From 5035cad61a103169576f0215cbf9f357062dbe14 Mon Sep 17 00:00:00 2001 From: =?utf8?q?F=C3=A1bio=20Madeira?= Date: Fri, 21 Apr 2017 15:55:51 +0100 Subject: [PATCH] JWS-109 & JWS-116 Regenerated the JABAWS JavaDoc (with eclipse java 8) and moved it to docs/. --- website/dm_javadoc/allclasses-frame.html | 225 --- website/dm_javadoc/allclasses-noframe.html | 225 --- website/dm_javadoc/compbio/data/msa/Category.html | 390 ----- .../dm_javadoc/compbio/data/msa/JABAService.html | 233 --- .../dm_javadoc/compbio/data/msa/JManagement.html | 272 ---- website/dm_javadoc/compbio/data/msa/Metadata.html | 282 ---- website/dm_javadoc/compbio/data/msa/MsaWS.html | 433 ----- .../dm_javadoc/compbio/data/msa/RegistryWS.html | 426 ----- .../compbio/data/msa/SequenceAnnotation.html | 445 ----- .../compbio/data/msa/class-use/Category.html | 233 --- .../compbio/data/msa/class-use/JABAService.html | 230 --- .../compbio/data/msa/class-use/JManagement.html | 190 --- .../compbio/data/msa/class-use/Metadata.html 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-ResultNotAvailableException -
-ResultNotAvailableExceptionBean -
-RunnerConfig -
-Score -
-ScoreManager -
-ScoreManager.ScoreHolder -
-SequenceAnnotation -
-SequenceUtil -
-Services -
-ServicesUtil -
-SMERFSConstraints -
-TestAllServices -
-TestAllServicesResponse -
-TestService -
-TestServiceResponse -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-UnsupportedRuntimeExceptionBean -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WrongParameterExceptionBean -
-WSTester -
-
- - - diff --git a/website/dm_javadoc/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html deleted file mode 100644 index 6d881ce..0000000 --- a/website/dm_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,225 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
AAConClient -
-Align -
-Alignment -
-AlignmentMetadata -
-AlignResponse -
-Analize -
-AnalizeResponse -
-Argument -
-CancelJob -
-CancelJobResponse -
-Category -
-ChunkHolder -
-ClustalAlignmentUtil -
-ConservationMethod -
-CustomAlign -
-CustomAlignResponse -
-CustomAnalize -
-CustomAnalizeResponse -
-DisorderMethod -
-FastaReader -
-FastaSequence -
-GetAnnotation -
-GetAnnotationResponse -
-GetJobStatus -
-GetJobStatusResponse -
-GetLastTested -
-GetLastTestedOn -
-GetLastTestedOnResponse -
-GetLastTestedResponse -
-GetLimit -
-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-GetServiceCategories -
-GetServiceCategoriesResponse -
-GetServiceDescription -
-GetServiceDescriptionResponse -
-GetSupportedServices -
-GetSupportedServicesResponse -
-IOHelper -
-IsOperating -
-IsOperatingResponse -
-JABAService -
-JManagement -
-JobExecutionException -
-JobStatus -
-JobSubmissionException -
-JobSubmissionExceptionBean -
-Jws2Client -
-Limit -
-LimitExceededException -
-LimitExceededExceptionBean -
-LimitsManager -
-Metadata -
-MetadataHelper -
-MsaWS -
-Option -
-Parameter -
-Preset -
-PresetAlign -
-PresetAlignResponse -
-PresetAnalize -
-PresetAnalizeResponse -
-PresetManager -
-Program -
-PullExecStatistics -
-PullExecStatisticsResponse -
-Range -
-RegistryWS -
-ResultNotAvailableException -
-ResultNotAvailableExceptionBean -
-RunnerConfig -
-Score -
-ScoreManager -
-ScoreManager.ScoreHolder -
-SequenceAnnotation -
-SequenceUtil -
-Services -
-ServicesUtil -
-SMERFSConstraints -
-TestAllServices -
-TestAllServicesResponse -
-TestService -
-TestServiceResponse -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-UnsupportedRuntimeExceptionBean -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WrongParameterExceptionBean -
-WSTester -
-
- - - diff --git a/website/dm_javadoc/compbio/data/msa/Category.html b/website/dm_javadoc/compbio/data/msa/Category.html deleted file mode 100644 index b687e04..0000000 --- a/website/dm_javadoc/compbio/data/msa/Category.html +++ /dev/null @@ -1,390 +0,0 @@ - - - - - - -Category - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Class Category

-
-java.lang.Object
-  extended by compbio.data.msa.Category
-
-
-
-
public class Category
extends java.lang.Object
- - -

-Class that splits Services to categories. Services themselves have no - knowledge which category they belongs to. - - This class is responsible for initialization of all the categories (done - statically) and holds the category names as constrains. - - Two categories considered equals if their names are equals. -

- -

-

-
Version:
-
1.0 September 2011
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static java.lang.StringCATEGORY_ALIGNMENT - -
-          All of the Category names
-static java.lang.StringCATEGORY_CONSERVATION - -
-           
-static java.lang.StringCATEGORY_DISORDER - -
-           
- java.lang.Stringname - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
-static java.util.Set<Category>getCategories() - -
-           
- java.util.Set<Services>getServices() - -
-           
- inthashCode() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-CATEGORY_ALIGNMENT

-
-public static final java.lang.String CATEGORY_ALIGNMENT
-
-
All of the Category names -

-

-
See Also:
Constant Field Values
-
-
- -

-CATEGORY_DISORDER

-
-public static final java.lang.String CATEGORY_DISORDER
-
-
-
See Also:
Constant Field Values
-
-
- -

-CATEGORY_CONSERVATION

-
-public static final java.lang.String CATEGORY_CONSERVATION
-
-
-
See Also:
Constant Field Values
-
-
- -

-name

-
-public java.lang.String name
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-getServices

-
-public java.util.Set<Services> getServices()
-
-
-
-
-
-
- -

-getCategories

-
-public static java.util.Set<Category> getCategories()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/JABAService.html b/website/dm_javadoc/compbio/data/msa/JABAService.html deleted file mode 100644 index bb42279..0000000 --- a/website/dm_javadoc/compbio/data/msa/JABAService.html +++ /dev/null @@ -1,233 +0,0 @@ - - - - - - -JABAService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface JABAService

-
-
All Known Subinterfaces:
MsaWS<T>, RegistryWS, SequenceAnnotation<T>
-
-
-
-
public interface JABAService
- - -

-This is a marker interface, contains no methods -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - -
-Field Summary
-static java.lang.StringSERVICE_NAMESPACE - -
-           
-static java.lang.StringV2_SERVICE_NAMESPACE - -
-           
-  -

- - - - - - - - -
-Field Detail
- -

-SERVICE_NAMESPACE

-
-static final java.lang.String SERVICE_NAMESPACE
-
-
-
See Also:
Constant Field Values
-
-
- -

-V2_SERVICE_NAMESPACE

-
-static final java.lang.String V2_SERVICE_NAMESPACE
-
-
-
See Also:
Constant Field Values
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/JManagement.html b/website/dm_javadoc/compbio/data/msa/JManagement.html deleted file mode 100644 index 73a4653..0000000 --- a/website/dm_javadoc/compbio/data/msa/JManagement.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -JManagement - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface JManagement

-
-
All Known Subinterfaces:
MsaWS<T>, SequenceAnnotation<T>
-
-
-
-
public interface JManagement
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(java.lang.String jobId) - -
-          Stop running the job jobId but leave its output untouched
- JobStatusgetJobStatus(java.lang.String jobId) - -
-          Return the status of the job.
- ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
-          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
-  -

- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-boolean cancelJob(java.lang.String jobId)
-
-
Stop running the job jobId but leave its output untouched -

-

- -
Returns:
true if job was cancelled successfully, false otherwise -
Throws: -
java.security.InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
-
-
-
- -

-getJobStatus

-
-JobStatus getJobStatus(java.lang.String jobId)
-
-
Return the status of the job. -

-

-
Parameters:
jobId - - unique job identifier -
Returns:
JobStatus - status of the job -
Throws: -
java.security.InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
See Also:
JobStatus
-
-
-
- -

-pullExecStatistics

-
-ChunkHolder pullExecStatistics(java.lang.String jobId,
-                               long position)
-
-
Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

-

-
Parameters:
jobId - - unique job identifier
position - - next position within the file to read -
Returns:
ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read -
Throws: -
java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format and also if the position value is negative
See Also:
ChunkHolder
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/Metadata.html b/website/dm_javadoc/compbio/data/msa/Metadata.html deleted file mode 100644 index 84f3d78..0000000 --- a/website/dm_javadoc/compbio/data/msa/Metadata.html +++ /dev/null @@ -1,282 +0,0 @@ - - - - - - -Metadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface Metadata<T>

-
-
All Known Subinterfaces:
MsaWS<T>, SequenceAnnotation<T>
-
-
-
-
public interface Metadata<T>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T>getLimit(java.lang.String presetName) - -
-          Get a Limit for a preset.
- LimitsManager<T>getLimits() - -
-          List Limits supported by a web service.
- PresetManager<T>getPresets() - -
-          Get presets supported by a web service
- RunnerConfig<T>getRunnerOptions() - -
-          Get options supported by a web service
-  -

- - - - - - - - -
-Method Detail
- -

-getRunnerOptions

-
-RunnerConfig<T> getRunnerOptions()
-
-
Get options supported by a web service -

-

- -
Returns:
RunnerConfig the list of options and parameters supported by a - web service.
-
-
-
- -

-getPresets

-
-PresetManager<T> getPresets()
-
-
Get presets supported by a web service -

-

- -
Returns:
PresetManager the object contains information about presets - supported by a web service
-
-
-
- -

-getLimit

-
-Limit<T> getLimit(java.lang.String presetName)
-
-
Get a Limit for a preset. -

-

-
Parameters:
presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
Returns:
Limit
-
-
-
- -

-getLimits

-
-LimitsManager<T> getLimits()
-
-
List Limits supported by a web service. -

-

- -
Returns:
LimitManager
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html deleted file mode 100644 index 5227700..0000000 --- a/website/dm_javadoc/compbio/data/msa/MsaWS.html +++ /dev/null @@ -1,433 +0,0 @@ - - - - - - -MsaWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface MsaWS<T>

-
-
Type Parameters:
T - executable type / web service type
-
-
All Superinterfaces:
JABAService, JManagement, Metadata<T>
-
-
-
-
public interface MsaWS<T>
extends JABAService, JManagement, Metadata<T>
- - -

-Multiple Sequence Alignment (MSA) Web Services Interface -

- -

-

-
Author:
-
pvtroshin - - Date November 2010
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
-          Align a list of sequences with options.
- AlignmentgetResult(java.lang.String jobId) - -
-          Return the result of the job.
- java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
-  -

- - - - - - - - -
-Method Detail
- -

-align

-
-java.lang.String align(java.util.List<FastaSequence> sequences)
-                       throws UnsupportedRuntimeException,
-                              LimitExceededException,
-                              JobSubmissionException
-
-
Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
java.security.InvalidParameterException - thrown if input list of FASTA sequences is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
-
-
-
- -

-customAlign

-
-java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                             java.util.List<Option<T>> options)
-                             throws UnsupportedRuntimeException,
-                                    LimitExceededException,
-                                    JobSubmissionException,
-                                    WrongParameterException
-
-
Align a list of sequences with options. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
options - A list of Options -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
See Also:
Default Limit is used to decide whether the calculation will be - permitted or denied
-
-
-
- -

-presetAlign

-
-java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                             Preset<T> preset)
-                             throws UnsupportedRuntimeException,
-                                    LimitExceededException,
-                                    JobSubmissionException,
-                                    WrongParameterException
-
-
Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
preset - A list of Options -
Returns:
String - jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
See Also:
Preset
-
-
-
- -

-getResult

-
-Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
-
-
Return the result of the job. This method waits for the job - jobId to complete before return. -

-

-
-
-
-
Parameters:
jobId - a unique job identifier -
Returns:
Alignment -
Throws: -
ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
java.security.InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid - format
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/RegistryWS.html b/website/dm_javadoc/compbio/data/msa/RegistryWS.html deleted file mode 100644 index 8fa123c..0000000 --- a/website/dm_javadoc/compbio/data/msa/RegistryWS.html +++ /dev/null @@ -1,426 +0,0 @@ - - - - - - -RegistryWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface RegistryWS

-
-
All Superinterfaces:
JABAService
-
-
-
-
public interface RegistryWS
extends JABAService
- - -

-JABAWS services registry -

- -

-

-
Version:
-
1.0 June 2011
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetLastTested(Services service) - -
-          Number of seconds since the last test.
- java.util.DategetLastTestedOn(Services service) - -
-          The date and time the service has been verified to work last time
- java.util.Set<Category>getServiceCategories() - -
-          Gets the list of services per category.
- java.lang.StringgetServiceDescription(Services service) - -
-          Gives the description of the service.
- java.util.Set<Services>getSupportedServices() - -
-          List of services that are functioning on the server.
- booleanisOperating(Services service) - -
-          Check whether a particular web service is working on this server
- java.lang.StringtestAllServices() - -
-          Test all JABAWS services on the server
- java.lang.StringtestService(Services service) - -
-          Test a particular service
-  -

- - - - - - - - -
-Method Detail
- -

-getSupportedServices

-
-java.util.Set<Services> getSupportedServices()
-
-
List of services that are functioning on the server. This function - returns the results of testing performed some time ago by - testAllServices() or testService(Services) methods. The - time of last check can be obtained from - getLastTestedOn(Services) method -

-

-
-
-
- -
Returns:
the Set of Services which are functioning on the server
See Also:
testAllServices()
-
-
-
- -

-getLastTested

-
-int getLastTested(Services service)
-
-
Number of seconds since the last test. Returns 0 if the service was not - tested or tested less then a one second ago. -

-

-
-
-
-
Parameters:
service - -
Returns:
when last time tested
-
-
-
- -

-getLastTestedOn

-
-java.util.Date getLastTestedOn(Services service)
-
-
The date and time the service has been verified to work last time -

-

-
-
-
-
Parameters:
service - -
Returns:
the Date and time on which the service was last tested
-
-
-
- -

-testAllServices

-
-java.lang.String testAllServices()
-
-
Test all JABAWS services on the server -

-

-
-
-
- -
Returns:
the test log
-
-
-
- -

-testService

-
-java.lang.String testService(Services service)
-
-
Test a particular service -

-

-
-
-
-
Parameters:
service - -
Returns:
the testing log
-
-
-
- -

-isOperating

-
-boolean isOperating(Services service)
-
-
Check whether a particular web service is working on this server -

-

-
-
-
-
Parameters:
service - -
Returns:
true if the service was functioning in time of last testing.
-
-
-
- -

-getServiceDescription

-
-java.lang.String getServiceDescription(Services service)
-
-
Gives the description of the service. -

-

-
-
-
-
Parameters:
service - -
Returns:
String, plain text or html formatted piece, but NOT a full html - document
-
-
-
- -

-getServiceCategories

-
-java.util.Set<Category> getServiceCategories()
-
-
Gets the list of services per category. ServiceClassifier has the method - that returns Map> -

-

-
-
-
- -
Returns:
ServiceClassifier the object to represent relation between - Services and Categories
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/SequenceAnnotation.html b/website/dm_javadoc/compbio/data/msa/SequenceAnnotation.html deleted file mode 100644 index 741aa6d..0000000 --- a/website/dm_javadoc/compbio/data/msa/SequenceAnnotation.html +++ /dev/null @@ -1,445 +0,0 @@ - - - - - - -SequenceAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa -
-Interface SequenceAnnotation<T>

-
-
Type Parameters:
T - executable type / web service type
-
-
All Superinterfaces:
JABAService, JManagement, Metadata<T>
-
-
-
-
public interface SequenceAnnotation<T>
extends JABAService, JManagement, Metadata<T>
- - -

-Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated -

- -

-

-
Version:
-
1.0 November 2010
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from interface compbio.data.msa.JABAService
SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.Stringanalize(java.util.List<FastaSequence> sequences) - -
-          Analyse the sequences.
- java.lang.StringcustomAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- ScoreManagergetAnnotation(java.lang.String jobId) - -
-          Return the result of the job.
- java.lang.StringpresetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.JManagement
cancelJob, getJobStatus, pullExecStatistics
-  - - - - - - - -
Methods inherited from interface compbio.data.msa.Metadata
getLimit, getLimits, getPresets, getRunnerOptions
-  -

- - - - - - - - -
-Method Detail
- -

-analize

-
-java.lang.String analize(java.util.List<FastaSequence> sequences)
-                         throws UnsupportedRuntimeException,
-                                LimitExceededException,
-                                JobSubmissionException
-
-
Analyse the sequences. The actual analysis algorithm is defined by the - type T. - - Any dataset containing a greater number of sequences or the average - length of the sequences are greater then defined in the default Limit - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
-
-
-
- -

-customAnalize

-
-java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
-                               java.util.List<Option<T>> options)
-                               throws UnsupportedRuntimeException,
-                                      LimitExceededException,
-                                      JobSubmissionException,
-                                      WrongParameterException
-
-
Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
options - A list of Options -
Returns:
jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
See Also:
Option
-
-
-
- -

-presetAnalize

-
-java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
-                               Preset<T> preset)
-                               throws UnsupportedRuntimeException,
-                                      LimitExceededException,
-                                      JobSubmissionException,
-                                      WrongParameterException
-
-
Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

-

-
-
-
-
Parameters:
sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
preset - A list of Options -
Returns:
String - jobId - unique identifier for the job -
Throws: -
JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
-
-
-
- -

-getAnnotation

-
-ScoreManager getAnnotation(java.lang.String jobId)
-                           throws ResultNotAvailableException
-
-
Return the result of the job. -

-

-
-
-
-
Parameters:
jobId - a unique job identifier -
Returns:
the Map with the sequence names, sequence group names or the word - 'Alignment' in case of alignments and values the represented by a - Set of Score objects. The alignment can be represented in as - little as one key->value pair in this map, the list of sequences - will be represented by multiple key->value mappings. If multiple - annotations were calculated, then they are represented as a Set - of Scores. -
Throws: -
ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/Category.html b/website/dm_javadoc/compbio/data/msa/class-use/Category.html deleted file mode 100644 index f0dacbc..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/Category.html +++ /dev/null @@ -1,233 +0,0 @@ - - - - - - -Uses of Class compbio.data.msa.Category - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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- - - -
-
-

-Uses of Class
compbio.data.msa.Category

-
- - - - - - - - - - - - - -
-Packages that use Category
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
-  -

- - - - - -
-Uses of Category in compbio.data.msa
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.msa that return types with arguments of type Category
-static java.util.Set<Category>Category.getCategories() - -
-           
- java.util.Set<Category>RegistryWS.getServiceCategories() - -
-          Gets the list of services per category.
-  -

- - - - - -
-Uses of Category in compbio.data.msa.jaxws
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws that return types with arguments of type Category
- java.util.Set<Category>GetServiceCategoriesResponse.getReturn() - -
-           
-  -

- - - - - - - - - -
Method parameters in compbio.data.msa.jaxws with type arguments of type Category
- voidGetServiceCategoriesResponse.setReturn(java.util.Set<Category> _return) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
-
-

-Uses of Interface
compbio.data.msa.JABAService

-
- - - - - - - - - - - - - -
-Packages that use JABAService
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of JABAService in compbio.data.msa
-  -

- - - - - - - - - - - - - - - - - -
Subinterfaces of JABAService in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceRegistryWS - -
-          JABAWS services registry
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

- - - - - -
-Uses of JABAService in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return JABAService
-static JABAServiceJws2Client.connect(java.lang.String host, - Services service) - -
-          Connects to a web service by the host and the service name web service - type
-  -

-

- - - - - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.JManagement

-
- - - - - - - - - -
-Packages that use JManagement
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of JManagement in compbio.data.msa
-  -

- - - - - - - - - - - - - -
Subinterfaces of JManagement in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.Metadata

-
- - - - - - - - - -
-Packages that use Metadata
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of Metadata in compbio.data.msa
-  -

- - - - - - - - - - - - - -
Subinterfaces of Metadata in compbio.data.msa
- interfaceMsaWS<T> - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
- interfaceSequenceAnnotation<T> - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Interface
compbio.data.msa.MsaWS

-
-No usage of compbio.data.msa.MsaWS -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/RegistryWS.html b/website/dm_javadoc/compbio/data/msa/class-use/RegistryWS.html deleted file mode 100644 index 9e8ad7a..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/RegistryWS.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.RegistryWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.RegistryWS

-
- - - - - - - - - -
-Packages that use RegistryWS
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of RegistryWS in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return RegistryWS
-static RegistryWSJws2Client.connectToRegistry(java.lang.String host) - -
-          Get a connection of JABAWS registry
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.SequenceAnnotation

-
- - - - - - - - - -
-Packages that use SequenceAnnotation
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - -
-Uses of SequenceAnnotation in compbio.ws.client
-  -

- - - - - - - - - -
Methods in compbio.ws.client that return SequenceAnnotation
-static SequenceAnnotation<compbio.ws.server.AAConWS>AAConClient.connect() - -
-          Connects to a AACon web service by the host and the service name
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/Align.html b/website/dm_javadoc/compbio/data/msa/jaxws/Align.html deleted file mode 100644 index abac99f..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/Align.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Align - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class Align

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.Align
-
-
-
-
public class Align
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
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Align() - -
-           
-  - - - - - - - - - - - - - - - -
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- java.util.List<FastaSequence>getFastaSequences() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
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-  - - - - - - - -
Methods inherited from class java.lang.Object
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-Align

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-public Align()
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-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
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-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
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- -compbio.data.msa.jaxws -
-Class AlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.AlignResponse
-
-
-
-
public class AlignResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AlignResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
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Methods inherited from class java.lang.Object
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-AlignResponse

-
-public AlignResponse()
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-
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-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
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-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
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-
Parameters:
_return - the value for the _return property
-
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- -compbio.data.msa.jaxws -
-Class Analize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.Analize
-
-
-
-
public class Analize
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Analize() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.util.List<FastaSequence>getFastaSequences() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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-Constructor Detail
- -

-Analize

-
-public Analize()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
- -
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- -compbio.data.msa.jaxws -
-Class AnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.AnalizeResponse
-
-
-
-
public class AnalizeResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
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-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-AnalizeResponse

-
-public AnalizeResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
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- -compbio.data.msa.jaxws -
-Class CancelJob

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJob
-
-
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-
public class CancelJob
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CancelJob() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetJobId() - -
-           
- voidsetJobId(java.lang.String jobId) - -
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
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-CancelJob

-
-public CancelJob()
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-
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-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
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- -compbio.data.msa.jaxws -
-Class CancelJobResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJobResponse
-
-
-
-
public class CancelJobResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CancelJobResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- booleanisReturn() - -
-           
- voidsetReturn(boolean _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-CancelJobResponse

-
-public CancelJobResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-isReturn

-
-public boolean isReturn()
-
-
- -
Returns:
returns boolean
-
-
-
- -

-setReturn

-
-public void setReturn(boolean _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class CustomAlign

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlign
-
-
-
-
public class CustomAlign
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAlign() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.List<FastaSequence>getFastaSequences() - -
-           
- java.util.List<Option>getOptions() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidsetOptions(java.util.List<Option> options) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAlign

-
-public CustomAlign()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getOptions

-
-public java.util.List<Option> getOptions()
-
-
- -
Returns:
returns List
-
-
-
- -

-setOptions

-
-public void setOptions(java.util.List<Option> options)
-
-
-
Parameters:
options - the value for the options property
-
-
- -
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- -compbio.data.msa.jaxws -
-Class CustomAlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlignResponse
-
-
-
-
public class CustomAlignResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAlignResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAlignResponse

-
-public CustomAlignResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class CustomAnalize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalize
-
-
-
-
public class CustomAnalize
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAnalize() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.List<FastaSequence>getFastaSequences() - -
-           
- java.util.List<Option>getOptions() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidsetOptions(java.util.List<Option> options) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAnalize

-
-public CustomAnalize()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getOptions

-
-public java.util.List<Option> getOptions()
-
-
- -
Returns:
returns List
-
-
-
- -

-setOptions

-
-public void setOptions(java.util.List<Option> options)
-
-
-
Parameters:
options - the value for the options property
-
-
- -
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- -

- -compbio.data.msa.jaxws -
-Class CustomAnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalizeResponse
-
-
-
-
public class CustomAnalizeResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CustomAnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
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-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-CustomAnalizeResponse

-
-public CustomAnalizeResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
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- -compbio.data.msa.jaxws -
-Class GetAnnotation

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotation
-
-
-
-
public class GetAnnotation
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetAnnotation() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetJobId() - -
-           
- voidsetJobId(java.lang.String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetAnnotation

-
-public GetAnnotation()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetAnnotationResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotationResponse
-
-
-
-
public class GetAnnotationResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetAnnotationResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ScoreManagergetReturn() - -
-           
- voidsetReturn(ScoreManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetAnnotationResponse

-
-public GetAnnotationResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public ScoreManager getReturn()
-
-
- -
Returns:
returns ScoreManager
-
-
-
- -

-setReturn

-
-public void setReturn(ScoreManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetJobStatus.html deleted file mode 100644 index 8be85d1..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetJobStatus.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetJobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetJobStatus

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatus
-
-
-
-
public class GetJobStatus
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetJobStatus() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetJobId() - -
-           
- voidsetJobId(java.lang.String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetJobStatus

-
-public GetJobStatus()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
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- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetJobStatusResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatusResponse
-
-
-
-
public class GetJobStatusResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetJobStatusResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- JobStatusgetReturn() - -
-           
- voidsetReturn(JobStatus _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetJobStatusResponse

-
-public GetJobStatusResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public JobStatus getReturn()
-
-
- -
Returns:
returns JobStatus
-
-
-
- -

-setReturn

-
-public void setReturn(JobStatus _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
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- -compbio.data.msa.jaxws -
-Class GetLastTested

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTested
-
-
-
-
public class GetLastTested
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTested() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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-GetLastTested

-
-public GetLastTested()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
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- -

- -compbio.data.msa.jaxws -
-Class GetLastTestedOn

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOn
-
-
-
-
public class GetLastTestedOn
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedOn() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedOn

-
-public GetLastTestedOn()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLastTestedOnResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOnResponse
-
-
-
-
public class GetLastTestedOnResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedOnResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.util.DategetReturn() - -
-           
- voidsetReturn(java.util.Date _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedOnResponse

-
-public GetLastTestedOnResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.util.Date getReturn()
-
-
- -
Returns:
returns Date
-
-
-
- -

-setReturn

-
-public void setReturn(java.util.Date _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLastTestedResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedResponse
-
-
-
-
public class GetLastTestedResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLastTestedResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- intgetReturn() - -
-           
- voidsetReturn(int _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLastTestedResponse

-
-public GetLastTestedResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public int getReturn()
-
-
- -
Returns:
returns int
-
-
-
- -

-setReturn

-
-public void setReturn(int _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLimit

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimit
-
-
-
-
public class GetLimit
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimit() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetPresetName() - -
-           
- voidsetPresetName(java.lang.String presetName) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimit

-
-public GetLimit()
-
-
- - - - - - - - -
-Method Detail
- -

-getPresetName

-
-public java.lang.String getPresetName()
-
-
- -
Returns:
returns String
-
-
-
- -

-setPresetName

-
-public void setPresetName(java.lang.String presetName)
-
-
-
Parameters:
presetName - the value for the presetName property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLimitResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitResponse
-
-
-
-
public class GetLimitResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimitResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- LimitgetReturn() - -
-           
- voidsetReturn(Limit _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimitResponse

-
-public GetLimitResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Limit getReturn()
-
-
- -
Returns:
returns Limit
-
-
-
- -

-setReturn

-
-public void setReturn(Limit _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetLimits

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimits
-
-
-
-
public class GetLimits
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimits() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimits

-
-public GetLimits()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html deleted file mode 100644 index d2e6749..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetLimitsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitsResponse
-
-
-
-
public class GetLimitsResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetLimitsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- LimitsManagergetReturn() - -
-           
- voidsetReturn(LimitsManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetLimitsResponse

-
-public GetLimitsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public LimitsManager getReturn()
-
-
- -
Returns:
returns LimitsManager
-
-
-
- -

-setReturn

-
-public void setReturn(LimitsManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetPresets.html deleted file mode 100644 index fe0fc7b..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetPresets.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetPresets - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetPresets

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresets
-
-
-
-
public class GetPresets
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetPresets() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetPresets

-
-public GetPresets()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetPresetsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresetsResponse
-
-
-
-
public class GetPresetsResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetPresetsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- PresetManagergetReturn() - -
-           
- voidsetReturn(PresetManager _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetPresetsResponse

-
-public GetPresetsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public PresetManager getReturn()
-
-
- -
Returns:
returns PresetManager
-
-
-
- -

-setReturn

-
-public void setReturn(PresetManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetResult.html deleted file mode 100644 index a203834..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetResult.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResult - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetResult

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResult
-
-
-
-
public class GetResult
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetResult() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetJobId() - -
-           
- voidsetJobId(java.lang.String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetResult

-
-public GetResult()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetResultResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResultResponse
-
-
-
-
public class GetResultResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetResultResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- AlignmentgetReturn() - -
-           
- voidsetReturn(Alignment _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetResultResponse

-
-public GetResultResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public Alignment getReturn()
-
-
- -
Returns:
returns Alignment
-
-
-
- -

-setReturn

-
-public void setReturn(Alignment _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetRunnerOptions

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptions
-
-
-
-
public class GetRunnerOptions
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetRunnerOptions() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetRunnerOptions

-
-public GetRunnerOptions()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetRunnerOptionsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptionsResponse
-
-
-
-
public class GetRunnerOptionsResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetRunnerOptionsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- RunnerConfiggetReturn() - -
-           
- voidsetReturn(RunnerConfig _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetRunnerOptionsResponse

-
-public GetRunnerOptionsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public RunnerConfig getReturn()
-
-
- -
Returns:
returns RunnerConfig
-
-
-
- -

-setReturn

-
-public void setReturn(RunnerConfig _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html deleted file mode 100644 index 01d2dbd..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetServiceCategories - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetServiceCategories

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceCategories
-
-
-
-
public class GetServiceCategories
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetServiceCategories() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetServiceCategories

-
-public GetServiceCategories()
-
-
- -
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- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetServiceCategoriesResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceCategoriesResponse
-
-
-
-
public class GetServiceCategoriesResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetServiceCategoriesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<Category>getReturn() - -
-           
- voidsetReturn(java.util.Set<Category> _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetServiceCategoriesResponse

-
-public GetServiceCategoriesResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.util.Set<Category> getReturn()
-
-
- -
Returns:
returns Set
-
-
-
- -

-setReturn

-
-public void setReturn(java.util.Set<Category> _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html deleted file mode 100644 index 411c255..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetServiceDescription - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetServiceDescription

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceDescription
-
-
-
-
public class GetServiceDescription
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetServiceDescription() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetServiceDescription

-
-public GetServiceDescription()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetServiceDescriptionResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceDescriptionResponse
-
-
-
-
public class GetServiceDescriptionResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetServiceDescriptionResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetServiceDescriptionResponse

-
-public GetServiceDescriptionResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html deleted file mode 100644 index 0741857..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetSupportedServices - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetSupportedServices

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServices
-
-
-
-
public class GetSupportedServices
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetSupportedServices() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetSupportedServices

-
-public GetSupportedServices()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html deleted file mode 100644 index 27f5e1e..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetSupportedServicesResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetSupportedServicesResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServicesResponse
-
-
-
-
public class GetSupportedServicesResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
GetSupportedServicesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<Services>getReturn() - -
-           
- voidsetReturn(java.util.Set<Services> _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-GetSupportedServicesResponse

-
-public GetSupportedServicesResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.util.Set<Services> getReturn()
-
-
- -
Returns:
returns Set
-
-
-
- -

-setReturn

-
-public void setReturn(java.util.Set<Services> _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/IsOperating.html b/website/dm_javadoc/compbio/data/msa/jaxws/IsOperating.html deleted file mode 100644 index 3a2c34e..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/IsOperating.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperating - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class IsOperating

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperating
-
-
-
-
public class IsOperating
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
IsOperating() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-IsOperating

-
-public IsOperating()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html deleted file mode 100644 index aa5e99b..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperatingResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class IsOperatingResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperatingResponse
-
-
-
-
public class IsOperatingResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
IsOperatingResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- booleanisReturn() - -
-           
- voidsetReturn(boolean _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-IsOperatingResponse

-
-public IsOperatingResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-isReturn

-
-public boolean isReturn()
-
-
- -
Returns:
returns boolean
-
-
-
- -

-setReturn

-
-public void setReturn(boolean _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html b/website/dm_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html deleted file mode 100644 index 2765e48..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -JobSubmissionExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class JobSubmissionExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.JobSubmissionExceptionBean
-
-
-
-
public class JobSubmissionExceptionBean
extends java.lang.Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
JobSubmissionExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetMessage() - -
-           
- voidsetMessage(java.lang.String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobSubmissionExceptionBean

-
-public JobSubmissionExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public java.lang.String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html b/website/dm_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html deleted file mode 100644 index f9ca55f..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html +++ /dev/null @@ -1,434 +0,0 @@ - - - - - - -LimitExceededExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class LimitExceededExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.LimitExceededExceptionBean
-
-
-
-
public class LimitExceededExceptionBean
extends java.lang.Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetActualNumberofSequences() - -
-           
- java.lang.StringgetMessage() - -
-           
- intgetNumberOfSequencesAllowed() - -
-           
- intgetSequenceLenghtActual() - -
-           
- intgetSequenceLenghtAllowed() - -
-           
- voidsetActualNumberofSequences(int actualNumberofSequences) - -
-           
- voidsetMessage(java.lang.String message) - -
-           
- voidsetNumberOfSequencesAllowed(int numberOfSequencesAllowed) - -
-           
- voidsetSequenceLenghtActual(int sequenceLenghtActual) - -
-           
- voidsetSequenceLenghtAllowed(int sequenceLenghtAllowed) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitExceededExceptionBean

-
-public LimitExceededExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getActualNumberofSequences

-
-public int getActualNumberofSequences()
-
-
- -
Returns:
returns int
-
-
-
- -

-setActualNumberofSequences

-
-public void setActualNumberofSequences(int actualNumberofSequences)
-
-
-
Parameters:
actualNumberofSequences - the value for the actualNumberofSequences property
-
-
-
- -

-getMessage

-
-public java.lang.String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
-
- -

-getNumberOfSequencesAllowed

-
-public int getNumberOfSequencesAllowed()
-
-
- -
Returns:
returns int
-
-
-
- -

-setNumberOfSequencesAllowed

-
-public void setNumberOfSequencesAllowed(int numberOfSequencesAllowed)
-
-
-
Parameters:
numberOfSequencesAllowed - the value for the numberOfSequencesAllowed property
-
-
-
- -

-getSequenceLenghtActual

-
-public int getSequenceLenghtActual()
-
-
- -
Returns:
returns int
-
-
-
- -

-setSequenceLenghtActual

-
-public void setSequenceLenghtActual(int sequenceLenghtActual)
-
-
-
Parameters:
sequenceLenghtActual - the value for the sequenceLenghtActual property
-
-
-
- -

-getSequenceLenghtAllowed

-
-public int getSequenceLenghtAllowed()
-
-
- -
Returns:
returns int
-
-
-
- -

-setSequenceLenghtAllowed

-
-public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
-
-
-
Parameters:
sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html deleted file mode 100644 index ee781da..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class PresetAlign

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlign
-
-
-
-
public class PresetAlign
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAlign() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.List<FastaSequence>getFastaSequences() - -
-           
- PresetgetPreset() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidsetPreset(Preset preset) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PresetAlign

-
-public PresetAlign()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getPreset

-
-public Preset getPreset()
-
-
- -
Returns:
returns Preset
-
-
-
- -

-setPreset

-
-public void setPreset(Preset preset)
-
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-
Parameters:
preset - the value for the preset property
-
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- -

- -compbio.data.msa.jaxws -
-Class PresetAlignResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlignResponse
-
-
-
-
public class PresetAlignResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAlignResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
- -

-PresetAlignResponse

-
-public PresetAlignResponse()
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-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class PresetAnalize

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalize
-
-
-
-
public class PresetAnalize
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAnalize() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.List<FastaSequence>getFastaSequences() - -
-           
- PresetgetPreset() - -
-           
- voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidsetPreset(Preset preset) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PresetAnalize

-
-public PresetAnalize()
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-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

-
-public java.util.List<FastaSequence> getFastaSequences()
-
-
- -
Returns:
returns List
-
-
-
- -

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
-
- -

-getPreset

-
-public Preset getPreset()
-
-
- -
Returns:
returns Preset
-
-
-
- -

-setPreset

-
-public void setPreset(Preset preset)
-
-
-
Parameters:
preset - the value for the preset property
-
-
- -
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- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class PresetAnalizeResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalizeResponse
-
-
-
-
public class PresetAnalizeResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PresetAnalizeResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PresetAnalizeResponse

-
-public PresetAnalizeResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class PullExecStatistics

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatistics
-
-
-
-
public class PullExecStatistics
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PullExecStatistics() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetJobId() - -
-           
- longgetPosition() - -
-           
- voidsetJobId(java.lang.String jobId) - -
-           
- voidsetPosition(long position) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PullExecStatistics

-
-public PullExecStatistics()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-
-
- -
Returns:
returns String
-
-
-
- -

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
-
- -

-getPosition

-
-public long getPosition()
-
-
- -
Returns:
returns long
-
-
-
- -

-setPosition

-
-public void setPosition(long position)
-
-
-
Parameters:
position - the value for the position property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class PullExecStatisticsResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatisticsResponse
-
-
-
-
public class PullExecStatisticsResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PullExecStatisticsResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ChunkHoldergetReturn() - -
-           
- voidsetReturn(ChunkHolder _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-PullExecStatisticsResponse

-
-public PullExecStatisticsResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public ChunkHolder getReturn()
-
-
- -
Returns:
returns ChunkHolder
-
-
-
- -

-setReturn

-
-public void setReturn(ChunkHolder _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class ResultNotAvailableExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
-
-
-
-
public class ResultNotAvailableExceptionBean
extends java.lang.Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ResultNotAvailableExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetMessage() - -
-           
- voidsetMessage(java.lang.String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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- - - - - - - - -
-Constructor Detail
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-ResultNotAvailableExceptionBean

-
-public ResultNotAvailableExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public java.lang.String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
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- -compbio.data.msa.jaxws -
-Class TestAllServices

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServices
-
-
-
-
public class TestAllServices
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestAllServices() - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-TestAllServices

-
-public TestAllServices()
-
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- -
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- -compbio.data.msa.jaxws -
-Class TestAllServicesResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServicesResponse
-
-
-
-
public class TestAllServicesResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestAllServicesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-TestAllServicesResponse

-
-public TestAllServicesResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class TestService

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestService
-
-
-
-
public class TestService
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestService() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- ServicesgetArg0() - -
-           
- voidsetArg0(Services arg0) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-TestService

-
-public TestService()
-
-
- - - - - - - - -
-Method Detail
- -

-getArg0

-
-public Services getArg0()
-
-
- -
Returns:
returns Services
-
-
-
- -

-setArg0

-
-public void setArg0(Services arg0)
-
-
-
Parameters:
arg0 - the value for the arg0 property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class TestServiceResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.TestServiceResponse
-
-
-
-
public class TestServiceResponse
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestServiceResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetReturn() - -
-           
- voidsetReturn(java.lang.String _return) - -
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-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-TestServiceResponse

-
-public TestServiceResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

-
-public java.lang.String getReturn()
-
-
- -
Returns:
returns String
-
-
-
- -

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
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- -

- -compbio.data.msa.jaxws -
-Class UnsupportedRuntimeExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
-
-
-
-
public class UnsupportedRuntimeExceptionBean
extends java.lang.Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
UnsupportedRuntimeExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetMessage() - -
-           
- voidsetMessage(java.lang.String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-UnsupportedRuntimeExceptionBean

-
-public UnsupportedRuntimeExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public java.lang.String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
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Parameters:
message - the value for the message property
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- -compbio.data.msa.jaxws -
-Class WrongParameterExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.WrongParameterExceptionBean
-
-
-
-
public class WrongParameterExceptionBean
extends java.lang.Object
- - -

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

- -

-

- -

- - - - - - - - - - - -
-Constructor Summary
WrongParameterExceptionBean() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetMessage() - -
-           
- voidsetMessage(java.lang.String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-WrongParameterExceptionBean

-
-public WrongParameterExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

-
-public java.lang.String getMessage()
-
-
- -
Returns:
returns String
-
-
-
- -

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
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-Uses of Class
compbio.data.msa.jaxws.Align

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-

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compbio.data.msa.jaxws.AlignResponse

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-No usage of compbio.data.msa.jaxws.AlignResponse -

-

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compbio.data.msa.jaxws.Analize

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-

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-Uses of Class
compbio.data.msa.jaxws.AnalizeResponse

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-No usage of compbio.data.msa.jaxws.AnalizeResponse -

-

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compbio.data.msa.jaxws.CancelJob

-
-No usage of compbio.data.msa.jaxws.CancelJob -

-

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compbio.data.msa.jaxws.CancelJobResponse

-
-No usage of compbio.data.msa.jaxws.CancelJobResponse -

-

- - - - - - - - - - - - - - - -
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compbio.data.msa.jaxws.CustomAlign

-
-No usage of compbio.data.msa.jaxws.CustomAlign -

-

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compbio.data.msa.jaxws.CustomAlignResponse

-
-No usage of compbio.data.msa.jaxws.CustomAlignResponse -

-

- - - - - - - - - - - - - - - -
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compbio.data.msa.jaxws.CustomAnalize

-
-No usage of compbio.data.msa.jaxws.CustomAnalize -

-

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compbio.data.msa.jaxws.CustomAnalizeResponse

-
-No usage of compbio.data.msa.jaxws.CustomAnalizeResponse -

-

- - - - - - - - - - - - - - - -
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compbio.data.msa.jaxws.GetAnnotation

-
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-

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compbio.data.msa.jaxws.GetAnnotationResponse

-
-No usage of compbio.data.msa.jaxws.GetAnnotationResponse -

-

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compbio.data.msa.jaxws.GetJobStatus

-
-No usage of compbio.data.msa.jaxws.GetJobStatus -

-

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compbio.data.msa.jaxws.GetJobStatusResponse

-
-No usage of compbio.data.msa.jaxws.GetJobStatusResponse -

-

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compbio.data.msa.jaxws.GetLastTested

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compbio.data.msa.jaxws.GetLastTestedOn

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compbio.data.msa.jaxws.GetLastTestedOnResponse

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compbio.data.msa.jaxws.GetLastTestedResponse

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compbio.data.msa.jaxws.GetLimit

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compbio.data.msa.jaxws.GetLimitResponse

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compbio.data.msa.jaxws.GetLimits

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compbio.data.msa.jaxws.GetLimitsResponse

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compbio.data.msa.jaxws.GetPresets

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compbio.data.msa.jaxws.GetPresetsResponse

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compbio.data.msa.jaxws.GetResult

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compbio.data.msa.jaxws.GetResultResponse

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compbio.data.msa.jaxws.GetRunnerOptions

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compbio.data.msa.jaxws.GetRunnerOptionsResponse

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compbio.data.msa.jaxws.GetServiceCategories

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compbio.data.msa.jaxws.GetServiceCategoriesResponse

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compbio.data.msa.jaxws.GetServiceDescription

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compbio.data.msa.jaxws.GetServiceDescriptionResponse

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compbio.data.msa.jaxws.GetSupportedServices

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compbio.data.msa.jaxws.GetSupportedServicesResponse

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compbio.data.msa.jaxws.IsOperatingResponse

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compbio.data.msa.jaxws.JobSubmissionExceptionBean

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compbio.data.msa.jaxws.LimitExceededExceptionBean

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compbio.data.msa.jaxws.PresetAlign

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compbio.data.msa.jaxws.PresetAlignResponse

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compbio.data.msa.jaxws.PresetAnalize

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compbio.data.msa.jaxws.PresetAnalizeResponse

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compbio.data.msa.jaxws.PullExecStatistics

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compbio.data.msa.jaxws.PullExecStatisticsResponse

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compbio.data.msa.jaxws.ResultNotAvailableExceptionBean

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compbio.data.msa.jaxws.TestAllServices

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compbio.data.msa.jaxws.TestAllServicesResponse

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compbio.data.msa.jaxws.TestService

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compbio.data.msa.jaxws.TestServiceResponse

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compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean

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compbio.data.msa.jaxws.WrongParameterExceptionBean

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-Classes  - -
-Align -
-AlignResponse -
-Analize -
-AnalizeResponse -
-CancelJob -
-CancelJobResponse -
-CustomAlign -
-CustomAlignResponse -
-CustomAnalize -
-CustomAnalizeResponse -
-GetAnnotation -
-GetAnnotationResponse -
-GetJobStatus -
-GetJobStatusResponse -
-GetLastTested -
-GetLastTestedOn -
-GetLastTestedOnResponse -
-GetLastTestedResponse -
-GetLimit -
-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-GetServiceCategories -
-GetServiceCategoriesResponse -
-GetServiceDescription -
-GetServiceDescriptionResponse -
-GetSupportedServices -
-GetSupportedServicesResponse -
-IsOperating -
-IsOperatingResponse -
-JobSubmissionExceptionBean -
-LimitExceededExceptionBean -
-PresetAlign -
-PresetAlignResponse -
-PresetAnalize -
-PresetAnalizeResponse -
-PullExecStatistics -
-PullExecStatisticsResponse -
-ResultNotAvailableExceptionBean -
-TestAllServices -
-TestAllServicesResponse -
-TestService -
-TestServiceResponse -
-UnsupportedRuntimeExceptionBean -
-WrongParameterExceptionBean
- - - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/package-summary.html b/website/dm_javadoc/compbio/data/msa/jaxws/package-summary.html deleted file mode 100644 index 5df13cc..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/package-summary.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -compbio.data.msa.jaxws - - - - - - - - - - - - -
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-Package compbio.data.msa.jaxws -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
Align 
AlignResponse 
Analize 
AnalizeResponse 
CancelJob 
CancelJobResponse 
CustomAlign 
CustomAlignResponse 
CustomAnalize 
CustomAnalizeResponse 
GetAnnotation 
GetAnnotationResponse 
GetJobStatus 
GetJobStatusResponse 
GetLastTested 
GetLastTestedOn 
GetLastTestedOnResponse 
GetLastTestedResponse 
GetLimit 
GetLimitResponse 
GetLimits 
GetLimitsResponse 
GetPresets 
GetPresetsResponse 
GetResult 
GetResultResponse 
GetRunnerOptions 
GetRunnerOptionsResponse 
GetServiceCategories 
GetServiceCategoriesResponse 
GetServiceDescription 
GetServiceDescriptionResponse 
GetSupportedServices 
GetSupportedServicesResponse 
IsOperating 
IsOperatingResponse 
JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
PresetAlign 
PresetAlignResponse 
PresetAnalize 
PresetAnalizeResponse 
PullExecStatistics 
PullExecStatisticsResponse 
ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
TestAllServices 
TestAllServicesResponse 
TestService 
TestServiceResponse 
UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
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-Package compbio.data.msa -

-Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Interface Summary
JABAServiceThis is a marker interface, contains no methods
JManagement 
Metadata<T> 
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
RegistryWSJABAWS services registry
SequenceAnnotation<T>Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  - -

- - - - - - - - - -
-Class Summary
CategoryClass that splits Services to categories.
-  - -

-

-Package compbio.data.msa Description -

- -

-Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

- -

-

-
Version:
-
1.0 April 2010
-
Author:
-
Peter Troshin
-
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-
- - - - - - - - - - - - - - - - - -
-Packages that use compbio.data.msa
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.data.msa used by compbio.data.msa
Category - -
-          Class that splits Services to categories.
JABAService - -
-          This is a marker interface, contains no methods
JManagement - -
-           
Metadata - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.msa used by compbio.data.msa.jaxws
Category - -
-          Class that splits Services to categories.
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.msa used by compbio.ws.client
JABAService - -
-          This is a marker interface, contains no methods
RegistryWS - -
-          JABAWS services registry
SequenceAnnotation - -
-          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
-  -

-

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- - - -
- -

- -compbio.data.sequence -
-Class Alignment

-
-java.lang.Object
-  extended by compbio.data.sequence.Alignment
-
-
-
-
@Immutable
-public final class Alignment
extends java.lang.Object
- - -

-Multiple sequence alignment. - - Does not give any guarantees on the content of individual FastaSequece - records. It does not guarantee neither the uniqueness of the names of - sequences nor it guarantees the uniqueness of the sequences. -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
See Also:
FastaSequence, -AlignmentMetadata
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
Alignment(java.util.List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
Alignment(java.util.List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-          Please note that this implementation does not take the order of sequences - into account!
- AlignmentMetadatagetMetadata() - -
-           
- java.util.List<FastaSequence>getSequences() - -
-           
- intgetSize() - -
-           
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Alignment

-
-public Alignment(java.util.List<FastaSequence> sequences,
-                 Program program,
-                 char gapchar)
-
-
-
Parameters:
sequences -
program -
gapchar -
-
-
- -

-Alignment

-
-public Alignment(java.util.List<FastaSequence> sequences,
-                 AlignmentMetadata metadata)
-
-
-
Parameters:
sequences -
metadata -
-
- - - - - - - - -
-Method Detail
- -

-getSequences

-
-public java.util.List<FastaSequence> getSequences()
-
-
- -
Returns:
list of FastaSequence records
-
-
-
- -

-getSize

-
-public int getSize()
-
-
- -
Returns:
a number of sequence in the alignment
-
-
-
- -

-getMetadata

-
-public AlignmentMetadata getMetadata()
-
-
- -
Returns:
AlignmentMetadata object
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
Please note that this implementation does not take the order of sequences - into account! -

-

-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html deleted file mode 100644 index fc54c81..0000000 --- a/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -AlignmentMetadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class AlignmentMetadata

-
-java.lang.Object
-  extended by compbio.data.sequence.AlignmentMetadata
-
-
-
-
@Immutable
-public class AlignmentMetadata
extends java.lang.Object
- - -

-Alignment metadata e.g. method/program being used to generate the alignment - and its parameters -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
AlignmentMetadata(Program program, - char gapchar) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- chargetGapchar() - -
-           
- ProgramgetProgram() - -
-           
- inthashCode() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-AlignmentMetadata

-
-public AlignmentMetadata(Program program,
-                         char gapchar)
-
-
- - - - - - - - -
-Method Detail
- -

-getProgram

-
-public Program getProgram()
-
-
-
-
-
-
- -

-getGapchar

-
-public char getGapchar()
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index f451ac5..0000000 --- a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html +++ /dev/null @@ -1,387 +0,0 @@ - - - - - - -ClustalAlignmentUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.data.sequence -
-Class ClustalAlignmentUtil

-
-java.lang.Object
-  extended by compbio.data.sequence.ClustalAlignmentUtil
-
-
-
-
public final class ClustalAlignmentUtil
extends java.lang.Object
- - -

-Tools to read and write clustal formated files -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
Petr Troshin based on jimp class
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static chargapchar - -
-          Dash char to be used as gap char in the alignments
-  - - - - - - - - - - -
-Constructor Summary
ClustalAlignmentUtil() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleanisValidClustalFile(java.io.InputStream input) - -
-          Please note this method closes the input stream provided as a parameter
-static AlignmentreadClustalFile(java.io.File file) - -
-           
-static AlignmentreadClustalFile(java.io.InputStream instream) - -
-          Read Clustal formatted alignment.
-static voidwriteClustalAlignment(java.io.Writer out, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-gapchar

-
-public static final char gapchar
-
-
Dash char to be used as gap char in the alignments -

-

-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ClustalAlignmentUtil

-
-public ClustalAlignmentUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-readClustalFile

-
-public static Alignment readClustalFile(java.io.InputStream instream)
-                                 throws java.io.IOException,
-                                        UnknownFileFormatException
-
-
Read Clustal formatted alignment. Limitations: Does not read consensus - - Sequence names as well as the sequences are not guaranteed to be unique! -

-

- -
Throws: -
{@link - IOException} -
{@link - UnknownFileFormatException} -
java.io.IOException -
UnknownFileFormatException
-
-
-
- -

-isValidClustalFile

-
-public static boolean isValidClustalFile(java.io.InputStream input)
-
-
Please note this method closes the input stream provided as a parameter -

-

-
Parameters:
input - -
Returns:
true if the file is recognised as Clustal formatted alignment, - false otherwise
-
-
-
- -

-writeClustalAlignment

-
-public static void writeClustalAlignment(java.io.Writer out,
-                                         Alignment alignment)
-                                  throws java.io.IOException
-
-
Write Clustal formatted alignment Limitations: does not record the - consensus. Potential bug - records 60 chars length alignment where - Clustal would have recorded 50 chars. -

-

-
Parameters:
out -
alignment - -
Throws: -
java.io.IOException
-
-
-
- -

-readClustalFile

-
-public static Alignment readClustalFile(java.io.File file)
-                                 throws UnknownFileFormatException,
-                                        java.io.IOException
-
-
- -
Throws: -
UnknownFileFormatException -
java.io.IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/ConservationMethod.html b/website/dm_javadoc/compbio/data/sequence/ConservationMethod.html deleted file mode 100644 index 1c35f81..0000000 --- a/website/dm_javadoc/compbio/data/sequence/ConservationMethod.html +++ /dev/null @@ -1,605 +0,0 @@ - - - - - - -ConservationMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum ConservationMethod

-
-java.lang.Object
-  extended by java.lang.Enum<ConservationMethod>
-      extended by compbio.data.sequence.ConservationMethod
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<ConservationMethod>
-
-
-
-
public enum ConservationMethod
extends java.lang.Enum<ConservationMethod>
- - -

-Enumeration listing of all the supported methods. -

- -

-

-
Author:
-
Agnieszka Golicz & Peter Troshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
ARMON - -
-           
GERSTEIN - -
-           
JORES - -
-           
KABAT - -
-           
KARLIN - -
-           
LANDGRAF - -
-           
MIRNY - -
-           
NOT_LANCET - -
-           
SANDER - -
-           
SCHNEIDER - -
-           
SHENKIN - -
-           
SMERFS - -
-           
TAYLOR_GAPS - -
-           
TAYLOR_NO_GAPS - -
-           
THOMPSON - -
-           
VALDAR - -
-           
WILLIAMSON - -
-           
ZVELIBIL - -
-           
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static ConservationMethodgetMethod(java.lang.String meth) - -
-           
-static ConservationMethodvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static ConservationMethod[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-KABAT

-
-public static final ConservationMethod KABAT
-
-
-
-
-
- -

-JORES

-
-public static final ConservationMethod JORES
-
-
-
-
-
- -

-SCHNEIDER

-
-public static final ConservationMethod SCHNEIDER
-
-
-
-
-
- -

-SHENKIN

-
-public static final ConservationMethod SHENKIN
-
-
-
-
-
- -

-GERSTEIN

-
-public static final ConservationMethod GERSTEIN
-
-
-
-
-
- -

-TAYLOR_GAPS

-
-public static final ConservationMethod TAYLOR_GAPS
-
-
-
-
-
- -

-TAYLOR_NO_GAPS

-
-public static final ConservationMethod TAYLOR_NO_GAPS
-
-
-
-
-
- -

-ZVELIBIL

-
-public static final ConservationMethod ZVELIBIL
-
-
-
-
-
- -

-KARLIN

-
-public static final ConservationMethod KARLIN
-
-
-
-
-
- -

-ARMON

-
-public static final ConservationMethod ARMON
-
-
-
-
-
- -

-THOMPSON

-
-public static final ConservationMethod THOMPSON
-
-
-
-
-
- -

-NOT_LANCET

-
-public static final ConservationMethod NOT_LANCET
-
-
-
-
-
- -

-MIRNY

-
-public static final ConservationMethod MIRNY
-
-
-
-
-
- -

-WILLIAMSON

-
-public static final ConservationMethod WILLIAMSON
-
-
-
-
-
- -

-LANDGRAF

-
-public static final ConservationMethod LANDGRAF
-
-
-
-
-
- -

-SANDER

-
-public static final ConservationMethod SANDER
-
-
-
-
-
- -

-VALDAR

-
-public static final ConservationMethod VALDAR
-
-
-
-
-
- -

-SMERFS

-
-public static final ConservationMethod SMERFS
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static ConservationMethod[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (ConservationMethod c : ConservationMethod.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static ConservationMethod valueOf(java.lang.String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
-
- -

-getMethod

-
-public static ConservationMethod getMethod(java.lang.String meth)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/DisorderMethod.html b/website/dm_javadoc/compbio/data/sequence/DisorderMethod.html deleted file mode 100644 index c3be12a..0000000 --- a/website/dm_javadoc/compbio/data/sequence/DisorderMethod.html +++ /dev/null @@ -1,322 +0,0 @@ - - - - - - -DisorderMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum DisorderMethod

-
-java.lang.Object
-  extended by java.lang.Enum<DisorderMethod>
-      extended by compbio.data.sequence.DisorderMethod
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<DisorderMethod>
-
-
-
-
public enum DisorderMethod
extends java.lang.Enum<DisorderMethod>
- - -

-

- -

- - - - - - - - - - - - - -
-Enum Constant Summary
Disembl - -
-           
JRonn - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static DisorderMethodvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static DisorderMethod[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-JRonn

-
-public static final DisorderMethod JRonn
-
-
-
-
-
- -

-Disembl

-
-public static final DisorderMethod Disembl
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static DisorderMethod[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (DisorderMethod c : DisorderMethod.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static DisorderMethod valueOf(java.lang.String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/FastaReader.html b/website/dm_javadoc/compbio/data/sequence/FastaReader.html deleted file mode 100644 index ac48bd5..0000000 --- a/website/dm_javadoc/compbio/data/sequence/FastaReader.html +++ /dev/null @@ -1,415 +0,0 @@ - - - - - - -FastaReader - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class FastaReader

-
-java.lang.Object
-  extended by compbio.data.sequence.FastaReader
-
-
-
All Implemented Interfaces:
java.util.Iterator<FastaSequence>
-
-
-
-
public class FastaReader
extends java.lang.Object
implements java.util.Iterator<FastaSequence>
- - -

-Reads files with FASTA formatted sequences. All the information in the FASTA - header is preserved including trailing white spaces. All the white spaces are - removed from the sequence. - - Examples of the correct input: - - 

- 
- >zedpshvyzg
- GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
- 
- >xovkactesa
- CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
- FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
- FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
- DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
- 
- >ntazzewyvv
- CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
- EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
- EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
-   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
-   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
-   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
- 
-    > 12 d t y wi               k       jbke    
-   KLSHHDCD
-    N
-     H
-     HSKCTEPHCGNSHQMLHRDP
-     CCDQCQSWEAENWCASMRKAILF
- 
-
-

- -

-

-
Version:
-
1.0 April 2011
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
FastaReader(java.io.InputStream inputStream) - -
-          This class will not close the incoming stream! So the client should do - so.
FastaReader(java.lang.String inputFile) - -
-          Header data can contain non-ASCII symbols and read in UTF8
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidclose() - -
-          Call this method to close the connection to the input file if you want to - free up the resources.
- booleanhasNext() - -
-          
- FastaSequencenext() - -
-          Reads the next FastaSequence from the input
- voidremove() - -
-          Not implemented
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-FastaReader

-
-public FastaReader(java.lang.String inputFile)
-            throws java.io.FileNotFoundException
-
-
Header data can contain non-ASCII symbols and read in UTF8 -

-

-
Parameters:
inputFile - the file containing the list of FASTA formatted sequences to - read from -
Throws: -
java.io.FileNotFoundException - if the input file is not found -
java.lang.IllegalStateException - if the close method was called on this instance
-
-
- -

-FastaReader

-
-public FastaReader(java.io.InputStream inputStream)
-            throws java.io.FileNotFoundException
-
-
This class will not close the incoming stream! So the client should do - so. -

-

-
Parameters:
inputStream - -
Throws: -
java.io.FileNotFoundException
-
- - - - - - - - -
-Method Detail
- -

-hasNext

-
-public boolean hasNext()
-
-
-

-

-
Specified by:
hasNext in interface java.util.Iterator<FastaSequence>
-
-
- -
Throws: -
java.lang.IllegalStateException - if the close method was called on this instance
-
-
-
- -

-next

-
-public FastaSequence next()
-
-
Reads the next FastaSequence from the input -

-

-
Specified by:
next in interface java.util.Iterator<FastaSequence>
-
-
- -
Throws: -
java.lang.AssertionError - if the header or the sequence is missing -
java.lang.IllegalStateException - if the close method was called on this instance
-
-
-
- -

-remove

-
-public void remove()
-
-
Not implemented -

-

-
Specified by:
remove in interface java.util.Iterator<FastaSequence>
-
-
-
-
-
-
- -

-close

-
-public void close()
-
-
Call this method to close the connection to the input file if you want to - free up the resources. The connection will be closed on the JVM shutdown - if this method was not called explicitly. No further reading on this - instance of the FastaReader will be possible after calling this method. -

-

-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index 8d7a42a..0000000 --- a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -FastaSequence - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class FastaSequence

-
-java.lang.Object
-  extended by compbio.data.sequence.FastaSequence
-
-
-
-
@Immutable
-public class FastaSequence
extends java.lang.Object
- - -

-A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it stores e.g. it could be nucleotide, - protein or even gapped alignment sequence! The only guarantee it makes is - that the sequence does not contain white space characters e.g. spaces, new - lines etc -

- -

-

-
Version:
-
1.0 September 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
FastaSequence(java.lang.String id, - java.lang.String sequence) - -
-          Upon construction the any whitespace characters are removed from the - sequence
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static intcountMatchesInSequence(java.lang.String theString, - java.lang.String theRegExp) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetFormatedSequence(int width) - -
-          Format sequence per width letter in one string.
- java.lang.StringgetFormattedFasta() - -
-           
- java.lang.StringgetId() - -
-          Gets the value of id
- intgetLength() - -
-           
- java.lang.StringgetOnelineFasta() - -
-           
- java.lang.StringgetSequence() - -
-          Gets the value of sequence
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-          Same as oneLineFasta
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-FastaSequence

-
-public FastaSequence(java.lang.String id,
-                     java.lang.String sequence)
-
-
Upon construction the any whitespace characters are removed from the - sequence -

-

-
Parameters:
id -
sequence -
-
- - - - - - - - -
-Method Detail
- -

-getId

-
-public java.lang.String getId()
-
-
Gets the value of id -

-

- -
Returns:
the value of id
-
-
-
- -

-getSequence

-
-public java.lang.String getSequence()
-
-
Gets the value of sequence -

-

- -
Returns:
the value of sequence
-
-
-
- -

-countMatchesInSequence

-
-public static int countMatchesInSequence(java.lang.String theString,
-                                         java.lang.String theRegExp)
-
-
-
-
-
-
- -

-getFormattedFasta

-
-public java.lang.String getFormattedFasta()
-
-
-
-
-
-
- -

-getOnelineFasta

-
-public java.lang.String getOnelineFasta()
-
-
- -
Returns:
one line name, next line sequence, no matter what the sequence - length is
-
-
-
- -

-getFormatedSequence

-
-public java.lang.String getFormatedSequence(int width)
-
-
Format sequence per width letter in one string. Without spaces. -

-

- -
Returns:
multiple line formated sequence, one line width letters length
-
-
-
- -

-getLength

-
-public int getLength()
-
-
- -
Returns:
sequence length
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
Same as oneLineFasta -

-

-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index 95106cf..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Program.html +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - -Program - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum Program

-
-java.lang.Object
-  extended by java.lang.Enum<Program>
-      extended by compbio.data.sequence.Program
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<Program>
-
-
-
-
public enum Program
extends java.lang.Enum<Program>
- - -

-The list of programmes that can produce alignments -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CLUSTAL - -
-          ClustalW
MAFFT - -
-          Mafft
MUSCLE - -
-          Muscle
Probcons - -
-          Probcons
Tcoffee - -
-          Tcoffee
-  - - - - - - - - - - - - - - - -
-Method Summary
-static ProgramvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static Program[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-CLUSTAL

-
-public static final Program CLUSTAL
-
-
ClustalW -

-

-
-
-
- -

-MAFFT

-
-public static final Program MAFFT
-
-
Mafft -

-

-
-
-
- -

-MUSCLE

-
-public static final Program MUSCLE
-
-
Muscle -

-

-
-
-
- -

-Tcoffee

-
-public static final Program Tcoffee
-
-
Tcoffee -

-

-
-
-
- -

-Probcons

-
-public static final Program Probcons
-
-
Probcons -

-

-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static Program[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (Program c : Program.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static Program valueOf(java.lang.String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Range.html b/website/dm_javadoc/compbio/data/sequence/Range.html deleted file mode 100644 index 2006121..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Range.html +++ /dev/null @@ -1,394 +0,0 @@ - - - - - - -Range - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class Range

-
-java.lang.Object
-  extended by compbio.data.sequence.Range
-
-
-
All Implemented Interfaces:
java.lang.Comparable<Range>
-
-
-
-
public class Range
extends java.lang.Object
implements java.lang.Comparable<Range>
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
- intfrom - -
-           
- intto - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
Range(int from, - int to) - -
-           
Range(java.lang.String[] twoElementAr) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Range o) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-from

-
-public final int from
-
-
-
-
-
- -

-to

-
-public final int to
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-Range

-
-public Range(int from,
-             int to)
-
-
-
- -

-Range

-
-public Range(java.lang.String[] twoElementAr)
-
-
- - - - - - - - -
-Method Detail
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-compareTo

-
-public int compareTo(Range o)
-
-
-
Specified by:
compareTo in interface java.lang.Comparable<Range>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html deleted file mode 100644 index 589f5a4..0000000 --- a/website/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - -SMERFSConstraints - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum SMERFSConstraints

-
-java.lang.Object
-  extended by java.lang.Enum<SMERFSConstraints>
-      extended by compbio.data.sequence.SMERFSConstraints
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<SMERFSConstraints>
-
-
-
-
public enum SMERFSConstraints
extends java.lang.Enum<SMERFSConstraints>
- - -

-Enumeration defining two constraints for SMERFS columns score calculation. - MAX_SCORE gives the highest core of all the windows the column belongs to. - MID_SCORE gives the window score to the column in the middle. -

- -

-

-
Author:
-
Agnieszka Golicz & Peter Troshin
-
-
- -

- - - - - - - - - - - - - -
-Enum Constant Summary
MAX_SCORE - -
-           
MID_SCORE - -
-           
-  - - - - - - - - - - - - - - - - - - -
-Field Summary
-static SMERFSConstraintsDEFAULT_COLUMN_SCORE - -
-          Default column scoring schema
-static doubleDEFAULT_GAP_THRESHOLD - -
-          Default gap threshold value for SMERFS algorithm
-static intDEFAULT_WINDOW_SIZE - -
-          Default window size value for SMERFS algorithm
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static SMERFSConstraintsgetSMERFSColumnScore(java.lang.String score) - -
-           
-static SMERFSConstraintsvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static SMERFSConstraints[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-MAX_SCORE

-
-public static final SMERFSConstraints MAX_SCORE
-
-
-
-
-
- -

-MID_SCORE

-
-public static final SMERFSConstraints MID_SCORE
-
-
-
-
- - - - - - - - -
-Field Detail
- -

-DEFAULT_COLUMN_SCORE

-
-public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
-
-
Default column scoring schema -

-

-
-
-
- -

-DEFAULT_WINDOW_SIZE

-
-public static final int DEFAULT_WINDOW_SIZE
-
-
Default window size value for SMERFS algorithm -

-

-
See Also:
Constant Field Values
-
-
- -

-DEFAULT_GAP_THRESHOLD

-
-public static final double DEFAULT_GAP_THRESHOLD
-
-
Default gap threshold value for SMERFS algorithm -

-

-
See Also:
Constant Field Values
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static SMERFSConstraints[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (SMERFSConstraints c : SMERFSConstraints.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static SMERFSConstraints valueOf(java.lang.String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
-
- -

-getSMERFSColumnScore

-
-public static SMERFSConstraints getSMERFSColumnScore(java.lang.String score)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Score.html b/website/dm_javadoc/compbio/data/sequence/Score.html deleted file mode 100644 index 93e7259..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Score.html +++ /dev/null @@ -1,537 +0,0 @@ - - - - - - -Score - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class Score

-
-java.lang.Object
-  extended by compbio.data.sequence.Score
-
-
-
All Implemented Interfaces:
java.lang.Comparable<Score>
-
-
-
-
@Immutable
-public class Score
extends java.lang.Object
implements java.lang.Comparable<Score>
- - -

-A value class for AACon annotation results storage. The objects of this type - are immutable -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - -
-Constructor Summary
Score(java.lang.Enum<?> method, - java.util.ArrayList<java.lang.Float> scores) - -
-          Instantiate the Score
Score(java.lang.Enum<?> method, - java.util.ArrayList<java.lang.Float> scores, - java.util.TreeSet<Range> ranges) - -
-           
Score(java.lang.Enum<?> method, - float[] scores) - -
-           
Score(java.lang.Enum<?> method, - java.util.TreeSet<Range> ranges) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Score o) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetMethod() - -
-          Returns the ConservationMethod
- java.util.TreeSet<Range>getRanges() - -
-          Return Ranges if any Collections.EMPTY_SET otherwise
- java.util.ArrayList<java.lang.Float>getScores() - -
-          The column scores for the alignment
- inthashCode() - -
-           
- voidsetRanges(java.util.TreeSet<Range> ranges) - -
-           
- java.lang.StringtoString() - -
-           
-static voidwrite(java.util.TreeSet<Score> scores, - java.io.Writer writer) - -
-          Outputs the List of Score objects into the Output stream.
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Score

-
-public Score(java.lang.Enum<?> method,
-             java.util.ArrayList<java.lang.Float> scores)
-
-
Instantiate the Score -

-

-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
-
-
- -

-Score

-
-public Score(java.lang.Enum<?> method,
-             java.util.ArrayList<java.lang.Float> scores,
-             java.util.TreeSet<Range> ranges)
-
-
-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
ranges - The set of ranges i.e. parts of the sequence with specific - function, usually can be calculated based on scores
-
-
- -

-Score

-
-public Score(java.lang.Enum<?> method,
-             java.util.TreeSet<Range> ranges)
-
-
-
- -

-Score

-
-public Score(java.lang.Enum<?> method,
-             float[] scores)
-
-
- - - - - - - - -
-Method Detail
- -

-getMethod

-
-public java.lang.String getMethod()
-
-
Returns the ConservationMethod -

-

-
-
-
- -
Returns:
the ConservationMethod
-
-
-
- -

-getScores

-
-public java.util.ArrayList<java.lang.Float> getScores()
-
-
The column scores for the alignment -

-

-
-
-
- -
Returns:
the column scores for the alignment
-
-
-
- -

-getRanges

-
-public java.util.TreeSet<Range> getRanges()
-
-
Return Ranges if any Collections.EMPTY_SET otherwise -

-

-
-
-
- -
Returns:
ordered set of Range
-
-
-
- -

-setRanges

-
-public void setRanges(java.util.TreeSet<Range> ranges)
-
-
-
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-write

-
-public static void write(java.util.TreeSet<Score> scores,
-                         java.io.Writer writer)
-                  throws java.io.IOException
-
-
Outputs the List of Score objects into the Output stream. The output - format is as follows: - - 
- #MethodName <space separated list of values>
- 	  
- For example:
- 	 
- #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
- #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
- 
-
- - The maximum precision for values is 3 digits, but can be less. -

-

-
-
-
-
Parameters:
scores - the list of scores to output
writer - -
Throws: -
java.io.IOException - if the OutputStream cannot be written into -
java.lang.NullPointerException - if the output stream is null
-
-
-
- -

-compareTo

-
-public int compareTo(Score o)
-
-
-
Specified by:
compareTo in interface java.lang.Comparable<Score>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html b/website/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html deleted file mode 100644 index 0b3d81c..0000000 --- a/website/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html +++ /dev/null @@ -1,380 +0,0 @@ - - - - - - -ScoreManager.ScoreHolder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class ScoreManager.ScoreHolder

-
-java.lang.Object
-  extended by compbio.data.sequence.ScoreManager.ScoreHolder
-
-
-
Enclosing class:
ScoreManager
-
-
-
-
public static class ScoreManager.ScoreHolder
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
- java.lang.Stringid - -
-           
- java.util.TreeSet<Score>scores - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- intgetNumberOfScores() - -
-           
- ScoregetScoreByMethod(java.lang.Enum<?> method) - -
-           
- ScoregetScoreByMethod(java.lang.String method) - -
-           
- inthashCode() - -
-           
- voidwriteOut(java.io.Writer writer) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-id

-
-public java.lang.String id
-
-
-
-
-
- -

-scores

-
-public java.util.TreeSet<Score> scores
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-writeOut

-
-public void writeOut(java.io.Writer writer)
-              throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-getScoreByMethod

-
-public Score getScoreByMethod(java.lang.Enum<?> method)
-
-
-
-
-
-
- -

-getScoreByMethod

-
-public Score getScoreByMethod(java.lang.String method)
-
-
-
-
-
-
- -

-getNumberOfScores

-
-public int getNumberOfScores()
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/ScoreManager.html b/website/dm_javadoc/compbio/data/sequence/ScoreManager.html deleted file mode 100644 index fb95141..0000000 --- a/website/dm_javadoc/compbio/data/sequence/ScoreManager.html +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - -ScoreManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class ScoreManager

-
-java.lang.Object
-  extended by compbio.data.sequence.ScoreManager
-
-
-
-
public class ScoreManager
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Nested Class Summary
-static classScoreManager.ScoreHolder - -
-           
-  - - - - - - - - - - -
-Field Summary
-static java.lang.StringSINGLE_ENTRY_KEY - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Map<java.lang.String,java.util.TreeSet<Score>>asMap() - -
-           
- java.util.Set<Score>asSet() - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- ScoreManager.ScoreHoldergetAnnotationForSequence(java.lang.String seqId) - -
-           
- intgetNumberOfSeq() - -
-           
- inthashCode() - -
-           
-static ScoreManagernewInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data) - -
-           
-static ScoreManagernewInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap) - -
-           
-static ScoreManagernewInstanceSingleSequence(java.util.Set<Score> data) - -
-           
- voidwriteOut(java.io.Writer outStream) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-SINGLE_ENTRY_KEY

-
-public static final java.lang.String SINGLE_ENTRY_KEY
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Method Detail
- -

-newInstance

-
-public static ScoreManager newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data)
-
-
-
-
-
-
- -

-newInstanceSingleScore

-
-public static ScoreManager newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap)
-
-
-
-
-
-
- -

-newInstanceSingleSequence

-
-public static ScoreManager newInstanceSingleSequence(java.util.Set<Score> data)
-
-
-
-
-
-
- -

-asMap

-
-public java.util.Map<java.lang.String,java.util.TreeSet<Score>> asMap()
-
-
-
-
-
-
- -

-asSet

-
-public java.util.Set<Score> asSet()
-
-
-
-
-
-
- -

-getNumberOfSeq

-
-public int getNumberOfSeq()
-
-
-
-
-
-
- -

-getAnnotationForSequence

-
-public ScoreManager.ScoreHolder getAnnotationForSequence(java.lang.String seqId)
-
-
-
-
-
-
- -

-writeOut

-
-public void writeOut(java.io.Writer outStream)
-              throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index 4fd53ee..0000000 --- a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,946 +0,0 @@ - - - - - - -SequenceUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
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- -

- -compbio.data.sequence -
-Class SequenceUtil

-
-java.lang.Object
-  extended by compbio.data.sequence.SequenceUtil
-
-
-
-
public final class SequenceUtil
extends java.lang.Object
- - -

-Utility class for operations on sequences -

- -

-

-
Since:
-
1.0
-
Version:
-
2.0 June 2011
-
Author:
-
Peter Troshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static java.util.regex.PatternAA - -
-          Valid Amino acids
-static java.util.regex.PatternAMBIGUOUS_AA - -
-          Same as AA pattern but with two additional letters - XU
-static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE - -
-          Ambiguous nucleotide
-static java.util.regex.PatternDIGIT - -
-          A digit
-static java.util.regex.PatternNON_AA - -
-          inversion of AA pattern
-static java.util.regex.PatternNON_NUCLEOTIDE - -
-          Non nucleotide
-static java.util.regex.PatternNONWORD - -
-          Non word
-static java.util.regex.PatternNUCLEOTIDE - -
-          Nucleotides a, t, g, c, u
-static java.util.regex.PatternWHITE_SPACE - -
-          A whitespace character: [\t\n\x0B\f\r]
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static java.lang.StringcleanProteinSequence(java.lang.String sequence) - -
-          Remove all non AA chars from the sequence
-static java.lang.StringcleanSequence(java.lang.String sequence) - -
-          Removes all whitespace chars in the sequence string
-static voidcloseSilently(java.util.logging.Logger log, - java.io.Closeable stream) - -
-          Closes the Closable and logs the exception if any
-static java.lang.StringdeepCleanSequence(java.lang.String sequence) - -
-          Removes all special characters and digits as well as whitespace chars - from the sequence
-static booleanisAmbiguosProtein(java.lang.String sequence) - -
-          Check whether the sequence confirms to amboguous protein sequence
-static booleanisNonAmbNucleotideSequence(java.lang.String sequence) - -
-          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
-static booleanisNucleotideSequence(FastaSequence s) - -
-           
-static booleanisProteinSequence(java.lang.String sequence) - -
-           
-static java.util.List<FastaSequence>openInputStream(java.lang.String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static java.util.HashSet<Score>readAAConResults(java.io.InputStream results) - -
-          Read AACon result with no alignment files.
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>readDisembl(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>readGlobPlot(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.Map<java.lang.String,Score>readIUPred(java.io.File result) - -
-          Read IUPred output
-static java.util.Map<java.lang.String,Score>readJRonn(java.io.File result) - -
-           
-static java.util.Map<java.lang.String,Score>readJRonn(java.io.InputStream inStream) - -
-          Reader for JRonn horizontal file format
-static voidwriteFasta(java.io.OutputStream os, - java.util.List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static voidwriteFasta(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-static voidwriteFastaKeepTheStream(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, - int width) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-WHITE_SPACE

-
-public static final java.util.regex.Pattern WHITE_SPACE
-
-
A whitespace character: [\t\n\x0B\f\r] -

-

-
-
-
- -

-DIGIT

-
-public static final java.util.regex.Pattern DIGIT
-
-
A digit -

-

-
-
-
- -

-NONWORD

-
-public static final java.util.regex.Pattern NONWORD
-
-
Non word -

-

-
-
-
- -

-AA

-
-public static final java.util.regex.Pattern AA
-
-
Valid Amino acids -

-

-
-
-
- -

-NON_AA

-
-public static final java.util.regex.Pattern NON_AA
-
-
inversion of AA pattern -

-

-
-
-
- -

-AMBIGUOUS_AA

-
-public static final java.util.regex.Pattern AMBIGUOUS_AA
-
-
Same as AA pattern but with two additional letters - XU -

-

-
-
-
- -

-NUCLEOTIDE

-
-public static final java.util.regex.Pattern NUCLEOTIDE
-
-
Nucleotides a, t, g, c, u -

-

-
-
-
- -

-AMBIGUOUS_NUCLEOTIDE

-
-public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
-
-
Ambiguous nucleotide -

-

-
-
-
- -

-NON_NUCLEOTIDE

-
-public static final java.util.regex.Pattern NON_NUCLEOTIDE
-
-
Non nucleotide -

-

-
-
- - - - - - - - -
-Method Detail
- -

-isNucleotideSequence

-
-public static boolean isNucleotideSequence(FastaSequence s)
-
-
- -
Returns:
true is the sequence contains only letters a,c, t, g, u
-
-
-
- -

-isNonAmbNucleotideSequence

-
-public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
-
-
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -

-

-
-
-
-
- -

-cleanSequence

-
-public static java.lang.String cleanSequence(java.lang.String sequence)
-
-
Removes all whitespace chars in the sequence string -

-

-
Parameters:
sequence - -
Returns:
cleaned up sequence
-
-
-
- -

-deepCleanSequence

-
-public static java.lang.String deepCleanSequence(java.lang.String sequence)
-
-
Removes all special characters and digits as well as whitespace chars - from the sequence -

-

-
Parameters:
sequence - -
Returns:
cleaned up sequence
-
-
-
- -

-cleanProteinSequence

-
-public static java.lang.String cleanProteinSequence(java.lang.String sequence)
-
-
Remove all non AA chars from the sequence -

-

-
Parameters:
sequence - the sequence to clean -
Returns:
cleaned sequence
-
-
-
- -

-isProteinSequence

-
-public static boolean isProteinSequence(java.lang.String sequence)
-
-
-
Parameters:
sequence - -
Returns:
true is the sequence is a protein sequence, false overwise
-
-
-
- -

-isAmbiguosProtein

-
-public static boolean isAmbiguosProtein(java.lang.String sequence)
-
-
Check whether the sequence confirms to amboguous protein sequence -

-

-
Parameters:
sequence - -
Returns:
return true only if the sequence if ambiguous protein sequence - Return false otherwise. e.g. if the sequence is non-ambiguous - protein or DNA
-
-
-
- -

-writeFasta

-
-public static void writeFasta(java.io.OutputStream outstream,
-                              java.util.List<FastaSequence> sequences,
-                              int width)
-                       throws java.io.IOException
-
-
Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -

-

-
Parameters:
outstream -
sequences -
width - - the maximum number of characters to write in one line -
Throws: -
java.io.IOException
-
-
-
- -

-writeFastaKeepTheStream

-
-public static void writeFastaKeepTheStream(java.io.OutputStream outstream,
-                                           java.util.List<FastaSequence> sequences,
-                                           int width)
-                                    throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-readFasta

-
-public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
-                                               throws java.io.IOException
-
-
Reads fasta sequences from inStream into the list of FastaSequence - objects -

-

-
Parameters:
inStream - from -
Returns:
list of FastaSequence objects -
Throws: -
java.io.IOException
-
-
-
- -

-writeFasta

-
-public static void writeFasta(java.io.OutputStream os,
-                              java.util.List<FastaSequence> sequences)
-                       throws java.io.IOException
-
-
Writes FastaSequence in the file, each sequence will take one line only -

-

-
Parameters:
os -
sequences - -
Throws: -
java.io.IOException
-
-
-
- -

-readIUPred

-
-public static java.util.Map<java.lang.String,Score> readIUPred(java.io.File result)
-                                                        throws java.io.IOException,
-                                                               UnknownFileFormatException
-
-
Read IUPred output -

-

-
Parameters:
result - -
Returns:
Map key->sequence name, value->Score -
Throws: -
java.io.IOException -
UnknownFileFormatException
-
-
-
- -

-readJRonn

-
-public static java.util.Map<java.lang.String,Score> readJRonn(java.io.File result)
-                                                       throws java.io.IOException,
-                                                              UnknownFileFormatException
-
-
- -
Throws: -
java.io.IOException -
UnknownFileFormatException
-
-
-
- -

-readJRonn

-
-public static java.util.Map<java.lang.String,Score> readJRonn(java.io.InputStream inStream)
-                                                       throws java.io.IOException,
-                                                              UnknownFileFormatException
-
-
Reader for JRonn horizontal file format - - 
- >Foobar M G D T T A G 0.48 0.42
- 0.42 0.48 0.52 0.53 0.54
- 
- 
- Where all values are tab delimited
-

-

-
Parameters:
inStream - the InputStream connected to the JRonn output file
-
Returns:
Map key=sequence name value=Score
-
Throws:
-
java.io.IOException - is thrown if the inStream has problems accessing the data
-
UnknownFileFormatException - is thrown if the inStream represents an unknown source of
- data, i.e. not a JRonn output

-

-
-
- -

-closeSilently

-
-public static final void closeSilently(java.util.logging.Logger log,
-                                       java.io.Closeable stream)
-
-
Closes the Closable and logs the exception if any -

-

-
Parameters:
log -
stream -
-
-
-
- -

-readDisembl

-
-public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readDisembl(java.io.InputStream input)
-                                                                            throws java.io.IOException,
-                                                                                   UnknownFileFormatException
-
-
> Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

-

-
Parameters:
input - the InputStream -
Returns:
Map key=sequence name, value=set of score -
Throws: -
java.io.IOException -
UnknownFileFormatException
-
-
-
- -

-readGlobPlot

-
-public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readGlobPlot(java.io.InputStream input)
-                                                                             throws java.io.IOException,
-                                                                                    UnknownFileFormatException
-
-
> Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

-

-
Parameters:
input - -
Returns:
Map key=sequence name, value=set of score -
Throws: -
java.io.IOException -
UnknownFileFormatException
-
-
-
- -

-readAAConResults

-
-public static java.util.HashSet<Score> readAAConResults(java.io.InputStream results)
-
-
Read AACon result with no alignment files. This method leaves incoming - InputStream open! -

-

-
Parameters:
results - output file of AAConservation -
Returns:
Map with keys ConservationMethod -> float[]
-
-
-
- -

-openInputStream

-
-public static java.util.List<FastaSequence> openInputStream(java.lang.String inFilePath)
-                                                     throws java.io.IOException,
-                                                            UnknownFileFormatException
-
-
Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -

-

-
Parameters:
inFilePath - the path to the input file -
Returns:
the List of FastaSequence objects -
Throws: -
java.io.IOException - if the file denoted by inFilePath cannot be read -
UnknownFileFormatException - if the inFilePath points to the file which format cannot be - recognised
-
-
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- -compbio.data.sequence -
-Class UnknownFileFormatException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.data.sequence.UnknownFileFormatException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class UnknownFileFormatException
extends java.lang.Exception
- - -

-

-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Constructor Summary
UnknownFileFormatException() - -
-           
UnknownFileFormatException(java.io.File file, - java.lang.Throwable cause) - -
-           
UnknownFileFormatException(java.lang.String message) - -
-           
UnknownFileFormatException(java.lang.String message, - java.lang.Throwable cause) - -
-           
UnknownFileFormatException(java.lang.Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException()
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(java.io.File file,
-                                  java.lang.Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(java.lang.String message,
-                                  java.lang.Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(java.lang.String message)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(java.lang.Throwable cause)
-
-
- -
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index 7855bee..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,281 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.Alignment

-
- - - - - - - - - - - - - - - - - -
-Packages that use Alignment
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Alignment in compbio.data.msa
-  -

- - - - - - - - - -
Methods in compbio.data.msa that return Alignment
- AlignmentMsaWS.getResult(java.lang.String jobId) - -
-          Return the result of the job.
-  -

- - - - - -
-Uses of Alignment in compbio.data.msa.jaxws
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws that return Alignment
- AlignmentGetResultResponse.getReturn() - -
-           
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws with parameters of type Alignment
- voidGetResultResponse.setReturn(Alignment _return) - -
-           
-  -

- - - - - -
-Uses of Alignment in compbio.data.sequence
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Alignment
-static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) - -
-           
-static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) - -
-          Read Clustal formatted alignment.
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Alignment
-static voidClustalAlignmentUtil.writeClustalAlignment(java.io.Writer out, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  -

-

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-Uses of Class
compbio.data.sequence.AlignmentMetadata

-
- - - - - - - - - -
-Packages that use AlignmentMetadata
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of AlignmentMetadata in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return AlignmentMetadata
- AlignmentMetadataAlignment.getMetadata() - -
-           
-  -

- - - - - - - - -
Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
Alignment(java.util.List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
-  -

-

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html deleted file mode 100644 index 3252b0a..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ClustalAlignmentUtil - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

-
-No usage of compbio.data.sequence.ClustalAlignmentUtil -

-

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-Uses of Class
compbio.data.sequence.ConservationMethod

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-Packages that use ConservationMethod
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of ConservationMethod in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return ConservationMethod
-static ConservationMethodConservationMethod.getMethod(java.lang.String meth) - -
-           
-static ConservationMethodConservationMethod.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static ConservationMethod[]ConservationMethod.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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-Uses of Class
compbio.data.sequence.DisorderMethod

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-Packages that use DisorderMethod
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of DisorderMethod in compbio.data.sequence
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- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return DisorderMethod
-static DisorderMethodDisorderMethod.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static DisorderMethod[]DisorderMethod.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

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-Uses of Class
compbio.data.sequence.FastaReader

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-No usage of compbio.data.sequence.FastaReader -

-

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-Uses of Class
compbio.data.sequence.FastaSequence

-
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-Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa with type arguments of type FastaSequence
- java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- java.lang.StringSequenceAnnotation.analize(java.util.List<FastaSequence> sequences) - -
-          Analyse the sequences.
- java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
-          Align a list of sequences with options.
- java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
-          Analyse the sequences according to custom settings defined in options - list.
- java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
- java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
-          Analyse the sequences according to the preset settings.
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.msa.jaxws
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
- java.util.List<FastaSequence>PresetAnalize.getFastaSequences() - -
-           
- java.util.List<FastaSequence>PresetAlign.getFastaSequences() - -
-           
- java.util.List<FastaSequence>CustomAnalize.getFastaSequences() - -
-           
- java.util.List<FastaSequence>CustomAlign.getFastaSequences() - -
-           
- java.util.List<FastaSequence>Analize.getFastaSequences() - -
-           
- java.util.List<FastaSequence>Align.getFastaSequences() - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
- voidPresetAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidPresetAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidCustomAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidCustomAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidAnalize.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
- voidAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return FastaSequence
- FastaSequenceFastaReader.next() - -
-          Reads the next FastaSequence from the input
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
- java.util.List<FastaSequence>Alignment.getSequences() - -
-           
-static java.util.List<FastaSequence>SequenceUtil.openInputStream(java.lang.String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type FastaSequence
-static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.sequence with type arguments of type FastaSequence
-static voidSequenceUtil.writeFasta(java.io.OutputStream os, - java.util.List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static voidSequenceUtil.writeFasta(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-static voidSequenceUtil.writeFastaKeepTheStream(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, - int width) - -
-           
-  -

- - - - - - - - - - - -
Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
Alignment(java.util.List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
-           
Alignment(java.util.List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.metadata
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.metadata with type arguments of type FastaSequence
-static intLimit.getAvgSequenceLength(java.util.List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- booleanLimit.isExceeded(java.util.List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
-static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
-           
-  -

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compbio.data.sequence.Program

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-Packages that use Program
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Program in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Program
- ProgramAlignmentMetadata.getProgram() - -
-           
-static ProgramProgram.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static Program[]Program.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - - - - - - - -
Constructors in compbio.data.sequence with parameters of type Program
Alignment(java.util.List<FastaSequence> sequences, - Program program, - char gapchar) - -
-           
AlignmentMetadata(Program program, - char gapchar) - -
-           
-  -

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-Uses of Class
compbio.data.sequence.Range

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-Packages that use Range
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Range in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type Range
- java.util.TreeSet<Range>Score.getRanges() - -
-          Return Ranges if any Collections.EMPTY_SET otherwise
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Range
- intRange.compareTo(Range o) - -
-           
-  -

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Method parameters in compbio.data.sequence with type arguments of type Range
- voidScore.setRanges(java.util.TreeSet<Range> ranges) - -
-           
-  -

- - - - - - - - - - - -
Constructor parameters in compbio.data.sequence with type arguments of type Range
Score(java.lang.Enum<?> method, - java.util.ArrayList<java.lang.Float> scores, - java.util.TreeSet<Range> ranges) - -
-           
Score(java.lang.Enum<?> method, - java.util.TreeSet<Range> ranges) - -
-           
-  -

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-Uses of Class
compbio.data.sequence.SMERFSConstraints

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-Packages that use SMERFSConstraints
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of SMERFSConstraints in compbio.data.sequence
-  -

- - - - - - - - - -
Fields in compbio.data.sequence declared as SMERFSConstraints
-static SMERFSConstraintsSMERFSConstraints.DEFAULT_COLUMN_SCORE - -
-          Default column scoring schema
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return SMERFSConstraints
-static SMERFSConstraintsSMERFSConstraints.getSMERFSColumnScore(java.lang.String score) - -
-           
-static SMERFSConstraintsSMERFSConstraints.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static SMERFSConstraints[]SMERFSConstraints.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

-

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-Uses of Class
compbio.data.sequence.Score

-
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-Packages that use Score
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of Score in compbio.data.sequence
-  -

- - - - - - - - - -
Fields in compbio.data.sequence with type parameters of type Score
- java.util.TreeSet<Score>ScoreManager.ScoreHolder.scores - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return Score
- ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.Enum<?> method) - -
-           
- ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.String method) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type Score
- java.util.Map<java.lang.String,java.util.TreeSet<Score>>ScoreManager.asMap() - -
-           
- java.util.Set<Score>ScoreManager.asSet() - -
-           
-static java.util.HashSet<Score>SequenceUtil.readAAConResults(java.io.InputStream results) - -
-          Read AACon result with no alignment files.
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) - -
-          Read IUPred output
-static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) - -
-           
-static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) - -
-          Reader for JRonn horizontal file format
-  -

- - - - - - - - - -
Methods in compbio.data.sequence with parameters of type Score
- intScore.compareTo(Score o) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.sequence with type arguments of type Score
-static ScoreManagerScoreManager.newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleSequence(java.util.Set<Score> data) - -
-           
-static voidScore.write(java.util.TreeSet<Score> scores, - java.io.Writer writer) - -
-          Outputs the List of Score objects into the Output stream.
-  -

-

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-Uses of Class
compbio.data.sequence.ScoreManager.ScoreHolder

-
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-Packages that use ScoreManager.ScoreHolder
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of ScoreManager.ScoreHolder in compbio.data.sequence
-  -

- - - - - - - - - -
Methods in compbio.data.sequence that return ScoreManager.ScoreHolder
- ScoreManager.ScoreHolderScoreManager.getAnnotationForSequence(java.lang.String seqId) - -
-           
-  -

-

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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ScoreManager.html b/website/dm_javadoc/compbio/data/sequence/class-use/ScoreManager.html deleted file mode 100644 index 7d550fa..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/ScoreManager.html +++ /dev/null @@ -1,271 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ScoreManager - - - - - - - - - - - - -
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-Uses of Class
compbio.data.sequence.ScoreManager

-
- - - - - - - - - - - - - - - - - -
-Packages that use ScoreManager
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.msa
-  -

- - - - - - - - - -
Methods in compbio.data.msa that return ScoreManager
- ScoreManagerSequenceAnnotation.getAnnotation(java.lang.String jobId) - -
-          Return the result of the job.
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.msa.jaxws
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws that return ScoreManager
- ScoreManagerGetAnnotationResponse.getReturn() - -
-           
-  -

- - - - - - - - - -
Methods in compbio.data.msa.jaxws with parameters of type ScoreManager
- voidGetAnnotationResponse.setReturn(ScoreManager _return) - -
-           
-  -

- - - - - -
-Uses of ScoreManager in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that return ScoreManager
-static ScoreManagerScoreManager.newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap) - -
-           
-static ScoreManagerScoreManager.newInstanceSingleSequence(java.util.Set<Score> data) - -
-           
-  -

-

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compbio.data.sequence.SequenceUtil

-
-No usage of compbio.data.sequence.SequenceUtil -

-

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compbio.data.sequence.UnknownFileFormatException

-
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-Packages that use UnknownFileFormatException
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
-  -

- - - - - -
-Uses of UnknownFileFormatException in compbio.data.sequence
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.data.sequence that throw UnknownFileFormatException
-static java.util.List<FastaSequence>SequenceUtil.openInputStream(java.lang.String inFilePath) - -
-          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
-static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) - -
-           
-static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) - -
-          Read Clustal formatted alignment.
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) - -
-          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
-static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) - -
-          Read IUPred output
-static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) - -
-           
-static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) - -
-          Reader for JRonn horizontal file format
-  -

-

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-Classes  - -
-Alignment -
-AlignmentMetadata -
-ClustalAlignmentUtil -
-FastaReader -
-FastaSequence -
-Range -
-Score -
-ScoreManager -
-ScoreManager.ScoreHolder -
-SequenceUtil
- - - - - - -
-Enums  - -
-ConservationMethod -
-DisorderMethod -
-Program -
-SMERFSConstraints
- - - - - - -
-Exceptions  - -
-UnknownFileFormatException
- - - - diff --git a/website/dm_javadoc/compbio/data/sequence/package-summary.html b/website/dm_javadoc/compbio/data/sequence/package-summary.html deleted file mode 100644 index 08becab..0000000 --- a/website/dm_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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-Package compbio.data.sequence -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
AlignmentMultiple sequence alignment.
AlignmentMetadataAlignment metadata e.g.
ClustalAlignmentUtilTools to read and write clustal formated files
FastaReaderReads files with FASTA formatted sequences.
FastaSequenceA FASTA formatted sequence.
Range 
ScoreA value class for AACon annotation results storage.
ScoreManager 
ScoreManager.ScoreHolder 
SequenceUtilUtility class for operations on sequences
-  - -

- - - - - - - - - - - - - - - - - - - - - -
-Enum Summary
ConservationMethodEnumeration listing of all the supported methods.
DisorderMethod 
ProgramThe list of programmes that can produce alignments
SMERFSConstraintsEnumeration defining two constraints for SMERFS columns score calculation.
-  - -

- - - - - - - - - -
-Exception Summary
UnknownFileFormatException 
-  - -

-

-Package compbio.data.sequence Description -

- -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services. -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
Petr Troshin
-
-
- - - - - - - - - - - - - - - -
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-Hierarchy For Package compbio.data.sequence -

-
-
-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Enum Hierarchy -

- -
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-Uses of Package
compbio.data.sequence

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use compbio.data.sequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
ScoreManager - -
-           
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa.jaxws
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
ScoreManager - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.sequence
Alignment - -
-          Multiple sequence alignment.
AlignmentMetadata - -
-          Alignment metadata e.g.
ConservationMethod - -
-          Enumeration listing of all the supported methods.
DisorderMethod - -
-           
FastaSequence - -
-          A FASTA formatted sequence.
Program - -
-          The list of programmes that can produce alignments
Range - -
-           
Score - -
-          A value class for AACon annotation results storage.
ScoreManager - -
-           
ScoreManager.ScoreHolder - -
-           
SMERFSConstraints - -
-          Enumeration defining two constraints for SMERFS columns score calculation.
UnknownFileFormatException - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.metadata
FastaSequence - -
-          A FASTA formatted sequence.
-  -

-

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- - - -
- -

- -compbio.metadata -
-Interface Argument<T>

-
-
Type Parameters:
T - executable type
-
-
All Known Implementing Classes:
Option, Parameter
-
-
-
-
public interface Argument<T>
- - -

-An unmodifiable view for the options and parameters, with one exception - it - allows to set a value -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Parameter, -Option
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetDefaultValue() - -
-           
- java.lang.StringgetDescription() - -
-           
- java.net.URLgetFurtherDetails() - -
-           
- java.lang.StringgetName() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-           
- voidsetValue(java.lang.String defaultValue) - -
-          Set default values for the parameter or an option
-  -

- - - - - - - - -
-Method Detail
- -

-getFurtherDetails

-
-java.net.URL getFurtherDetails()
-
-
-
-
-
-
- -

-getDefaultValue

-
-java.lang.String getDefaultValue()
-
-
-
-
-
-
- -

-getDescription

-
-java.lang.String getDescription()
-
-
-
-
-
-
- -

-getName

-
-java.lang.String getName()
-
-
-
-
-
-
- -

-getPossibleValues

-
-java.util.List<java.lang.String> getPossibleValues()
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-void setValue(java.lang.String defaultValue)
-              throws WrongParameterException
-
-
Set default values for the parameter or an option -

-

-
Parameters:
defaultValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
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- - - diff --git a/website/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html deleted file mode 100644 index 808122d..0000000 --- a/website/dm_javadoc/compbio/metadata/ChunkHolder.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -ChunkHolder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.metadata -
-Class ChunkHolder

-
-java.lang.Object
-  extended by compbio.metadata.ChunkHolder
-
-
-
-
public class ChunkHolder
extends java.lang.Object
- - -

-Represents a chunk of a string data together with the position in a file for - the next read operation. -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
ChunkHolder(java.lang.String chunk, - long position) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetChunk() - -
-           
- longgetNextPosition() - -
-           
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ChunkHolder

-
-public ChunkHolder(java.lang.String chunk,
-                   long position)
-
-
- - - - - - - - -
-Method Detail
- -

-getChunk

-
-public java.lang.String getChunk()
-
-
-
-
-
-
- -

-getNextPosition

-
-public long getNextPosition()
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
- -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 17cd825..0000000 --- a/website/dm_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class JobExecutionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobExecutionException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class JobExecutionException
extends java.lang.Exception
- - -

-JobExecutionException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides DrmaaException -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
JobExecutionException(java.lang.String message) - -
-           
JobExecutionException(java.lang.String message, - java.lang.Throwable cause) - -
-           
JobExecutionException(java.lang.Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobExecutionException

-
-public JobExecutionException(java.lang.String message)
-
-
-
- -

-JobExecutionException

-
-public JobExecutionException(java.lang.Throwable cause)
-
-
-
- -

-JobExecutionException

-
-public JobExecutionException(java.lang.String message,
-                             java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 612053a..0000000 --- a/website/dm_javadoc/compbio/metadata/JobStatus.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -JobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.metadata -
-Enum JobStatus

-
-java.lang.Object
-  extended by java.lang.Enum<JobStatus>
-      extended by compbio.metadata.JobStatus
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<JobStatus>
-
-
-
-
public enum JobStatus
extends java.lang.Enum<JobStatus>
- - -

-The status of the job. -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CANCELLED - -
-          Jobs that has been cancelled
COLLECTED - -
-          Results has been collected
FAILED - -
-          Failed jobs
FINISHED - -
-          Finished jobs
PENDING - -
-          Jobs which are in the queue and awaiting execution reported for cluster - jobs only
RUNNING - -
-          Jobs that are running
STARTED - -
-          Job calculation has been started.
SUBMITTED - -
-          Job has been submitted.
UNDEFINED - -
-          Represents jobs with unknown status
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JobStatusvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static JobStatus[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Enum Constant Detail
- -

-PENDING

-
-public static final JobStatus PENDING
-
-
Jobs which are in the queue and awaiting execution reported for cluster - jobs only -

-

-
-
-
- -

-RUNNING

-
-public static final JobStatus RUNNING
-
-
Jobs that are running -

-

-
-
-
- -

-CANCELLED

-
-public static final JobStatus CANCELLED
-
-
Jobs that has been cancelled -

-

-
-
-
- -

-FINISHED

-
-public static final JobStatus FINISHED
-
-
Finished jobs -

-

-
-
-
- -

-FAILED

-
-public static final JobStatus FAILED
-
-
Failed jobs -

-

-
-
-
- -

-UNDEFINED

-
-public static final JobStatus UNDEFINED
-
-
Represents jobs with unknown status -

-

-
-
-
- -

-STARTED

-
-public static final JobStatus STARTED
-
-
Job calculation has been started. First status reported by the local - engine -

-

-
-
-
- -

-SUBMITTED

-
-public static final JobStatus SUBMITTED
-
-
Job has been submitted. This status is only set for cluster jobs -

-

-
-
-
- -

-COLLECTED

-
-public static final JobStatus COLLECTED
-
-
Results has been collected -

-

-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static JobStatus[] values()
-
-
Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
-for (JobStatus c : JobStatus.values())
-    System.out.println(c);
-
-

-

- -
Returns:
an array containing the constants of this enum type, in -the order they are declared
-
-
-
- -

-valueOf

-
-public static JobStatus valueOf(java.lang.String name)
-
-
Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index 667937a..0000000 --- a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -JobSubmissionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class JobSubmissionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
-
-
-
-
public class JobSubmissionException
extends java.lang.Exception
- - -

-Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException. If - this exception is thrown the task has not been calculated -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
JobSubmissionException(java.lang.String message) - -
-           
JobSubmissionException(java.lang.String message, - java.lang.Throwable cause) - -
-           
JobSubmissionException(java.lang.Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-JobSubmissionException

-
-public JobSubmissionException(java.lang.String message)
-
-
-
- -

-JobSubmissionException

-
-public JobSubmissionException(java.lang.Throwable cause)
-
-
-
- -

-JobSubmissionException

-
-public JobSubmissionException(java.lang.String message,
-                              java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index edb3712..0000000 --- a/website/dm_javadoc/compbio/metadata/Limit.html +++ /dev/null @@ -1,478 +0,0 @@ - - - - - - -Limit - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Limit<T>

-
-java.lang.Object
-  extended by compbio.metadata.Limit<T>
-
-
-
Type Parameters:
T - the type of an executable for which this limit is defined.
-
-
-
public class Limit<T>
extends java.lang.Object
- - -

-A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. Also contains static method for determining the - number of sequence and their average length in the List -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
pvtroshin
-
See Also:
LimitsManager
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
Limit(int seqNumber, - int seqLength, - java.lang.String preset) - -
-          Instantiate the limit
Limit(int seqNumber, - int seqLength, - java.lang.String preset, - boolean isDefault) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- intgetAvgSeqLength() - -
-           
-static intgetAvgSequenceLength(java.util.List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- java.lang.StringgetPreset() - -
-           
- intgetSeqNumber() - -
-           
- inthashCode() - -
-           
- booleanisDefault() - -
-           
- booleanisExceeded(java.util.List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             java.lang.String preset)
-
-
Instantiate the limit -

-

-
Parameters:
seqNumber - the maximum number of sequences allowed for calculation. - Required
seqLength - the average length of the sequence, optional
preset - the name of preset if any, optional -
Throws: -
java.lang.IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
-
-
- -

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             java.lang.String preset,
-             boolean isDefault)
-
-
- - - - - - - - -
-Method Detail
- -

-getPreset

-
-public java.lang.String getPreset()
-
-
-
-
-
-
- -

-getAvgSeqLength

-
-public int getAvgSeqLength()
-
-
- -
Returns:
the allowed average sequence length
-
-
-
- -

-getSeqNumber

-
-public int getSeqNumber()
-
-
- -
Returns:
the maximum number of sequences allowed
-
-
-
- -

-isDefault

-
-public boolean isDefault()
-
-
- -
Returns:
true is this is a default limit to be used, false otherwise
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-isExceeded

-
-public boolean isExceeded(java.util.List<FastaSequence> data)
-
-
Checks if the number of sequences or their average length in the dataset - exceeds this limit. -

-

-
Parameters:
data - the dataset to measure -
Returns:
true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise. First check the number of sequences - in the dataset and if it exceeds the limit return true - irrespective of the average length. If the number of sequences in - the dataset is less than the limit and average length is defined, - then check whether the total number of letters (number of - sequence multiplied by the average sequence length) is greater - then the total number of letters in the dataset. Returns true if - the total number of letters in the dataset is greater than the - limit, false otherwise.
-
-
-
- -

-getAvgSequenceLength

-
-public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
-
-
Calculates an average sequence length of the dataset -

-

-
Parameters:
data - -
Returns:
an average sequence length in the input dataset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index f020137..0000000 --- a/website/dm_javadoc/compbio/metadata/LimitExceededException.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -LimitExceededException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class LimitExceededException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.LimitExceededException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class LimitExceededException
extends JobSubmissionException
- - -

-This exception is thrown if the task larger in size that the limit that - applies to the calculation. -

- -

-

-
Version:
-
1.0 February 2010
-
Author:
-
pvtroshin
-
See Also:
Limit, -Serialized Form
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededException(java.lang.String message) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetActualNumberofSequences() - -
-           
- intgetNumberOfSequencesAllowed() - -
-           
- intgetSequenceLenghtActual() - -
-           
- intgetSequenceLenghtAllowed() - -
-           
-static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitExceededException

-
-public LimitExceededException(java.lang.String message)
-
-
- - - - - - - - -
-Method Detail
- -

-newLimitExceeded

-
-public static LimitExceededException newLimitExceeded(Limit<?> limit,
-                                                      java.util.List<FastaSequence> seqs)
-
-
-
-
-
-
- -

-getNumberOfSequencesAllowed

-
-public int getNumberOfSequencesAllowed()
-
-
-
-
-
-
- -

-getActualNumberofSequences

-
-public int getActualNumberofSequences()
-
-
-
-
-
-
- -

-getSequenceLenghtAllowed

-
-public int getSequenceLenghtAllowed()
-
-
-
-
-
-
- -

-getSequenceLenghtActual

-
-public int getSequenceLenghtActual()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index cbf7e5e..0000000 --- a/website/dm_javadoc/compbio/metadata/LimitsManager.html +++ /dev/null @@ -1,363 +0,0 @@ - - - - - - -LimitsManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class LimitsManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.LimitsManager<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class LimitsManager<T>
extends java.lang.Object
- - -

-A collection of Limits -

- -

-

-
Version:
-
1.0 January 2010
-
Author:
-
pvtroshin
-
See Also:
Limit
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitsManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T>getDefaultLimit() - -
-           
- Limit<T>getLimitByName(java.lang.String presetName) - -
-           
- java.util.List<Limit<T>>getLimits() - -
-           
- java.lang.StringtoString() - -
-           
- voidvalidate(PresetManager<T> presets) - -
-          Validate Limits
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-LimitsManager

-
-public LimitsManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getLimits

-
-public java.util.List<Limit<T>> getLimits()
-
-
- -
Returns:
all limits defined for an executable T
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-getLimitByName

-
-public Limit<T> getLimitByName(java.lang.String presetName)
-
-
-
Parameters:
presetName - -
Returns:
Limit defined for the executable T and presetName. If no limit is - defined for the presetName then default Limit is returned. If - presetName is empty or null than the default Limit will be - returned. If not limit defined for the type T than NULL will be - returned
-
-
-
- -

-getDefaultLimit

-
-public Limit<T> getDefaultLimit()
-
-
- -
Returns:
the default Limit for an executable type T
-
-
-
- -

-validate

-
-public void validate(PresetManager<T> presets)
-              throws javax.xml.bind.ValidationException
-
-
Validate Limits -

-

-
Parameters:
presets - -
Throws: -
javax.xml.bind.ValidationException - if any of the Limit defined is found to be invalid. That is - when - - 1) No default limit is defined - - 2) More than 1 default limit is defined - - 3) Limit's preset name does not match any presets for type T
See Also:
Limit, -Preset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html deleted file mode 100644 index 77b8754..0000000 --- a/website/dm_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,714 +0,0 @@ - - - - - - -Option - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Option<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-
-
-
Type Parameters:
T - type of executable
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
Direct Known Subclasses:
Parameter
-
-
-
-
public class Option<T>
extends java.lang.Object
implements Argument<T>
- - -

-Command line option/flag or multiple exclusive options with no value. Example - -protein, -dna, -auto -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
Option(java.lang.String name, - java.lang.String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) - -
-          Adds an option to the optionName list
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetDefaultValue() - -
-          A default value of the option.
- java.lang.StringgetDescription() - -
-          A long description of the Option
- java.net.URLgetFurtherDetails() - -
-          The URL where further details about the option can be found
- java.lang.StringgetName() - -
-          Human readable name of the option
- java.util.List<java.lang.String>getOptionNames() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-          List of possible optionNames
- inthashCode() - -
-           
- booleanisRequired() - -
-          Flag that indicated that this option must be specified in the command - line for an executable to run
- voidsetDefaultValue(java.lang.String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetDescription(java.lang.String description) - -
-           
- voidsetFurtherDetails(java.net.URL furtherDetails) - -
-           
- voidsetName(java.lang.String name) - -
-           
- voidsetOptionNames(java.util.Set<java.lang.String> optionNames) - -
-           
- voidsetRequired(boolean isRequired) - -
-           
- voidsetValue(java.lang.String dValue) - -
-          Set default values for the parameter or an option
- java.lang.StringtoCommand(java.lang.String nameValueSeparator) - -
-          Convert the option to the command string.
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Option

-
-public Option(java.lang.String name,
-              java.lang.String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getName

-
-public java.lang.String getName()
-
-
Human readable name of the option -

-

-
Specified by:
getName in interface Argument<T>
-
-
-
-
-
-
- -

-setName

-
-public void setName(java.lang.String name)
-
-
-
-
-
-
-
-
-
- -

-getDescription

-
-public java.lang.String getDescription()
-
-
A long description of the Option -

-

-
Specified by:
getDescription in interface Argument<T>
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(java.lang.String description)
-
-
-
-
-
-
-
-
-
- -

-getFurtherDetails

-
-public java.net.URL getFurtherDetails()
-
-
The URL where further details about the option can be found -

-

-
Specified by:
getFurtherDetails in interface Argument<T>
-
-
-
-
-
-
- -

-setFurtherDetails

-
-public void setFurtherDetails(java.net.URL furtherDetails)
-
-
-
-
-
-
-
-
-
- -

-getDefaultValue

-
-public java.lang.String getDefaultValue()
-
-
A default value of the option. Defaults to command line argument name - e.g. -auto -

-

-
Specified by:
getDefaultValue in interface Argument<T>
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(java.lang.String defaultVal)
-                     throws WrongParameterException
-
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
-
-
-
Parameters:
defaultVal - -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
-
- -

-isRequired

-
-public boolean isRequired()
-
-
Flag that indicated that this option must be specified in the command - line for an executable to run -

-

-
-
-
- -
Returns:
true is the option is required, false otherwise
-
-
-
- -

-setRequired

-
-public void setRequired(boolean isRequired)
-
-
-
-
-
-
-
-
-
- -

-getOptionNames

-
-public java.util.List<java.lang.String> getOptionNames()
-
-
-
-
-
- -
Returns:
List of option names
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(java.util.Set<java.lang.String> optionNames)
-
-
-
-
-
-
-
-
-
- -

-addOptionNames

-
-public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
-
-
Adds an option to the optionName list -

-

-
-
-
-
Parameters:
value - -
Returns:
modified optionName list
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-toCommand

-
-public java.lang.String toCommand(java.lang.String nameValueSeparator)
-
-
Convert the option to the command string. -

-

-
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-getPossibleValues

-
-public java.util.List<java.lang.String> getPossibleValues()
-
-
List of possible optionNames -

-

-
Specified by:
getPossibleValues in interface Argument<T>
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-public void setValue(java.lang.String dValue)
-              throws WrongParameterException
-
-
Description copied from interface: Argument
-
Set default values for the parameter or an option -

-

-
Specified by:
setValue in interface Argument<T>
-
-
-
Parameters:
dValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index 7d92155..0000000 --- a/website/dm_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -Parameter - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Parameter<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-      extended by compbio.metadata.Parameter<T>
-
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
-
public class Parameter<T>
extends Option<T>
- - -

-A single value containing an option supported by the web service e.g. - seqType=protein. Where seqType is a optionName and protein is one of - possibleValues -

- -

-

-
Version:
-
1.0 November 2009
-
Author:
-
pvtroshin
-
See Also:
Option, -Argument
-
- -

- - - - - - - - - - - -
-Constructor Summary
Parameter(java.lang.String name, - java.lang.String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) - -
-          Adds an option to the optionName list
- java.util.Set<java.lang.String>addPossibleValues(java.lang.String... value) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetOptionName() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-          List is more convenient to work with
- ValueConstraingetValidValue() - -
-           
- inthashCode() - -
-           
- voidsetDefaultValue(java.lang.String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetOptionName(java.lang.String optionName) - -
-           
- voidsetOptionNames(java.util.Set<java.lang.String> optionName) - -
-           
- voidsetPossibleValues(java.util.Set<java.lang.String> possibleValues) - -
-           
- voidsetValidValue(ValueConstrain validValue) - -
-           
- java.lang.StringtoCommand(java.lang.String nameValueSeparator) - -
-          Convert the option to the command string.
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class compbio.metadata.Option
getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Parameter

-
-public Parameter(java.lang.String name,
-                 java.lang.String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getValidValue

-
-public ValueConstrain getValidValue()
-
-
-
-
-
-
- -

-setValidValue

-
-public void setValidValue(ValueConstrain validValue)
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class Option<T>
-
-
-
-
-
-
- -

-toCommand

-
-public java.lang.String toCommand(java.lang.String nameValueSeparator)
-
-
Description copied from class: Option
-
Convert the option to the command string. -

-

-
Overrides:
toCommand in class Option<T>
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class Option<T>
-
-
-
-
-
-
- -

-getPossibleValues

-
-public java.util.List<java.lang.String> getPossibleValues()
-
-
List is more convenient to work with -

-

-
Specified by:
getPossibleValues in interface Argument<T>
Overrides:
getPossibleValues in class Option<T>
-
-
- -
Returns:
List of String
-
-
-
- -

-setPossibleValues

-
-public void setPossibleValues(java.util.Set<java.lang.String> possibleValues)
-
-
-
-
-
-
- -

-addPossibleValues

-
-public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Option<T>
-
-
-
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(java.util.Set<java.lang.String> optionName)
-
-
-
Overrides:
setOptionNames in class Option<T>
-
-
-
-
-
-
- -

-addOptionNames

-
-public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
-
-
Description copied from class: Option
-
Adds an option to the optionName list -

-

-
Overrides:
addOptionNames in class Option<T>
-
-
- -
Returns:
modified optionName list
-
-
-
- -

-getOptionName

-
-public java.lang.String getOptionName()
-
-
-
-
-
-
- -

-setOptionName

-
-public void setOptionName(java.lang.String optionName)
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(java.lang.String defaultVal)
-                     throws WrongParameterException
-
-
Description copied from class: Option
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
Overrides:
setDefaultValue in class Option<T>
-
-
- -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index 87f3a9b..0000000 --- a/website/dm_javadoc/compbio/metadata/Preset.html +++ /dev/null @@ -1,455 +0,0 @@ - - - - - - -Preset - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Preset<T>

-
-java.lang.Object
-  extended by compbio.metadata.Preset<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class Preset<T>
extends java.lang.Object
- - -

-Collection of Options and Parameters with their values -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
See Also:
Option, -Parameter
-
- -

- - - - - - - - - - - -
-Constructor Summary
Preset() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- java.lang.StringgetDescription() - -
-           
- java.lang.StringgetName() - -
-           
- java.util.List<java.lang.String>getOptions() - -
-           
- inthashCode() - -
-           
- voidsetDescription(java.lang.String description) - -
-           
- voidsetName(java.lang.String name) - -
-           
- voidsetOptions(java.util.List<java.lang.String> option) - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Preset

-
-public Preset()
-
-
- - - - - - - - -
-Method Detail
- -

-setOptions

-
-public void setOptions(java.util.List<java.lang.String> option)
-
-
-
-
-
-
- -

-setName

-
-public void setName(java.lang.String name)
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(java.lang.String description)
-
-
-
-
-
-
- -

-getOptions

-
-public java.util.List<java.lang.String> getOptions()
-
-
- -
Returns:
a List of Options as a String
-
-
-
- -

-getName

-
-public java.lang.String getName()
-
-
- -
Returns:
- name of the Preset
-
-
-
- -

-getDescription

-
-public java.lang.String getDescription()
-
-
- -
Returns:
- a long description of the Preset
-
-
-
- -

-getArguments

-
-public java.util.List<Option<T>> getArguments(RunnerConfig<T> rconfig)
-                                       throws WrongParameterException
-
-
Converts list of options as String to type Option -

-

-
Parameters:
rconfig - -
Returns:
List of Options -
Throws: -
WrongParameterException - if the value of the parameter is invalid @see - Parameter
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index a7c1ab7..0000000 --- a/website/dm_javadoc/compbio/metadata/PresetManager.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - -PresetManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class PresetManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.PresetManager<T>
-
-
-
Type Parameters:
T - type of executable.
-
-
-
public class PresetManager<T>
extends java.lang.Object
- - -

-Collection of presets and methods to manipulate them @see Preset -

- -

-

-
Version:
-
1.0 December 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringLOCAL_ENGINE_LIMIT_PRESET - -
-           
-  - - - - - - - - - - -
-Constructor Summary
PresetManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Preset<T>getPresetByName(java.lang.String presetName) - -
-           
- java.util.List<Preset<T>>getPresets() - -
-           
- java.lang.StringgetRunnerClassName() - -
-           
- voidsetPresets(java.util.List<Preset<T>> presets) - -
-           
- voidsetRunnerClassName(java.lang.String runnerClassName) - -
-           
- java.lang.StringtoString() - -
-           
- voidvalidate(RunnerConfig<T> options) - -
-          Checks whether preset option and parameter are defined in RunnerConfig - object.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Field Detail
- -

-LOCAL_ENGINE_LIMIT_PRESET

-
-public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-PresetManager

-
-public PresetManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getPresets

-
-public java.util.List<Preset<T>> getPresets()
-
-
-
-
-
-
- -

-setPresets

-
-public void setPresets(java.util.List<Preset<T>> presets)
-
-
-
-
-
-
- -

-getRunnerClassName

-
-public java.lang.String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name of type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(java.lang.String runnerClassName)
-
-
-
-
-
-
- -

-getPresetByName

-
-public Preset<T> getPresetByName(java.lang.String presetName)
-
-
-
Parameters:
presetName - -
Returns:
preset by its name, null if no preset found
-
-
-
- -

-validate

-
-public void validate(RunnerConfig<T> options)
-              throws javax.xml.bind.ValidationException
-
-
Checks whether preset option and parameter are defined in RunnerConfig - object. - - TODO handle parameters with values properly! -

-

- -
Throws: -
javax.xml.bind.ValidationException - if preset is found to be invalid.
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html deleted file mode 100644 index 95f5a4c..0000000 --- a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -ResultNotAvailableException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class ResultNotAvailableException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.ResultNotAvailableException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class ResultNotAvailableException
extends java.lang.Exception
- - -

-ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides lower level exceptions - like DrmaaException -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
See Also:
Serialized Form
-
- -

- - - - - - - - - - - - - - - - - -
-Constructor Summary
ResultNotAvailableException(java.lang.String message) - -
-           
ResultNotAvailableException(java.lang.String message, - java.lang.Throwable cause) - -
-           
ResultNotAvailableException(java.lang.Throwable cause) - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(java.lang.String message)
-
-
-
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(java.lang.Throwable cause)
-
-
-
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(java.lang.String message,
-                                   java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index a03dfef..0000000 --- a/website/dm_javadoc/compbio/metadata/RunnerConfig.html +++ /dev/null @@ -1,706 +0,0 @@ - - - - - - -RunnerConfig - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class RunnerConfig<T>

-
-java.lang.Object
-  extended by compbio.metadata.RunnerConfig<T>
-
-
-
Type Parameters:
T - type of an Executable
-
-
-
@NotThreadSafe
-public class RunnerConfig<T>
extends java.lang.Object
- - -

-The list of Parameters and Options supported by executable. - The lists is defined in and loaded from Parameters.xml file. -

- -

-

-
Version:
-
1.0 October 2009
-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
RunnerConfig() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidaddOption(Option<T> option) - -
-          Adds Option to the internal list of options
- voidaddParameter(Parameter<T> param) - -
-          Adds parameter to the internal parameter list
- RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- Option<T>getArgument(java.lang.String name) - -
-          Returns the argument by its name if found, NULL otherwise.
- Option<T>getArgumentByOptionName(java.lang.String optionName) - -
-          Returns the argument by option name, NULL if the argument is not found
- java.util.List<Option<T>>getArguments() - -
-          Returns list of Parameter and Option supported by current - runner
- java.util.List<Option<T>>getOptions() - -
-          Returns the list of the Options supported by the executable of type T
- java.util.List<Parameter<T>>getParameters() - -
-          Returns the list of parameters supported executable of type T.
- java.lang.StringgetPrmSeparator() - -
-           
- java.lang.StringgetRunnerClassName() - -
-           
- booleanremoveArgument(java.lang.String name) - -
-          Removes the argument Argument if found.
- booleanremoveArgumentByOptionName(java.lang.String optionName) - -
-          Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor.
- voidsetOptions(java.util.List<Option<T>> parameters) - -
-          Adds the list of options or parameters to the internal list of options
- voidsetParameters(java.util.List<Parameter<T>> parameters) - -
-          Sets the list of parameters as internal list
- voidsetPrmSeparator(java.lang.String prmSeparator) - -
-          Sets name value separator character
- voidsetRunnerClassName(java.lang.String runnerClassName) - -
-          Set the name of a runner class
- java.lang.StringtoString() - -
-           
- voidvalidate() - -
-          Validate the value of the argument.
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-RunnerConfig

-
-public RunnerConfig()
-
-
- - - - - - - - -
-Method Detail
- -

-copyAndValidateRConfig

-
-public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
-
-
-
-
-
-
- -

-getOptions

-
-public java.util.List<Option<T>> getOptions()
-
-
Returns the list of the Options supported by the executable of type T -

-

- -
Returns:
list of Option supported by type T
See Also:
Option
-
-
-
- -

-addParameter

-
-public void addParameter(Parameter<T> param)
-
-
Adds parameter to the internal parameter list -

-

-
Parameters:
param - the Parameter to add
See Also:
Parameter
-
-
-
- -

-addOption

-
-public void addOption(Option<T> option)
-
-
Adds Option to the internal list of options -

-

-
Parameters:
option - the Option to add
-
-
-
- -

-getArguments

-
-public java.util.List<Option<T>> getArguments()
-
-
Returns list of Parameter and Option supported by current - runner -

-

- -
Returns:
list of Option and Parameter supported by type T
-
-
-
- -

-getPrmSeparator

-
-public java.lang.String getPrmSeparator()
-
-
- -
Returns:
name value separator character
-
-
-
- -

-setPrmSeparator

-
-public void setPrmSeparator(java.lang.String prmSeparator)
-
-
Sets name value separator character -

-

-
Parameters:
prmSeparator - the separator char
-
-
-
- -

-setOptions

-
-public void setOptions(java.util.List<Option<T>> parameters)
-
-
Adds the list of options or parameters to the internal list of options -

-

-
Parameters:
parameters - the list of parameters to add
-
-
-
- -

-getRunnerClassName

-
-public java.lang.String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name for type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(java.lang.String runnerClassName)
-
-
Set the name of a runner class -

-

-
Parameters:
runnerClassName - the name of the executable wrapping class
-
-
-
- -

-setParameters

-
-public void setParameters(java.util.List<Parameter<T>> parameters)
-
-
Sets the list of parameters as internal list -

-

-
Parameters:
parameters - the list of parameters
-
-
-
- -

-getParameters

-
-public java.util.List<Parameter<T>> getParameters()
-
-
Returns the list of parameters supported executable of type T. Where - Parameter is an Option with value. -

-

- -
Returns:
List of Parameter supported by type T.
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
-
- -

-getArgument

-
-public Option<T> getArgument(java.lang.String name)
-
-
Returns the argument by its name if found, NULL otherwise. Where the - Argument is a common interface for Option and Parameter - therefore this method can return either. If you need to retrieve the - Option by its optionNames use @link - getArgumentByOptionName(String) method. The - difference between option name and optionName is explained by the - following example: - - 
- Sequence type
-         
-         --nuc - Assume the sequences are nucleotide.
-         --amino - Assume the sequences are amino acid. 
-         --amino
-         --nuc
-         --auto
-
- - In the example, the "Sequence type" is a name whereas --amino, --nuc and - --auto are all optionNames. This dichotomy only manifests in - Option never in Parameters as the latter can - only have single element -

-

-
Parameters:
name - the Parameter of Option name -
Returns:
Argument
-
-
-
- -

-removeArgument

-
-public boolean removeArgument(java.lang.String name)
-
-
Removes the argument Argument if found. Where Argument is either - Option or Parameter. -

-

-
Parameters:
name - of the argument -
Returns:
true if argument was removed, false otherwise
-
-
-
- -

-getArgumentByOptionName

-
-public Option<T> getArgumentByOptionName(java.lang.String optionName)
-
-
Returns the argument by option name, NULL if the argument is not found -

-

-
Parameters:
optionName - - the optionName. This is not the same as an Option name. - - For example: - - 
-            Output sequences order
-                          --inputorder - Output order: same as input. 
-                           --reorder - Output order: aligned. Default: same as input
-                          --inputorder
-                          --reorder
-
- - The name of the option in the example is - "Output sequences order" whereas optionNames are - "--inputorder" and "--reorder". If you need to retrieve the - Option or Parameter by its names use - getArgument(String) method -
Returns:
Option
-
-
-
- -

-removeArgumentByOptionName

-
-public boolean removeArgumentByOptionName(java.lang.String optionName)
-
-
Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -

-

-
Parameters:
optionName - the optionName of the option, do not confuse with the name! -
Returns:
true if argument with optionName exists and was removed, false - otherwise
See Also:
for destinctions - between optionNames and the name of the Option
-
-
-
- -

-validate

-
-public void validate()
-              throws javax.xml.bind.ValidationException
-
-
Validate the value of the argument. Checks whether the argument value is - in the valid values range. -

-

- -
Throws: -
javax.xml.bind.ValidationException - if any of the arguments found invalid which is when -
-
  • Parameter value outside ValueConstrain boundary
    • -
  • Parameter name is not listed in possible values
    • -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index 81522aa..0000000 --- a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class UnsupportedRuntimeException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.UnsupportedRuntimeException
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable
    -
    -
    -
    -
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    - - -

    -Indicates that the server could not execute native executables. e.g. If Mafft - (unix executable) is asked to be run on Windows. In context of JABAWS this - exception indicates that the service is deployed but is not able to run. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date February 2010
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    UnsupportedRuntimeException(java.lang.String message) - -
    -           
    UnsupportedRuntimeException(java.lang.Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(java.lang.String message)
    -
    -
    -
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(java.lang.Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html deleted file mode 100644 index 81fd428..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - -ValueConstrain.Type - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Enum ValueConstrain.Type

    -
    -java.lang.Object
-  extended by java.lang.Enum<ValueConstrain.Type>
-      extended by compbio.metadata.ValueConstrain.Type
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<ValueConstrain.Type>
    -
    -
    -
    Enclosing class:
    ValueConstrain
    -
    -
    -
    -
    public static enum ValueConstrain.Type
    extends java.lang.Enum<ValueConstrain.Type>
    - - -

    -

    - -

    - - - - - - - - - - - - - -
    -Enum Constant Summary
    Float - -
    -           
    Integer - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static ValueConstrain.TypevalueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -Integer

    -
    -public static final ValueConstrain.Type Integer
    -
    -
    -
    -
    -
    - -

    -Float

    -
    -public static final ValueConstrain.Type Float
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static ValueConstrain.Type[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (ValueConstrain.Type c : ValueConstrain.Type.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static ValueConstrain.Type valueOf(java.lang.String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
    java.lang.NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 5326aba..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class ValueConstrain

    -
    -java.lang.Object
-  extended by compbio.metadata.ValueConstrain
-
    -
    -
    -
    public class ValueConstrain
    extends java.lang.Object
    - - -

    -The type and the lower and upper boundaries for numerical value. -

    - -

    -

    -
    Version:
    -
    1.0 November 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classValueConstrain.Type - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ValueConstrain() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(java.lang.Object obj) - -
    -           
    - java.lang.NumbergetMax() - -
    -           
    - java.lang.NumbergetMin() - -
    -           
    - ValueConstrain.TypegetType() - -
    -           
    - inthashCode() - -
    -           
    - voidsetMax(java.lang.String max) - -
    -           
    - voidsetMin(java.lang.String min) - -
    -           
    - voidsetType(ValueConstrain.Type type) - -
    -           
    - java.lang.StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ValueConstrain

    -
    -public ValueConstrain()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getType

    -
    -public ValueConstrain.Type getType()
    -
    -
    -
    -
    -
    -
    - -

    -setType

    -
    -public void setType(ValueConstrain.Type type)
    -
    -
    -
    -
    -
    -
    - -

    -getMax

    -
    -public java.lang.Number getMax()
    -
    -
    -
    -
    -
    -
    - -

    -setMax

    -
    -public void setMax(java.lang.String max)
    -
    -
    -
    -
    -
    -
    - -

    -getMin

    -
    -public java.lang.Number getMin()
    -
    -
    -
    -
    -
    -
    - -

    -setMin

    -
    -public void setMin(java.lang.String min)
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(java.lang.Object obj)
    -
    -
    -
    Overrides:
    equals in class java.lang.Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public java.lang.String toString()
    -
    -
    -
    Overrides:
    toString in class java.lang.Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class java.lang.Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index 8d45c0c..0000000 --- a/website/dm_javadoc/compbio/metadata/WrongParameterException.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -WrongParameterException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class WrongParameterException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.WrongParameterException
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable
    -
    -
    -
    -
    public class WrongParameterException
    extends java.lang.Exception
    - - -

    -WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value. -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    WrongParameterException(Option<?> option) - -
    -           
    WrongParameterException(java.lang.String message) - -
    -           
    WrongParameterException(java.lang.String message, - java.lang.Throwable cause) - -
    -           
    WrongParameterException(java.lang.Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WrongParameterException

    -
    -public WrongParameterException(Option<?> option)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(java.lang.String message)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(java.lang.Throwable cause)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(java.lang.String message,
-                               java.lang.Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index 8d33f7d..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Argument.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.metadata.Argument - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
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    -

    -Uses of Interface
    compbio.metadata.Argument

    -
    - - - - - - - - - -
    -Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Argument in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.metadata that implement Argument
    - classOption<T> - -
    -          Command line option/flag or multiple exclusive options with no value.
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html deleted file mode 100644 index 53c6afd..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ChunkHolder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
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    -

    -Uses of Class
    compbio.metadata.ChunkHolder

    -
    - - - - - - - - - - - - - -
    -Packages that use ChunkHolder
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return ChunkHolder
    - ChunkHolderJManagement.pullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return ChunkHolder
    - ChunkHolderPullExecStatisticsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    - voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html deleted file mode 100644 index 075e64e..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobExecutionException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.JobExecutionException

    -
    -No usage of compbio.metadata.JobExecutionException -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html deleted file mode 100644 index d0833ac..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html +++ /dev/null @@ -1,264 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobStatus - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.JobStatus

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use JobStatus
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return JobStatus
    - JobStatusJManagement.getJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return JobStatus
    - JobStatusGetJobStatusResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type JobStatus
    - voidGetJobStatusResponse.setReturn(JobStatus _return) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return JobStatus
    -static JobStatusJobStatus.valueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JobStatus[]JobStatus.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html deleted file mode 100644 index 01c870a..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html +++ /dev/null @@ -1,264 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.JobSubmissionException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.metadata.JobSubmissionException

    -
    - - - - - - - - - - - - - -
    -Packages that use JobSubmissionException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw JobSubmissionException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringSequenceAnnotation.analize(java.util.List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Subclasses of JobSubmissionException in compbio.metadata
    - classLimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    - classUnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Limit.html b/website/dm_javadoc/compbio/metadata/class-use/Limit.html deleted file mode 100644 index 308485e..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Limit.html +++ /dev/null @@ -1,296 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Limit - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.Limit

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use Limit
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return Limit
    - Limit<T>Metadata.getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Limit
    - LimitGetLimitResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Limit
    - voidGetLimitResponse.setReturn(Limit _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Limit
    - Limit<T>LimitsManager.getDefaultLimit() - -
    -           
    - Limit<T>LimitsManager.getLimitByName(java.lang.String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Limit
    - java.util.List<Limit<T>>LimitsManager.getLimits() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Limit
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html deleted file mode 100644 index b7a4899..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/LimitExceededException.html +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.LimitExceededException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.LimitExceededException

    -
    - - - - - - - - - - - - - -
    -Packages that use LimitExceededException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw LimitExceededException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringSequenceAnnotation.analize(java.util.List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return LimitExceededException
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html deleted file mode 100644 index f889d04..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/LimitsManager.html +++ /dev/null @@ -1,225 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.LimitsManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.LimitsManager

    -
    - - - - - - - - - - - - - -
    -Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return LimitsManager
    - LimitsManager<T>Metadata.getLimits() - -
    -          List Limits supported by a web service.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return LimitsManager
    - LimitsManagerGetLimitsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type LimitsManager
    - voidGetLimitsResponse.setReturn(LimitsManager _return) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Option.html b/website/dm_javadoc/compbio/metadata/class-use/Option.html deleted file mode 100644 index 3abb8b9..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Option.html +++ /dev/null @@ -1,385 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Option - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.metadata.Option

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use Option
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa with type arguments of type Option
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    - java.util.List<Option>CustomAnalize.getOptions() - -
    -           
    - java.util.List<Option>CustomAlign.getOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    - voidCustomAnalize.setOptions(java.util.List<Option> options) - -
    -           
    - voidCustomAlign.setOptions(java.util.List<Option> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.metadata
    -  -

    - - - - - - - - - -
    Subclasses of Option in compbio.metadata
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Option
    - Option<T>RunnerConfig.getArgument(java.lang.String name) - -
    -          Returns the argument by its name if found, NULL otherwise.
    - Option<T>RunnerConfig.getArgumentByOptionName(java.lang.String optionName) - -
    -          Returns the argument by option name, NULL if the argument is not found
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Option
    - java.util.List<Option<T>>RunnerConfig.getArguments() - -
    -          Returns list of Parameter and Option supported by current - runner
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - java.util.List<Option<T>>RunnerConfig.getOptions() - -
    -          Returns the list of the Options supported by the executable of type T
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Option
    - voidRunnerConfig.addOption(Option<T> option) - -
    -          Adds Option to the internal list of options
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Option
    - voidRunnerConfig.setOptions(java.util.List<Option<T>> parameters) - -
    -          Adds the list of options or parameters to the internal list of options
    -  -

    - - - - - - - - -
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.Parameter

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    -Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Parameter in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Parameter
    - java.util.List<Parameter<T>>RunnerConfig.getParameters() - -
    -          Returns the list of parameters supported executable of type T.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Parameter
    - voidRunnerConfig.addParameter(Parameter<T> param) - -
    -          Adds parameter to the internal parameter list
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Parameter
    - voidRunnerConfig.setParameters(java.util.List<Parameter<T>> parameters) - -
    -          Sets the list of parameters as internal list
    -  -

    -

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    -Uses of Class
    compbio.metadata.Preset

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use Preset
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Preset
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Preset
    - PresetPresetAnalize.getPreset() - -
    -           
    - PresetPresetAlign.getPreset() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    - voidPresetAnalize.setPreset(Preset preset) - -
    -           
    - voidPresetAlign.setPreset(Preset preset) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return Preset
    - Preset<T>PresetManager.getPresetByName(java.lang.String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Preset
    - java.util.List<Preset<T>>PresetManager.getPresets() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Preset
    - voidPresetManager.setPresets(java.util.List<Preset<T>> presets) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.PresetManager

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use PresetManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return PresetManager
    - PresetManager<T>Metadata.getPresets() - -
    -          Get presets supported by a web service
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return PresetManager
    - PresetManagerGetPresetsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type PresetManager
    - voidGetPresetsResponse.setReturn(PresetManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type PresetManager
    - voidLimitsManager.validate(PresetManager<T> presets) - -
    -          Validate Limits
    -  -

    -

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    compbio.metadata.ResultNotAvailableException

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    -Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw ResultNotAvailableException
    - ScoreManagerSequenceAnnotation.getAnnotation(java.lang.String jobId) - -
    -          Return the result of the job.
    - AlignmentMsaWS.getResult(java.lang.String jobId) - -
    -          Return the result of the job.
    -  -

    -

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    compbio.metadata.RunnerConfig

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    - - - - - - - - - - - - - - - - - -
    -Packages that use RunnerConfig
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return RunnerConfig
    - RunnerConfig<T>Metadata.getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return RunnerConfig
    - RunnerConfigGetRunnerOptionsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type RunnerConfig
    - voidGetRunnerOptionsResponse.setReturn(RunnerConfig _return) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata with parameters of type RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidPresetManager.validate(RunnerConfig<T> options) - -
    -          Checks whether preset option and parameter are defined in RunnerConfig - object.
    -  -

    -

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    compbio.metadata.UnsupportedRuntimeException

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    -Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringSequenceAnnotation.analize(java.util.List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain.Type in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain.Type
    - ValueConstrain.TypeValueConstrain.getType() - -
    -           
    -static ValueConstrain.TypeValueConstrain.Type.valueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]ValueConstrain.Type.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    - voidValueConstrain.setType(ValueConstrain.Type type) - -
    -           
    -  -

    -

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    compbio.metadata.ValueConstrain

    -
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    -Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain
    - ValueConstrainParameter.getValidValue() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain
    - voidParameter.setValidValue(ValueConstrain validValue) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.WrongParameterException

    -
    - - - - - - - - - - - - - -
    -Packages that use WrongParameterException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw WrongParameterException
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringSequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - java.lang.StringSequenceAnnotation.presetAnalize(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that throw WrongParameterException
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidParameter.setDefaultValue(java.lang.String defaultVal) - -
    -           
    - voidOption.setDefaultValue(java.lang.String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidArgument.setValue(java.lang.String defaultValue) - -
    -          Set default values for the parameter or an option
    - voidOption.setValue(java.lang.String dValue) - -
    -           
    -  -

    -

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    -Argument
    - - - - - - -
    -Classes  - -
    -ChunkHolder -
    -Limit -
    -LimitsManager -
    -Option -
    -Parameter -
    -Preset -
    -PresetManager -
    -RunnerConfig -
    -ValueConstrain
    - - - - - - -
    -Enums  - -
    -JobStatus -
    -ValueConstrain.Type
    - - - - - - -
    -Exceptions  - -
    -JobExecutionException -
    -JobSubmissionException -
    -LimitExceededException -
    -ResultNotAvailableException -
    -UnsupportedRuntimeException -
    -WrongParameterException
    - - - - diff --git a/website/dm_javadoc/compbio/metadata/package-summary.html b/website/dm_javadoc/compbio/metadata/package-summary.html deleted file mode 100644 index c125c20..0000000 --- a/website/dm_javadoc/compbio/metadata/package-summary.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -compbio.metadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -

    -Package compbio.metadata -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. -

    -See: -
    -          Description -

    - - - - - - - - - -
    -Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ChunkHolderRepresents a chunk of a string data together with the position in a file for - the next read operation.
    Limit<T>A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing an option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    -  - -

    - - - - - - - - - - - - - -
    -Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThis exception is thrown if the task larger in size that the limit that - applies to the calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  - -

    -

    -Package compbio.metadata Description -

    - -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    Peter Troshin
    -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/package-tree.html b/website/dm_javadoc/compbio/metadata/package-tree.html deleted file mode 100644 index 5da66c5..0000000 --- a/website/dm_javadoc/compbio/metadata/package-tree.html +++ /dev/null @@ -1,178 +0,0 @@ - - - - - - -compbio.metadata Class Hierarchy - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Hierarchy For Package compbio.metadata -

    -
    -
    -
    Package Hierarchies:
    All Packages
    -
    -

    -Class Hierarchy -

    - -

    -Interface Hierarchy -

    - -

    -Enum Hierarchy -

    - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/package-use.html b/website/dm_javadoc/compbio/metadata/package-use.html deleted file mode 100644 index 799729a..0000000 --- a/website/dm_javadoc/compbio/metadata/package-use.html +++ /dev/null @@ -1,410 +0,0 @@ - - - - - - -Uses of Package compbio.metadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Package
    compbio.metadata

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa.jaxws
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.metadata
    Argument - -
    -          An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing an option supported by the web service e.g.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    ValueConstrain - -
    -          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type - -
    -           
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/AAConClient.html b/website/dm_javadoc/compbio/ws/client/AAConClient.html deleted file mode 100644 index 3a4b469..0000000 --- a/website/dm_javadoc/compbio/ws/client/AAConClient.html +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - -AAConClient - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class AAConClient

    -
    -java.lang.Object
-  extended by compbio.ws.client.AAConClient
-
    -
    -
    -
    public class AAConClient
    extends java.lang.Object
    - - -

    -A command line client for AACon web service -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Method Summary
    -static SequenceAnnotation<compbio.ws.server.AAConWS>connect() - -
    -          Connects to a AACon web service by the host and the service name
    -static voidmain(java.lang.String[] args) - -
    -          Starts command line client, if no parameters are supplied prints help.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -connect

    -
    -public static SequenceAnnotation<compbio.ws.server.AAConWS> connect()
-                                                             throws javax.xml.ws.WebServiceException
    -
    -
    Connects to a AACon web service by the host and the service name -

    -

    - -
    Returns:
    AlignmentAnnotation -
    Throws: -
    javax.xml.ws.WebServiceException - if cannot connect to a web service
    -
    -
    -
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
    -
    -
    Starts command line client, if no parameters are supplied prints help. -

    -

    -
    Parameters:
    args - Usage: ACTION [OPTIONS] - - -i= - full path to fasta or Clustal formatted - alignment file - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits. Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write results - -f= - the name of the file with the list - of parameters to use. Please note that -r and -f options - cannot be used together. Conservation is calculated with - either a preset or parameters from the file, but not both!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/IOHelper.html b/website/dm_javadoc/compbio/ws/client/IOHelper.html deleted file mode 100644 index 3044d88..0000000 --- a/website/dm_javadoc/compbio/ws/client/IOHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -IOHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class IOHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.IOHelper
-
    -
    -
    -
    public class IOHelper
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    IOHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IOHelper

    -
    -public IOHelper()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/Jws2Client.html deleted file mode 100644 index c94a02b..0000000 --- a/website/dm_javadoc/compbio/ws/client/Jws2Client.html +++ /dev/null @@ -1,399 +0,0 @@ - - - - - - -Jws2Client - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class Jws2Client

    -
    -java.lang.Object
-  extended by compbio.ws.client.Jws2Client
-
    -
    -
    -
    public class Jws2Client
    extends java.lang.Object
    - - -

    -A command line client for JAva Bioinformatics Analysis Web Services -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static JABAServiceconnect(java.lang.String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static RegistryWSconnectToRegistry(java.lang.String host) - -
    -          Get a connection of JABAWS registry
    -static java.util.Set<Services>getServices(java.lang.String hostname) - -
    -           
    -static voidmain(java.lang.String[] args) - -
    -          Starts command line client, if no parameter are supported print help.
    -static voidtestService(java.lang.String hostname, - Services service, - java.io.PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -static booleanvalidURL(java.lang.String urlstr) - -
    -          Attempt to construct the URL object from the string
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -validURL

    -
    -public static boolean validURL(java.lang.String urlstr)
    -
    -
    Attempt to construct the URL object from the string -

    -

    -
    Parameters:
    urlstr - -
    Returns:
    true if it succeed false otherwise
    -
    -
    -
    - -

    -testService

    -
    -public static void testService(java.lang.String hostname,
-                               Services service,
-                               java.io.PrintWriter writer)
-                        throws java.net.ConnectException,
-                               javax.xml.ws.WebServiceException
    -
    -
    Asks registry to test the service on the host hostname -

    -

    -
    Parameters:
    hostname -
    service -
    writer - -
    Throws: -
    java.net.ConnectException -
    javax.xml.ws.WebServiceException
    -
    -
    -
    - -

    -getServices

    -
    -public static java.util.Set<Services> getServices(java.lang.String hostname)
-                                           throws javax.xml.ws.WebServiceException,
-                                                  java.net.ConnectException
    -
    -
    - -
    Throws: -
    javax.xml.ws.WebServiceException -
    java.net.ConnectException
    -
    -
    -
    - -

    -connect

    -
    -public static JABAService connect(java.lang.String host,
-                                  Services service)
-                           throws javax.xml.ws.WebServiceException,
-                                  java.net.ConnectException
    -
    -
    Connects to a web service by the host and the service name web service - type -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    service - the name of the JABAWS service to connect to -
    Returns:
    JABAService -
    Throws: -
    javax.xml.ws.WebServiceException -
    java.net.ConnectException - if fails to connect to the service on the host
    -
    -
    -
    - -

    -connectToRegistry

    -
    -public static RegistryWS connectToRegistry(java.lang.String host)
-                                    throws javax.xml.ws.WebServiceException,
-                                           java.net.ConnectException
    -
    -
    Get a connection of JABAWS registry -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba -
    Returns:
    compbio.data.msa.RegistryWS - instance of a RegistryWS web - service -
    Throws: -
    javax.xml.ws.WebServiceException -
    java.net.ConnectException
    -
    -
    -
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
    -
    -
    Starts command line client, if no parameter are supported print help. Two - parameters are required for successful call the JWS2 host name and a - service name. -

    -

    -
    Parameters:
    args - Usage: -h=host_and_context - -s=serviceName ACTION [OPTIONS] - - -h= - a full URL to the JWS2 web server - including context path e.g. http://10.31.1.159:8080/ws - - -s= - one of [MafftWS, MuscleWS, ClustalWS, - TcoffeeWS, ProbconsWS] ACTIONS: - - -i= - full path to fasta formatted sequence file, - from which to align sequences - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write an - alignment -f= - the name of the file with - the list of parameters to use. Please note that -r and -f - options cannot be used together. Alignment is done with either - preset or a parameters from the file, but not both!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/MetadataHelper.html b/website/dm_javadoc/compbio/ws/client/MetadataHelper.html deleted file mode 100644 index eea55ff..0000000 --- a/website/dm_javadoc/compbio/ws/client/MetadataHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -MetadataHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class MetadataHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.MetadataHelper
-
    -
    -
    -
    public class MetadataHelper
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    MetadataHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MetadataHelper

    -
    -public MetadataHelper()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/Services.html b/website/dm_javadoc/compbio/ws/client/Services.html deleted file mode 100644 index 49183a3..0000000 --- a/website/dm_javadoc/compbio/ws/client/Services.html +++ /dev/null @@ -1,762 +0,0 @@ - - - - - - -Services - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Enum Services

    -
    -java.lang.Object
-  extended by java.lang.Enum<Services>
-      extended by compbio.ws.client.Services
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Services>
    -
    -
    -
    -
    public enum Services
    extends java.lang.Enum<Services>
    - - -

    -List of web services currently supported by JABAWS version 2 -

    - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    AAConWS - -
    -           
    ClustalOWS - -
    -           
    ClustalWS - -
    -           
    DisemblWS - -
    -           
    GlobPlotWS - -
    -           
    IUPredWS - -
    -           
    JronnWS - -
    -           
    MafftWS - -
    -           
    MuscleWS - -
    -           
    ProbconsWS - -
    -           
    TcoffeeWS - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringAACON_INFO - -
    -           
    -static java.lang.StringCLUSTAL_INFO - -
    -           
    -static java.lang.StringCLUSTAL_OMEGA_INFO - -
    -           
    -static java.lang.StringDISEMBL_INFO - -
    -           
    -static java.lang.StringGLOBPLOT_INFO - -
    -           
    -static java.lang.StringIUPRED_INFO - -
    -           
    -static java.lang.StringJRONN_INFO - -
    -           
    -static java.lang.StringMAFFT_INFO - -
    -           
    -static java.lang.StringMUSCLE_INFO - -
    -           
    -static java.lang.StringPROBCONS_INFO - -
    -           
    -static java.lang.StringTCOFFEE_INFO - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ServicesgetService(java.lang.String servName) - -
    -           
    - java.lang.StringgetServiceInfo() - -
    -           
    -static voidmain(java.lang.String[] args) - -
    -           
    -static java.lang.StringtoString(java.util.Set<Services> services) - -
    -           
    -static ServicesvalueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -MafftWS

    -
    -public static final Services MafftWS
    -
    -
    -
    -
    -
    - -

    -MuscleWS

    -
    -public static final Services MuscleWS
    -
    -
    -
    -
    -
    - -

    -ClustalWS

    -
    -public static final Services ClustalWS
    -
    -
    -
    -
    -
    - -

    -ClustalOWS

    -
    -public static final Services ClustalOWS
    -
    -
    -
    -
    -
    - -

    -TcoffeeWS

    -
    -public static final Services TcoffeeWS
    -
    -
    -
    -
    -
    - -

    -ProbconsWS

    -
    -public static final Services ProbconsWS
    -
    -
    -
    -
    -
    - -

    -AAConWS

    -
    -public static final Services AAConWS
    -
    -
    -
    -
    -
    - -

    -JronnWS

    -
    -public static final Services JronnWS
    -
    -
    -
    -
    -
    - -

    -DisemblWS

    -
    -public static final Services DisemblWS
    -
    -
    -
    -
    -
    - -

    -GlobPlotWS

    -
    -public static final Services GlobPlotWS
    -
    -
    -
    -
    -
    - -

    -IUPredWS

    -
    -public static final Services IUPredWS
    -
    -
    -
    -
    - - - - - - - - -
    -Field Detail
    - -

    -AACON_INFO

    -
    -public static final java.lang.String AACON_INFO
    -
    -
    -
    -
    -
    - -

    -CLUSTAL_INFO

    -
    -public static final java.lang.String CLUSTAL_INFO
    -
    -
    -
    -
    -
    - -

    -CLUSTAL_OMEGA_INFO

    -
    -public static final java.lang.String CLUSTAL_OMEGA_INFO
    -
    -
    -
    -
    -
    - -

    -DISEMBL_INFO

    -
    -public static final java.lang.String DISEMBL_INFO
    -
    -
    -
    -
    -
    - -

    -GLOBPLOT_INFO

    -
    -public static final java.lang.String GLOBPLOT_INFO
    -
    -
    -
    -
    -
    - -

    -IUPRED_INFO

    -
    -public static final java.lang.String IUPRED_INFO
    -
    -
    -
    -
    -
    - -

    -TCOFFEE_INFO

    -
    -public static final java.lang.String TCOFFEE_INFO
    -
    -
    -
    -
    -
    - -

    -MUSCLE_INFO

    -
    -public static final java.lang.String MUSCLE_INFO
    -
    -
    -
    -
    -
    - -

    -PROBCONS_INFO

    -
    -public static final java.lang.String PROBCONS_INFO
    -
    -
    -
    -
    -
    - -

    -JRONN_INFO

    -
    -public static final java.lang.String JRONN_INFO
    -
    -
    -
    -
    -
    - -

    -MAFFT_INFO

    -
    -public static final java.lang.String MAFFT_INFO
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Services[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (Services c : Services.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static Services valueOf(java.lang.String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
    java.lang.NullPointerException - if the argument is null
    -
    -
    -
    - -

    -getService

    -
    -public static Services getService(java.lang.String servName)
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public static java.lang.String toString(java.util.Set<Services> services)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceInfo

    -
    -public java.lang.String getServiceInfo()
    -
    -
    -
    -
    -
    -
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/ServicesUtil.html b/website/dm_javadoc/compbio/ws/client/ServicesUtil.html deleted file mode 100644 index f0dc95b..0000000 --- a/website/dm_javadoc/compbio/ws/client/ServicesUtil.html +++ /dev/null @@ -1,309 +0,0 @@ - - - - - - -ServicesUtil - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class ServicesUtil

    -
    -java.lang.Object
-  extended by compbio.ws.client.ServicesUtil
-
    -
    -
    -
    public class ServicesUtil
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ServicesUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static java.lang.Class<? extends compbio.engine.client.Executable<?>>getRunnerByJobDirectory(java.io.File jobdir) - -
    -           
    -static ServicesgetServiceByJobDirectory(java.io.File jobdir) - -
    -           
    -static ServicesgetServiceByRunner(java.lang.Class<? extends compbio.engine.client.Executable> class1) - -
    -           
    -static java.lang.Class<? extends compbio.engine.client.Executable<?>>getServiceImpl(Services service) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ServicesUtil

    -
    -public ServicesUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getServiceByRunner

    -
    -public static Services getServiceByRunner(java.lang.Class<? extends compbio.engine.client.Executable> class1)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceImpl

    -
    -public static java.lang.Class<? extends compbio.engine.client.Executable<?>> getServiceImpl(Services service)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerByJobDirectory

    -
    -public static java.lang.Class<? extends compbio.engine.client.Executable<?>> getRunnerByJobDirectory(java.io.File jobdir)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceByJobDirectory

    -
    -public static Services getServiceByJobDirectory(java.io.File jobdir)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html deleted file mode 100644 index d97a870..0000000 --- a/website/dm_javadoc/compbio/ws/client/WSTester.html +++ /dev/null @@ -1,368 +0,0 @@ - - - - - - -WSTester - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class WSTester

    -
    -java.lang.Object
-  extended by compbio.ws.client.WSTester
-
    -
    -
    -
    public class WSTester
    extends java.lang.Object
    - - -

    -Class for testing web services -

    - -

    -

    -
    Version:
    -
    1.0 February 2010
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringfastaAlignment - -
    -           
    -static java.lang.StringfastaInput - -
    -          Sequences to be used as input for all WS
    -  - - - - - - - - - - -
    -Constructor Summary
    WSTester(java.lang.String hostname, - java.io.PrintWriter writer) - -
    -          Construct an instance of JABAWS tester
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancheckService(Services service) - -
    -          Test JABA web service
    -static - - - - -
    -<T> void
    -    		main(java.lang.String[] args) - -
    -          Test JWS2 web services
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -fastaInput

    -
    -public static final java.lang.String fastaInput
    -
    -
    Sequences to be used as input for all WS -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -fastaAlignment

    -
    -public static final java.lang.String fastaAlignment
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -WSTester

    -
    -public WSTester(java.lang.String hostname,
-                java.io.PrintWriter writer)
    -
    -
    Construct an instance of JABAWS tester -

    -

    -
    Parameters:
    hostname - - fully qualified host and context name of JABAWS e.g. - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    writer - a PrintWriter instance to writer test log to.
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static <T> void main(java.lang.String[] args)
-                 throws java.io.IOException
    -
    -
    Test JWS2 web services -

    -

    -
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested -
    Throws: -
    java.io.IOException
    -
    -
    -
    - -

    -checkService

    -
    -public boolean checkService(Services service)
-                     throws java.net.ConnectException,
-                            javax.xml.ws.WebServiceException
    -
    -
    Test JABA web service -

    -

    -
    Parameters:
    service - the service to test -
    Returns:
    true if the service works as expected, false otherwise -
    Throws: -
    javax.xml.ws.WebServiceException -
    java.net.ConnectException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.ws.client.Services

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use Services
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - -
    -Uses of Services in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that return types with arguments of type Services
    - java.util.Set<Services>Category.getServices() - -
    -           
    - java.util.Set<Services>RegistryWS.getSupportedServices() - -
    -          List of services that are functioning on the server.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Services
    - intRegistryWS.getLastTested(Services service) - -
    -          Number of seconds since the last test.
    - java.util.DateRegistryWS.getLastTestedOn(Services service) - -
    -          The date and time the service has been verified to work last time
    - java.lang.StringRegistryWS.getServiceDescription(Services service) - -
    -          Gives the description of the service.
    - booleanRegistryWS.isOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - java.lang.StringRegistryWS.testService(Services service) - -
    -          Test a particular service
    -  -

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    Methods in compbio.data.msa.jaxws that return Services
    - ServicesTestService.getArg0() - -
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    -           
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    -           
    - voidGetLastTested.setArg0(Services arg0) - -
    -           
    -  -

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    Method parameters in compbio.data.msa.jaxws with type arguments of type Services
    - voidGetSupportedServicesResponse.setReturn(java.util.Set<Services> _return) - -
    -           
    -  -

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    -Uses of Services in compbio.ws.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Services
    -static ServicesServices.getService(java.lang.String servName) - -
    -           
    -static ServicesServicesUtil.getServiceByJobDirectory(java.io.File jobdir) - -
    -           
    -static ServicesServicesUtil.getServiceByRunner(java.lang.Class<? extends compbio.engine.client.Executable> class1) - -
    -           
    -static ServicesServices.valueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]Services.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type Services
    -static java.util.Set<Services>Jws2Client.getServices(java.lang.String hostname) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client with parameters of type Services
    - booleanWSTester.checkService(Services service) - -
    -          Test JABA web service
    -static JABAServiceJws2Client.connect(java.lang.String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static java.lang.Class<? extends compbio.engine.client.Executable<?>>ServicesUtil.getServiceImpl(Services service) - -
    -           
    -static voidJws2Client.testService(java.lang.String hostname, - Services service, - java.io.PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.client with type arguments of type Services
    -static java.lang.StringServices.toString(java.util.Set<Services> services) - -
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    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AAConClientA command line client for AACon web service
    IOHelper 
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    MetadataHelper 
    ServicesUtil 
    WSTesterClass for testing web services
    -  - -

    - - - - - - - - - -
    -Enum Summary
    ServicesList of web services currently supported by JABAWS version 2
    -  - -

    -

    -Package compbio.ws.client Description -

    - -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    - -

    -

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    1.0 April 2010
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    -Packages that use compbio.ws.client
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.data.msa
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.data.msa.jaxws
    Services - -
    -          List of web services currently supported by JABAWS version 2
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    -compbio.data.*
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    compbio.data.msa.Category
    -public static final java.lang.StringCATEGORY_ALIGNMENT"Alignment"
    -public static final java.lang.StringCATEGORY_CONSERVATION"Conservation"
    -public static final java.lang.StringCATEGORY_DISORDER"Protein Disorder"
    - -

    - -

    - - - - - - - - - - - - - - - - - -
    compbio.data.msa.JABAService
    -public static final java.lang.StringSERVICE_NAMESPACE"http://msa.data.compbio/01/01/2010/"
    -public static final java.lang.StringV2_SERVICE_NAMESPACE"http://msa.data.compbio/01/12/2010/"
    - -

    - -

    - - - - - - - - - - - - -
    compbio.data.sequence.ClustalAlignmentUtil
    -public static final chargapchar45
    - -

    - -

    - - - - - - - - - - - - -
    compbio.data.sequence.ScoreManager
    -public static final java.lang.StringSINGLE_ENTRY_KEY"Alignment"
    - -

    - -

    - - - - - - - - - - - - - - - - - -
    compbio.data.sequence.SMERFSConstraints
    -public static final doubleDEFAULT_GAP_THRESHOLD0.1
    -public static final intDEFAULT_WINDOW_SIZE7
    - -

    - -

    - - - - - -
    -compbio.metadata.*
    - -

    - - - - - - - - - - - - -
    compbio.metadata.PresetManager<T>
    -public static final java.lang.StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    - -

    - -

    - - - - - -
    -compbio.ws.*
    - -

    - - - - - - - - - - - - - - - - - -
    compbio.ws.client.WSTester
    -public static final java.lang.StringfastaAlignment">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
    -public static final java.lang.StringfastaInput">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"
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    -
    AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Valid Amino acids -
    AACON_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    AAConClient - Class in compbio.ws.client
    A command line client for AACon web service
    addOption(Option<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds Option to the internal list of options -
    addOptionNames(String...) - -Method in class compbio.metadata.Option -
    Adds an option to the optionName list -
    addOptionNames(String...) - -Method in class compbio.metadata.Parameter -
      -
    addParameter(Parameter<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds parameter to the internal parameter list -
    addPossibleValues(String...) - -Method in class compbio.metadata.Parameter -
      -
    Align - Class in compbio.data.msa.jaxws
     
    Align() - -Constructor for class compbio.data.msa.jaxws.Align -
      -
    align(List<FastaSequence>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with default settings. -
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - -Constructor for class compbio.data.sequence.Alignment -
      -
    Alignment(List<FastaSequence>, AlignmentMetadata) - -Constructor for class compbio.data.sequence.Alignment -
      -
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - -Constructor for class compbio.data.sequence.AlignmentMetadata -
      -
    AlignResponse - Class in compbio.data.msa.jaxws
     
    AlignResponse() - -Constructor for class compbio.data.msa.jaxws.AlignResponse -
      -
    AMBIGUOUS_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Same as AA pattern but with two additional letters - XU -
    AMBIGUOUS_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Ambiguous nucleotide -
    Analize - Class in compbio.data.msa.jaxws
     
    Analize() - -Constructor for class compbio.data.msa.jaxws.Analize -
      -
    analize(List<FastaSequence>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences. -
    AnalizeResponse - Class in compbio.data.msa.jaxws
     
    AnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.AnalizeResponse -
      -
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
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    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    Limit(int, int, String) - -Constructor for class compbio.metadata.Limit -
    Instantiate the limit -
    Limit(int, int, String, boolean) - -Constructor for class compbio.metadata.Limit -
      -
    LimitExceededException - Exception in compbio.metadata
    This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitExceededException(String) - -Constructor for exception compbio.metadata.LimitExceededException -
      -
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    LimitExceededExceptionBean() - -Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - -Constructor for class compbio.metadata.LimitsManager -
      -
    LOCAL_ENGINE_LIMIT_PRESET - -Static variable in class compbio.metadata.PresetManager -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    MAFFT_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    main(String[]) - -Static method in class compbio.ws.client.AAConClient -
    Starts command line client, if no parameters are supplied prints help. -
    main(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Starts command line client, if no parameter are supported print help. -
    main(String[]) - -Static method in enum compbio.ws.client.Services -
      -
    main(String[]) - -Static method in class compbio.ws.client.WSTester -
    Test JWS2 web services -
    Metadata<T> - Interface in compbio.data.msa
     
    MetadataHelper - Class in compbio.ws.client
     
    MetadataHelper() - -Constructor for class compbio.ws.client.MetadataHelper -
      -
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    MUSCLE_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    -
    - - - - - - - - - - - - - - - -
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    -N

    -
    -
    name - -Variable in class compbio.data.msa.Category -
      -
    newInstance(Map<String, Set<Score>>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleScore(Map<String, Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleSequence(Set<Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newLimitExceeded(Limit<?>, List<FastaSequence>) - -Static method in exception compbio.metadata.LimitExceededException -
      -
    next() - -Method in class compbio.data.sequence.FastaReader -
    Reads the next FastaSequence from the input -
    NON_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    inversion of AA pattern -
    NON_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non nucleotide -
    NONWORD - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non word -
    NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Nucleotides a, t, g, c, u -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -
    -
    openInputStream(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - -Constructor for class compbio.metadata.Option -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -
    -
    Parameter<T> - Class in compbio.metadata
    A single value containing an option supported by the web service e.g.
    Parameter(String, String) - -Constructor for class compbio.metadata.Parameter -
      -
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - -Constructor for class compbio.metadata.Preset -
      -
    PresetAlign - Class in compbio.data.msa.jaxws
     
    PresetAlign() - -Constructor for class compbio.data.msa.jaxws.PresetAlign -
      -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with preset. -
    PresetAlignResponse - Class in compbio.data.msa.jaxws
     
    PresetAlignResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    PresetAnalize - Class in compbio.data.msa.jaxws
     
    PresetAnalize() - -Constructor for class compbio.data.msa.jaxws.PresetAnalize -
      -
    presetAnalize(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to the preset settings. -
    PresetAnalizeResponse - Class in compbio.data.msa.jaxws
     
    PresetAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - -Constructor for class compbio.metadata.PresetManager -
      -
    PROBCONS_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    PullExecStatistics - Class in compbio.data.msa.jaxws
     
    PullExecStatistics() - -Constructor for class compbio.data.msa.jaxws.PullExecStatistics -
      -
    pullExecStatistics(String, long) - -Method in interface compbio.data.msa.JManagement -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. -
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
     
    PullExecStatisticsResponse() - -Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    Range - Class in compbio.data.sequence
     
    Range(int, int) - -Constructor for class compbio.data.sequence.Range -
      -
    Range(String[]) - -Constructor for class compbio.data.sequence.Range -
      -
    readAAConResults(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read AACon result with no alignment files. -
    readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Read Clustal formatted alignment. -
    readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    readDisembl(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readFasta(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads fasta sequences from inStream into the list of FastaSequence - objects -
    readGlobPlot(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readIUPred(File) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read IUPred output -
    readJRonn(File) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    readJRonn(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reader for JRonn horizontal file format -
    RegistryWS - Interface in compbio.data.msa
    JABAWS services registry
    remove() - -Method in class compbio.data.sequence.FastaReader -
    Not implemented -
    removeArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument Argument if found. -
    removeArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    ResultNotAvailableException(String) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(String, Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    ResultNotAvailableExceptionBean() - -Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - -Constructor for class compbio.metadata.RunnerConfig -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -S

    -
    -
    Score - Class in compbio.data.sequence
    A value class for AACon annotation results storage.
    Score(Enum<?>, ArrayList<Float>) - -Constructor for class compbio.data.sequence.Score -
    Instantiate the Score -
    Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, float[]) - -Constructor for class compbio.data.sequence.Score -
      -
    ScoreManager - Class in compbio.data.sequence
     
    ScoreManager.ScoreHolder - Class in compbio.data.sequence
     
    scores - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    SequenceAnnotation<T> - Interface in compbio.data.msa
    Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 2
    ServicesUtil - Class in compbio.ws.client
     
    ServicesUtil() - -Constructor for class compbio.ws.client.ServicesUtil -
      -
    setActualNumberofSequences(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetServiceDescription -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.TestService -
      -
    setDefaultValue(String) - -Method in class compbio.metadata.Option -
    Sets one of the values defined in optionList as default. -
    setDefaultValue(String) - -Method in class compbio.metadata.Parameter -
      -
    setDescription(String) - -Method in class compbio.metadata.Option -
      -
    setDescription(String) - -Method in class compbio.metadata.Preset -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Align -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Analize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setFurtherDetails(URL) - -Method in class compbio.metadata.Option -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setMax(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    setMin(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setName(String) - -Method in class compbio.metadata.Option -
      -
    setName(String) - -Method in class compbio.metadata.Preset -
      -
    setNumberOfSequencesAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setOptionName(String) - -Method in class compbio.metadata.Parameter -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Option -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setOptions(List<String>) - -Method in class compbio.metadata.Preset -
      -
    setOptions(List<Option<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Adds the list of options or parameters to the internal list of options -
    setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Sets the list of parameters as internal list -
    setPosition(long) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setPossibleValues(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setPresetName(String) - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    setPresets(List<Preset<T>>) - -Method in class compbio.metadata.PresetManager -
      -
    setPrmSeparator(String) - -Method in class compbio.metadata.RunnerConfig -
    Sets name value separator character -
    setRanges(TreeSet<Range>) - -Method in class compbio.data.sequence.Score -
      -
    setRequired(boolean) - -Method in class compbio.metadata.Option -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    setReturn(ScoreManager) - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    setReturn(JobStatus) - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    setReturn(Date) - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    setReturn(int) - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    setReturn(Limit) - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    setReturn(LimitsManager) - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    setReturn(PresetManager) - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    setReturn(Alignment) - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    setReturn(RunnerConfig) - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    setReturn(Set<Category>) - -Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    setReturn(Set<Services>) - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    setReturn(ChunkHolder) - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.PresetManager -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.RunnerConfig -
    Set the name of a runner class -
    setSequenceLenghtActual(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setSequenceLenghtAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setType(ValueConstrain.Type) - -Method in class compbio.metadata.ValueConstrain -
      -
    setValidValue(ValueConstrain) - -Method in class compbio.metadata.Parameter -
      -
    setValue(String) - -Method in interface compbio.metadata.Argument -
    Set default values for the parameter or an option -
    setValue(String) - -Method in class compbio.metadata.Option -
      -
    SINGLE_ENTRY_KEY - -Static variable in class compbio.data.sequence.ScoreManager -
      -
    SMERFSConstraints - Enum in compbio.data.sequence
    Enumeration defining two constraints for SMERFS columns score calculation.
    -
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    TCOFFEE_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    TestAllServices - Class in compbio.data.msa.jaxws
     
    TestAllServices() - -Constructor for class compbio.data.msa.jaxws.TestAllServices -
      -
    testAllServices() - -Method in interface compbio.data.msa.RegistryWS -
    Test all JABAWS services on the server -
    TestAllServicesResponse - Class in compbio.data.msa.jaxws
     
    TestAllServicesResponse() - -Constructor for class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    TestService - Class in compbio.data.msa.jaxws
     
    TestService() - -Constructor for class compbio.data.msa.jaxws.TestService -
      -
    testService(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Test a particular service -
    testService(String, Services, PrintWriter) - -Static method in class compbio.ws.client.Jws2Client -
    Asks registry to test the service on the host hostname -
    TestServiceResponse - Class in compbio.data.msa.jaxws
     
    TestServiceResponse() - -Constructor for class compbio.data.msa.jaxws.TestServiceResponse -
      -
    to - -Variable in class compbio.data.sequence.Range -
      -
    toCommand(String) - -Method in class compbio.metadata.Option -
    Convert the option to the command string. -
    toCommand(String) - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.data.sequence.Alignment -
      -
    toString() - -Method in class compbio.data.sequence.FastaSequence -
    Same as oneLineFasta -
    toString() - -Method in class compbio.data.sequence.Range -
      -
    toString() - -Method in class compbio.data.sequence.Score -
      -
    toString() - -Method in class compbio.metadata.ChunkHolder -
      -
    toString() - -Method in class compbio.metadata.Limit -
      -
    toString() - -Method in class compbio.metadata.LimitsManager -
      -
    toString() - -Method in class compbio.metadata.Option -
      -
    toString() - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.metadata.Preset -
      -
    toString() - -Method in class compbio.metadata.PresetManager -
      -
    toString() - -Method in class compbio.metadata.RunnerConfig -
      -
    toString() - -Method in class compbio.metadata.ValueConstrain -
      -
    toString(Set<Services>) - -Static method in enum compbio.ws.client.Services -
      -
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    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(File, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeException(Throwable) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBean() - -Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
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    V2_SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    validate(PresetManager<T>) - -Method in class compbio.metadata.LimitsManager -
    Validate Limits -
    validate(RunnerConfig<T>) - -Method in class compbio.metadata.PresetManager -
    Checks whether preset option and parameter are defined in RunnerConfig - object. -
    validate() - -Method in class compbio.metadata.RunnerConfig -
    Validate the value of the argument. -
    validURL(String) - -Static method in class compbio.ws.client.Jws2Client -
    Attempt to construct the URL object from the string -
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - -Constructor for class compbio.metadata.ValueConstrain -
      -
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.Program -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.JobStatus -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.ws.client.Services -
    Returns the enum constant of this type with the specified name. -
    values() - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.Program -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.JobStatus -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.ws.client.Services -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
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    CancelJob - Class in compbio.data.msa.jaxws
     
    CancelJob() - -Constructor for class compbio.data.msa.jaxws.CancelJob -
      -
    cancelJob(String) - -Method in interface compbio.data.msa.JManagement -
    Stop running the job jobId but leave its output untouched -
    CancelJobResponse - Class in compbio.data.msa.jaxws
     
    CancelJobResponse() - -Constructor for class compbio.data.msa.jaxws.CancelJobResponse -
      -
    Category - Class in compbio.data.msa
    Class that splits Services to categories.
    CATEGORY_ALIGNMENT - -Static variable in class compbio.data.msa.Category -
    All of the Category names -
    CATEGORY_CONSERVATION - -Static variable in class compbio.data.msa.Category -
      -
    CATEGORY_DISORDER - -Static variable in class compbio.data.msa.Category -
      -
    checkService(Services) - -Method in class compbio.ws.client.WSTester -
    Test JABA web service -
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of a string data together with the position in a file for - the next read operation.
    ChunkHolder(String, long) - -Constructor for class compbio.metadata.ChunkHolder -
      -
    cleanProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Remove all non AA chars from the sequence -
    cleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all whitespace chars in the sequence string -
    close() - -Method in class compbio.data.sequence.FastaReader -
    Call this method to close the connection to the input file if you want to - free up the resources. -
    closeSilently(Logger, Closeable) - -Static method in class compbio.data.sequence.SequenceUtil -
    Closes the Closable and logs the exception if any -
    CLUSTAL_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    CLUSTAL_OMEGA_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - -Constructor for class compbio.data.sequence.ClustalAlignmentUtil -
      -
    compareTo(Range) - -Method in class compbio.data.sequence.Range -
      -
    compareTo(Score) - -Method in class compbio.data.sequence.Score -
      -
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    connect() - -Static method in class compbio.ws.client.AAConClient -
    Connects to a AACon web service by the host and the service name -
    connect(String, Services) - -Static method in class compbio.ws.client.Jws2Client -
    Connects to a web service by the host and the service name web service - type -
    connectToRegistry(String) - -Static method in class compbio.ws.client.Jws2Client -
    Get a connection of JABAWS registry -
    ConservationMethod - Enum in compbio.data.sequence
    Enumeration listing of all the supported methods.
    copyAndValidateRConfig(RunnerConfig<?>) - -Method in class compbio.metadata.RunnerConfig -
      -
    countMatchesInSequence(String, String) - -Static method in class compbio.data.sequence.FastaSequence -
      -
    CustomAlign - Class in compbio.data.msa.jaxws
     
    CustomAlign() - -Constructor for class compbio.data.msa.jaxws.CustomAlign -
      -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with options. -
    CustomAlignResponse - Class in compbio.data.msa.jaxws
     
    CustomAlignResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    CustomAnalize - Class in compbio.data.msa.jaxws
     
    CustomAnalize() - -Constructor for class compbio.data.msa.jaxws.CustomAnalize -
      -
    customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to custom settings defined in options - list. -
    CustomAnalizeResponse - Class in compbio.data.msa.jaxws
     
    CustomAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
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    WHITE_SPACE - -Static variable in class compbio.data.sequence.SequenceUtil -
    A whitespace character: [\t\n\x0B\f\r] -
    write(TreeSet<Score>, Writer) - -Static method in class compbio.data.sequence.Score -
    Outputs the List of Score objects into the Output stream. -
    writeClustalAlignment(Writer, Alignment) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Write Clustal formatted alignment Limitations: does not record the - consensus. -
    writeFasta(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -
    writeFasta(OutputStream, List<FastaSequence>) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes FastaSequence in the file, each sequence will take one line only -
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager -
      -
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    WrongParameterException(Option<?>) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String, Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    WrongParameterExceptionBean() - -Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester(String, PrintWriter) - -Constructor for class compbio.ws.client.WSTester -
    Construct an instance of JABAWS tester -
    -
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    deepCleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all special characters and digits as well as whitespace chars - from the sequence -
    DEFAULT_COLUMN_SCORE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default column scoring schema -
    DEFAULT_GAP_THRESHOLD - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default gap threshold value for SMERFS algorithm -
    DEFAULT_WINDOW_SIZE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default window size value for SMERFS algorithm -
    DIGIT - -Static variable in class compbio.data.sequence.SequenceUtil -
    A digit -
    DISEMBL_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    DisorderMethod - Enum in compbio.data.sequence
     
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    equals(Object) - -Method in class compbio.data.msa.Category -
      -
    equals(Object) - -Method in class compbio.data.sequence.Alignment -
    Please note that this implementation does not take the order of sequences - into account! -
    equals(Object) - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    equals(Object) - -Method in class compbio.data.sequence.FastaSequence -
      -
    equals(Object) - -Method in class compbio.data.sequence.Range -
      -
    equals(Object) - -Method in class compbio.data.sequence.Score -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    equals(Object) - -Method in class compbio.metadata.ChunkHolder -
      -
    equals(Object) - -Method in class compbio.metadata.Limit -
      -
    equals(Object) - -Method in class compbio.metadata.Option -
      -
    equals(Object) - -Method in class compbio.metadata.Parameter -
      -
    equals(Object) - -Method in class compbio.metadata.Preset -
      -
    equals(Object) - -Method in class compbio.metadata.RunnerConfig -
      -
    equals(Object) - -Method in class compbio.metadata.ValueConstrain -
      -
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    fastaAlignment - -Static variable in class compbio.ws.client.WSTester -
      -
    fastaInput - -Static variable in class compbio.ws.client.WSTester -
    Sequences to be used as input for all WS -
    FastaReader - Class in compbio.data.sequence
    Reads files with FASTA formatted sequences.
    FastaReader(String) - -Constructor for class compbio.data.sequence.FastaReader -
    Header data can contain non-ASCII symbols and read in UTF8 -
    FastaReader(InputStream) - -Constructor for class compbio.data.sequence.FastaReader -
    This class will not close the incoming stream! So the client should do - so. -
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - -Constructor for class compbio.data.sequence.FastaSequence -
    Upon construction the any whitespace characters are removed from the - sequence -
    from - -Variable in class compbio.data.sequence.Range -
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    -
    gapchar - -Static variable in class compbio.data.sequence.ClustalAlignmentUtil -
    Dash char to be used as gap char in the alignments -
    getActualNumberofSequences() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getActualNumberofSequences() - -Method in exception compbio.metadata.LimitExceededException -
      -
    GetAnnotation - Class in compbio.data.msa.jaxws
     
    GetAnnotation() - -Constructor for class compbio.data.msa.jaxws.GetAnnotation -
      -
    getAnnotation(String) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Return the result of the job. -
    getAnnotationForSequence(String) - -Method in class compbio.data.sequence.ScoreManager -
      -
    GetAnnotationResponse - Class in compbio.data.msa.jaxws
     
    GetAnnotationResponse() - -Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetServiceDescription -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.TestService -
      -
    getArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by its name if found, NULL otherwise. -
    getArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by option name, NULL if the argument is not found -
    getArguments(RunnerConfig<T>) - -Method in class compbio.metadata.Preset -
    Converts list of options as String to type Option -
    getArguments() - -Method in class compbio.metadata.RunnerConfig -
    Returns list of Parameter and Option supported by current - runner -
    getAvgSeqLength() - -Method in class compbio.metadata.Limit -
      -
    getAvgSequenceLength(List<FastaSequence>) - -Static method in class compbio.metadata.Limit -
    Calculates an average sequence length of the dataset -
    getCategories() - -Static method in class compbio.data.msa.Category -
      -
    getChunk() - -Method in class compbio.metadata.ChunkHolder -
      -
    getDefaultLimit() - -Method in class compbio.metadata.LimitsManager -
      -
    getDefaultValue() - -Method in interface compbio.metadata.Argument -
      -
    getDefaultValue() - -Method in class compbio.metadata.Option -
    A default value of the option. -
    getDescription() - -Method in interface compbio.metadata.Argument -
      -
    getDescription() - -Method in class compbio.metadata.Option -
    A long description of the Option -
    getDescription() - -Method in class compbio.metadata.Preset -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Align -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Analize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getFormatedSequence(int) - -Method in class compbio.data.sequence.FastaSequence -
    Format sequence per width letter in one string. -
    getFormattedFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getFurtherDetails() - -Method in interface compbio.metadata.Argument -
      -
    getFurtherDetails() - -Method in class compbio.metadata.Option -
    The URL where further details about the option can be found -
    getGapchar() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getId() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of id -
    getJobId() - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - -Constructor for class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobStatus(String) - -Method in interface compbio.data.msa.JManagement -
    Return the status of the job. -
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
     
    GetJobStatusResponse() - -Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    GetLastTested - Class in compbio.data.msa.jaxws
     
    GetLastTested() - -Constructor for class compbio.data.msa.jaxws.GetLastTested -
      -
    getLastTested(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Number of seconds since the last test. -
    GetLastTestedOn - Class in compbio.data.msa.jaxws
     
    GetLastTestedOn() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getLastTestedOn(Services) - -Method in interface compbio.data.msa.RegistryWS -
    The date and time the service has been verified to work last time -
    GetLastTestedOnResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedOnResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    GetLastTestedResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getLength() - -Method in class compbio.data.sequence.FastaSequence -
      -
    GetLimit - Class in compbio.data.msa.jaxws
     
    GetLimit() - -Constructor for class compbio.data.msa.jaxws.GetLimit -
      -
    getLimit(String) - -Method in interface compbio.data.msa.Metadata -
    Get a Limit for a preset. -
    getLimitByName(String) - -Method in class compbio.metadata.LimitsManager -
      -
    GetLimitResponse - Class in compbio.data.msa.jaxws
     
    GetLimitResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitResponse -
      -
    GetLimits - Class in compbio.data.msa.jaxws
     
    GetLimits() - -Constructor for class compbio.data.msa.jaxws.GetLimits -
      -
    getLimits() - -Method in interface compbio.data.msa.Metadata -
    List Limits supported by a web service. -
    getLimits() - -Method in class compbio.metadata.LimitsManager -
      -
    GetLimitsResponse - Class in compbio.data.msa.jaxws
     
    GetLimitsResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getMax() - -Method in class compbio.metadata.ValueConstrain -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    getMetadata() - -Method in class compbio.data.sequence.Alignment -
      -
    getMethod(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
      -
    getMethod() - -Method in class compbio.data.sequence.Score -
    Returns the ConservationMethod -
    getMin() - -Method in class compbio.metadata.ValueConstrain -
      -
    getName() - -Method in interface compbio.metadata.Argument -
      -
    getName() - -Method in class compbio.metadata.Option -
    Human readable name of the option -
    getName() - -Method in class compbio.metadata.Preset -
      -
    getNextPosition() - -Method in class compbio.metadata.ChunkHolder -
      -
    getNumberOfScores() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getNumberOfSeq() - -Method in class compbio.data.sequence.ScoreManager -
      -
    getNumberOfSequencesAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getNumberOfSequencesAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getOnelineFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getOptionName() - -Method in class compbio.metadata.Parameter -
      -
    getOptionNames() - -Method in class compbio.metadata.Option -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getOptions() - -Method in class compbio.metadata.Preset -
      -
    getOptions() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of the Options supported by the executable of type T -
    getParameters() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of parameters supported executable of type T. -
    getPosition() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getPossibleValues() - -Method in interface compbio.metadata.Argument -
      -
    getPossibleValues() - -Method in class compbio.metadata.Option -
    List of possible optionNames -
    getPossibleValues() - -Method in class compbio.metadata.Parameter -
    List is more convenient to work with -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getPreset() - -Method in class compbio.metadata.Limit -
      -
    getPresetByName(String) - -Method in class compbio.metadata.PresetManager -
      -
    getPresetName() - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    GetPresets - Class in compbio.data.msa.jaxws
     
    GetPresets() - -Constructor for class compbio.data.msa.jaxws.GetPresets -
      -
    getPresets() - -Method in interface compbio.data.msa.Metadata -
    Get presets supported by a web service -
    getPresets() - -Method in class compbio.metadata.PresetManager -
      -
    GetPresetsResponse - Class in compbio.data.msa.jaxws
     
    GetPresetsResponse() - -Constructor for class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getPrmSeparator() - -Method in class compbio.metadata.RunnerConfig -
      -
    getProgram() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getRanges() - -Method in class compbio.data.sequence.Score -
    Return Ranges if any Collections.EMPTY_SET otherwise -
    GetResult - Class in compbio.data.msa.jaxws
     
    GetResult() - -Constructor for class compbio.data.msa.jaxws.GetResult -
      -
    getResult(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the result of the job. -
    GetResultResponse - Class in compbio.data.msa.jaxws
     
    GetResultResponse() - -Constructor for class compbio.data.msa.jaxws.GetResultResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    getRunnerByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getRunnerClassName() - -Method in class compbio.metadata.PresetManager -
      -
    getRunnerClassName() - -Method in class compbio.metadata.RunnerConfig -
      -
    GetRunnerOptions - Class in compbio.data.msa.jaxws
     
    GetRunnerOptions() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptions -
      -
    getRunnerOptions() - -Method in interface compbio.data.msa.Metadata -
    Get options supported by a web service -
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
     
    GetRunnerOptionsResponse() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getScoreByMethod(Enum<?>) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScoreByMethod(String) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScores() - -Method in class compbio.data.sequence.Score -
    The column scores for the alignment -
    getSeqNumber() - -Method in class compbio.metadata.Limit -
      -
    getSequence() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of sequence -
    getSequenceLenghtActual() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtActual() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequenceLenghtAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequences() - -Method in class compbio.data.sequence.Alignment -
      -
    getService(String) - -Static method in enum compbio.ws.client.Services -
      -
    getServiceByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceByRunner(Class<? extends Executable>) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    GetServiceCategories - Class in compbio.data.msa.jaxws
     
    GetServiceCategories() - -Constructor for class compbio.data.msa.jaxws.GetServiceCategories -
      -
    getServiceCategories() - -Method in interface compbio.data.msa.RegistryWS -
    Gets the list of services per category. -
    GetServiceCategoriesResponse - Class in compbio.data.msa.jaxws
     
    GetServiceCategoriesResponse() - -Constructor for class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    GetServiceDescription - Class in compbio.data.msa.jaxws
     
    GetServiceDescription() - -Constructor for class compbio.data.msa.jaxws.GetServiceDescription -
      -
    getServiceDescription(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Gives the description of the service. -
    GetServiceDescriptionResponse - Class in compbio.data.msa.jaxws
     
    GetServiceDescriptionResponse() - -Constructor for class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    getServiceImpl(Services) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceInfo() - -Method in enum compbio.ws.client.Services -
      -
    getServices() - -Method in class compbio.data.msa.Category -
      -
    getServices(String) - -Static method in class compbio.ws.client.Jws2Client -
      -
    getSize() - -Method in class compbio.data.sequence.Alignment -
      -
    getSMERFSColumnScore(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
      -
    GetSupportedServices - Class in compbio.data.msa.jaxws
     
    GetSupportedServices() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServices -
      -
    getSupportedServices() - -Method in interface compbio.data.msa.RegistryWS -
    List of services that are functioning on the server. -
    GetSupportedServicesResponse - Class in compbio.data.msa.jaxws
     
    GetSupportedServicesResponse() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getType() - -Method in class compbio.metadata.ValueConstrain -
      -
    getValidValue() - -Method in class compbio.metadata.Parameter -
      -
    GLOBPLOT_INFO - -Static variable in enum compbio.ws.client.Services -
      -
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    hashCode() - -Method in class compbio.data.msa.Category -
      -
    hashCode() - -Method in class compbio.data.sequence.Alignment -
      -
    hashCode() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    hashCode() - -Method in class compbio.data.sequence.FastaSequence -
      -
    hashCode() - -Method in class compbio.data.sequence.Range -
      -
    hashCode() - -Method in class compbio.data.sequence.Score -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    hashCode() - -Method in class compbio.metadata.ChunkHolder -
      -
    hashCode() - -Method in class compbio.metadata.Limit -
      -
    hashCode() - -Method in class compbio.metadata.Option -
      -
    hashCode() - -Method in class compbio.metadata.Parameter -
      -
    hashCode() - -Method in class compbio.metadata.Preset -
      -
    hashCode() - -Method in class compbio.metadata.ValueConstrain -
      -
    hasNext() - -Method in class compbio.data.sequence.FastaReader -
    -
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    id - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    IOHelper - Class in compbio.ws.client
     
    IOHelper() - -Constructor for class compbio.ws.client.IOHelper -
      -
    isAmbiguosProtein(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Check whether the sequence confirms to amboguous protein sequence -
    isDefault() - -Method in class compbio.metadata.Limit -
      -
    isExceeded(List<FastaSequence>) - -Method in class compbio.metadata.Limit -
    Checks if the number of sequences or their average length in the dataset - exceeds this limit. -
    isNonAmbNucleotideSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -
    isNucleotideSequence(FastaSequence) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    IsOperating - Class in compbio.data.msa.jaxws
     
    IsOperating() - -Constructor for class compbio.data.msa.jaxws.IsOperating -
      -
    isOperating(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Check whether a particular web service is working on this server -
    IsOperatingResponse - Class in compbio.data.msa.jaxws
     
    IsOperatingResponse() - -Constructor for class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isRequired() - -Method in class compbio.metadata.Option -
    Flag that indicated that this option must be specified in the command - line for an executable to run -
    isReturn() - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    isReturn() - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Please note this method closes the input stream provided as a parameter -
    IUPRED_INFO - -Static variable in enum compbio.ws.client.Services -
      -
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    JABAService - Interface in compbio.data.msa
    This is a marker interface, contains no methods
    JManagement - Interface in compbio.data.msa
     
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobExecutionException(String) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(String, Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(String, Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobSubmissionExceptionBean() - -Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    JRONN_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
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    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
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    -Class compbio.metadata.JobSubmissionException extends java.lang.Exception implements Serializable
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    -Serialized Fields
    - -

    -numberOfSequencesAllowed

    -
    -int numberOfSequencesAllowed
    -
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    -
    -int actualNumberofSequences
    -
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    -
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    -

    -aSequenceLenghtAllowed

    -
    -int aSequenceLenghtAllowed
    -
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    -

    -aSequenceLenghtActual

    -
    -int aSequenceLenghtActual
    -
    -
    -
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    - -

    - - - - - -
    -Class compbio.metadata.ResultNotAvailableException extends java.lang.Exception implements Serializable
    - -

    -serialVersionUID: -5475613614578761L - -

    - -

    - - - - - -
    -Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    - -

    -serialVersionUID: -86624836785110293L - -

    - -

    - - - - - -
    -Class compbio.metadata.WrongParameterException extends java.lang.Exception implements Serializable
    - -

    -serialVersionUID: -547775417557345769L - -

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    + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/Alignment.html b/website/docs/dm_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..93f7f2d --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,473 @@ + + + + + +Alignment + + + + + + + + +
    + + +
    Skip navigation links
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    compbio.data.sequence
    +

    Class Alignment

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Alignment
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Alignment
+extends java.lang.Object
      +
      Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. It does not guarantee neither the uniqueness of the names of + sequences nor it guarantees the uniqueness of the sequences.
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      FastaSequence, +AlignmentMetadata
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Alignment

          +
          protected Alignment()
          +
          • +
        + + + +
          +
        • +

          Alignment

          +
          public Alignment(java.util.List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
          +
          +
          Parameters:
          +
          sequences -
          +
          program -
          +
          gapchar -
          +
          +
          • +
        + + + +
          +
        • +

          Alignment

          +
          public Alignment(java.util.List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
          +
          +
          Parameters:
          +
          sequences -
          +
          metadata -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getSequences

          +
          public java.util.List<FastaSequence> getSequences()
          +
          +
          Returns:
          +
          list of FastaSequence records
          +
          +
          • +
        + + + +
          +
        • +

          getSize

          +
          public int getSize()
          +
          +
          Returns:
          +
          a number of sequence in the alignment
          +
          +
          • +
        + + + +
          +
        • +

          getMetadata

          +
          public AlignmentMetadata getMetadata()
          +
          +
          Returns:
          +
          AlignmentMetadata object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          Please note that this implementation does not take the order of sequences + into account!
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/docs/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..c9b3675 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,393 @@ + + + + + +AlignmentMetadata + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class AlignmentMetadata

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.AlignmentMetadata
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public class AlignmentMetadata
+extends java.lang.Object
      +
      Alignment metadata e.g. method/program being used to generate the alignment + and its parameters
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          program

          +
          private Program program
          +
          • +
        + + + +
          +
        • +

          gapchar

          +
          private char gapchar
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AlignmentMetadata

          +
          private AlignmentMetadata()
          +
          • +
        + + + +
          +
        • +

          AlignmentMetadata

          +
          public AlignmentMetadata(Program program,
+                         char gapchar)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getProgram

          +
          public Program getProgram()
          +
          • +
        + + + +
          +
        • +

          getGapchar

          +
          public char getGapchar()
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/docs/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..eeb48b2 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,488 @@ + + + + + +ClustalAlignmentUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ClustalAlignmentUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ClustalAlignmentUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class ClustalAlignmentUtil
+extends java.lang.Object
      +
      Tools to read and write clustal formated files
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      Petr Troshin based on jimp class
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static chargapchar +
        Dash char to be used as gap char in the alignments
        +
        private static java.util.logging.Loggerlog 
        private static intmaxNameLength 
        private static intminNameHolderLength 
        private static intoneLineAlignmentLength 
        private static java.lang.Stringspacer 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleanisValidClustalFile(java.io.InputStream input) +
        Please note this method closes the input stream provided as a parameter
        +
        static AlignmentreadClustalFile(java.io.File file) 
        static AlignmentreadClustalFile(java.io.InputStream instream) +
        Read Clustal formatted alignment.
        +
        static voidwriteClustalAlignment(java.io.Writer out, + Alignment alignment) +
        Write Clustal formatted alignment Limitations: does not record the + consensus.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final java.util.logging.Logger log
          +
          • +
        + + + +
          +
        • +

          gapchar

          +
          public static final char gapchar
          +
          Dash char to be used as gap char in the alignments
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          minNameHolderLength

          +
          private static final int minNameHolderLength
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          oneLineAlignmentLength

          +
          private static final int oneLineAlignmentLength
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClustalAlignmentUtil

          +
          public ClustalAlignmentUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          readClustalFile

          +
          public static Alignment readClustalFile(java.io.InputStream instream)
+                                 throws java.io.IOException,
+                                        UnknownFileFormatException
          +
          Read Clustal formatted alignment. Limitations: Does not read consensus + + Sequence names as well as the sequences are not guaranteed to be unique!
          +
          +
          Throws:
          +
          {@link - IOException}
          +
          {@link - UnknownFileFormatException}
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          isValidClustalFile

          +
          public static boolean isValidClustalFile(java.io.InputStream input)
          +
          Please note this method closes the input stream provided as a parameter
          +
          +
          Parameters:
          +
          input -
          +
          Returns:
          +
          true if the file is recognised as Clustal formatted alignment, + false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          writeClustalAlignment

          +
          public static void writeClustalAlignment(java.io.Writer out,
+                                         Alignment alignment)
+                                  throws java.io.IOException
          +
          Write Clustal formatted alignment Limitations: does not record the + consensus. Potential bug - records 60 chars length alignment where + Clustal would have recorded 50 chars.
          +
          +
          Parameters:
          +
          out -
          +
          alignment -
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
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    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/ConservationMethod.html b/website/docs/dm_javadoc/compbio/data/sequence/ConservationMethod.html new file mode 100644 index 0000000..5daae21 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/ConservationMethod.html @@ -0,0 +1,551 @@ + + + + + +ConservationMethod + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum ConservationMethod

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<ConservationMethod>
      +
      +
      +
      +
      public enum ConservationMethod
+extends java.lang.Enum<ConservationMethod>
      +
      Enumeration listing of all the supported methods.
      +
      +
      Author:
      +
      Agnieszka Golicz & Peter Troshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static ConservationMethod[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (ConservationMethod c : ConservationMethod.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static ConservationMethod valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/DisemblResult.html b/website/docs/dm_javadoc/compbio/data/sequence/DisemblResult.html new file mode 100644 index 0000000..e6ac83b --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/DisemblResult.html @@ -0,0 +1,356 @@ + + + + + +DisemblResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum DisemblResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<DisemblResult>
        • +
      • +
          +
        • compbio.data.sequence.DisemblResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<DisemblResult>
      +
      +
      +
      +
       enum DisemblResult
+extends java.lang.Enum<DisemblResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        COILS +
        These contains ranges and scores
        +
        HOTLOOPS 
        REM465 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static DisemblResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static DisemblResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static DisemblResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (DisemblResult c : DisemblResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static DisemblResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/DisorderMethod.html b/website/docs/dm_javadoc/compbio/data/sequence/DisorderMethod.html new file mode 100644 index 0000000..12e02b1 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/DisorderMethod.html @@ -0,0 +1,341 @@ + + + + + +DisorderMethod + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum DisorderMethod

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<DisorderMethod>
        • +
      • +
          +
        • compbio.data.sequence.DisorderMethod
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<DisorderMethod>
      +
      +
      +
      +
      public enum DisorderMethod
+extends java.lang.Enum<DisorderMethod>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Disembl 
        JRonn 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static DisorderMethodvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static DisorderMethod[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static DisorderMethod[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (DisorderMethod c : DisorderMethod.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static DisorderMethod valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/FastaReader.html b/website/docs/dm_javadoc/compbio/data/sequence/FastaReader.html new file mode 100644 index 0000000..787a7cc --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/FastaReader.html @@ -0,0 +1,497 @@ + + + + + +FastaReader + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class FastaReader

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.FastaReader
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.Iterator<FastaSequence>
      +
      +
      +
      +
      public class FastaReader
+extends java.lang.Object
+implements java.util.Iterator<FastaSequence>
      +
      Reads files with FASTA formatted sequences. All the information in the FASTA + header is preserved including trailing white spaces. All the white spaces are + removed from the sequence. + + Examples of the correct input: + + 
      + 
+ >zedpshvyzg
+ GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
+ 
+ >xovkactesa
+ CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
+ FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
+ FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
+ DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
+ 
+ >ntazzewyvv
+ CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
+ EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
+ EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
+   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
+   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
+   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
+ 
+    > 12 d t y wi               k       jbke    
+   KLSHHDCD
+    N
+     H
+     HSKCTEPHCGNSHQMLHRDP
+     CCDQCQSWEAENWCASMRKAILF
+ 
+
      +
      +
      Version:
      +
      1.0 April 2011
      +
      Author:
      +
      Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringDELIM +
        Delimiter for the scanner
        +
        private java.util.Scannerinput 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        FastaReader(java.io.InputStream inputStream) +
        This class will not close the incoming stream! So the client should do + so.
        +
        FastaReader(java.lang.String inputFile) +
        Header data can contain non-ASCII symbols and read in UTF8
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        voidclose() +
        Call this method to close the connection to the input file if you want to + free up the resources.
        +
        booleanhasNext()
        FastaSequencenext() +
        Reads the next FastaSequence from the input
        +
        voidremove() +
        Not implemented
        +
        private static FastaSequencetoFastaSequence(java.lang.String singleFastaEntry) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
          +
        • + + +

          Methods inherited from interface java.util.Iterator

          +forEachRemaining
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          input

          +
          private final java.util.Scanner input
          +
          • +
        + + + +
          +
        • +

          DELIM

          +
          private final java.lang.String DELIM
          +
          Delimiter for the scanner
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FastaReader

          +
          public FastaReader(java.lang.String inputFile)
+            throws java.io.FileNotFoundException
          +
          Header data can contain non-ASCII symbols and read in UTF8
          +
          +
          Parameters:
          +
          inputFile - the file containing the list of FASTA formatted sequences to + read from
          +
          Throws:
          +
          java.io.FileNotFoundException - if the input file is not found
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          +
          • +
        + + + +
          +
        • +

          FastaReader

          +
          public FastaReader(java.io.InputStream inputStream)
+            throws java.io.FileNotFoundException
          +
          This class will not close the incoming stream! So the client should do + so.
          +
          +
          Parameters:
          +
          inputStream -
          +
          Throws:
          +
          java.io.FileNotFoundException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          hasNext

          +
          public boolean hasNext()
          +
          +
          Specified by:
          +
          hasNext in interface java.util.Iterator<FastaSequence>
          +
          Throws:
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          +
          • +
        + + + +
          +
        • +

          next

          +
          public FastaSequence next()
          +
          Reads the next FastaSequence from the input
          +
          +
          Specified by:
          +
          next in interface java.util.Iterator<FastaSequence>
          +
          Throws:
          +
          java.lang.AssertionError - if the header or the sequence is missing
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          MismatchException - - if there were no more FastaSequence's.
          +
          +
          • +
        + + + +
          +
        • +

          remove

          +
          public void remove()
          +
          Not implemented
          +
          +
          Specified by:
          +
          remove in interface java.util.Iterator<FastaSequence>
          +
          +
          • +
        + + + +
          +
        • +

          close

          +
          public void close()
          +
          Call this method to close the connection to the input file if you want to + free up the resources. The connection will be closed on the JVM shutdown + if this method was not called explicitly. No further reading on this + instance of the FastaReader will be possible after calling this method.
          +
          • +
        + + + +
          +
        • +

          toFastaSequence

          +
          private static FastaSequence toFastaSequence(java.lang.String singleFastaEntry)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/docs/dm_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..b01dc15 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,526 @@ + + + + + +FastaSequence + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class FastaSequence

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.FastaSequence
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public class FastaSequence
+extends java.lang.Object
      +
      A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it stores e.g. it could be nucleotide, + protein or even gapped alignment sequence! The only guarantee it makes is + that the sequence does not contain white space characters e.g. spaces, new + lines etc
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringid +
        Sequence id
        +
        private java.lang.Stringsequence +
        Returns the string representation of sequence
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        FastaSequence() 
        FastaSequence(java.lang.String id, + java.lang.String sequence) +
        Upon construction the any whitespace characters are removed from the + sequence
        +
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          id

          +
          private java.lang.String id
          +
          Sequence id
          +
          • +
        + + + +
          +
        • +

          sequence

          +
          private java.lang.String sequence
          +
          Returns the string representation of sequence
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FastaSequence

          +
          FastaSequence()
          +
          • +
        + + + +
          +
        • +

          FastaSequence

          +
          public FastaSequence(java.lang.String id,
+                     java.lang.String sequence)
          +
          Upon construction the any whitespace characters are removed from the + sequence
          +
          +
          Parameters:
          +
          id -
          +
          sequence -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getId

          +
          public java.lang.String getId()
          +
          Gets the value of id
          +
          +
          Returns:
          +
          the value of id
          +
          +
          • +
        + + + +
          +
        • +

          getSequence

          +
          public java.lang.String getSequence()
          +
          Gets the value of sequence
          +
          +
          Returns:
          +
          the value of sequence
          +
          +
          • +
        + + + +
          +
        • +

          countMatchesInSequence

          +
          public static int countMatchesInSequence(java.lang.String theString,
+                                         java.lang.String theRegExp)
          +
          • +
        + + + +
          +
        • +

          getFormattedFasta

          +
          public java.lang.String getFormattedFasta()
          +
          • +
        + + + +
          +
        • +

          getOnelineFasta

          +
          public java.lang.String getOnelineFasta()
          +
          +
          Returns:
          +
          one line name, next line sequence, no matter what the sequence + length is
          +
          +
          • +
        + + + +
          +
        • +

          getFormatedSequence

          +
          public java.lang.String getFormatedSequence(int width)
          +
          Format sequence per width letter in one string. Without spaces.
          +
          +
          Returns:
          +
          multiple line formated sequence, one line width letters length
          +
          +
          • +
        + + + +
          +
        • +

          getLength

          +
          public int getLength()
          +
          +
          Returns:
          +
          sequence length
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          Same as oneLineFasta
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/GlobProtResult.html b/website/docs/dm_javadoc/compbio/data/sequence/GlobProtResult.html new file mode 100644 index 0000000..d7d03b3 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/GlobProtResult.html @@ -0,0 +1,392 @@ + + + + + +GlobProtResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum GlobProtResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<GlobProtResult>
        • +
      • +
          +
        • compbio.data.sequence.GlobProtResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<GlobProtResult>
      +
      +
      +
      +
       enum GlobProtResult
+extends java.lang.Enum<GlobProtResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Disorder +
        This a range with no scores
        +
        Dydx +
        This a score with no range
        +
        GlobDoms +
        This a range with no scores
        +
        RawScore +
        This a score with no range
        +
        SmoothedScore +
        This a score with no range
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static GlobProtResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static GlobProtResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          GlobDoms

          +
          public static final GlobProtResult GlobDoms
          +
          This a range with no scores
          +
          • +
        + + + +
          +
        • +

          Disorder

          +
          public static final GlobProtResult Disorder
          +
          This a range with no scores
          +
          • +
        + + + +
          +
        • +

          Dydx

          +
          public static final GlobProtResult Dydx
          +
          This a score with no range
          +
          • +
        + + + +
          +
        • +

          SmoothedScore

          +
          public static final GlobProtResult SmoothedScore
          +
          This a score with no range
          +
          • +
        + + + +
          +
        • +

          RawScore

          +
          public static final GlobProtResult RawScore
          +
          This a score with no range
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static GlobProtResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (GlobProtResult c : GlobProtResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static GlobProtResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/IUPredResult.html b/website/docs/dm_javadoc/compbio/data/sequence/IUPredResult.html new file mode 100644 index 0000000..4a81c35 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/IUPredResult.html @@ -0,0 +1,375 @@ + + + + + +IUPredResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum IUPredResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<IUPredResult>
        • +
      • +
          +
        • compbio.data.sequence.IUPredResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<IUPredResult>
      +
      +
      +
      +
       enum IUPredResult
+extends java.lang.Enum<IUPredResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Glob +
        Globular domains
        +
        Long +
        Long disorder
        +
        Short +
        Short disorder
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static IUPredResultgetType(java.io.File file) 
        static IUPredResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static IUPredResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          Short

          +
          public static final IUPredResult Short
          +
          Short disorder
          +
          • +
        + + + +
          +
        • +

          Long

          +
          public static final IUPredResult Long
          +
          Long disorder
          +
          • +
        + + + +
          +
        • +

          Glob

          +
          public static final IUPredResult Glob
          +
          Globular domains
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static IUPredResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (IUPredResult c : IUPredResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static IUPredResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + +
          +
        • +

          getType

          +
          static IUPredResult getType(java.io.File file)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/Program.html b/website/docs/dm_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..cbc83ab --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,442 @@ + + + + + +Program + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum Program

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<Program>
        • +
      • +
          +
        • compbio.data.sequence.Program
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<Program>
      +
      +
      +
      +
      public enum Program
+extends java.lang.Enum<Program>
      +
      The list of programmes that can produce alignments
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static ProgramvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static Program[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          CLUSTAL

          +
          public static final Program CLUSTAL
          +
          ClustalW
          +
          • +
        + + + +
          +
        • +

          ClustalO

          +
          public static final Program ClustalO
          +
          ClustalO
          +
          • +
        + + + +
          +
        • +

          Mafft

          +
          public static final Program Mafft
          +
          Mafft
          +
          • +
        + + + +
          +
        • +

          Muscle

          +
          public static final Program Muscle
          +
          Muscle
          +
          • +
        + + + +
          +
        • +

          Tcoffee

          +
          public static final Program Tcoffee
          +
          Tcoffee
          +
          • +
        + + + +
          +
        • +

          Probcons

          +
          public static final Program Probcons
          +
          Probcons
          +
          • +
        + + + +
          +
        • +

          MSAprobs

          +
          public static final Program MSAprobs
          +
          MSAprobs
          +
          • +
        + + + +
          +
        • +

          GLprobs

          +
          public static final Program GLprobs
          +
          GLprobs
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static Program[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (Program c : Program.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static Program valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html new file mode 100644 index 0000000..1ef78f4 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html @@ -0,0 +1,477 @@ + + + + + +RNAStructReader.AlifoldLine + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.AlifoldLine

    +
    +
    + +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringregex 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static RNAStructReader.AlifoldLinevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static RNAStructReader.AlifoldLine[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          regex

          +
          java.lang.String regex
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.AlifoldLine[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.AlifoldLine c : RNAStructReader.AlifoldLine.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.AlifoldLine valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html new file mode 100644 index 0000000..bedddac --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html @@ -0,0 +1,417 @@ + + + + + +RNAStructReader.AlifoldResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.AlifoldResult

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.AlifoldResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.AlifoldResult c : RNAStructReader.AlifoldResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.AlifoldResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html new file mode 100644 index 0000000..c7076c7 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html @@ -0,0 +1,381 @@ + + + + + +RNAStructReader.RNAOut + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.RNAOut

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        ENERGY 
        FREQ 
        OTHER 
        SEQ 
        STRUCT 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static RNAStructReader.RNAOutvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static RNAStructReader.RNAOut[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.RNAOut[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.RNAOut c : RNAStructReader.RNAOut.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.RNAOut valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.html b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.html new file mode 100644 index 0000000..27515c4 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructReader.html @@ -0,0 +1,647 @@ + + + + + +RNAStructReader + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class RNAStructReader

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.RNAStructReader
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class RNAStructReader
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.StringalignmentP 
        (package private) static java.lang.Stringbracket 
        (package private) static java.lang.StringcentStructP 
        (package private) static java.lang.StringenergyP 
        (package private) static java.lang.StringensembleFreqP 
        (package private) static java.lang.StringfloatP 
        (package private) static java.lang.StringfreeEnergyP 
        (package private) static java.lang.StringfreqP 
        (package private) static java.lang.StringjustStructP 
        (package private) static java.lang.StringMEAStructP 
        (package private) static java.lang.StringmfeStructP 
        (package private) static java.lang.StringnotData 
        (package private) static java.lang.Stringps 
        (package private) static java.lang.StringPStructP 
        (package private) static java.lang.Strings 
        (package private) static java.lang.StringseqP 
        (package private) static java.lang.StringstochBTStructP 
        (package private) static java.lang.StringstructP 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        RNAStructReader() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          s

          +
          static java.lang.String s
          +
          • +
        + + + +
          +
        • +

          bracket

          +
          static java.lang.String bracket
          +
          • +
        + + + +
          +
        • +

          notData

          +
          static java.lang.String notData
          +
          • +
        + + + +
          +
        • +

          seqP

          +
          static java.lang.String seqP
          +
          • +
        + + + +
          +
        • +

          structP

          +
          static java.lang.String structP
          +
          • +
        + + + +
          +
        • +

          floatP

          +
          static java.lang.String floatP
          +
          • +
        + + + +
          +
        • +

          energyP

          +
          static java.lang.String energyP
          +
          • +
        + + + +
          +
        • +

          freqP

          +
          static java.lang.String freqP
          +
          • +
        + + + +
          +
        • +

          ps

          +
          static java.lang.String ps
          +
          • +
        + + + +
          +
        • +

          alignmentP

          +
          static java.lang.String alignmentP
          +
          • +
        + + + +
          +
        • +

          mfeStructP

          +
          static java.lang.String mfeStructP
          +
          • +
        + + + +
          +
        • +

          justStructP

          +
          static java.lang.String justStructP
          +
          • +
        + + + +
          +
        • +

          stochBTStructP

          +
          static java.lang.String stochBTStructP
          +
          • +
        + + + +
          +
        • +

          PStructP

          +
          static java.lang.String PStructP
          +
          • +
        + + + +
          +
        • +

          centStructP

          +
          static java.lang.String centStructP
          +
          • +
        + + + +
          +
        • +

          MEAStructP

          +
          static java.lang.String MEAStructP
          +
          • +
        + + + +
          +
        • +

          freeEnergyP

          +
          static java.lang.String freeEnergyP
          +
          • +
        + + + +
          +
        • +

          ensembleFreqP

          +
          static java.lang.String ensembleFreqP
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RNAStructReader

          +
          public RNAStructReader()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          readRNAStructStream

          +
          public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout)
+                                                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          newSetScore

          +
          private static java.util.TreeSet<Score> newSetScore(java.lang.Enum<?> res,
+                                                    java.util.List<java.lang.Float> scores)
          +
          • +
        + + + +
          +
        • +

          newEmptyScore

          +
          public static java.util.TreeSet<Score> newEmptyScore(java.lang.Enum<?> res)
          +
          • +
        + + + +
          +
        • +

          readRNAStructStream

          +
          public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout,
+                                                        java.io.InputStream alifold)
+                                                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/RNAStructScoreManager.html b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructScoreManager.html new file mode 100644 index 0000000..674ad8b --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/RNAStructScoreManager.html @@ -0,0 +1,392 @@ + + + + + +RNAStructScoreManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class RNAStructScoreManager

    +
    +
    + +
    +
      +
    • +
      +
      +
      public class RNAStructScoreManager
+extends ScoreManager
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RNAStructScoreManager

          +
          private RNAStructScoreManager()
          +
          • +
        + + + +
          +
        • +

          RNAStructScoreManager

          +
          public RNAStructScoreManager(java.util.List<java.lang.String> structs,
+                             java.util.List<java.util.TreeSet<Score>> data)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newInstance

          +
          public static RNAStructScoreManager newInstance(java.util.List<java.lang.String> structs,
+                                                java.util.List<java.util.TreeSet<Score>> data)
          +
          • +
        + + + +
          +
        • +

          getStructs

          +
          public java.util.List<java.lang.String> getStructs()
          +
          • +
        + + + +
          +
        • +

          getData

          +
          public java.util.List<java.util.TreeSet<Score>> getData()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class ScoreManager
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/Range.html b/website/docs/dm_javadoc/compbio/data/sequence/Range.html new file mode 100644 index 0000000..df1504c --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/Range.html @@ -0,0 +1,410 @@ + + + + + +Range + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class Range

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Range
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Comparable<Range>
      +
      +
      +
      +
      public class Range
+extends java.lang.Object
+implements java.lang.Comparable<Range>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        intfrom 
        intto 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Range() 
         Range(int from, + int to) 
         Range(java.lang.String[] twoElementAr) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intcompareTo(Range o) 
        booleanequals(java.lang.Object obj) 
        inthashCode() 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          from

          +
          public final int from
          +
          • +
        + + + +
          +
        • +

          to

          +
          public final int to
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Range

          +
          private Range()
          +
          • +
        + + + +
          +
        • +

          Range

          +
          public Range(int from,
+             int to)
          +
          • +
        + + + +
          +
        • +

          Range

          +
          public Range(java.lang.String[] twoElementAr)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          compareTo

          +
          public int compareTo(Range o)
          +
          +
          Specified by:
          +
          compareTo in interface java.lang.Comparable<Range>
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/docs/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html new file mode 100644 index 0000000..612d54f --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html @@ -0,0 +1,440 @@ + + + + + +SMERFSConstraints + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum SMERFSConstraints

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<SMERFSConstraints>
        • +
      • +
          +
        • compbio.data.sequence.SMERFSConstraints
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<SMERFSConstraints>
      +
      +
      +
      +
      public enum SMERFSConstraints
+extends java.lang.Enum<SMERFSConstraints>
      +
      Enumeration defining two constraints for SMERFS columns score calculation. + MAX_SCORE gives the highest core of all the windows the column belongs to. + MID_SCORE gives the window score to the column in the middle.
      +
      +
      Author:
      +
      Agnieszka Golicz & Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        MAX_SCORE 
        MID_SCORE 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static SMERFSConstraintsgetSMERFSColumnScore(java.lang.String score) 
        static SMERFSConstraintsvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static SMERFSConstraints[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          DEFAULT_COLUMN_SCORE

          +
          public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
          +
          Default column scoring schema
          +
          • +
        + + + +
          +
        • +

          DEFAULT_WINDOW_SIZE

          +
          public static final int DEFAULT_WINDOW_SIZE
          +
          Default window size value for SMERFS algorithm
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          DEFAULT_GAP_THRESHOLD

          +
          public static final double DEFAULT_GAP_THRESHOLD
          +
          Default gap threshold value for SMERFS algorithm
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static SMERFSConstraints[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (SMERFSConstraints c : SMERFSConstraints.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static SMERFSConstraints valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + +
          +
        • +

          getSMERFSColumnScore

          +
          public static SMERFSConstraints getSMERFSColumnScore(java.lang.String score)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/Score.html b/website/docs/dm_javadoc/compbio/data/sequence/Score.html new file mode 100644 index 0000000..174bd07 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/Score.html @@ -0,0 +1,624 @@ + + + + + +Score + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class Score

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Score
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Comparable<Score>
      +
      +
      +
      +
      @Immutable
+public class Score
+extends java.lang.Object
+implements java.lang.Comparable<Score>
      +
      A value class for AACon annotation results storage. The objects of this type + are immutable
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmethod 
        (package private) static java.text.NumberFormatNUMBER_FORMAT 
        private java.util.TreeSet<Range>ranges 
        private java.util.ArrayList<java.lang.Float>scores 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Score() 
         Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores) +
        Instantiate the Score
        +
         Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores, + java.util.TreeSet<Range> ranges) 
         Score(java.lang.Enum<?> method, + float[] scores) 
         Score(java.lang.Enum<?> method, + java.util.TreeSet<Range> ranges) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intcompareTo(Score o) 
        booleanequals(java.lang.Object obj) 
        java.lang.StringgetMethod() +
        Returns the ConservationMethod
        +
        java.util.TreeSet<Range>getRanges() +
        Return Ranges if any Collections.EMPTY_SET otherwise
        +
        java.util.ArrayList<java.lang.Float>getScores() +
        The column scores for the alignment
        +
        inthashCode() 
        voidsetRanges(java.util.TreeSet<Range> ranges) 
        private java.util.ArrayList<java.lang.Float>toList(float[] values) 
        java.lang.StringtoString() 
        static voidwrite(java.util.TreeSet<Score> scores, + java.io.Writer writer) +
        Outputs the List of Score objects into the Output stream.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          NUMBER_FORMAT

          +
          static final java.text.NumberFormat NUMBER_FORMAT
          +
          • +
        + + + +
          +
        • +

          method

          +
          private final java.lang.String method
          +
          • +
        + + + +
          +
        • +

          ranges

          +
          private java.util.TreeSet<Range> ranges
          +
          • +
        + + + +
          +
        • +

          scores

          +
          private java.util.ArrayList<java.lang.Float> scores
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Score

          +
          private Score()
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.Float> scores)
          +
          Instantiate the Score
          +
          +
          Parameters:
          +
          method - the ConservationMethod with which scores were + calculated
          +
          scores - the actual conservation values for each column of the + alignment
          +
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.Float> scores,
+             java.util.TreeSet<Range> ranges)
          +
          +
          Parameters:
          +
          method - the ConservationMethod with which scores were + calculated
          +
          scores - the actual conservation values for each column of the + alignment
          +
          ranges - The set of ranges i.e. parts of the sequence with specific + function, usually can be calculated based on scores
          +
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.TreeSet<Range> ranges)
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             float[] scores)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toList

          +
          private java.util.ArrayList<java.lang.Float> toList(float[] values)
          +
          • +
        + + + +
          +
        • +

          getMethod

          +
          public java.lang.String getMethod()
          +
          Returns the ConservationMethod
          +
          +
          Returns:
          +
          the ConservationMethod
          +
          +
          • +
        + + + +
          +
        • +

          getScores

          +
          public java.util.ArrayList<java.lang.Float> getScores()
          +
          The column scores for the alignment
          +
          +
          Returns:
          +
          the column scores for the alignment
          +
          +
          • +
        + + + +
          +
        • +

          getRanges

          +
          public java.util.TreeSet<Range> getRanges()
          +
          Return Ranges if any Collections.EMPTY_SET otherwise
          +
          +
          Returns:
          +
          ordered set of Range
          +
          +
          • +
        + + + +
          +
        • +

          setRanges

          +
          public void setRanges(java.util.TreeSet<Range> ranges)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          write

          +
          public static void write(java.util.TreeSet<Score> scores,
+                         java.io.Writer writer)
+                  throws java.io.IOException
          +
          Outputs the List of Score objects into the Output stream. The output + format is as follows: + + 
          + 
+ #MethodName [comma separated list of ranges] <space separated list of values>
+ 	  
+ For example:
+ 	 
+ #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
+ #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
+ #COILS 22-33, 44-56 0.121 3.212
+ 
+
          + + The maximum precision for values is 3 digits, but can be less.
          +
          +
          Parameters:
          +
          scores - the list of scores to output
          +
          writer -
          +
          Throws:
          +
          java.io.IOException - if the OutputStream cannot be written into
          +
          java.lang.NullPointerException - if the output stream is null
          +
          +
          • +
        + + + +
          +
        • +

          compareTo

          +
          public int compareTo(Score o)
          +
          +
          Specified by:
          +
          compareTo in interface java.lang.Comparable<Score>
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html b/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html new file mode 100644 index 0000000..cc214b3 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html @@ -0,0 +1,419 @@ + + + + + +ScoreManager.ScoreHolder + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ScoreManager.ScoreHolder

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ScoreManager.ScoreHolder
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Enclosing class:
      +
      ScoreManager
      +
      +
      +
      +
      public static class ScoreManager.ScoreHolder
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        java.lang.Stringid 
        java.util.TreeSet<Score>scores 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private ScoreHolder() 
        (package private)ScoreHolder(java.lang.String id, + java.util.Set<Score> scores) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          id

          +
          public java.lang.String id
          +
          • +
        + + + +
          +
        • +

          scores

          +
          public java.util.TreeSet<Score> scores
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ScoreHolder

          +
          private ScoreHolder()
          +
          • +
        + + + +
          +
        • +

          ScoreHolder

          +
          ScoreHolder(java.lang.String id,
+            java.util.Set<Score> scores)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          writeOut

          +
          public void writeOut(java.io.Writer writer)
+              throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getScoreByMethod

          +
          public Score getScoreByMethod(java.lang.Enum<?> method)
          +
          • +
        + + + +
          +
        • +

          getScoreByMethod

          +
          public Score getScoreByMethod(java.lang.String method)
          +
          • +
        + + + +
          +
        • +

          getNumberOfScores

          +
          public int getNumberOfScores()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.html b/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.html new file mode 100644 index 0000000..dcdbdbd --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.html @@ -0,0 +1,507 @@ + + + + + +ScoreManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ScoreManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ScoreManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Direct Known Subclasses:
      +
      RNAStructScoreManager
      +
      +
      +
      +
      public class ScoreManager
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ScoreManager

          +
          protected ScoreManager()
          +
          • +
        + + + +
          +
        • +

          ScoreManager

          +
          private ScoreManager(java.lang.String id,
+                     java.util.Set<Score> data)
          +
          • +
        + + + +
          +
        • +

          ScoreManager

          +
          private ScoreManager(java.util.Map<java.lang.String,java.util.Set<Score>> data)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newInstance

          +
          public static ScoreManager newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data)
          +
          • +
        + + + +
          +
        • +

          newInstanceSingleScore

          +
          public static ScoreManager newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap)
          +
          • +
        + + + +
          +
        • +

          newInstanceSingleSequence

          +
          public static ScoreManager newInstanceSingleSequence(java.util.Set<Score> data)
          +
          • +
        + + + +
          +
        • +

          asMap

          +
          public java.util.Map<java.lang.String,java.util.TreeSet<Score>> asMap()
          +
          • +
        + + + +
          +
        • +

          asSet

          +
          public java.util.Set<Score> asSet()
          +
          • +
        + + + +
          +
        • +

          getNumberOfSeq

          +
          public int getNumberOfSeq()
          +
          • +
        + + + + + + + +
          +
        • +

          writeOut

          +
          public void writeOut(java.io.Writer outStream)
+              throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/docs/dm_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..9e9e4db --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,1147 @@ + + + + + +SequenceUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class SequenceUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.SequenceUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class SequenceUtil
+extends java.lang.Object
      +
      Utility class for operations on sequences
      +
      +
      Since:
      +
      1.0
      +
      Version:
      +
      2.0 June 2011
      +
      Author:
      +
      Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.util.regex.PatternAA +
        Valid Amino acids
        +
        static java.util.regex.PatternAMBIGUOUS_AA +
        Same as AA pattern but with two additional letters - XU
        +
        static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE +
        Ambiguous nucleotide
        +
        static java.util.regex.PatternDIGIT +
        A digit
        +
        private static java.lang.StringJRONN_WRONG_FORMAT_MESSAGE 
        static java.util.regex.PatternNON_AA +
        inversion of AA pattern
        +
        static java.util.regex.PatternNON_NUCLEOTIDE +
        Non nucleotide
        +
        static java.util.regex.PatternNONWORD +
        Non word
        +
        static java.util.regex.PatternNUCLEOTIDE +
        Nucleotides a, t, g, c, u
        +
        static java.util.regex.PatternWHITE_SPACE +
        A whitespace character: [\t\n\x0B\f\r]
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private SequenceUtil() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.StringcleanProteinSequence(java.lang.String sequence) +
        Remove all non AA chars from the sequence
        +
        static java.lang.StringcleanSequence(java.lang.String sequence) +
        Removes all whitespace chars in the sequence string
        +
        static voidcloseSilently(java.util.logging.Logger log, + java.io.Closeable stream) +
        Closes the Closable and logs the exception if any
        +
        private static float[]convertToNumber(java.lang.String[] annotValues) 
        static java.lang.StringdeepCleanSequence(java.lang.String sequence) +
        Removes all special characters and digits as well as whitespace chars + from the sequence
        +
        static booleanisAmbiguosProtein(java.lang.String sequence) +
        Check whether the sequence confirms to amboguous protein sequence
        +
        static booleanisNonAmbNucleotideSequence(java.lang.String sequence) +
        Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
        +
        static booleanisNucleotideSequence(FastaSequence s) 
        static booleanisProteinSequence(java.lang.String sequence) 
        static java.util.List<FastaSequence>openInputStream(java.lang.String inFilePath) +
        Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
        +
        private static java.util.TreeSet<Range>parseIUPredDomains(java.util.Scanner scan) +
        # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
        +
        private static float[]parseIUPredScores(java.util.Scanner scan) 
        private static java.util.TreeSet<Range>parseRanges(java.lang.Enum resultType, + java.lang.String lines) +
        Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
        +
        static java.util.HashSet<Score>readAAConResults(java.io.InputStream results) +
        Read AACon result with no alignment files.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) +
        Reads fasta sequences from inStream into the list of FastaSequence + objects
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
        static voidwriteClustal(java.io.OutputStream outStream, + java.util.List<FastaSequence> sequences, + char gapChar) 
        static voidwriteFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) +
        Writes FastaSequence in the file, each sequence will take one line only
        +
        static voidwriteFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) +
        Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
        +
        static voidwriteFastaKeepTheStream(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          WHITE_SPACE

          +
          public static final java.util.regex.Pattern WHITE_SPACE
          +
          A whitespace character: [\t\n\x0B\f\r]
          +
          • +
        + + + +
          +
        • +

          DIGIT

          +
          public static final java.util.regex.Pattern DIGIT
          +
          A digit
          +
          • +
        + + + +
          +
        • +

          NONWORD

          +
          public static final java.util.regex.Pattern NONWORD
          +
          Non word
          +
          • +
        + + + +
          +
        • +

          AA

          +
          public static final java.util.regex.Pattern AA
          +
          Valid Amino acids
          +
          • +
        + + + +
          +
        • +

          NON_AA

          +
          public static final java.util.regex.Pattern NON_AA
          +
          inversion of AA pattern
          +
          • +
        + + + +
          +
        • +

          AMBIGUOUS_AA

          +
          public static final java.util.regex.Pattern AMBIGUOUS_AA
          +
          Same as AA pattern but with two additional letters - XU
          +
          • +
        + + + +
          +
        • +

          NUCLEOTIDE

          +
          public static final java.util.regex.Pattern NUCLEOTIDE
          +
          Nucleotides a, t, g, c, u
          +
          • +
        + + + +
          +
        • +

          AMBIGUOUS_NUCLEOTIDE

          +
          public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
          +
          Ambiguous nucleotide
          +
          • +
        + + + +
          +
        • +

          NON_NUCLEOTIDE

          +
          public static final java.util.regex.Pattern NON_NUCLEOTIDE
          +
          Non nucleotide
          +
          • +
        + + + +
          +
        • +

          JRONN_WRONG_FORMAT_MESSAGE

          +
          private static final java.lang.String JRONN_WRONG_FORMAT_MESSAGE
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SequenceUtil

          +
          private SequenceUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isNucleotideSequence

          +
          public static boolean isNucleotideSequence(FastaSequence s)
          +
          +
          Returns:
          +
          true is the sequence contains only letters a,c, t, g, u
          +
          +
          • +
        + + + +
          +
        • +

          isNonAmbNucleotideSequence

          +
          public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
          +
          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
          +
          • +
        + + + +
          +
        • +

          cleanSequence

          +
          public static java.lang.String cleanSequence(java.lang.String sequence)
          +
          Removes all whitespace chars in the sequence string
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          cleaned up sequence
          +
          +
          • +
        + + + +
          +
        • +

          deepCleanSequence

          +
          public static java.lang.String deepCleanSequence(java.lang.String sequence)
          +
          Removes all special characters and digits as well as whitespace chars + from the sequence
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          cleaned up sequence
          +
          +
          • +
        + + + +
          +
        • +

          cleanProteinSequence

          +
          public static java.lang.String cleanProteinSequence(java.lang.String sequence)
          +
          Remove all non AA chars from the sequence
          +
          +
          Parameters:
          +
          sequence - the sequence to clean
          +
          Returns:
          +
          cleaned sequence
          +
          +
          • +
        + + + +
          +
        • +

          isProteinSequence

          +
          public static boolean isProteinSequence(java.lang.String sequence)
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          true is the sequence is a protein sequence, false overwise
          +
          +
          • +
        + + + +
          +
        • +

          isAmbiguosProtein

          +
          public static boolean isAmbiguosProtein(java.lang.String sequence)
          +
          Check whether the sequence confirms to amboguous protein sequence
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          return true only if the sequence if ambiguous protein sequence + Return false otherwise. e.g. if the sequence is non-ambiguous + protein or DNA
          +
          +
          • +
        + + + +
          +
        • +

          writeFasta

          +
          public static void writeFasta(java.io.OutputStream outstream,
+                              java.util.List<FastaSequence> sequences,
+                              int width)
+                       throws java.io.IOException
          +
          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
          +
          +
          Parameters:
          +
          outstream -
          +
          sequences -
          +
          width - - the maximum number of characters to write in one line
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeFastaKeepTheStream

          +
          public static void writeFastaKeepTheStream(java.io.OutputStream outstream,
+                                           java.util.List<FastaSequence> sequences,
+                                           int width)
+                                    throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          readFasta

          +
          public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
+                                               throws java.io.IOException
          +
          Reads fasta sequences from inStream into the list of FastaSequence + objects
          +
          +
          Parameters:
          +
          inStream - from
          +
          Returns:
          +
          list of FastaSequence objects
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeFasta

          +
          public static void writeFasta(java.io.OutputStream os,
+                              java.util.List<FastaSequence> sequences)
+                       throws java.io.IOException
          +
          Writes FastaSequence in the file, each sequence will take one line only
          +
          +
          Parameters:
          +
          os -
          +
          sequences -
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          readIUPred

          +
          public static java.util.Map<java.lang.String,Score> readIUPred(java.io.File result)
+                                                        throws java.io.IOException,
+                                                               UnknownFileFormatException
          +
          Read IUPred output
          +
          +
          Parameters:
          +
          result -
          +
          Returns:
          +
          Map key->sequence name, value->Score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          readIUPred

          +
          private static java.util.Map<java.lang.String,Score> readIUPred(java.io.InputStream input,
+                                                                IUPredResult type)
+                                                         throws java.io.IOException,
+                                                                UnknownFileFormatException
          +
          ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
          +
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          parseIUPredDomains

          +
          private static java.util.TreeSet<Range> parseIUPredDomains(java.util.Scanner scan)
          +
          # P53_HUMA + + Number of globular domains: 2 + + globular domain 1. 98 - 269 + + globular domain 2. 431 - 482 + + >P53_HUMA + + meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp
          +
          +
          Parameters:
          +
          scan -
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          readJRonn

          +
          public static java.util.Map<java.lang.String,Score> readJRonn(java.io.InputStream inStream)
+                                                       throws java.io.IOException,
+                                                              UnknownFileFormatException
          +
          Reader for JRonn horizontal file format + + 
          + >Foobar M G D T T A G 0.48 0.42
+ 0.42 0.48 0.52 0.53 0.54
+ 
+ 
          + Where all values are tab delimited
          +
          +
          Parameters:
          +
          inStream - the InputStream connected to the JRonn output file
          +
          Returns:
          +
          Map key=sequence name value=Score
          +
          Throws:
          +
          java.io.IOException - is thrown if the inStream has problems accessing the data
          +
          UnknownFileFormatException - is thrown if the inStream represents an unknown source of + data, i.e. not a JRonn output
          +
          +
          • +
        + + + + + + + +
          +
        • +

          closeSilently

          +
          public static final void closeSilently(java.util.logging.Logger log,
+                                       java.io.Closeable stream)
          +
          Closes the Closable and logs the exception if any
          +
          +
          Parameters:
          +
          log -
          +
          stream -
          +
          +
          • +
        + + + +
          +
        • +

          readDisembl

          +
          public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readDisembl(java.io.InputStream input)
+                                                                            throws java.io.IOException,
+                                                                                   UnknownFileFormatException
          +
          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
          +
          +
          Parameters:
          +
          input - the InputStream
          +
          Returns:
          +
          Map key=sequence name, value=set of score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          parseRanges

          +
          private static java.util.TreeSet<Range> parseRanges(java.lang.Enum resultType,
+                                                    java.lang.String lines)
          +
          Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
          +
          +
          Parameters:
          +
          lines -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          readGlobPlot

          +
          public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readGlobPlot(java.io.InputStream input)
+                                                                             throws java.io.IOException,
+                                                                                    UnknownFileFormatException
          +
          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
          +
          +
          Parameters:
          +
          input -
          +
          Returns:
          +
          Map key=sequence name, value=set of score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          readAAConResults

          +
          public static java.util.HashSet<Score> readAAConResults(java.io.InputStream results)
          +
          Read AACon result with no alignment files. This method leaves incoming + InputStream open!
          +
          +
          Parameters:
          +
          results - output file of AAConservation
          +
          Returns:
          +
          Map with keys ConservationMethod -> float[]
          +
          +
          • +
        + + + +
          +
        • +

          openInputStream

          +
          public static java.util.List<FastaSequence> openInputStream(java.lang.String inFilePath)
+                                                     throws java.io.IOException,
+                                                            UnknownFileFormatException
          +
          Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
          +
          +
          Parameters:
          +
          inFilePath - the path to the input file
          +
          Returns:
          +
          the List of FastaSequence objects
          +
          Throws:
          +
          java.io.IOException - if the file denoted by inFilePath cannot be read
          +
          UnknownFileFormatException - if the inFilePath points to the file which format cannot be + recognised
          +
          +
          • +
        + + + +
          +
        • +

          writeClustal

          +
          public static void writeClustal(java.io.OutputStream outStream,
+                                java.util.List<FastaSequence> sequences,
+                                char gapChar)
+                         throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/docs/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..1a267df --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,367 @@ + + + + + +UnknownFileFormatException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class UnknownFileFormatException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.data.sequence.UnknownFileFormatException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class UnknownFileFormatException
+extends java.lang.Exception
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.io.Filefile 
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          file

          +
          java.io.File file
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException()
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.io.File file,
+                                  java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.String message,
+                                  java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/docs/dm_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..cbabfd4 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,190 @@ + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + +
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    compbio.data.sequence.Alignment

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    +
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    + +
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    +
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    + +
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    Uses of Class
    compbio.data.sequence.IUPredResult

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      Packages that use IUPredResult 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
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    Uses of Class
    compbio.data.sequence.Range

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      Packages that use Range 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
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        Uses of Range in compbio.data.sequence

        + + + + + + + + + + + + +
        Fields in compbio.data.sequence with type parameters of type Range 
        Modifier and TypeField and Description
        private java.util.TreeSet<Range>Score.ranges 
        + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return types with arguments of type Range 
        Modifier and TypeMethod and Description
        java.util.TreeSet<Range>Score.getRanges() +
        Return Ranges if any Collections.EMPTY_SET otherwise
        +
        private static java.util.TreeSet<Range>SequenceUtil.parseIUPredDomains(java.util.Scanner scan) +
        # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
        +
        private static java.util.TreeSet<Range>SequenceUtil.parseRanges(java.lang.Enum resultType, + java.lang.String lines) +
        Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
        +
        + + + + + + + + + + + + +
        Methods in compbio.data.sequence with parameters of type Range 
        Modifier and TypeMethod and Description
        intRange.compareTo(Range o) 
        + + + + + + + + + + + + +
        Method parameters in compbio.data.sequence with type arguments of type Range 
        Modifier and TypeMethod and Description
        voidScore.setRanges(java.util.TreeSet<Range> ranges) 
        + + + + + + + + + + + + + +
        Constructor parameters in compbio.data.sequence with type arguments of type Range 
        Constructor and Description
        Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores, + java.util.TreeSet<Range> ranges) 
        Score(java.lang.Enum<?> method, + java.util.TreeSet<Range> ranges) 
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    Uses of Class
    compbio.data.sequence.Score

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      Packages that use Score 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
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        Uses of Score in compbio.data.sequence

        + + + + + + + + + + + + +
        Fields in compbio.data.sequence with type parameters of type Score 
        Modifier and TypeField and Description
        java.util.TreeSet<Score>ScoreManager.ScoreHolder.scores 
        + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return Score 
        Modifier and TypeMethod and Description
        ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.Enum<?> method) 
        ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.String method) 
        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return types with arguments of type Score 
        Modifier and TypeMethod and Description
        java.util.Map<java.lang.String,java.util.TreeSet<Score>>ScoreManager.asMap() 
        java.util.Set<Score>ScoreManager.asSet() 
        java.util.List<java.util.TreeSet<Score>>RNAStructScoreManager.getData() 
        static java.util.TreeSet<Score>RNAStructReader.newEmptyScore(java.lang.Enum<?> res) 
        private static java.util.TreeSet<Score>RNAStructReader.newSetScore(java.lang.Enum<?> res, + java.util.List<java.lang.Float> scores) 
        static java.util.HashSet<Score>SequenceUtil.readAAConResults(java.io.InputStream results) +
        Read AACon result with no alignment files.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
        + + + + + + + + + + + + +
        Methods in compbio.data.sequence with parameters of type Score 
        Modifier and TypeMethod and Description
        intScore.compareTo(Score o) 
        + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Method parameters in compbio.data.sequence with type arguments of type Score 
        Modifier and TypeMethod and Description
        static RNAStructScoreManagerRNAStructScoreManager.newInstance(java.util.List<java.lang.String> structs, + java.util.List<java.util.TreeSet<Score>> data) 
        static ScoreManagerScoreManager.newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data) 
        static ScoreManagerScoreManager.newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap) 
        static ScoreManagerScoreManager.newInstanceSingleSequence(java.util.Set<Score> data) 
        static voidScore.write(java.util.TreeSet<Score> scores, + java.io.Writer writer) +
        Outputs the List of Score objects into the Output stream.
        +
        + + + + + + + + + + + + + + + + + + + +
        Constructor parameters in compbio.data.sequence with type arguments of type Score 
        Constructor and Description
        RNAStructScoreManager(java.util.List<java.lang.String> structs, + java.util.List<java.util.TreeSet<Score>> data) 
        ScoreHolder(java.lang.String id, + java.util.Set<Score> scores) 
        ScoreManager(java.util.Map<java.lang.String,java.util.Set<Score>> data) 
        ScoreManager(java.lang.String id, + java.util.Set<Score> data) 
        +
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    Uses of Class
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      Packages that use UnknownFileFormatException 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
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        Uses of UnknownFileFormatException in compbio.data.sequence

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that throw UnknownFileFormatException 
        Modifier and TypeMethod and Description
        private static float[]SequenceUtil.convertToNumber(java.lang.String[] annotValues) 
        static java.util.List<FastaSequence>SequenceUtil.openInputStream(java.lang.String inFilePath) +
        Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
        +
        private static float[]SequenceUtil.parseIUPredScores(java.util.Scanner scan) 
        static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) 
        static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) +
        Read Clustal formatted alignment.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
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    compbio.data.sequence

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    Classes

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    Enums

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    Exceptions

    + +
    + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/package-summary.html b/website/docs/dm_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..36bae81 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,291 @@ + + + + + +compbio.data.sequence + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
    + + +
    + +
    +

    Package compbio.data.sequence

    +
    +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    +
    +

    See: Description

    +
    +
    + + + + +

    Package compbio.data.sequence Description

    +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services.
    +
    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Petr Troshin
    +
    +
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/data/sequence/package-tree.html b/website/docs/dm_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..c1c6cba --- /dev/null +++ b/website/docs/dm_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,181 @@ + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + +
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    +

    Hierarchy For Package compbio.data.sequence

    +Package Hierarchies: + +
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    Class Hierarchy

    + +

    Enum Hierarchy

    + +
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    Uses of Package
    compbio.data.sequence

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    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/Argument.html b/website/docs/dm_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..9a87c74 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,324 @@ + + + + + +Argument + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
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      • +
    +
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    + + +
    +
    compbio.metadata
    +

    Interface Argument<T>

    +
    +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      All Known Implementing Classes:
      +
      Option, Parameter
      +
      +
      +
      +
      public interface Argument<T>
      +
      An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
      +
      +
      Author:
      +
      pvtroshin + + Date December 2009
      +
      See Also:
      +
      Parameter, +Option
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFurtherDetails

          +
          java.lang.String getFurtherDetails()
          +
          • +
        + + + +
          +
        • +

          getDefaultValue

          +
          java.lang.String getDefaultValue()
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          java.lang.String getDescription()
          +
          • +
        + + + +
          +
        • +

          getName

          +
          java.lang.String getName()
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          java.util.List<java.lang.String> getPossibleValues()
          +
          +
          Returns:
          +
          List of values allowed for an Argument
          +
          +
          • +
        + + + +
          +
        • +

          setValue

          +
          void setValue(java.lang.String defaultValue)
+       throws WrongParameterException
          +
          Set default values for the parameter or an option
          +
          +
          Parameters:
          +
          defaultValue - the value to be set
          +
          Throws:
          +
          WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
          +
          See Also:
          +
          ValueConstrain
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/docs/dm_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..e3abfc4 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,409 @@ + + + + + +ChunkHolder + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ChunkHolder

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.ChunkHolder
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ChunkHolder
+extends java.lang.Object
      +
      Represents a chunk of a string data together with the position in a file for + the next read operation.
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringchunk 
        (package private) longposition 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private ChunkHolder() 
         ChunkHolder(java.lang.String chunk, + long position) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          chunk

          +
          java.lang.String chunk
          +
          • +
        + + + +
          +
        • +

          position

          +
          long position
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ChunkHolder

          +
          private ChunkHolder()
          +
          • +
        + + + +
          +
        • +

          ChunkHolder

          +
          public ChunkHolder(java.lang.String chunk,
+                   long position)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getChunk

          +
          public java.lang.String getChunk()
          +
          • +
        + + + +
          +
        • +

          getNextPosition

          +
          public long getNextPosition()
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/docs/dm_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..715ac15 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,337 @@ + + + + + +JobExecutionException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class JobExecutionException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.JobExecutionException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class JobExecutionException
+extends java.lang.Exception
      +
      JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.String message,
+                             java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/JobStatus.html b/website/docs/dm_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..7a76709 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,462 @@ + + + + + +JobStatus + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Enum JobStatus

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<JobStatus>
        • +
      • +
          +
        • compbio.metadata.JobStatus
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<JobStatus>
      +
      +
      +
      +
      public enum JobStatus
+extends java.lang.Enum<JobStatus>
      +
      The status of the job.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        CANCELLED +
        Jobs that has been cancelled
        +
        COLLECTED +
        Results has been collected
        +
        FAILED +
        Failed jobs
        +
        FINISHED +
        Finished jobs
        +
        PENDING +
        Jobs which are in the queue and awaiting execution reported for cluster + jobs only
        +
        RUNNING +
        Jobs that are running
        +
        STARTED +
        Job calculation has been started.
        +
        SUBMITTED +
        Job has been submitted.
        +
        UNDEFINED +
        Represents jobs with unknown status
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static JobStatusvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static JobStatus[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          PENDING

          +
          public static final JobStatus PENDING
          +
          Jobs which are in the queue and awaiting execution reported for cluster + jobs only
          +
          • +
        + + + +
          +
        • +

          RUNNING

          +
          public static final JobStatus RUNNING
          +
          Jobs that are running
          +
          • +
        + + + +
          +
        • +

          CANCELLED

          +
          public static final JobStatus CANCELLED
          +
          Jobs that has been cancelled
          +
          • +
        + + + +
          +
        • +

          FINISHED

          +
          public static final JobStatus FINISHED
          +
          Finished jobs
          +
          • +
        + + + +
          +
        • +

          FAILED

          +
          public static final JobStatus FAILED
          +
          Failed jobs
          +
          • +
        + + + +
          +
        • +

          UNDEFINED

          +
          public static final JobStatus UNDEFINED
          +
          Represents jobs with unknown status
          +
          • +
        + + + +
          +
        • +

          STARTED

          +
          public static final JobStatus STARTED
          +
          Job calculation has been started. First status reported by the local + engine
          +
          • +
        + + + +
          +
        • +

          SUBMITTED

          +
          public static final JobStatus SUBMITTED
          +
          Job has been submitted. This status is only set for cluster jobs
          +
          • +
        + + + +
          +
        • +

          COLLECTED

          +
          public static final JobStatus COLLECTED
          +
          Results has been collected
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static JobStatus[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (JobStatus c : JobStatus.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static JobStatus valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/docs/dm_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..e96f00b --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,339 @@ + + + + + +JobSubmissionException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class JobSubmissionException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.JobSubmissionException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      Direct Known Subclasses:
      +
      LimitExceededException, UnsupportedRuntimeException
      +
      +
      +
      +
      public class JobSubmissionException
+extends java.lang.Exception
      +
      Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException. If + this exception is thrown the task has not been calculated
      +
      +
      Author:
      +
      pvtroshin + + Date December 2009
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.String message,
+                              java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/Limit.html b/website/docs/dm_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..b15ed36 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,594 @@ + + + + + +Limit + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Limit<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Limit<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - the type of an executable for which this limit is defined.
      +
      +
      +
      +
      public class Limit<T>
+extends java.lang.Object
      +
      A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. Also contains static method for determining the + number of sequence and their average length in the List
      +
      +
      Version:
      +
      1.0 January 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      LimitsManager
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) booleanisDefault 
        private java.lang.Stringpreset 
        private intseqLength 
        private intseqNumber 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Limit() 
         Limit(int seqNumber, + int seqLength, + java.lang.String preset) +
        Instantiate the limit
        +
         Limit(int seqNumber, + int seqLength, + java.lang.String preset, + boolean isDefault) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          preset

          +
          private java.lang.String preset
          +
          • +
        + + + +
          +
        • +

          seqNumber

          +
          private int seqNumber
          +
          • +
        + + + +
          +
        • +

          seqLength

          +
          private int seqLength
          +
          • +
        + + + +
          +
        • +

          isDefault

          +
          boolean isDefault
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Limit

          +
          private Limit()
          +
          • +
        + + + +
          +
        • +

          Limit

          +
          public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset)
          +
          Instantiate the limit
          +
          +
          Parameters:
          +
          seqNumber - the maximum number of sequences allowed for calculation. + Required
          +
          seqLength - the average length of the sequence, optional
          +
          preset - the name of preset if any, optional
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
          +
          +
          • +
        + + + +
          +
        • +

          Limit

          +
          public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset,
+             boolean isDefault)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPreset

          +
          public java.lang.String getPreset()
          +
          • +
        + + + +
          +
        • +

          getAvgSeqLength

          +
          public int getAvgSeqLength()
          +
          +
          Returns:
          +
          the allowed average sequence length
          +
          +
          • +
        + + + +
          +
        • +

          getSeqNumber

          +
          public int getSeqNumber()
          +
          +
          Returns:
          +
          the maximum number of sequences allowed
          +
          +
          • +
        + + + +
          +
        • +

          isDefault

          +
          public boolean isDefault()
          +
          +
          Returns:
          +
          true is this is a default limit to be used, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          numberOfLetters

          +
          long numberOfLetters()
          +
          • +
        + + + +
          +
        • +

          isExceeded

          +
          public boolean isExceeded(java.util.List<FastaSequence> data)
          +
          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
          +
          +
          Parameters:
          +
          data - the dataset to measure
          +
          Returns:
          +
          true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise. First check the number of sequences + in the dataset and if it exceeds the limit return true + irrespective of the average length. If the number of sequences in + the dataset is less than the limit and average length is defined, + then check whether the total number of letters (number of + sequence multiplied by the average sequence length) is greater + then the total number of letters in the dataset. Returns true if + the total number of letters in the dataset is greater than the + limit, false otherwise.
          +
          +
          • +
        + + + +
          +
        • +

          getAvgSequenceLength

          +
          public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
          +
          Calculates an average sequence length of the dataset
          +
          +
          Parameters:
          +
          data -
          +
          Returns:
          +
          an average sequence length in the input dataset
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/docs/dm_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..defd848 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,454 @@ + + + + + +LimitExceededException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class LimitExceededException

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class LimitExceededException
+extends JobSubmissionException
      +
      This exception is thrown if the task larger in size that the limit that + applies to the calculation.
      +
      +
      Version:
      +
      1.0 February 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Limit, +Serialized Form
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          numberOfSequencesAllowed

          +
          int numberOfSequencesAllowed
          +
          • +
        + + + +
          +
        • +

          actualNumberofSequences

          +
          int actualNumberofSequences
          +
          • +
        + + + +
          +
        • +

          aSequenceLenghtAllowed

          +
          int aSequenceLenghtAllowed
          +
          • +
        + + + +
          +
        • +

          aSequenceLenghtActual

          +
          int aSequenceLenghtActual
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LimitExceededException

          +
          public LimitExceededException(java.lang.String message)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getNumberOfSequencesAllowed

          +
          public int getNumberOfSequencesAllowed()
          +
          • +
        + + + +
          +
        • +

          getActualNumberofSequences

          +
          public int getActualNumberofSequences()
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtAllowed

          +
          public int getSequenceLenghtAllowed()
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtActual

          +
          public int getSequenceLenghtActual()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/LimitsManager.html b/website/docs/dm_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..5165948 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,427 @@ + + + + + +LimitsManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class LimitsManager<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.LimitsManager<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      +
      public class LimitsManager<T>
+extends java.lang.Object
      +
      A collection of Limits
      +
      +
      Version:
      +
      1.0 January 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Limit
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          java.lang.String runnerClassName
          +
          • +
        + + + +
          +
        • +

          limit

          +
          java.util.List<Limit<T>> limit
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LimitsManager

          +
          public LimitsManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getLimits

          +
          public java.util.List<Limit<T>> getLimits()
          +
          +
          Returns:
          +
          all limits defined for an executable T
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getLimitByName

          +
          public Limit<T> getLimitByName(java.lang.String presetName)
          +
          +
          Parameters:
          +
          presetName -
          +
          Returns:
          +
          Limit defined for the executable T and presetName. If no limit is + defined for the presetName then default Limit is returned. If + presetName is empty or null than the default Limit will be + returned. If not limit defined for the type T than NULL will be + returned
          +
          +
          • +
        + + + +
          +
        • +

          getDefaultLimit

          +
          public Limit<T> getDefaultLimit()
          +
          +
          Returns:
          +
          the default Limit for an executable type T
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate(PresetManager<T> presets)
+              throws javax.xml.bind.ValidationException
          +
          Validate Limits
          +
          +
          Parameters:
          +
          presets -
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if any of the Limit defined is found to be invalid. That is + when + + 1) No default limit is defined + + 2) More than 1 default limit is defined + + 3) Limit's preset name does not match any presets for type T
          +
          See Also:
          +
          Limit, +Preset
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/Option.html b/website/docs/dm_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..ad8a2c5 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/Option.html @@ -0,0 +1,831 @@ + + + + + +Option + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Option<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Option<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of executable
      +
      +
      +
      All Implemented Interfaces:
      +
      Argument<T>
      +
      +
      +
      Direct Known Subclasses:
      +
      Parameter
      +
      +
      +
      +
      public class Option<T>
+extends java.lang.Object
+implements Argument<T>
      +
      Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.net.URLbasicURL 
        protected java.lang.StringdefaultValue 
        protected java.lang.Stringdescription 
        protected java.lang.StringfurtherDetails 
        protected booleanisRequired 
        protected java.lang.Stringname 
        (package private) java.util.Set<java.lang.String>optionNames 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        Option() 
        Option(java.lang.String name, + java.lang.String description) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) +
        Adds an option to the optionName list
        +
        booleanequals(java.lang.Object obj) 
        java.net.URLgetBasicURL() 
        java.lang.StringgetDefaultValue() +
        A default value of the option.
        +
        java.lang.StringgetDescription() +
        A long description of the Option
        +
        java.lang.StringgetFurtherDetails() +
        The URL where further details about the option can be found
        +
        java.lang.StringgetName() +
        Human readable name of the option
        +
        java.util.List<java.lang.String>getOptionNames() 
        java.util.List<java.lang.String>getPossibleValues() +
        List of possible optionNames
        +
        inthashCode() 
        booleanisRequired() +
        Flag that indicated that this option must be specified in the command + line for an executable to run
        +
        voidsetBasicURL(java.net.URL url) 
        voidsetDefaultValue(java.lang.String defaultVal) +
        Sets one of the values defined in optionList as default.
        +
        voidsetDescription(java.lang.String description) 
        voidsetFurtherDetails(java.lang.String furtherDetails) 
        voidsetName(java.lang.String name) 
        voidsetOptionNames(java.util.Set<java.lang.String> optionNames) 
        voidsetRequired(boolean isRequired) 
        voidsetValue(java.lang.String dValue) +
        Set default values for the parameter or an option
        +
        java.lang.StringtoCommand(java.lang.String nameValueSeparator) +
        Convert the option to the command string.
        +
        java.lang.StringtoString() 
        (package private) voidvalidate() +
        Validate the option
        +
        (package private) static booleanvalueExist(java.lang.String testValue, + java.util.List<java.lang.String> values) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          description

          +
          protected java.lang.String description
          +
          • +
        + + + +
          +
        • +

          optionNames

          +
          java.util.Set<java.lang.String> optionNames
          +
          • +
        + + + +
          +
        • +

          name

          +
          protected java.lang.String name
          +
          • +
        + + + +
          +
        • +

          isRequired

          +
          protected boolean isRequired
          +
          • +
        + + + +
          +
        • +

          furtherDetails

          +
          protected java.lang.String furtherDetails
          +
          • +
        + + + +
          +
        • +

          defaultValue

          +
          protected java.lang.String defaultValue
          +
          • +
        + + + +
          +
        • +

          basicURL

          +
          private java.net.URL basicURL
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Option

          +
          Option()
          +
          • +
        + + + +
          +
        • +

          Option

          +
          public Option(java.lang.String name,
+              java.lang.String description)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getName

          +
          public java.lang.String getName()
          +
          Human readable name of the option
          +
          +
          Specified by:
          +
          getName in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setName

          +
          public void setName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setBasicURL

          +
          public void setBasicURL(java.net.URL url)
          +
          • +
        + + + +
          +
        • +

          getBasicURL

          +
          public java.net.URL getBasicURL()
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          public java.lang.String getDescription()
          +
          A long description of the Option
          +
          +
          Specified by:
          +
          getDescription in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setDescription

          +
          public void setDescription(java.lang.String description)
          +
          • +
        + + + +
          +
        • +

          getFurtherDetails

          +
          public java.lang.String getFurtherDetails()
          +
          The URL where further details about the option can be found
          +
          +
          Specified by:
          +
          getFurtherDetails in interface Argument<T>
          +
          Throws:
          +
          java.net.MalformedURLException
          +
          +
          • +
        + + + +
          +
        • +

          setFurtherDetails

          +
          public void setFurtherDetails(java.lang.String furtherDetails)
          +
          • +
        + + + +
          +
        • +

          getDefaultValue

          +
          public java.lang.String getDefaultValue()
          +
          A default value of the option. Defaults to command line argument name + e.g. -auto
          +
          +
          Specified by:
          +
          getDefaultValue in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setDefaultValue

          +
          public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
          +
          Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception
          +
          +
          Parameters:
          +
          defaultVal -
          +
          Throws:
          +
          WrongParameterException - is thrown if the defaultValue is not found in optionList
          +
          +
          • +
        + + + +
          +
        • +

          valueExist

          +
          static boolean valueExist(java.lang.String testValue,
+                          java.util.List<java.lang.String> values)
          +
          • +
        + + + +
          +
        • +

          isRequired

          +
          public boolean isRequired()
          +
          Flag that indicated that this option must be specified in the command + line for an executable to run
          +
          +
          Returns:
          +
          true is the option is required, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          setRequired

          +
          public void setRequired(boolean isRequired)
          +
          • +
        + + + +
          +
        • +

          getOptionNames

          +
          public java.util.List<java.lang.String> getOptionNames()
          +
          +
          Returns:
          +
          List of option names
          +
          +
          • +
        + + + +
          +
        • +

          setOptionNames

          +
          public void setOptionNames(java.util.Set<java.lang.String> optionNames)
          +
          • +
        + + + +
          +
        • +

          addOptionNames

          +
          public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
          +
          Adds an option to the optionName list
          +
          +
          Parameters:
          +
          value -
          +
          Returns:
          +
          modified optionName list
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toCommand

          +
          public java.lang.String toCommand(java.lang.String nameValueSeparator)
          +
          Convert the option to the command string.
          +
          +
          Returns:
          +
          If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          public java.util.List<java.lang.String> getPossibleValues()
          +
          List of possible optionNames
          +
          +
          Specified by:
          +
          getPossibleValues in interface Argument<T>
          +
          Returns:
          +
          List of values allowed for an Argument
          +
          +
          • +
        + + + +
          +
        • +

          setValue

          +
          public void setValue(java.lang.String dValue)
+              throws WrongParameterException
          +
          Description copied from interface: Argument
          +
          Set default values for the parameter or an option
          +
          +
          Specified by:
          +
          setValue in interface Argument<T>
          +
          Parameters:
          +
          dValue - the value to be set
          +
          Throws:
          +
          WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
          +
          See Also:
          +
          ValueConstrain
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Validate the option
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - is the option is invalid. This happens if option does not + have a default value but have multiple option names, or no + option names is defined
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/Parameter.html b/website/docs/dm_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..dcd568d --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,655 @@ + + + + + +Parameter + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Parameter<T>

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Argument<T>
      +
      +
      +
      +
      public class Parameter<T>
+extends Option<T>
      +
      A single value containing an option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues
      +
      +
      Version:
      +
      1.0 November 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Option, +Argument
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          possibleValues

          +
          java.util.Set<java.lang.String> possibleValues
          +
          • +
        + + + + +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Parameter

          +
          private Parameter()
          +
          • +
        + + + +
          +
        • +

          Parameter

          +
          public Parameter(java.lang.String name,
+                 java.lang.String description)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          setValidValue

          +
          public void setValidValue(ValueConstrain validValue)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          toCommand

          +
          public java.lang.String toCommand(java.lang.String nameValueSeparator)
          +
          Description copied from class: Option
          +
          Convert the option to the command string.
          +
          +
          Overrides:
          +
          toCommand in class Option<T>
          +
          Returns:
          +
          If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          public java.util.List<java.lang.String> getPossibleValues()
          +
          List is more convenient to work with
          +
          +
          Specified by:
          +
          getPossibleValues in interface Argument<T>
          +
          Overrides:
          +
          getPossibleValues in class Option<T>
          +
          Returns:
          +
          List of String
          +
          +
          • +
        + + + +
          +
        • +

          setPossibleValues

          +
          public void setPossibleValues(java.util.Set<java.lang.String> possibleValues)
          +
          • +
        + + + +
          +
        • +

          addPossibleValues

          +
          public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          setOptionNames

          +
          public void setOptionNames(java.util.Set<java.lang.String> optionName)
          +
          +
          Overrides:
          +
          setOptionNames in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          addOptionNames

          +
          public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
          +
          Description copied from class: Option
          +
          Adds an option to the optionName list
          +
          +
          Overrides:
          +
          addOptionNames in class Option<T>
          +
          Returns:
          +
          modified optionName list
          +
          +
          • +
        + + + +
          +
        • +

          getOptionName

          +
          public java.lang.String getOptionName()
          +
          • +
        + + + +
          +
        • +

          setOptionName

          +
          public void setOptionName(java.lang.String optionName)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          java.lang.String getValue()
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Description copied from class: Option
          +
          Validate the option
          +
          +
          Overrides:
          +
          validate in class Option<T>
          +
          Throws:
          +
          javax.xml.bind.ValidationException - is the option is invalid. This happens if option does not + have a default value but have multiple option names, or no + option names is defined
          +
          +
          • +
        + + + +
          +
        • +

          isValidValue

          +
          boolean isValidValue(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          setDefaultValue

          +
          public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
          +
          Description copied from class: Option
          +
          Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception
          +
          +
          Overrides:
          +
          setDefaultValue in class Option<T>
          +
          Throws:
          +
          WrongParameterException - is thrown if the defaultValue is not found in optionList
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/Preset.html b/website/docs/dm_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..a7e8369 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,557 @@ + + + + + +Preset + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Preset<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Preset<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      +
      public class Preset<T>
+extends java.lang.Object
      +
      Collection of Options and Parameters with their values
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Option, +Parameter
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringdescription 
        (package private) java.lang.Stringname 
        (package private) java.util.List<java.lang.String>option 
        private static java.lang.StringSPACE 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Preset() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) booleancontainValue(java.lang.String option) 
        booleanequals(java.lang.Object obj) 
        java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) +
        Converts list of options as String to type Option
        +
        java.lang.StringgetDescription() 
        java.lang.StringgetName() 
        (package private) java.lang.StringgetName(java.lang.String option) 
        java.util.List<java.lang.String>getOptions() 
        (package private) java.lang.StringgetValue(java.lang.String option) 
        inthashCode() 
        voidsetDescription(java.lang.String description) 
        voidsetName(java.lang.String name) 
        voidsetOptions(java.util.List<java.lang.String> option) 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          name

          +
          java.lang.String name
          +
          • +
        + + + +
          +
        • +

          description

          +
          java.lang.String description
          +
          • +
        + + + +
          +
        • +

          option

          +
          java.util.List<java.lang.String> option
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Preset

          +
          public Preset()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<java.lang.String> option)
          +
          • +
        + + + +
          +
        • +

          setName

          +
          public void setName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setDescription

          +
          public void setDescription(java.lang.String description)
          +
          • +
        + + + +
          +
        • +

          getOptions

          +
          public java.util.List<java.lang.String> getOptions()
          +
          +
          Returns:
          +
          a List of Options as a String
          +
          +
          • +
        + + + +
          +
        • +

          getName

          +
          public java.lang.String getName()
          +
          +
          Returns:
          +
          - name of the Preset
          +
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          public java.lang.String getDescription()
          +
          +
          Returns:
          +
          - a long description of the Preset
          +
          +
          • +
        + + + + + + + +
          +
        • +

          containValue

          +
          boolean containValue(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          getName

          +
          java.lang.String getName(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          java.lang.String getValue(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/PresetManager.html b/website/docs/dm_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..7f77c68 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,513 @@ + + + + + +PresetManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class PresetManager<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.PresetManager<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of executable.
      +
      +
      +
      +
      public class PresetManager<T>
+extends java.lang.Object
      +
      Collection of presets and methods to manipulate them @see Preset
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          java.lang.String runnerClassName
          +
          • +
        + + + +
          +
        • +

          preset

          +
          java.util.List<Preset<T>> preset
          +
          • +
        + + + +
          +
        • +

          LOCAL_ENGINE_LIMIT_PRESET

          +
          public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetManager

          +
          public PresetManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPresets

          +
          public java.util.List<Preset<T>> getPresets()
          +
          • +
        + + + +
          +
        • +

          setPresets

          +
          public void setPresets(java.util.List<Preset<T>> presets)
          +
          • +
        + + + +
          +
        • +

          getRunnerClassName

          +
          public java.lang.String getRunnerClassName()
          +
          +
          Returns:
          +
          fully qualified class name of type T
          +
          +
          • +
        + + + +
          +
        • +

          setRunnerClassName

          +
          public void setRunnerClassName(java.lang.String runnerClassName)
          +
          • +
        + + + +
          +
        • +

          getPresetByName

          +
          public Preset<T> getPresetByName(java.lang.String presetName)
          +
          +
          Parameters:
          +
          presetName -
          +
          Returns:
          +
          preset by its name, null if no preset found
          +
          +
          • +
        + + + +
          +
        • +

          isComposite

          +
          boolean isComposite(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          containsValue

          +
          boolean containsValue(java.util.List<java.lang.String> values,
+                      java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          isNumeric

          +
          boolean isNumeric(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate(RunnerConfig<T> options)
+              throws javax.xml.bind.ValidationException
          +
          Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly!
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if preset is found to be invalid.
          +
          +
          • +
        + + + +
          +
        • +

          getArgument

          +
          Argument<T> getArgument(RunnerConfig<T> options,
+                        java.lang.String optionName)
+                 throws javax.xml.bind.ValidationException
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/docs/dm_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..3404204 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,338 @@ + + + + + +ResultNotAvailableException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ResultNotAvailableException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.ResultNotAvailableException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class ResultNotAvailableException
+extends java.lang.Exception
      +
      ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides lower level exceptions + like DrmaaException
      +
      +
      Author:
      +
      pvtroshin + + Date October 2009
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.String message,
+                                   java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/docs/dm_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..d59f007 --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,790 @@ + + + + + +RunnerConfig + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
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    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class RunnerConfig<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.RunnerConfig<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of an Executable
      +
      +
      +
      +
      @NotThreadSafe
+public class RunnerConfig<T>
+extends java.lang.Object
      +
      The list of Parameters and Options supported by executable. + The lists is defined in and loaded from Parameters.xml file.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.util.List<Option<T>>arguments 
        (package private) java.util.List<Option<T>>options 
        (package private) java.util.List<Parameter<T>>parameters 
        (package private) java.lang.StringprmSeparator 
        private java.lang.StringrunnerClassName +
        The class name of a runnable e.g.
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        RunnerConfig() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          private java.lang.String runnerClassName
          +
          The class name of a runnable e.g. T
          +
          • +
        + + + +
          +
        • +

          options

          +
          java.util.List<Option<T>> options
          +
          • +
        + + + +
          +
        • +

          prmSeparator

          +
          java.lang.String prmSeparator
          +
          • +
        + + + +
          +
        • +

          parameters

          +
          java.util.List<Parameter<T>> parameters
          +
          • +
        + + + +
          +
        • +

          arguments

          +
          java.util.List<Option<T>> arguments
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RunnerConfig

          +
          public RunnerConfig()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getOptions

          +
          public java.util.List<Option<T>> getOptions()
          +
          Returns the list of the Options supported by the executable of type T
          +
          +
          Returns:
          +
          list of Option supported by type T
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          addParameter

          +
          public void addParameter(Parameter<T> param)
          +
          Adds parameter to the internal parameter list
          +
          +
          Parameters:
          +
          param - the Parameter to add
          +
          See Also:
          +
          Parameter
          +
          +
          • +
        + + + +
          +
        • +

          addOption

          +
          public void addOption(Option<T> option)
          +
          Adds Option to the internal list of options
          +
          +
          Parameters:
          +
          option - the Option to add
          +
          +
          • +
        + + + +
          +
        • +

          getArguments

          +
          public java.util.List<Option<T>> getArguments()
          +
          Returns list of Parameter and Option supported by current + runner
          +
          +
          Returns:
          +
          list of Option and Parameter supported by type T
          +
          +
          • +
        + + + +
          +
        • +

          getPrmSeparator

          +
          public java.lang.String getPrmSeparator()
          +
          +
          Returns:
          +
          name value separator character
          +
          +
          • +
        + + + +
          +
        • +

          setPrmSeparator

          +
          public void setPrmSeparator(java.lang.String prmSeparator)
          +
          Sets name value separator character
          +
          +
          Parameters:
          +
          prmSeparator - the separator char
          +
          +
          • +
        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<Option<T>> parameters)
          +
          Adds the list of options or parameters to the internal list of options
          +
          +
          Parameters:
          +
          parameters - the list of parameters to add
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerClassName

          +
          public java.lang.String getRunnerClassName()
          +
          +
          Returns:
          +
          fully qualified class name for type T
          +
          +
          • +
        + + + +
          +
        • +

          setRunnerClassName

          +
          public void setRunnerClassName(java.lang.String runnerClassName)
          +
          Set the name of a runner class
          +
          +
          Parameters:
          +
          runnerClassName - the name of the executable wrapping class
          +
          +
          • +
        + + + +
          +
        • +

          setParameters

          +
          public void setParameters(java.util.List<Parameter<T>> parameters)
          +
          Sets the list of parameters as internal list
          +
          +
          Parameters:
          +
          parameters - the list of parameters
          +
          +
          • +
        + + + +
          +
        • +

          getParameters

          +
          public java.util.List<Parameter<T>> getParameters()
          +
          Returns the list of parameters supported executable of type T. Where + Parameter is an Option with value.
          +
          +
          Returns:
          +
          List of Parameter supported by type T.
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getArgument

          +
          public Option<T> getArgument(java.lang.String name)
          +
          Returns the argument by its name if found, NULL otherwise. Where the + Argument is a common interface for Option and Parameter + therefore this method can return either. If you need to retrieve the + Option by its optionNames use @link + getArgumentByOptionName(String) method. The + difference between option name and optionName is explained by the + following example: + + 
          + Sequence type
+         
+         --nuc - Assume the sequences are nucleotide.
+         --amino - Assume the sequences are amino acid. 
+         --amino
+         --nuc
+         --auto
+
          + + In the example, the "Sequence type" is a name whereas --amino, --nuc and + --auto are all optionNames. This dichotomy only manifests in + Option never in Parameters as the latter can + only have single element
          +
          +
          Parameters:
          +
          name - the Parameter of Option name
          +
          Returns:
          +
          Argument
          +
          +
          • +
        + + + +
          +
        • +

          removeArgument

          +
          public boolean removeArgument(java.lang.String name)
          +
          Removes the argument Argument if found. Where Argument is either + Option or Parameter.
          +
          +
          Parameters:
          +
          name - of the argument
          +
          Returns:
          +
          true if argument was removed, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getArgumentByOptionName

          +
          public Option<T> getArgumentByOptionName(java.lang.String optionName)
          +
          Returns the argument by option name, NULL if the argument is not found
          +
          +
          Parameters:
          +
          optionName - - the optionName. This is not the same as an Option name. + + For example: + + 
          +            Output sequences order
+                          --inputorder - Output order: same as input. 
+                           --reorder - Output order: aligned. Default: same as input
+                          --inputorder
+                          --reorder
+
          + + The name of the option in the example is + "Output sequences order" whereas optionNames are + "--inputorder" and "--reorder". If you need to retrieve the + Option or Parameter by its names use + getArgument(String) method
          +
          Returns:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          removeArgumentByOptionName

          +
          public boolean removeArgumentByOptionName(java.lang.String optionName)
          +
          Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
          +
          +
          Parameters:
          +
          optionName - the optionName of the option, do not confuse with the name!
          +
          Returns:
          +
          true if argument with optionName exists and was removed, false + otherwise
          +
          See Also:
          +
          for destinctions + between optionNames and the name of the Option
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate()
+              throws javax.xml.bind.ValidationException
          +
          Validate the value of the argument. Checks whether the argument value is + in the valid values range.
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if any of the arguments found invalid which is when +
          +
        • Parameter value outside ValueConstrain boundary
          • +
        • Parameter name is not listed in possible values
          • +
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/docs/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..6a1ba1e --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,326 @@ + + + + + +UnsupportedRuntimeException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class UnsupportedRuntimeException

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class UnsupportedRuntimeException
+extends JobSubmissionException
      +
      Indicates that the server could not execute native executables. e.g. If Mafft + (unix executable) is asked to be run on Windows. In context of JABAWS this + exception indicates that the service is deployed but is not able to run.
      +
      +
      Author:
      +
      pvtroshin + + Date February 2010
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          UnsupportedRuntimeException

          +
          public UnsupportedRuntimeException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          UnsupportedRuntimeException

          +
          public UnsupportedRuntimeException(java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..98fc57b --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,345 @@ + + + + + +ValueConstrain.Type + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Enum ValueConstrain.Type

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Float 
        Integer 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static ValueConstrain.TypevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static ValueConstrain.Type[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static ValueConstrain.Type[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (ValueConstrain.Type c : ValueConstrain.Type.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static ValueConstrain.Type valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..ef6e17b --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,545 @@ + + + + + +ValueConstrain + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ValueConstrain

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.ValueConstrain
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ValueConstrain
+extends java.lang.Object
      +
      The type and the lower and upper boundaries for numerical value.
      +
      +
      Version:
      +
      1.0 November 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Nested Class Summary

        + + + + + + + + + + +
        Nested Classes 
        Modifier and TypeClass and Description
        static class ValueConstrain.Type 
        +
        • +
      + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringmax 
        (package private) java.lang.Stringmin 
        (package private) ValueConstrain.Typetype 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ValueConstrain() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) voidcheckValue(java.lang.String value) +
        Validate that the value is within the constrain boundaries
        +
        booleanequals(java.lang.Object obj) 
        java.lang.NumbergetMax() 
        java.lang.NumbergetMin() 
        ValueConstrain.TypegetType() 
        inthashCode() 
        (package private) booleanhasMaxValue() 
        (package private) booleanhasMinValue() 
        voidsetMax(java.lang.String max) 
        voidsetMin(java.lang.String min) 
        voidsetType(ValueConstrain.Type type) 
        java.lang.StringtoString() 
        (package private) voidvalidate() +
        Validate the ValueConstrain object.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ValueConstrain

          +
          public ValueConstrain()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + + + + + +
          +
        • +

          getMax

          +
          public java.lang.Number getMax()
          +
          • +
        + + + +
          +
        • +

          setMax

          +
          public void setMax(java.lang.String max)
          +
          • +
        + + + +
          +
        • +

          getMin

          +
          public java.lang.Number getMin()
          +
          • +
        + + + +
          +
        • +

          setMin

          +
          public void setMin(java.lang.String min)
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hasMinValue

          +
          boolean hasMinValue()
          +
          • +
        + + + +
          +
        • +

          hasMaxValue

          +
          boolean hasMaxValue()
          +
          • +
        + + + +
          +
        • +

          checkValue

          +
          void checkValue(java.lang.String value)
          +
          Validate that the value is within the constrain boundaries
          +
          +
          Parameters:
          +
          value -
          +
          Throws:
          +
          java.lang.IndexOutOfBoundsException - when the value is outside the defined boundaries
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Validate the ValueConstrain object. For the ValueConstrain object the + type and at least one boundary has to be defined
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - - if the type or no boundaries are defined
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/docs/dm_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..e3e040c --- /dev/null +++ b/website/docs/dm_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,350 @@ + + + + + +WrongParameterException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class WrongParameterException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.WrongParameterException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class WrongParameterException
+extends java.lang.Exception
      +
      WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
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        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(Option<?> option)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.String message,
+                               java.lang.Throwable cause)
          +
          • +
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      PackageDescription
      compbio.metadata +
      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
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      PackageDescription
      compbio.metadata +
      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
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        + + + + + + + + + + + + + + + + +
        Methods in compbio.metadata that return JobStatus 
        Modifier and TypeMethod and Description
        static JobStatusJobStatus.valueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static JobStatus[]JobStatus.values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
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      PackageDescription
      compbio.metadata +
      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
      +
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      • +
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        Uses of Option in compbio.metadata

        + + + + + + + + + + + + +
        Subclasses of Option in compbio.metadata 
        Modifier and TypeClass and Description
        class Parameter<T> +
        A single value containing an option supported by the web service e.g.
        +
        + + + + + + + + + + + + + + + + +
        Fields in compbio.metadata with type parameters of type Option 
        Modifier and TypeField and Description
        (package private) java.util.List<Option<T>>RunnerConfig.arguments 
        (package private) java.util.List<Option<T>>RunnerConfig.options 
        + + + + + + + + + + + + + + + + +
        Methods in compbio.metadata that return Option 
        Modifier and TypeMethod and Description
        Option<T>RunnerConfig.getArgument(java.lang.String name) +
        Returns the argument by its name if found, NULL otherwise.
        +
        Option<T>RunnerConfig.getArgumentByOptionName(java.lang.String optionName) +
        Returns the argument by option name, NULL if the argument is not found
        +
        + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.metadata that return types with arguments of type Option 
        Modifier and TypeMethod and Description
        java.util.List<Option<T>>RunnerConfig.getArguments() +
        Returns list of Parameter and Option supported by current + runner
        +
        java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) +
        Converts list of options as String to type Option
        +
        java.util.List<Option<T>>RunnerConfig.getOptions() +
        Returns the list of the Options supported by the executable of type T
        +
        + + + + + + + + + + + + +
        Methods in compbio.metadata with parameters of type Option 
        Modifier and TypeMethod and Description
        voidRunnerConfig.addOption(Option<T> option) +
        Adds Option to the internal list of options
        +
        + + + + + + + + + + + + +
        Method parameters in compbio.metadata with type arguments of type Option 
        Modifier and TypeMethod and Description
        voidRunnerConfig.setOptions(java.util.List<Option<T>> parameters) +
        Adds the list of options or parameters to the internal list of options
        +
        + + + + + + + + + + +
        Constructors in compbio.metadata with parameters of type Option 
        Constructor and Description
        WrongParameterException(Option<?> option) 
        +
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      PackageDescription
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      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
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      PackageDescription
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      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
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    compbio.metadata

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    Package compbio.metadata

    +
    +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    +
    +

    See: Description

    +
    +
    +
      +
    • + + + + + + + + + + + + +
      Interface Summary 
      InterfaceDescription
      Argument<T> +
      An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
      +
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      ChunkHolder +
      Represents a chunk of a string data together with the position in a file for + the next read operation.
      +
      Limit<T> +
      A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
      +
      LimitsManager<T> +
      A collection of Limits
      +
      Option<T> +
      Command line option/flag or multiple exclusive options with no value.
      +
      Parameter<T> +
      A single value containing an option supported by the web service e.g.
      +
      Preset<T> +
      Collection of Options and Parameters with their values
      +
      PresetManager<T> +
      Collection of presets and methods to manipulate them @see Preset
      +
      RunnerConfig<T> +
      The list of Parameters and Options supported by executable.
      +
      ValueConstrain +
      The type and the lower and upper boundaries for numerical value.
      +
      +
      • +
    • + + + + + + + + + + + + + + + + +
      Enum Summary 
      EnumDescription
      JobStatus +
      The status of the job.
      +
      ValueConstrain.Type 
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Exception Summary 
      ExceptionDescription
      JobExecutionException +
      JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
      +
      JobSubmissionException +
      Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
      +
      LimitExceededException +
      This exception is thrown if the task larger in size that the limit that + applies to the calculation.
      +
      ResultNotAvailableException +
      ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
      +
      UnsupportedRuntimeException +
      Indicates that the server could not execute native executables.
      +
      WrongParameterException +
      WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
      +
      +
      • +
    + + + +

    Package compbio.metadata Description

    +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS)
    +
    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
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    Hierarchy For Package compbio.metadata

    +Package Hierarchies: + +
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    Class Hierarchy

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    Enum Hierarchy

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    • java.lang.Object +
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    Uses of Package
    compbio.metadata

    +
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    +
      +
    • + + + + + + + + + + + + +
      Packages that use compbio.metadata 
      PackageDescription
      compbio.metadata +
      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
      +
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Classes in compbio.metadata used by compbio.metadata 
      Class and Description
      Argument +
      An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
      +
      JobStatus +
      The status of the job.
      +
      JobSubmissionException +
      Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
      +
      Limit +
      A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
      +
      LimitExceededException +
      This exception is thrown if the task larger in size that the limit that + applies to the calculation.
      +
      Option +
      Command line option/flag or multiple exclusive options with no value.
      +
      Parameter +
      A single value containing an option supported by the web service e.g.
      +
      Preset +
      Collection of Options and Parameters with their values
      +
      PresetManager +
      Collection of presets and methods to manipulate them @see Preset
      +
      RunnerConfig +
      The list of Parameters and Options supported by executable.
      +
      ValueConstrain +
      The type and the lower and upper boundaries for numerical value.
      +
      ValueConstrain.Type 
      WrongParameterException +
      WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
      +
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    Constant Field Values

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    Contents

    + +
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    compbio.data.*

    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.data.sequence.ClustalAlignmentUtil 
      Modifier and TypeConstant FieldValue
      + +public static final chargapchar45
      + +private static final intmaxNameLength30
      + +private static final intminNameHolderLength10
      + +private static final intoneLineAlignmentLength60
      + +private static final java.lang.Stringspacer" "
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.FastaReader 
      Modifier and TypeConstant FieldValue
      + +private final java.lang.StringDELIM">"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.ScoreManager 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringSINGLE_ENTRY_KEY"Alignment"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.SequenceUtil 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringJRONN_WRONG_FORMAT_MESSAGE"Jronn file must be in the following format:\n>sequence_name\n M\tV\tS\n0.43\t0.22\t0.65\nWhere first line is the sequence name,\nsecond line is the tab delimited sequence,\nthird line contains tab delimited disorder prediction values.\nNo lines are allowed between these three. Additionally, the number of sequence residues must be equal to the number of the disorder values."
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.data.sequence.SMERFSConstraints 
      Modifier and TypeConstant FieldValue
      + +public static final doubleDEFAULT_GAP_THRESHOLD0.1
      + +public static final intDEFAULT_WINDOW_SIZE7
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.UnknownFileFormatException 
      Modifier and TypeConstant FieldValue
      + +private static final longserialVersionUID196629543695636854L
      +
      • +
    + + + +

    compbio.metadata.*

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    How This API Document Is Organized

    +
    This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.
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      Deprecated API

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      The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.

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      Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.

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      Constant Field Values

      +

      The Constant Field Values page lists the static final fields and their values.

      +
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    A

    +
    +
    AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Valid Amino acids
    +
    +
    actualNumberofSequences - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds Option to the internal list of options
    +
    +
    addOptionNames(String...) - Method in class compbio.metadata.Option
    +
    +
    Adds an option to the optionName list
    +
    +
    addOptionNames(String...) - Method in class compbio.metadata.Parameter
    +
     
    +
    addParameter(Parameter<T>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds parameter to the internal parameter list
    +
    +
    addPossibleValues(String...) - Method in class compbio.metadata.Parameter
    +
     
    +
    AlifoldLine(String) - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
     
    +
    AlifoldResult() - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
     
    +
    Alignment - Class in compbio.data.sequence
    +
    +
    Multiple sequence alignment.
    +
    +
    Alignment() - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    Alignment(List<FastaSequence>, AlignmentMetadata) - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    AlignmentMetadata - Class in compbio.data.sequence
    +
    +
    Alignment metadata e.g.
    +
    +
    AlignmentMetadata() - Constructor for class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    AlignmentMetadata(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    alignmentP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    AMBIGUOUS_AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Same as AA pattern but with two additional letters - XU
    +
    +
    AMBIGUOUS_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Ambiguous nucleotide
    +
    +
    Argument<T> - Interface in compbio.metadata
    +
    +
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +
    +
    arguments - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    aSequenceLenghtActual - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    aSequenceLenghtAllowed - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    asMap() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    asSet() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    J

    +
    +
    JobExecutionException - Exception in compbio.metadata
    +
    +
    JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    +
    +
    JobExecutionException(String) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    JobExecutionException(Throwable) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    JobExecutionException(String, Throwable) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    JobStatus - Enum in compbio.metadata
    +
    +
    The status of the job.
    +
    +
    JobStatus() - Constructor for enum compbio.metadata.JobStatus
    +
     
    +
    JobSubmissionException - Exception in compbio.metadata
    +
    +
    Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    +
    +
    JobSubmissionException(String) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JobSubmissionException(Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JobSubmissionException(String, Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JRONN_WRONG_FORMAT_MESSAGE - Static variable in class compbio.data.sequence.SequenceUtil
    +
     
    +
    justStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    L

    +
    +
    Limit<T> - Class in compbio.metadata
    +
    +
    A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    +
    +
    Limit() - Constructor for class compbio.metadata.Limit
    +
     
    +
    Limit(int, int, String) - Constructor for class compbio.metadata.Limit
    +
    +
    Instantiate the limit
    +
    +
    Limit(int, int, String, boolean) - Constructor for class compbio.metadata.Limit
    +
     
    +
    limit - Variable in class compbio.metadata.LimitsManager
    +
     
    +
    LimitExceededException - Exception in compbio.metadata
    +
    +
    This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    +
    +
    LimitExceededException(String) - Constructor for exception compbio.metadata.LimitExceededException
    +
     
    +
    LimitsManager<T> - Class in compbio.metadata
    +
    +
    A collection of Limits
    +
    +
    LimitsManager() - Constructor for class compbio.metadata.LimitsManager
    +
     
    +
    LOCAL_ENGINE_LIMIT_PRESET - Static variable in class compbio.metadata.PresetManager
    +
     
    +
    log - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
    +
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    + +
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    + + + diff --git a/website/docs/dm_javadoc/index-files/index-12.html b/website/docs/dm_javadoc/index-files/index-12.html new file mode 100644 index 0000000..c77991e --- /dev/null +++ b/website/docs/dm_javadoc/index-files/index-12.html @@ -0,0 +1,145 @@ + + + + + +M-Index + + + + + + + + +
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    M

    +
    +
    main(String[]) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    max - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    maxNameLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    MEAStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    metadata - Variable in class compbio.data.sequence.Alignment
    +
     
    +
    method - Variable in class compbio.data.sequence.Score
    +
     
    +
    mfeStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    min - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    minNameHolderLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
    +
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    N

    +
    +
    name - Variable in class compbio.metadata.Option
    +
     
    +
    name - Variable in class compbio.metadata.Preset
    +
     
    +
    newEmptyScore(Enum<?>) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    newInstance(List<String>, List<TreeSet<Score>>) - Static method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    newInstance(Map<String, Set<Score>>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newInstanceSingleScore(Map<String, Score>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newInstanceSingleSequence(Set<Score>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - Static method in exception compbio.metadata.LimitExceededException
    +
     
    +
    newSetScore(Enum<?>, List<Float>) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    next() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Reads the next FastaSequence from the input
    +
    +
    NON_AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    inversion of AA pattern
    +
    +
    NON_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Non nucleotide
    +
    +
    NONWORD - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Non word
    +
    +
    notData - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Nucleotides a, t, g, c, u
    +
    +
    NUMBER_FORMAT - Static variable in class compbio.data.sequence.Score
    +
     
    +
    numberOfLetters() - Method in class compbio.metadata.Limit
    +
     
    +
    numberOfSequencesAllowed - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
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    + +
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    + + + diff --git a/website/docs/dm_javadoc/index-files/index-14.html b/website/docs/dm_javadoc/index-files/index-14.html new file mode 100644 index 0000000..c262678 --- /dev/null +++ b/website/docs/dm_javadoc/index-files/index-14.html @@ -0,0 +1,148 @@ + + + + + +O-Index + + + + + + + + +
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    Skip navigation links
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    O

    +
    +
    oneLineAlignmentLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    openInputStream(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
    +
    +
    Option<T> - Class in compbio.metadata
    +
    +
    Command line option/flag or multiple exclusive options with no value.
    +
    +
    Option() - Constructor for class compbio.metadata.Option
    +
     
    +
    Option(String, String) - Constructor for class compbio.metadata.Option
    +
     
    +
    option - Variable in class compbio.metadata.Preset
    +
     
    +
    optionNames - Variable in class compbio.metadata.Option
    +
     
    +
    options - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
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    +
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    + +
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    + + + diff --git a/website/docs/dm_javadoc/index-files/index-15.html b/website/docs/dm_javadoc/index-files/index-15.html new file mode 100644 index 0000000..7be93de --- /dev/null +++ b/website/docs/dm_javadoc/index-files/index-15.html @@ -0,0 +1,192 @@ + + + + + +P-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    P

    +
    +
    Parameter<T> - Class in compbio.metadata
    +
    +
    A single value containing an option supported by the web service e.g.
    +
    +
    Parameter() - Constructor for class compbio.metadata.Parameter
    +
     
    +
    Parameter(String, String) - Constructor for class compbio.metadata.Parameter
    +
     
    +
    parameters - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    parseIUPredDomains(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
    +
    +
    parseIUPredScores(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    parseRanges(Enum, String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
    +
    +
    position - Variable in class compbio.metadata.ChunkHolder
    +
     
    +
    possibleValues - Variable in class compbio.metadata.Parameter
    +
     
    +
    preset - Variable in class compbio.metadata.Limit
    +
     
    +
    Preset<T> - Class in compbio.metadata
    +
    +
    Collection of Options and Parameters with their values
    +
    +
    Preset() - Constructor for class compbio.metadata.Preset
    +
     
    +
    preset - Variable in class compbio.metadata.PresetManager
    +
     
    +
    PresetManager<T> - Class in compbio.metadata
    +
    +
    Collection of presets and methods to manipulate them @see Preset
    +
    +
    PresetManager() - Constructor for class compbio.metadata.PresetManager
    +
     
    +
    prmSeparator - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    program - Variable in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    Program - Enum in compbio.data.sequence
    +
    +
    The list of programmes that can produce alignments
    +
    +
    Program() - Constructor for enum compbio.data.sequence.Program
    +
     
    +
    ps - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    PStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/dm_javadoc/index-files/index-16.html b/website/docs/dm_javadoc/index-files/index-16.html new file mode 100644 index 0000000..e198f1f --- /dev/null +++ b/website/docs/dm_javadoc/index-files/index-16.html @@ -0,0 +1,275 @@ + + + + + +R-Index + + + + + + + + +
    + + +
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    + +
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    R

    +
    +
    Range - Class in compbio.data.sequence
    +
     
    +
    Range() - Constructor for class compbio.data.sequence.Range
    +
     
    +
    Range(int, int) - Constructor for class compbio.data.sequence.Range
    +
     
    +
    Range(String[]) - Constructor for class compbio.data.sequence.Range
    +
     
    +
    ranges - Variable in class compbio.data.sequence.Score
    +
     
    +
    readAAConResults(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Read AACon result with no alignment files.
    +
    +
    readClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Read Clustal formatted alignment.
    +
    +
    readClustalFile(File) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    readDisembl(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
    +
    +
    readFasta(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reads fasta sequences from inStream into the list of FastaSequence + objects
    +
    +
    readGlobPlot(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
    +
    +
    readIUPred(File) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Read IUPred output
    +
    +
    readIUPred(InputStream, IUPredResult) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
    +
    +
    readJRonn(File) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    readJRonn(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reader for JRonn horizontal file format
    +
    +
    readRNAStructStream(InputStream) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    readRNAStructStream(InputStream, InputStream) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    regex - Variable in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
     
    +
    remove() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Not implemented
    +
    +
    removeArgument(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Removes the argument Argument if found.
    +
    +
    removeArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
    +
    +
    ResultNotAvailableException - Exception in compbio.metadata
    +
    +
    ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +
    +
    ResultNotAvailableException(String) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    ResultNotAvailableException(Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    ResultNotAvailableException(String, Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    RNAOut() - Constructor for enum compbio.data.sequence.RNAStructReader.RNAOut
    +
     
    +
    RNAStructReader - Class in compbio.data.sequence
    +
     
    +
    RNAStructReader() - Constructor for class compbio.data.sequence.RNAStructReader
    +
     
    +
    RNAStructReader.AlifoldLine - Enum in compbio.data.sequence
    +
     
    +
    RNAStructReader.AlifoldResult - Enum in compbio.data.sequence
    +
     
    +
    RNAStructReader.RNAOut - Enum in compbio.data.sequence
    +
     
    +
    RNAStructScoreManager - Class in compbio.data.sequence
    +
     
    +
    RNAStructScoreManager() - Constructor for class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    RNAStructScoreManager(List<String>, List<TreeSet<Score>>) - Constructor for class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    runnerClassName - Variable in class compbio.metadata.LimitsManager
    +
     
    +
    runnerClassName - Variable in class compbio.metadata.PresetManager
    +
     
    +
    runnerClassName - Variable in class compbio.metadata.RunnerConfig
    +
    +
    The class name of a runnable e.g.
    +
    +
    RunnerConfig<T> - Class in compbio.metadata
    +
    +
    The list of Parameters and Options supported by executable.
    +
    +
    RunnerConfig() - Constructor for class compbio.metadata.RunnerConfig
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
    +
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    + +
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    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    S

    +
    +
    s - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    Score - Class in compbio.data.sequence
    +
    +
    A value class for AACon annotation results storage.
    +
    +
    Score() - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, ArrayList<Float>) - Constructor for class compbio.data.sequence.Score
    +
    +
    Instantiate the Score
    +
    +
    Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, float[]) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    ScoreHolder() - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    ScoreHolder(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    ScoreManager - Class in compbio.data.sequence
    +
     
    +
    ScoreManager() - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager(Map<String, Set<Score>>) - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager.ScoreHolder - Class in compbio.data.sequence
    +
     
    +
    scores - Variable in class compbio.data.sequence.Score
    +
     
    +
    scores - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    seqLength - Variable in class compbio.metadata.Limit
    +
     
    +
    seqNumber - Variable in class compbio.metadata.Limit
    +
     
    +
    seqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    seqScores - Variable in class compbio.data.sequence.ScoreManager
    +
     
    +
    sequence - Variable in class compbio.data.sequence.FastaSequence
    +
    +
    Returns the string representation of sequence
    +
    +
    sequences - Variable in class compbio.data.sequence.Alignment
    +
     
    +
    SequenceUtil - Class in compbio.data.sequence
    +
    +
    Utility class for operations on sequences
    +
    +
    SequenceUtil() - Constructor for class compbio.data.sequence.SequenceUtil
    +
     
    +
    serialVersionUID - Static variable in exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.JobExecutionException
    +
    +
    Default stable serial for serialization
    +
    +
    serialVersionUID - Static variable in exception compbio.metadata.JobSubmissionException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.ResultNotAvailableException
    +
    +
    Default stable serial for serialization
    +
    +
    serialVersionUID - Static variable in exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.WrongParameterException
    +
    +
    Default stable serial for serialization
    +
    +
    setBasicURL(URL) - Method in class compbio.metadata.Option
    +
     
    +
    setDefaultValue(String) - Method in class compbio.metadata.Option
    +
    +
    Sets one of the values defined in optionList as default.
    +
    +
    setDefaultValue(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    setDescription(String) - Method in class compbio.metadata.Option
    +
     
    +
    setDescription(String) - Method in class compbio.metadata.Preset
    +
     
    +
    setFurtherDetails(String) - Method in class compbio.metadata.Option
    +
     
    +
    setMax(String) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setMin(String) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setName(String) - Method in class compbio.metadata.Option
    +
     
    +
    setName(String) - Method in class compbio.metadata.Preset
    +
     
    +
    setOptionName(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    setOptionNames(Set<String>) - Method in class compbio.metadata.Option
    +
     
    +
    setOptionNames(Set<String>) - Method in class compbio.metadata.Parameter
    +
     
    +
    setOptions(List<String>) - Method in class compbio.metadata.Preset
    +
     
    +
    setOptions(List<Option<T>>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds the list of options or parameters to the internal list of options
    +
    +
    setParameters(List<Parameter<T>>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Sets the list of parameters as internal list
    +
    +
    setPossibleValues(Set<String>) - Method in class compbio.metadata.Parameter
    +
     
    +
    setPresets(List<Preset<T>>) - Method in class compbio.metadata.PresetManager
    +
     
    +
    setPrmSeparator(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Sets name value separator character
    +
    +
    setRanges(TreeSet<Range>) - Method in class compbio.data.sequence.Score
    +
     
    +
    setRequired(boolean) - Method in class compbio.metadata.Option
    +
     
    +
    setRunnerClassName(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    setRunnerClassName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Set the name of a runner class
    +
    +
    setType(ValueConstrain.Type) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setValidValue(ValueConstrain) - Method in class compbio.metadata.Parameter
    +
     
    +
    setValue(String) - Method in interface compbio.metadata.Argument
    +
    +
    Set default values for the parameter or an option
    +
    +
    setValue(String) - Method in class compbio.metadata.Option
    +
     
    +
    SINGLE_ENTRY_KEY - Static variable in class compbio.data.sequence.ScoreManager
    +
     
    +
    SMERFSConstraints - Enum in compbio.data.sequence
    +
    +
    Enumeration defining two constraints for SMERFS columns score calculation.
    +
    +
    SMERFSConstraints() - Constructor for enum compbio.data.sequence.SMERFSConstraints
    +
     
    +
    SPACE - Static variable in class compbio.metadata.Preset
    +
     
    +
    spacer - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    stochBTStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    structP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
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    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    T

    +
    +
    to - Variable in class compbio.data.sequence.Range
    +
     
    +
    toCommand(String) - Method in class compbio.metadata.Option
    +
    +
    Convert the option to the command string.
    +
    +
    toCommand(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    toFastaSequence(String) - Static method in class compbio.data.sequence.FastaReader
    +
     
    +
    toList(float[]) - Method in class compbio.data.sequence.Score
    +
     
    +
    toString() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    toString() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Same as oneLineFasta
    +
    +
    toString() - Method in class compbio.data.sequence.Range
    +
     
    +
    toString() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    toString() - Method in class compbio.data.sequence.Score
    +
     
    +
    toString() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    toString() - Method in class compbio.metadata.Limit
    +
     
    +
    toString() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    toString() - Method in class compbio.metadata.Option
    +
     
    +
    toString() - Method in class compbio.metadata.Parameter
    +
     
    +
    toString() - Method in class compbio.metadata.Preset
    +
     
    +
    toString() - Method in class compbio.metadata.PresetManager
    +
     
    +
    toString() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    toString() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    type - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    Type() - Constructor for enum compbio.metadata.ValueConstrain.Type
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
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    + +
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    U

    +
    +
    UnknownFileFormatException - Exception in compbio.data.sequence
    +
     
    +
    UnknownFileFormatException() - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(File, Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(String, Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(String) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnsupportedRuntimeException - Exception in compbio.metadata
    +
    +
    Indicates that the server could not execute native executables.
    +
    +
    UnsupportedRuntimeException(String) - Constructor for exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    UnsupportedRuntimeException(Throwable) - Constructor for exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
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    + + +
    Skip navigation links
    + + + + +
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    + +
    + + +
    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    B

    +
    +
    basicURL - Variable in class compbio.metadata.Option
    +
     
    +
    bracket - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
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    Skip navigation links
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    V

    +
    +
    validate() - Method in class compbio.metadata.Limit
    +
     
    +
    validate(PresetManager<T>) - Method in class compbio.metadata.LimitsManager
    +
    +
    Validate Limits
    +
    +
    validate() - Method in class compbio.metadata.Option
    +
    +
    Validate the option
    +
    +
    validate() - Method in class compbio.metadata.Parameter
    +
     
    +
    validate(RunnerConfig<T>) - Method in class compbio.metadata.PresetManager
    +
    +
    Checks whether preset option and parameter are defined in RunnerConfig + object.
    +
    +
    validate() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Validate the value of the argument.
    +
    +
    validate() - Method in class compbio.metadata.ValueConstrain
    +
    +
    Validate the ValueConstrain object.
    +
    +
    validValue - Variable in class compbio.metadata.Parameter
    +
     
    +
    ValueConstrain - Class in compbio.metadata
    +
    +
    The type and the lower and upper boundaries for numerical value.
    +
    +
    ValueConstrain() - Constructor for class compbio.metadata.ValueConstrain
    +
     
    +
    ValueConstrain.Type - Enum in compbio.metadata
    +
     
    +
    valueExist(String, List<String>) - Static method in class compbio.metadata.Option
    +
     
    +
    valueOf(String) - Static method in enum compbio.data.sequence.ConservationMethod
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.DisemblResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.DisorderMethod
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.GlobProtResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.IUPredResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.Program
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.RNAOut
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.metadata.JobStatus
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.metadata.ValueConstrain.Type
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    values() - Static method in enum compbio.data.sequence.ConservationMethod
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.DisemblResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.DisorderMethod
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.GlobProtResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.IUPredResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.Program
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.RNAOut
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.metadata.JobStatus
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.metadata.ValueConstrain.Type
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    + + + + +
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    W

    +
    +
    WHITE_SPACE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    A whitespace character: [\t\n\x0B\f\r]
    +
    +
    write(TreeSet<Score>, Writer) - Static method in class compbio.data.sequence.Score
    +
    +
    Outputs the List of Score objects into the Output stream.
    +
    +
    writeClustal(OutputStream, List<FastaSequence>, char) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    writeClustalAlignment(Writer, Alignment) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Write Clustal formatted alignment Limitations: does not record the + consensus.
    +
    +
    writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +
    +
    writeFasta(OutputStream, List<FastaSequence>) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Writes FastaSequence in the file, each sequence will take one line only
    +
    +
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    writeOut(Writer) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    writeOut(Writer) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    WrongParameterException - Exception in compbio.metadata
    +
    +
    WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +
    +
    WrongParameterException(Option<?>) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(String) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(Throwable) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(String, Throwable) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    + + + + +
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    + +
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    + + + + +
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    + +
    + + +
    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    C

    +
    +
    centStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    checkValue(String) - Method in class compbio.metadata.ValueConstrain
    +
    +
    Validate that the value is within the constrain boundaries
    +
    +
    chunk - Variable in class compbio.metadata.ChunkHolder
    +
     
    +
    ChunkHolder - Class in compbio.metadata
    +
    +
    Represents a chunk of a string data together with the position in a file for + the next read operation.
    +
    +
    ChunkHolder() - Constructor for class compbio.metadata.ChunkHolder
    +
     
    +
    ChunkHolder(String, long) - Constructor for class compbio.metadata.ChunkHolder
    +
     
    +
    cleanProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Remove all non AA chars from the sequence
    +
    +
    cleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Removes all whitespace chars in the sequence string
    +
    +
    close() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Call this method to close the connection to the input file if you want to + free up the resources.
    +
    +
    closeSilently(Logger, Closeable) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Closes the Closable and logs the exception if any
    +
    +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    +
    +
    Tools to read and write clustal formated files
    +
    +
    ClustalAlignmentUtil() - Constructor for class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    compareTo(Range) - Method in class compbio.data.sequence.Range
    +
     
    +
    compareTo(Score) - Method in class compbio.data.sequence.Score
    +
     
    +
    compbio.data.sequence - package compbio.data.sequence
    +
    +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    +
    +
    compbio.metadata - package compbio.metadata
    +
    +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    +
    +
    ConservationMethod - Enum in compbio.data.sequence
    +
    +
    Enumeration listing of all the supported methods.
    +
    +
    ConservationMethod() - Constructor for enum compbio.data.sequence.ConservationMethod
    +
     
    +
    containsValue(List<String>, String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    containValue(String) - Method in class compbio.metadata.Preset
    +
     
    +
    convertToNumber(String[]) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    copyAndValidateRConfig(RunnerConfig<?>) - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    countMatchesInSequence(String, String) - Static method in class compbio.data.sequence.FastaSequence
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
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    + + + + +
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    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    D

    +
    +
    deepCleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Removes all special characters and digits as well as whitespace chars + from the sequence
    +
    +
    DEFAULT_COLUMN_SCORE - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default column scoring schema
    +
    +
    DEFAULT_GAP_THRESHOLD - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default gap threshold value for SMERFS algorithm
    +
    +
    DEFAULT_WINDOW_SIZE - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default window size value for SMERFS algorithm
    +
    +
    defaultValue - Variable in class compbio.metadata.Option
    +
     
    +
    DELIM - Variable in class compbio.data.sequence.FastaReader
    +
    +
    Delimiter for the scanner
    +
    +
    description - Variable in class compbio.metadata.Option
    +
     
    +
    description - Variable in class compbio.metadata.Preset
    +
     
    +
    DIGIT - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    A digit
    +
    +
    DisemblResult - Enum in compbio.data.sequence
    +
     
    +
    DisemblResult() - Constructor for enum compbio.data.sequence.DisemblResult
    +
     
    +
    DisorderMethod - Enum in compbio.data.sequence
    +
     
    +
    DisorderMethod() - Constructor for enum compbio.data.sequence.DisorderMethod
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    Skip navigation links
    + + + + +
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    + + +
    Skip navigation links
    + + + + +
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    + +
    A B C D E F G H I J L M N O P R S T U V W  + + +

    E

    +
    +
    energyP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    ensembleFreqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Alignment
    +
    +
    Please note that this implementation does not take the order of sequences + into account!
    +
    +
    equals(Object) - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Range
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Score
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    equals(Object) - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Limit
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Option
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Parameter
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Preset
    +
     
    +
    equals(Object) - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    equals(Object) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    +A B C D E F G H I J L M N O P R S T U V W 
    + +
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    + + + + +
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    A B C D E F G H I J L M N O P R S T U V W  + + +

    F

    +
    +
    FastaReader - Class in compbio.data.sequence
    +
    +
    Reads files with FASTA formatted sequences.
    +
    +
    FastaReader(String) - Constructor for class compbio.data.sequence.FastaReader
    +
    +
    Header data can contain non-ASCII symbols and read in UTF8
    +
    +
    FastaReader(InputStream) - Constructor for class compbio.data.sequence.FastaReader
    +
    +
    This class will not close the incoming stream! So the client should do + so.
    +
    +
    FastaSequence - Class in compbio.data.sequence
    +
    +
    A FASTA formatted sequence.
    +
    +
    FastaSequence() - Constructor for class compbio.data.sequence.FastaSequence
    +
     
    +
    FastaSequence(String, String) - Constructor for class compbio.data.sequence.FastaSequence
    +
    +
    Upon construction the any whitespace characters are removed from the + sequence
    +
    +
    file - Variable in exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    floatP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    freeEnergyP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    freqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    from - Variable in class compbio.data.sequence.Range
    +
     
    +
    furtherDetails - Variable in class compbio.metadata.Option
    +
     
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    G

    +
    +
    gapchar - Variable in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    gapchar - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Dash char to be used as gap char in the alignments
    +
    +
    getActualNumberofSequences() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getAnnotationForSequence(String) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    getArgument(RunnerConfig<T>, String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    getArgument(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the argument by its name if found, NULL otherwise.
    +
    +
    getArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the argument by option name, NULL if the argument is not found
    +
    +
    getArguments(RunnerConfig<T>) - Method in class compbio.metadata.Preset
    +
    +
    Converts list of options as String to type Option
    +
    +
    getArguments() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns list of Parameter and Option supported by current + runner
    +
    +
    getAvgSeqLength() - Method in class compbio.metadata.Limit
    +
     
    +
    getAvgSequenceLength(List<FastaSequence>) - Static method in class compbio.metadata.Limit
    +
    +
    Calculates an average sequence length of the dataset
    +
    +
    getBasicURL() - Method in class compbio.metadata.Option
    +
     
    +
    getChunk() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    getData() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    getDefaultLimit() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    getDefaultValue() - Method in interface compbio.metadata.Argument
    +
     
    +
    getDefaultValue() - Method in class compbio.metadata.Option
    +
    +
    A default value of the option.
    +
    +
    getDescription() - Method in interface compbio.metadata.Argument
    +
     
    +
    getDescription() - Method in class compbio.metadata.Option
    +
    +
    A long description of the Option
    +
    +
    getDescription() - Method in class compbio.metadata.Preset
    +
     
    +
    getFormatedSequence(int) - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Format sequence per width letter in one string.
    +
    +
    getFormattedFasta() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getFurtherDetails() - Method in interface compbio.metadata.Argument
    +
     
    +
    getFurtherDetails() - Method in class compbio.metadata.Option
    +
    +
    The URL where further details about the option can be found
    +
    +
    getGapchar() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    getId() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Gets the value of id
    +
    +
    getLength() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getLimitByName(String) - Method in class compbio.metadata.LimitsManager
    +
     
    +
    getLimits() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    getMax() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getMetadata() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getMethod(String) - Static method in enum compbio.data.sequence.ConservationMethod
    +
     
    +
    getMethod() - Method in class compbio.data.sequence.Score
    +
    +
    Returns the ConservationMethod
    +
    +
    getMin() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getName() - Method in interface compbio.metadata.Argument
    +
     
    +
    getName() - Method in class compbio.metadata.Option
    +
    +
    Human readable name of the option
    +
    +
    getName() - Method in class compbio.metadata.Preset
    +
     
    +
    getName(String) - Method in class compbio.metadata.Preset
    +
     
    +
    getNextPosition() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    getNumberOfScores() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getNumberOfSeq() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    getNumberOfSequencesAllowed() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getOnelineFasta() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getOptionName() - Method in class compbio.metadata.Parameter
    +
     
    +
    getOptionNames() - Method in class compbio.metadata.Option
    +
     
    +
    getOptions() - Method in class compbio.metadata.Preset
    +
     
    +
    getOptions() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the list of the Options supported by the executable of type T
    +
    +
    getParameters() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the list of parameters supported executable of type T.
    +
    +
    getPossibleValues() - Method in interface compbio.metadata.Argument
    +
     
    +
    getPossibleValues() - Method in class compbio.metadata.Option
    +
    +
    List of possible optionNames
    +
    +
    getPossibleValues() - Method in class compbio.metadata.Parameter
    +
    +
    List is more convenient to work with
    +
    +
    getPreset() - Method in class compbio.metadata.Limit
    +
     
    +
    getPresetByName(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    getPresets() - Method in class compbio.metadata.PresetManager
    +
     
    +
    getPrmSeparator() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    getProgram() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    getRanges() - Method in class compbio.data.sequence.Score
    +
    +
    Return Ranges if any Collections.EMPTY_SET otherwise
    +
    +
    getRunnerClassName() - Method in class compbio.metadata.PresetManager
    +
     
    +
    getRunnerClassName() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    getScoreByMethod(Enum<?>) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getScoreByMethod(String) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getScores() - Method in class compbio.data.sequence.Score
    +
    +
    The column scores for the alignment
    +
    +
    getSeqNumber() - Method in class compbio.metadata.Limit
    +
     
    +
    getSequence() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Gets the value of sequence
    +
    +
    getSequenceLenghtActual() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getSequenceLenghtAllowed() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getSequences() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getSize() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getSMERFSColumnScore(String) - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
     
    +
    getStructs() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    getType(File) - Static method in enum compbio.data.sequence.IUPredResult
    +
     
    +
    getType() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getValidValue() - Method in class compbio.metadata.Parameter
    +
     
    +
    getValue() - Method in class compbio.metadata.Parameter
    +
     
    +
    getValue(String) - Method in class compbio.metadata.Preset
    +
     
    +
    GlobProtResult - Enum in compbio.data.sequence
    +
     
    +
    GlobProtResult() - Constructor for enum compbio.data.sequence.GlobProtResult
    +
     
    +
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    H

    +
    +
    hashCode() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.Range
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.Score
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    hashCode() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    hashCode() - Method in class compbio.metadata.Limit
    +
     
    +
    hashCode() - Method in class compbio.metadata.Option
    +
     
    +
    hashCode() - Method in class compbio.metadata.Parameter
    +
     
    +
    hashCode() - Method in class compbio.metadata.Preset
    +
     
    +
    hashCode() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hasMaxValue() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hasMinValue() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hasNext() - Method in class compbio.data.sequence.FastaReader
    +
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    I

    +
    +
    id - Variable in class compbio.data.sequence.FastaSequence
    +
    +
    Sequence id
    +
    +
    id - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    identify(String) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    identifyLine(String) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    input - Variable in class compbio.data.sequence.FastaReader
    +
     
    +
    isAmbiguosProtein(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Check whether the sequence confirms to amboguous protein sequence
    +
    +
    isComposite(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    isDefault - Variable in class compbio.metadata.Limit
    +
     
    +
    isDefault() - Method in class compbio.metadata.Limit
    +
     
    +
    isExceeded(List<FastaSequence>) - Method in class compbio.metadata.Limit
    +
    +
    Checks if the number of sequences or their average length in the dataset + exceeds this limit.
    +
    +
    isNonAmbNucleotideSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
    +
    +
    isNucleotideSequence(FastaSequence) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    isNumeric(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    isProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    isRequired - Variable in class compbio.metadata.Option
    +
     
    +
    isRequired() - Method in class compbio.metadata.Option
    +
    +
    Flag that indicated that this option must be specified in the command + line for an executable to run
    +
    +
    isValidClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Please note this method closes the input stream provided as a parameter
    +
    +
    isValidValue(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    IUPredResult - Enum in compbio.data.sequence
    +
     
    +
    IUPredResult() - Constructor for enum compbio.data.sequence.IUPredResult
    +
     
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    PackageDescription
    compbio.data.sequence +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
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    compbio.metadata +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
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+} +ul { + list-style-type:disc; +} +code, tt { + font-family:'DejaVu Sans Mono', monospace; + font-size:14px; + padding-top:4px; + margin-top:8px; + line-height:1.4em; +} +dt code { + font-family:'DejaVu Sans Mono', monospace; + font-size:14px; + padding-top:4px; +} +table tr td dt code { + font-family:'DejaVu Sans Mono', monospace; + font-size:14px; + vertical-align:top; + padding-top:4px; +} +sup { + font-size:8px; +} +/* +Document title and Copyright styles +*/ +.clear { + clear:both; + height:0px; + overflow:hidden; +} +.aboutLanguage { + float:right; + padding:0px 21px; + font-size:11px; + z-index:200; + margin-top:-9px; +} +.legalCopy { + margin-left:.5em; +} +.bar a, .bar a:link, .bar a:visited, .bar a:active { + color:#FFFFFF; + text-decoration:none; +} +.bar a:hover, .bar a:focus { + color:#bb7a2a; +} +.tab { + background-color:#0066FF; + color:#ffffff; + padding:8px; + width:5em; + font-weight:bold; +} +/* +Navigation bar styles +*/ +.bar { + background-color:#4D7A97; + color:#FFFFFF; + padding:.8em .5em .4em .8em; + height:auto;/*height:1.8em;*/ + font-size:11px; + margin:0; +} +.topNav { + background-color:#4D7A97; + color:#FFFFFF; + float:left; + padding:0; + width:100%; + clear:right; + height:2.8em; + padding-top:10px; + overflow:hidden; + font-size:12px; +} +.bottomNav { + margin-top:10px; + background-color:#4D7A97; + color:#FFFFFF; + float:left; + padding:0; + width:100%; + clear:right; + height:2.8em; + padding-top:10px; + overflow:hidden; + font-size:12px; +} +.subNav { + background-color:#dee3e9; + float:left; + width:100%; + overflow:hidden; + font-size:12px; +} +.subNav div { + clear:left; + float:left; + padding:0 0 5px 6px; + text-transform:uppercase; +} +ul.navList, ul.subNavList { + float:left; + margin:0 25px 0 0; + padding:0; +} +ul.navList li{ + list-style:none; + float:left; + padding: 5px 6px; + text-transform:uppercase; +} +ul.subNavList li{ + list-style:none; + float:left; +} +.topNav a:link, .topNav a:active, .topNav a:visited, .bottomNav a:link, .bottomNav a:active, .bottomNav a:visited { + color:#FFFFFF; + text-decoration:none; + text-transform:uppercase; +} +.topNav a:hover, .bottomNav a:hover { + text-decoration:none; + color:#bb7a2a; + text-transform:uppercase; +} +.navBarCell1Rev { + background-color:#F8981D; + color:#253441; + margin: auto 5px; +} +.skipNav { + position:absolute; + top:auto; + left:-9999px; + overflow:hidden; +} +/* +Page header and footer styles +*/ +.header, .footer { + clear:both; + margin:0 20px; + padding:5px 0 0 0; +} +.indexHeader { + margin:10px; + position:relative; +} +.indexHeader span{ + margin-right:15px; +} +.indexHeader h1 { + font-size:13px; +} +.title { + color:#2c4557; + margin:10px 0; +} +.subTitle { + margin:5px 0 0 0; +} +.header ul { + margin:0 0 15px 0; + padding:0; +} +.footer ul { + margin:20px 0 5px 0; +} +.header ul li, .footer ul li { + list-style:none; + font-size:13px; +} +/* +Heading styles +*/ +div.details ul.blockList ul.blockList ul.blockList li.blockList h4, div.details ul.blockList ul.blockList ul.blockListLast li.blockList h4 { + background-color:#dee3e9; + border:1px solid #d0d9e0; + margin:0 0 6px -8px; + padding:7px 5px; +} +ul.blockList ul.blockList ul.blockList li.blockList h3 { + background-color:#dee3e9; + border:1px solid #d0d9e0; + margin:0 0 6px -8px; + padding:7px 5px; +} +ul.blockList ul.blockList li.blockList h3 { + padding:0; + margin:15px 0; +} +ul.blockList li.blockList h2 { + padding:0px 0 20px 0; +} +/* +Page layout container styles +*/ +.contentContainer, .sourceContainer, .classUseContainer, .serializedFormContainer, .constantValuesContainer { + clear:both; + padding:10px 20px; + position:relative; +} +.indexContainer { + margin:10px; + position:relative; + font-size:12px; +} +.indexContainer h2 { + font-size:13px; + padding:0 0 3px 0; +} +.indexContainer ul { + margin:0; + padding:0; +} +.indexContainer ul li { + list-style:none; + padding-top:2px; +} +.contentContainer .description dl dt, .contentContainer .details dl dt, .serializedFormContainer dl dt { + font-size:12px; + font-weight:bold; + margin:10px 0 0 0; + color:#4E4E4E; +} +.contentContainer .description dl dd, .contentContainer .details dl dd, .serializedFormContainer dl dd { + margin:5px 0 10px 0px; + font-size:14px; + font-family:'DejaVu Sans Mono',monospace; +} +.serializedFormContainer dl.nameValue dt { + margin-left:1px; + font-size:1.1em; + display:inline; + font-weight:bold; +} +.serializedFormContainer dl.nameValue dd { + margin:0 0 0 1px; + font-size:1.1em; + display:inline; +} +/* +List styles +*/ +ul.horizontal li { + display:inline; + font-size:0.9em; +} +ul.inheritance { + margin:0; + padding:0; +} +ul.inheritance li { + display:inline; + list-style:none; +} +ul.inheritance li ul.inheritance { + margin-left:15px; + padding-left:15px; + padding-top:1px; +} +ul.blockList, ul.blockListLast { + margin:10px 0 10px 0; + padding:0; +} +ul.blockList li.blockList, ul.blockListLast li.blockList { + list-style:none; + margin-bottom:15px; + line-height:1.4; +} +ul.blockList ul.blockList li.blockList, ul.blockList ul.blockListLast li.blockList { + padding:0px 20px 5px 10px; + border:1px solid #ededed; + background-color:#f8f8f8; +} +ul.blockList ul.blockList ul.blockList li.blockList, ul.blockList ul.blockList ul.blockListLast li.blockList { + padding:0 0 5px 8px; + background-color:#ffffff; + border:none; +} +ul.blockList ul.blockList ul.blockList ul.blockList li.blockList { + margin-left:0; + padding-left:0; + padding-bottom:15px; + border:none; +} +ul.blockList ul.blockList ul.blockList ul.blockList li.blockListLast { + list-style:none; + border-bottom:none; + padding-bottom:0; +} +table tr td dl, table tr td dl dt, table tr td dl dd { + margin-top:0; + margin-bottom:1px; +} +/* +Table styles +*/ +.overviewSummary, .memberSummary, .typeSummary, .useSummary, .constantsSummary, .deprecatedSummary { + width:100%; + border-left:1px solid #EEE; + border-right:1px solid #EEE; + border-bottom:1px solid #EEE; +} +.overviewSummary, .memberSummary { + padding:0px; +} +.overviewSummary caption, .memberSummary caption, .typeSummary caption, +.useSummary caption, .constantsSummary caption, .deprecatedSummary caption { + position:relative; + text-align:left; + background-repeat:no-repeat; + color:#253441; + font-weight:bold; + clear:none; + overflow:hidden; + padding:0px; + padding-top:10px; + padding-left:1px; + margin:0px; + white-space:pre; +} +.overviewSummary caption a:link, .memberSummary caption a:link, .typeSummary caption a:link, +.useSummary caption a:link, .constantsSummary caption a:link, .deprecatedSummary caption a:link, +.overviewSummary caption a:hover, .memberSummary caption a:hover, .typeSummary caption a:hover, +.useSummary caption a:hover, .constantsSummary caption a:hover, .deprecatedSummary caption a:hover, +.overviewSummary caption a:active, .memberSummary caption a:active, .typeSummary caption a:active, +.useSummary caption a:active, .constantsSummary caption a:active, .deprecatedSummary caption a:active, +.overviewSummary caption a:visited, .memberSummary caption a:visited, .typeSummary caption a:visited, +.useSummary caption a:visited, .constantsSummary caption a:visited, .deprecatedSummary caption a:visited { + color:#FFFFFF; +} +.overviewSummary caption span, .memberSummary caption span, .typeSummary caption span, +.useSummary caption span, .constantsSummary caption span, .deprecatedSummary caption span { + white-space:nowrap; + padding-top:5px; + padding-left:12px; + padding-right:12px; + padding-bottom:7px; + display:inline-block; + float:left; + background-color:#F8981D; + border: none; + height:16px; +} +.memberSummary caption span.activeTableTab span { + white-space:nowrap; + padding-top:5px; + padding-left:12px; + padding-right:12px; + margin-right:3px; + display:inline-block; + float:left; + background-color:#F8981D; + height:16px; +} +.memberSummary caption span.tableTab span { + white-space:nowrap; + padding-top:5px; + padding-left:12px; + padding-right:12px; + margin-right:3px; + display:inline-block; + float:left; + background-color:#4D7A97; + height:16px; +} +.memberSummary caption span.tableTab, .memberSummary caption span.activeTableTab { + padding-top:0px; + padding-left:0px; + padding-right:0px; + background-image:none; + float:none; + display:inline; +} +.overviewSummary .tabEnd, .memberSummary .tabEnd, .typeSummary .tabEnd, +.useSummary .tabEnd, .constantsSummary .tabEnd, .deprecatedSummary .tabEnd { + display:none; + width:5px; + position:relative; + float:left; + background-color:#F8981D; +} +.memberSummary .activeTableTab .tabEnd { + display:none; + width:5px; + margin-right:3px; + position:relative; + float:left; + background-color:#F8981D; +} +.memberSummary .tableTab .tabEnd { + display:none; + width:5px; + margin-right:3px; + position:relative; + background-color:#4D7A97; + float:left; + +} +.overviewSummary td, .memberSummary td, .typeSummary td, +.useSummary td, .constantsSummary td, .deprecatedSummary td { + text-align:left; + padding:0px 0px 12px 10px; +} +th.colOne, th.colFirst, th.colLast, .useSummary th, .constantsSummary th, +td.colOne, td.colFirst, td.colLast, .useSummary td, .constantsSummary td{ + vertical-align:top; + padding-right:0px; + padding-top:8px; + padding-bottom:3px; +} +th.colFirst, th.colLast, th.colOne, .constantsSummary th { + background:#dee3e9; + text-align:left; + padding:8px 3px 3px 7px; +} +td.colFirst, th.colFirst { + white-space:nowrap; + font-size:13px; +} +td.colLast, th.colLast { + font-size:13px; +} +td.colOne, th.colOne { + font-size:13px; +} +.overviewSummary td.colFirst, .overviewSummary th.colFirst, +.useSummary td.colFirst, .useSummary th.colFirst, +.overviewSummary td.colOne, .overviewSummary th.colOne, +.memberSummary td.colFirst, .memberSummary th.colFirst, +.memberSummary td.colOne, .memberSummary th.colOne, +.typeSummary td.colFirst{ + width:25%; + vertical-align:top; +} +td.colOne a:link, td.colOne a:active, td.colOne a:visited, td.colOne a:hover, td.colFirst a:link, td.colFirst a:active, td.colFirst a:visited, td.colFirst a:hover, td.colLast a:link, td.colLast a:active, td.colLast a:visited, td.colLast a:hover, .constantValuesContainer td a:link, .constantValuesContainer td a:active, .constantValuesContainer td a:visited, .constantValuesContainer td a:hover { + font-weight:bold; +} +.tableSubHeadingColor { + background-color:#EEEEFF; +} +.altColor { + background-color:#FFFFFF; +} +.rowColor { + background-color:#EEEEEF; +} +/* +Content styles +*/ +.description pre { + margin-top:0; +} +.deprecatedContent { + margin:0; + padding:10px 0; +} +.docSummary { + padding:0; +} + +ul.blockList ul.blockList ul.blockList li.blockList h3 { + font-style:normal; +} + +div.block { + font-size:14px; + font-family:'DejaVu Serif', Georgia, "Times New Roman", Times, serif; +} + +td.colLast div { + padding-top:0px; +} + + +td.colLast a { + padding-bottom:3px; +} +/* +Formatting effect styles +*/ +.sourceLineNo { + color:green; + padding:0 30px 0 0; +} +h1.hidden { + visibility:hidden; + overflow:hidden; + font-size:10px; +} +.block { + display:block; + margin:3px 10px 2px 0px; + color:#474747; +} +.deprecatedLabel, .descfrmTypeLabel, .memberNameLabel, .memberNameLink, +.overrideSpecifyLabel, .packageHierarchyLabel, .paramLabel, .returnLabel, +.seeLabel, .simpleTagLabel, .throwsLabel, .typeNameLabel, .typeNameLink { + font-weight:bold; +} +.deprecationComment, .emphasizedPhrase, .interfaceName { + font-style:italic; +} + +div.block div.block span.deprecationComment, div.block div.block span.emphasizedPhrase, +div.block div.block span.interfaceName { + font-style:normal; +} + +div.contentContainer ul.blockList li.blockList h2{ + padding-bottom:0px; +} diff --git a/website/docs/full_javadoc/allclasses-frame.html b/website/docs/full_javadoc/allclasses-frame.html new file mode 100644 index 0000000..06100a6 --- /dev/null +++ b/website/docs/full_javadoc/allclasses-frame.html @@ -0,0 +1,235 @@ + + + + + +All Classes + + + + + +

    All Classes

    +
    + +
    + + diff --git a/website/docs/full_javadoc/allclasses-noframe.html b/website/docs/full_javadoc/allclasses-noframe.html new file mode 100644 index 0000000..9e0c103 --- /dev/null +++ b/website/docs/full_javadoc/allclasses-noframe.html @@ -0,0 +1,235 @@ + + + + + +All Classes + + + + + +

    All Classes

    +
    + +
    + + diff --git a/website/docs/full_javadoc/compbio/data/msa/Category.html b/website/docs/full_javadoc/compbio/data/msa/Category.html new file mode 100644 index 0000000..2f406e4 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/Category.html @@ -0,0 +1,468 @@ + + + + + +Category + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa
    +

    Class Category

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.Category
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Category
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          CATEGORY_ALIGNMENT

          +
          public static final java.lang.String CATEGORY_ALIGNMENT
          +
          All of the Category names
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          CATEGORY_DISORDER

          +
          public static final java.lang.String CATEGORY_DISORDER
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          CATEGORY_CONSERVATION

          +
          public static final java.lang.String CATEGORY_CONSERVATION
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          CATEGORY_PREDICTION

          +
          public static final java.lang.String CATEGORY_PREDICTION
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          name

          +
          public java.lang.String name
          +
          • +
        + + + +
          +
        • +

          services

          +
          java.util.Set<Services> services
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Category

          +
          private Category(java.lang.String name,
+                 java.util.Set<Services> services)
          +
          • +
        + + + +
          +
        • +

          Category

          +
          private Category()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getServices

          +
          public java.util.Set<Services> getServices()
          +
          • +
        + + + +
          +
        • +

          getCategories

          +
          public static java.util.Set<Category> getCategories()
          +
          • +
        + + + +
          +
        • +

          init

          +
          private static java.util.Set<Category> init()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/JABAService.html b/website/docs/full_javadoc/compbio/data/msa/JABAService.html new file mode 100644 index 0000000..e4af740 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/JABAService.html @@ -0,0 +1,283 @@ + + + + + +JABAService + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.data.msa
    +

    Interface JABAService

    +
    +
    +
    + +
    +
    + +
    +
    +
      +
    • + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/JManagement.html b/website/docs/full_javadoc/compbio/data/msa/JManagement.html new file mode 100644 index 0000000..4077b56 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/JManagement.html @@ -0,0 +1,301 @@ + + + + + +JManagement + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.data.msa
    +

    Interface JManagement

    +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Abstract Methods 
        Modifier and TypeMethod and Description
        booleancancelJob(java.lang.String jobId) +
        Stop running the job jobId but leave its output untouched
        +
        JobStatusgetJobStatus(java.lang.String jobId) +
        Return the status of the job.
        +
        ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) +
        Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
        +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          cancelJob

          +
          boolean cancelJob(java.lang.String jobId)
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          Throws:
          +
          java.security.InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          JobStatus getJobStatus(java.lang.String jobId)
          +
          Return the status of the job.
          +
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          Throws:
          +
          java.security.InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          pullExecStatistics

          +
          ChunkHolder pullExecStatistics(java.lang.String jobId,
+                               long position)
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          Throws:
          +
          java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format and also if the position value is negative
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/Metadata.html b/website/docs/full_javadoc/compbio/data/msa/Metadata.html new file mode 100644 index 0000000..f2a8b23 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/Metadata.html @@ -0,0 +1,302 @@ + + + + + +Metadata + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.data.msa
    +

    Interface Metadata<T>

    +
    +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getRunnerOptions

          +
          RunnerConfig<T> getRunnerOptions()
          +
          Get options supported by a web service
          +
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          PresetManager<T> getPresets()
          +
          Get presets supported by a web service
          +
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          Limit<T> getLimit(java.lang.String presetName)
          +
          Get a Limit for a preset.
          +
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + +
          +
        • +

          getLimits

          +
          LimitsManager<T> getLimits()
          +
          List Limits supported by a web service.
          +
          +
          Returns:
          +
          LimitManager
          +
          +
          • +
        +
        • +
      +
      • +
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    Skip navigation links
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/MsaWS.html b/website/docs/full_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..bd4efd9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,446 @@ + + + + + +MsaWS + + + + + + + + +
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    compbio.data.msa
    +

    Interface MsaWS<T>

    +
    +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          java.lang.String align(java.util.List<FastaSequence> sequences)
+                throws UnsupportedRuntimeException,
+                       LimitExceededException,
+                       JobSubmissionException
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          java.security.InvalidParameterException - thrown if input list of FASTA sequences is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + +
          +
        • +

          customAlign

          +
          java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                             java.util.List<Option<T>> options)
+                      throws UnsupportedRuntimeException,
+                             LimitExceededException,
+                             JobSubmissionException,
+                             WrongParameterException
          +
          Align a list of sequences with options.
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                             Preset<T> preset)
+                      throws UnsupportedRuntimeException,
+                             LimitExceededException,
+                             JobSubmissionException,
+                             WrongParameterException
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          java.security.InvalidParameterException - thrown if input list of FASTA sequence is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          Alignment getResult(java.lang.String jobId)
+             throws ResultNotAvailableException
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          java.security.InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid + format
          +
          +
          • +
        +
        • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/RegistryWS.html b/website/docs/full_javadoc/compbio/data/msa/RegistryWS.html new file mode 100644 index 0000000..683736d --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/RegistryWS.html @@ -0,0 +1,419 @@ + + + + + +RegistryWS + + + + + + + + +
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    compbio.data.msa
    +

    Interface RegistryWS

    +
    +
    +
    +
      +
    • +
      +
      All Superinterfaces:
      +
      JABAService
      +
      +
      +
      All Known Implementing Classes:
      +
      RegistryWS
      +
      +
      +
      +
      public interface RegistryWS
+extends JABAService
      +
      JABAWS services registry
      +
      +
      Version:
      +
      1.0 June 2011
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getSupportedServices

          +
          java.util.Set<Services> getSupportedServices()
          +
          List of services that are functioning on the server. This function + returns the results of testing performed some time ago by + testAllServices() or testService(Services) methods. The + time of last check can be obtained from + getLastTestedOn(Services) method
          +
          +
          Returns:
          +
          the Set of Services which are functioning on the server
          +
          See Also:
          +
          testAllServices()
          +
          +
          • +
        + + + +
          +
        • +

          getLastTested

          +
          int getLastTested(Services service)
          +
          Number of seconds since the last test. Returns 0 if the service was not + tested or tested less then a one second ago.
          +
          +
          Parameters:
          +
          service -
          +
          Returns:
          +
          when last time tested
          +
          +
          • +
        + + + +
          +
        • +

          getLastTestedOn

          +
          java.util.Date getLastTestedOn(Services service)
          +
          The date and time the service has been verified to work last time
          +
          +
          Parameters:
          +
          service -
          +
          Returns:
          +
          the Date and time on which the service was last tested
          +
          +
          • +
        + + + +
          +
        • +

          testAllServices

          +
          java.lang.String testAllServices()
          +
          Test all JABAWS services on the server
          +
          +
          Returns:
          +
          the test log
          +
          +
          • +
        + + + +
          +
        • +

          testService

          +
          java.lang.String testService(Services service)
          +
          Test a particular service
          +
          +
          Parameters:
          +
          service -
          +
          Returns:
          +
          the testing log
          +
          +
          • +
        + + + +
          +
        • +

          isOperating

          +
          boolean isOperating(Services service)
          +
          Check whether a particular web service is working on this server
          +
          +
          Parameters:
          +
          service -
          +
          Returns:
          +
          true if the service was functioning in time of last testing.
          +
          +
          • +
        + + + +
          +
        • +

          getServiceDescription

          +
          java.lang.String getServiceDescription(Services service)
          +
          Gives the description of the service.
          +
          +
          Parameters:
          +
          service -
          +
          Returns:
          +
          String, plain text or html formatted piece, but NOT a full html + document
          +
          +
          • +
        + + + +
          +
        • +

          getServiceCategories

          +
          java.util.Set<Category> getServiceCategories()
          +
          Gets the list of services per category. ServiceClassifier has the method + that returns Map>
          +
          +
          Returns:
          +
          ServiceClassifier the object to represent relation between + Services and Categories
          +
          +
          • +
        +
        • +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/SequenceAnnotation.html b/website/docs/full_javadoc/compbio/data/msa/SequenceAnnotation.html new file mode 100644 index 0000000..3d36bb9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/SequenceAnnotation.html @@ -0,0 +1,456 @@ + + + + + +SequenceAnnotation + + + + + + + + +
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    compbio.data.msa
    +

    Interface SequenceAnnotation<T>

    +
    +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          analize

          +
          java.lang.String analize(java.util.List<FastaSequence> sequences)
+                  throws UnsupportedRuntimeException,
+                         LimitExceededException,
+                         JobSubmissionException
          +
          Analyse the sequences. The actual analysis algorithm is defined by the + type T. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          +
          • +
        + + + +
          +
        • +

          customAnalize

          +
          java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
+                               java.util.List<Option<T>> options)
+                        throws UnsupportedRuntimeException,
+                               LimitExceededException,
+                               JobSubmissionException,
+                               WrongParameterException
          +
          Analyse the sequences according to custom settings defined in options + list. The actual analysis algorithm is defined by the type T. Default + Limit is used to decide whether the calculation will be permitted or + denied
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          presetAnalize

          +
          java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                               Preset<T> preset)
+                        throws UnsupportedRuntimeException,
+                               LimitExceededException,
+                               JobSubmissionException,
+                               WrongParameterException
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          +
          • +
        + + + +
          +
        • +

          getAnnotation

          +
          ScoreManager getAnnotation(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Return the result of the job.
          +
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          the Map with the sequence names, sequence group names or the word + 'Alignment' in case of alignments and values the represented by a + Set of Score objects. The alignment can be represented in as + little as one key->value pair in this map, the list of sequences + will be represented by multiple key->value mappings. If multiple + annotations were calculated, then they are represented as a Set + of Scores.
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
          +
          +
          • +
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        • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/Align.html new file mode 100644 index 0000000..b3b6023 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/Align.html @@ -0,0 +1,328 @@ + + + + + +Align + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class Align

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.Align
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Align
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Align

          +
          public Align()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        +
        • +
      +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html new file mode 100644 index 0000000..2ae1485 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html @@ -0,0 +1,328 @@ + + + + + +AlignResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class AlignResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.AlignResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class AlignResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AlignResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
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        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AlignResponse

          +
          public AlignResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/Analize.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/Analize.html new file mode 100644 index 0000000..c9b16f0 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/Analize.html @@ -0,0 +1,328 @@ + + + + + +Analize + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class Analize

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.Analize
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Analize
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Analize

          +
          public Analize()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html new file mode 100644 index 0000000..6052ab7 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html @@ -0,0 +1,328 @@ + + + + + +AnalizeResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class AnalizeResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.AnalizeResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class AnalizeResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AnalizeResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AnalizeResponse

          +
          public AnalizeResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJob.html new file mode 100644 index 0000000..728df6e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJob.html @@ -0,0 +1,328 @@ + + + + + +CancelJob + + + + + + + + +
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    +
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    + +
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    + + +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CancelJob

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CancelJob
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CancelJob
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringjobId 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        CancelJob() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetJobId() 
        voidsetJobId(java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          private java.lang.String jobId
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CancelJob

          +
          public CancelJob()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setJobId

          +
          public void setJobId(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - the value for the jobId property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html new file mode 100644 index 0000000..9c0dde3 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html @@ -0,0 +1,328 @@ + + + + + +CancelJobResponse + + + + + + + + +
    + + +
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    + + + +
    + +
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    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CancelJobResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CancelJobResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CancelJobResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private boolean_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        CancelJobResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleanisReturn() 
        voidsetReturn(boolean _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private boolean _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CancelJobResponse

          +
          public CancelJobResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isReturn

          +
          public boolean isReturn()
          +
          +
          Returns:
          +
          returns boolean
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(boolean _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html new file mode 100644 index 0000000..08775f5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html @@ -0,0 +1,375 @@ + + + + + +CustomAlign + + + + + + + + +
    + + +
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    +
    + + + +
    + +
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    + + +
    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class CustomAlign

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomAlign
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomAlign
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        + + + +
          +
        • +

          options

          +
          private java.util.List<Option> options
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomAlign

          +
          public CustomAlign()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        + + + +
          +
        • +

          getOptions

          +
          public java.util.List<Option> getOptions()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<Option> options)
          +
          +
          Parameters:
          +
          options - the value for the options property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
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    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html new file mode 100644 index 0000000..6670d50 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html @@ -0,0 +1,328 @@ + + + + + +CustomAlignResponse + + + + + + + + +
    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class CustomAlignResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomAlignResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomAlignResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomAlignResponse

          +
          public CustomAlignResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
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    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalize.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalize.html new file mode 100644 index 0000000..e795f6f --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalize.html @@ -0,0 +1,375 @@ + + + + + +CustomAnalize + + + + + + + + +
    + + +
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    +
    + + + +
    + +
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    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CustomAnalize

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomAnalize
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomAnalize
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        + + + +
          +
        • +

          options

          +
          private java.util.List<Option> options
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomAnalize

          +
          public CustomAnalize()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        + + + +
          +
        • +

          getOptions

          +
          public java.util.List<Option> getOptions()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<Option> options)
          +
          +
          Parameters:
          +
          options - the value for the options property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalizeResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalizeResponse.html new file mode 100644 index 0000000..72475f4 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomAnalizeResponse.html @@ -0,0 +1,328 @@ + + + + + +CustomAnalizeResponse + + + + + + + + +
    + + +
    Skip navigation links
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    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CustomAnalizeResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomAnalizeResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomAnalizeResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomAnalizeResponse

          +
          public CustomAnalizeResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFold.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFold.html new file mode 100644 index 0000000..9f0e5a2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFold.html @@ -0,0 +1,375 @@ + + + + + +CustomFold + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CustomFold

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomFold
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomFold
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          alignment

          +
          private Alignment alignment
          +
          • +
        + + + +
          +
        • +

          options

          +
          private java.util.List<Option> options
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomFold

          +
          public CustomFold()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getAlignment

          +
          public Alignment getAlignment()
          +
          +
          Returns:
          +
          returns Alignment
          +
          +
          • +
        + + + +
          +
        • +

          setAlignment

          +
          public void setAlignment(Alignment alignment)
          +
          +
          Parameters:
          +
          alignment - the value for the alignment property
          +
          +
          • +
        + + + +
          +
        • +

          getOptions

          +
          public java.util.List<Option> getOptions()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<Option> options)
          +
          +
          Parameters:
          +
          options - the value for the options property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFoldResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFoldResponse.html new file mode 100644 index 0000000..6848863 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/CustomFoldResponse.html @@ -0,0 +1,328 @@ + + + + + +CustomFoldResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class CustomFoldResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.CustomFoldResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CustomFoldResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        CustomFoldResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CustomFoldResponse

          +
          public CustomFoldResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/Fold.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/Fold.html new file mode 100644 index 0000000..ed2493d --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/Fold.html @@ -0,0 +1,328 @@ + + + + + +Fold + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class Fold

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.Fold
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Fold
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Alignmentalignment 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Fold() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Fold

          +
          public Fold()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getAlignment

          +
          public Alignment getAlignment()
          +
          +
          Returns:
          +
          returns Alignment
          +
          +
          • +
        + + + +
          +
        • +

          setAlignment

          +
          public void setAlignment(Alignment alignment)
          +
          +
          Parameters:
          +
          alignment - the value for the alignment property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/FoldResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/FoldResponse.html new file mode 100644 index 0000000..b472b91 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/FoldResponse.html @@ -0,0 +1,328 @@ + + + + + +FoldResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class FoldResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.FoldResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class FoldResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        FoldResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FoldResponse

          +
          public FoldResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html new file mode 100644 index 0000000..7d9b638 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html @@ -0,0 +1,328 @@ + + + + + +GetAnnotation + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetAnnotation

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetAnnotation
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetAnnotation
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringjobId 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetAnnotation() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetJobId() 
        voidsetJobId(java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          private java.lang.String jobId
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetAnnotation

          +
          public GetAnnotation()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setJobId

          +
          public void setJobId(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - the value for the jobId property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html new file mode 100644 index 0000000..3db8a5a --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html @@ -0,0 +1,328 @@ + + + + + +GetAnnotationResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetAnnotationResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetAnnotationResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetAnnotationResponse
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetAnnotationResponse

          +
          public GetAnnotationResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public ScoreManager getReturn()
          +
          +
          Returns:
          +
          returns ScoreManager
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(ScoreManager _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html new file mode 100644 index 0000000..47170bc --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html @@ -0,0 +1,328 @@ + + + + + +GetJobStatus + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetJobStatus

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetJobStatus
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetJobStatus
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringjobId 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetJobStatus() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetJobId() 
        voidsetJobId(java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          private java.lang.String jobId
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetJobStatus

          +
          public GetJobStatus()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setJobId

          +
          public void setJobId(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - the value for the jobId property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html new file mode 100644 index 0000000..9957d5e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html @@ -0,0 +1,328 @@ + + + + + +GetJobStatusResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetJobStatusResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetJobStatusResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetJobStatusResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private JobStatus_return 
        +
        • +
      + + + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetJobStatusResponse

          +
          public GetJobStatusResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public JobStatus getReturn()
          +
          +
          Returns:
          +
          returns JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(JobStatus _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html new file mode 100644 index 0000000..8a8b4b6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTested.html @@ -0,0 +1,328 @@ + + + + + +GetLastTested + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLastTested

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLastTested
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLastTested
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Servicesarg0 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetLastTested() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLastTested

          +
          public GetLastTested()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getArg0

          +
          public Services getArg0()
          +
          +
          Returns:
          +
          returns Services
          +
          +
          • +
        + + + +
          +
        • +

          setArg0

          +
          public void setArg0(Services arg0)
          +
          +
          Parameters:
          +
          arg0 - the value for the arg0 property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOn.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOn.html new file mode 100644 index 0000000..19f333e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOn.html @@ -0,0 +1,328 @@ + + + + + +GetLastTestedOn + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class GetLastTestedOn

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLastTestedOn
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLastTestedOn
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Servicesarg0 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetLastTestedOn() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLastTestedOn

          +
          public GetLastTestedOn()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getArg0

          +
          public Services getArg0()
          +
          +
          Returns:
          +
          returns Services
          +
          +
          • +
        + + + +
          +
        • +

          setArg0

          +
          public void setArg0(Services arg0)
          +
          +
          Parameters:
          +
          arg0 - the value for the arg0 property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html new file mode 100644 index 0000000..a1ca08a --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html @@ -0,0 +1,328 @@ + + + + + +GetLastTestedOnResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLastTestedOnResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLastTestedOnResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLastTestedOnResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.util.Date_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.DategetReturn() 
        voidsetReturn(java.util.Date _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.util.Date _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLastTestedOnResponse

          +
          public GetLastTestedOnResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.util.Date getReturn()
          +
          +
          Returns:
          +
          returns Date
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.util.Date _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html new file mode 100644 index 0000000..767d079 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html @@ -0,0 +1,328 @@ + + + + + +GetLastTestedResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLastTestedResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLastTestedResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLastTestedResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private int_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intgetReturn() 
        voidsetReturn(int _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private int _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLastTestedResponse

          +
          public GetLastTestedResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public int getReturn()
          +
          +
          Returns:
          +
          returns int
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(int _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimit.html new file mode 100644 index 0000000..7b1dc43 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimit.html @@ -0,0 +1,328 @@ + + + + + +GetLimit + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLimit

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLimit
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLimit
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringpresetName 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetLimit() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetPresetName() 
        voidsetPresetName(java.lang.String presetName) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          presetName

          +
          private java.lang.String presetName
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLimit

          +
          public GetLimit()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPresetName

          +
          public java.lang.String getPresetName()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setPresetName

          +
          public void setPresetName(java.lang.String presetName)
          +
          +
          Parameters:
          +
          presetName - the value for the presetName property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html new file mode 100644 index 0000000..cc721a5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html @@ -0,0 +1,328 @@ + + + + + +GetLimitResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLimitResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLimitResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLimitResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Limit_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetLimitResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        LimitgetReturn() 
        voidsetReturn(Limit _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private Limit _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLimitResponse

          +
          public GetLimitResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public Limit getReturn()
          +
          +
          Returns:
          +
          returns Limit
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(Limit _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
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    Skip navigation links
    + + + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimits.html new file mode 100644 index 0000000..becf088 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimits.html @@ -0,0 +1,237 @@ + + + + + +GetLimits + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
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      • +
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      • +
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      • +
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    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetLimits

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLimits
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLimits
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetLimits() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
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    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLimits

          +
          public GetLimits()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    • Summary: 
      • +
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      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html new file mode 100644 index 0000000..211d621 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html @@ -0,0 +1,328 @@ + + + + + +GetLimitsResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class GetLimitsResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetLimitsResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetLimitsResponse
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetLimitsResponse

          +
          public GetLimitsResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public LimitsManager getReturn()
          +
          +
          Returns:
          +
          returns LimitsManager
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(LimitsManager _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServices.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServices.html new file mode 100644 index 0000000..5b95e34 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServices.html @@ -0,0 +1,237 @@ + + + + + +GetNonoperatedServices + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetNonoperatedServices

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetNonoperatedServices
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetNonoperatedServices
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
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        • +
      +
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    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetNonoperatedServices

          +
          public GetNonoperatedServices()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    • Summary: 
      • +
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      • +
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    • Detail: 
      • +
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      • +
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      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html new file mode 100644 index 0000000..5ad4612 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetNonoperatedServicesResponse.html @@ -0,0 +1,328 @@ + + + + + +GetNonoperatedServicesResponse + + + + + + + + +
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    +
    compbio.data.msa.jaxws
    +

    Class GetNonoperatedServicesResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetNonoperatedServicesResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetNonoperatedServicesResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.util.Set<Services>_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.Set<Services>getReturn() 
        voidsetReturn(java.util.Set<Services> _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.util.Set<Services> _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetNonoperatedServicesResponse

          +
          public GetNonoperatedServicesResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.util.Set<Services> getReturn()
          +
          +
          Returns:
          +
          returns Set
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.util.Set<Services> _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresets.html new file mode 100644 index 0000000..33d7f25 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresets.html @@ -0,0 +1,237 @@ + + + + + +GetPresets + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
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      • +
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      • +
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      • +
    • Method
      • +
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      +
    • Detail: 
      • +
    • Field | 
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      • +
    +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetPresets

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetPresets
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetPresets
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetPresets() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetPresets

          +
          public GetPresets()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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      +
    • Summary: 
      • +
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      • +
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    • Detail: 
      • +
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      • +
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    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html new file mode 100644 index 0000000..3beb96c --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html @@ -0,0 +1,328 @@ + + + + + +GetPresetsResponse + + + + + + + + +
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    +
    compbio.data.msa.jaxws
    +

    Class GetPresetsResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetPresetsResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetPresetsResponse
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetPresetsResponse

          +
          public GetPresetsResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public PresetManager getReturn()
          +
          +
          Returns:
          +
          returns PresetManager
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(PresetManager _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResult.html new file mode 100644 index 0000000..e3bf035 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResult.html @@ -0,0 +1,328 @@ + + + + + +GetResult + + + + + + + + +
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    +
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    +
    compbio.data.msa.jaxws
    +

    Class GetResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetResult
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetResult
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringjobId 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetResult() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetJobId() 
        voidsetJobId(java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          private java.lang.String jobId
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetResult

          +
          public GetResult()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setJobId

          +
          public void setJobId(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - the value for the jobId property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html new file mode 100644 index 0000000..15c2ebe --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html @@ -0,0 +1,328 @@ + + + + + +GetResultResponse + + + + + + + + +
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    +
    + + + +
    + +
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    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class GetResultResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetResultResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetResultResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Alignment_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetResultResponse() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetResultResponse

          +
          public GetResultResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public Alignment getReturn()
          +
          +
          Returns:
          +
          returns Alignment
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(Alignment _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html new file mode 100644 index 0000000..c343aa2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html @@ -0,0 +1,237 @@ + + + + + +GetRunnerOptions + + + + + + + + +
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    + + + +
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    +
    +
      +
    • Summary: 
      • +
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      • +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetRunnerOptions

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetRunnerOptions
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetRunnerOptions
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GetRunnerOptions() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
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      +
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        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetRunnerOptions

          +
          public GetRunnerOptions()
          +
          • +
        +
        • +
      +
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    + + +
    Skip navigation links
    + + + + +
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      • +
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      • +
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    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html new file mode 100644 index 0000000..fca4b82 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html @@ -0,0 +1,328 @@ + + + + + +GetRunnerOptionsResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class GetRunnerOptionsResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetRunnerOptionsResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetRunnerOptionsResponse
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetRunnerOptionsResponse

          +
          public GetRunnerOptionsResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public RunnerConfig getReturn()
          +
          +
          Returns:
          +
          returns RunnerConfig
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(RunnerConfig _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
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      +
      • +
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    Skip navigation links
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html new file mode 100644 index 0000000..695fe88 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html @@ -0,0 +1,237 @@ + + + + + +GetServiceCategories + + + + + + + + +
    + + +
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    +
      +
    • Summary: 
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    compbio.data.msa.jaxws
    +

    Class GetServiceCategories

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetServiceCategories
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetServiceCategories
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
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    +
      +
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        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetServiceCategories

          +
          public GetServiceCategories()
          +
          • +
        +
        • +
      +
      • +
    +
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    + + +
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    Skip navigation links
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html new file mode 100644 index 0000000..a9a0efa --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html @@ -0,0 +1,328 @@ + + + + + +GetServiceCategoriesResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class GetServiceCategoriesResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetServiceCategoriesResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetServiceCategoriesResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.util.Set<Category>_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.Set<Category>getReturn() 
        voidsetReturn(java.util.Set<Category> _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.util.Set<Category> _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetServiceCategoriesResponse

          +
          public GetServiceCategoriesResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.util.Set<Category> getReturn()
          +
          +
          Returns:
          +
          returns Set
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.util.Set<Category> _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html new file mode 100644 index 0000000..b8bae63 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html @@ -0,0 +1,328 @@ + + + + + +GetServiceDescription + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class GetServiceDescription

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetServiceDescription
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetServiceDescription
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Servicesarg0 
        +
        • +
      + + + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetServiceDescription

          +
          public GetServiceDescription()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getArg0

          +
          public Services getArg0()
          +
          +
          Returns:
          +
          returns Services
          +
          +
          • +
        + + + +
          +
        • +

          setArg0

          +
          public void setArg0(Services arg0)
          +
          +
          Parameters:
          +
          arg0 - the value for the arg0 property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
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    + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescriptionResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescriptionResponse.html new file mode 100644 index 0000000..37d1726 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetServiceDescriptionResponse.html @@ -0,0 +1,328 @@ + + + + + +GetServiceDescriptionResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class GetServiceDescriptionResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetServiceDescriptionResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetServiceDescriptionResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetServiceDescriptionResponse

          +
          public GetServiceDescriptionResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html new file mode 100644 index 0000000..dae4390 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html @@ -0,0 +1,237 @@ + + + + + +GetSupportedServices + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
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      • +
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      • +
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    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class GetSupportedServices

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetSupportedServices
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetSupportedServices
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetSupportedServices

          +
          public GetSupportedServices()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    +
      +
    • Summary: 
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html new file mode 100644 index 0000000..9cb0c96 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/GetSupportedServicesResponse.html @@ -0,0 +1,328 @@ + + + + + +GetSupportedServicesResponse + + + + + + + + +
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    +
    compbio.data.msa.jaxws
    +

    Class GetSupportedServicesResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.GetSupportedServicesResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GetSupportedServicesResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.util.Set<Services>_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.Set<Services>getReturn() 
        voidsetReturn(java.util.Set<Services> _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.util.Set<Services> _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GetSupportedServicesResponse

          +
          public GetSupportedServicesResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.util.Set<Services> getReturn()
          +
          +
          Returns:
          +
          returns Set
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.util.Set<Services> _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperating.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperating.html new file mode 100644 index 0000000..0019185 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperating.html @@ -0,0 +1,328 @@ + + + + + +IsOperating + + + + + + + + +
    + + +
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    +
    + + + +
    + +
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    + + +
    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class IsOperating

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.IsOperating
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class IsOperating
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Servicesarg0 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        IsOperating() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          IsOperating

          +
          public IsOperating()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getArg0

          +
          public Services getArg0()
          +
          +
          Returns:
          +
          returns Services
          +
          +
          • +
        + + + +
          +
        • +

          setArg0

          +
          public void setArg0(Services arg0)
          +
          +
          Parameters:
          +
          arg0 - the value for the arg0 property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html new file mode 100644 index 0000000..a022ee5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html @@ -0,0 +1,328 @@ + + + + + +IsOperatingResponse + + + + + + + + +
    + + +
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    compbio.data.msa.jaxws
    +

    Class IsOperatingResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.IsOperatingResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class IsOperatingResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private boolean_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleanisReturn() 
        voidsetReturn(boolean _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private boolean _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          IsOperatingResponse

          +
          public IsOperatingResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isReturn

          +
          public boolean isReturn()
          +
          +
          Returns:
          +
          returns boolean
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(boolean _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html new file mode 100644 index 0000000..6577c55 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html @@ -0,0 +1,331 @@ + + + + + +JobSubmissionExceptionBean + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class JobSubmissionExceptionBean

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.JobSubmissionExceptionBean
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class JobSubmissionExceptionBean
+extends java.lang.Object
      +
      This class was generated by the JAX-WS RI. + JAX-WS RI 2.2.3-b01- + Generated source version: 2.2.3
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmessage 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetMessage() 
        voidsetMessage(java.lang.String message) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          message

          +
          private java.lang.String message
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobSubmissionExceptionBean

          +
          public JobSubmissionExceptionBean()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getMessage

          +
          public java.lang.String getMessage()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setMessage

          +
          public void setMessage(java.lang.String message)
          +
          +
          Parameters:
          +
          message - the value for the message property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html new file mode 100644 index 0000000..e0e06fa --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html @@ -0,0 +1,519 @@ + + + + + +LimitExceededExceptionBean + + + + + + + + +
    + + +
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    +
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    + +
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    + + +
    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class LimitExceededExceptionBean

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.LimitExceededExceptionBean
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class LimitExceededExceptionBean
+extends java.lang.Object
      +
      This class was generated by the JAX-WS RI. + JAX-WS RI 2.2.3-b01- + Generated source version: 2.2.3
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          actualNumberofSequences

          +
          private int actualNumberofSequences
          +
          • +
        + + + +
          +
        • +

          message

          +
          private java.lang.String message
          +
          • +
        + + + +
          +
        • +

          numberOfSequencesAllowed

          +
          private int numberOfSequencesAllowed
          +
          • +
        + + + +
          +
        • +

          sequenceLenghtActual

          +
          private int sequenceLenghtActual
          +
          • +
        + + + +
          +
        • +

          sequenceLenghtAllowed

          +
          private int sequenceLenghtAllowed
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LimitExceededExceptionBean

          +
          public LimitExceededExceptionBean()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getActualNumberofSequences

          +
          public int getActualNumberofSequences()
          +
          +
          Returns:
          +
          returns int
          +
          +
          • +
        + + + +
          +
        • +

          setActualNumberofSequences

          +
          public void setActualNumberofSequences(int actualNumberofSequences)
          +
          +
          Parameters:
          +
          actualNumberofSequences - the value for the actualNumberofSequences property
          +
          +
          • +
        + + + +
          +
        • +

          getMessage

          +
          public java.lang.String getMessage()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setMessage

          +
          public void setMessage(java.lang.String message)
          +
          +
          Parameters:
          +
          message - the value for the message property
          +
          +
          • +
        + + + +
          +
        • +

          getNumberOfSequencesAllowed

          +
          public int getNumberOfSequencesAllowed()
          +
          +
          Returns:
          +
          returns int
          +
          +
          • +
        + + + +
          +
        • +

          setNumberOfSequencesAllowed

          +
          public void setNumberOfSequencesAllowed(int numberOfSequencesAllowed)
          +
          +
          Parameters:
          +
          numberOfSequencesAllowed - the value for the numberOfSequencesAllowed property
          +
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtActual

          +
          public int getSequenceLenghtActual()
          +
          +
          Returns:
          +
          returns int
          +
          +
          • +
        + + + +
          +
        • +

          setSequenceLenghtActual

          +
          public void setSequenceLenghtActual(int sequenceLenghtActual)
          +
          +
          Parameters:
          +
          sequenceLenghtActual - the value for the sequenceLenghtActual property
          +
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtAllowed

          +
          public int getSequenceLenghtAllowed()
          +
          +
          Returns:
          +
          returns int
          +
          +
          • +
        + + + +
          +
        • +

          setSequenceLenghtAllowed

          +
          public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
          +
          +
          Parameters:
          +
          sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html new file mode 100644 index 0000000..fa5752f --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html @@ -0,0 +1,375 @@ + + + + + +PresetAlign + + + + + + + + +
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    Skip navigation links
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    +
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    +
    compbio.data.msa.jaxws
    +

    Class PresetAlign

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetAlign
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetAlign
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        + + + +
          +
        • +

          preset

          +
          private Preset preset
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetAlign

          +
          public PresetAlign()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        + + + +
          +
        • +

          getPreset

          +
          public Preset getPreset()
          +
          +
          Returns:
          +
          returns Preset
          +
          +
          • +
        + + + +
          +
        • +

          setPreset

          +
          public void setPreset(Preset preset)
          +
          +
          Parameters:
          +
          preset - the value for the preset property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html new file mode 100644 index 0000000..958892e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html @@ -0,0 +1,328 @@ + + + + + +PresetAlignResponse + + + + + + + + +
    + + +
    Skip navigation links
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    +
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    + +
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    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class PresetAlignResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetAlignResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetAlignResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetAlignResponse

          +
          public PresetAlignResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalize.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalize.html new file mode 100644 index 0000000..f218799 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalize.html @@ -0,0 +1,375 @@ + + + + + +PresetAnalize + + + + + + + + +
    + + +
    Skip navigation links
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    +
    + + + +
    + +
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    + + +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class PresetAnalize

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetAnalize
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetAnalize
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaSequences

          +
          private java.util.List<FastaSequence> fastaSequences
          +
          • +
        + + + +
          +
        • +

          preset

          +
          private Preset preset
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetAnalize

          +
          public PresetAnalize()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFastaSequences

          +
          public java.util.List<FastaSequence> getFastaSequences()
          +
          +
          Returns:
          +
          returns List
          +
          +
          • +
        + + + +
          +
        • +

          setFastaSequences

          +
          public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
          +
          +
          Parameters:
          +
          fastaSequences - the value for the fastaSequences property
          +
          +
          • +
        + + + +
          +
        • +

          getPreset

          +
          public Preset getPreset()
          +
          +
          Returns:
          +
          returns Preset
          +
          +
          • +
        + + + +
          +
        • +

          setPreset

          +
          public void setPreset(Preset preset)
          +
          +
          Parameters:
          +
          preset - the value for the preset property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html new file mode 100644 index 0000000..d5cf453 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html @@ -0,0 +1,328 @@ + + + + + +PresetAnalizeResponse + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.msa.jaxws
    +

    Class PresetAnalizeResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetAnalizeResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetAnalizeResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetAnalizeResponse

          +
          public PresetAnalizeResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFold.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFold.html new file mode 100644 index 0000000..56f1529 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFold.html @@ -0,0 +1,375 @@ + + + + + +PresetFold + + + + + + + + +
    + + +
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    +
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    compbio.data.msa.jaxws
    +

    Class PresetFold

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetFold
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetFold
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetFold

          +
          public PresetFold()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getAlignment

          +
          public Alignment getAlignment()
          +
          +
          Returns:
          +
          returns Alignment
          +
          +
          • +
        + + + +
          +
        • +

          setAlignment

          +
          public void setAlignment(Alignment alignment)
          +
          +
          Parameters:
          +
          alignment - the value for the alignment property
          +
          +
          • +
        + + + +
          +
        • +

          getPreset

          +
          public Preset getPreset()
          +
          +
          Returns:
          +
          returns Preset
          +
          +
          • +
        + + + +
          +
        • +

          setPreset

          +
          public void setPreset(Preset preset)
          +
          +
          Parameters:
          +
          preset - the value for the preset property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFoldResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFoldResponse.html new file mode 100644 index 0000000..d8ff9b6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PresetFoldResponse.html @@ -0,0 +1,328 @@ + + + + + +PresetFoldResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class PresetFoldResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PresetFoldResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PresetFoldResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        PresetFoldResponse() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetFoldResponse

          +
          public PresetFoldResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
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    Skip navigation links
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    +
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    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html new file mode 100644 index 0000000..aefb41d --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html @@ -0,0 +1,375 @@ + + + + + +PullExecStatistics + + + + + + + + +
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    +
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    compbio.data.msa.jaxws
    +

    Class PullExecStatistics

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PullExecStatistics
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PullExecStatistics
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringjobId 
        private longposition 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        PullExecStatistics() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetJobId() 
        longgetPosition() 
        voidsetJobId(java.lang.String jobId) 
        voidsetPosition(long position) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          private java.lang.String jobId
          +
          • +
        + + + +
          +
        • +

          position

          +
          private long position
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PullExecStatistics

          +
          public PullExecStatistics()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setJobId

          +
          public void setJobId(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - the value for the jobId property
          +
          +
          • +
        + + + +
          +
        • +

          getPosition

          +
          public long getPosition()
          +
          +
          Returns:
          +
          returns long
          +
          +
          • +
        + + + +
          +
        • +

          setPosition

          +
          public void setPosition(long position)
          +
          +
          Parameters:
          +
          position - the value for the position property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html new file mode 100644 index 0000000..bae3bf7 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html @@ -0,0 +1,328 @@ + + + + + +PullExecStatisticsResponse + + + + + + + + +
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    Skip navigation links
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    +
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    + +
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    + + +
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    +
    compbio.data.msa.jaxws
    +

    Class PullExecStatisticsResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.PullExecStatisticsResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class PullExecStatisticsResponse
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PullExecStatisticsResponse

          +
          public PullExecStatisticsResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public ChunkHolder getReturn()
          +
          +
          Returns:
          +
          returns ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(ChunkHolder _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html new file mode 100644 index 0000000..8a06919 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html @@ -0,0 +1,331 @@ + + + + + +ResultNotAvailableExceptionBean + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class ResultNotAvailableExceptionBean

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ResultNotAvailableExceptionBean
+extends java.lang.Object
      +
      This class was generated by the JAX-WS RI. + JAX-WS RI 2.2.3-b01- + Generated source version: 2.2.3
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmessage 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetMessage() 
        voidsetMessage(java.lang.String message) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          message

          +
          private java.lang.String message
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ResultNotAvailableExceptionBean

          +
          public ResultNotAvailableExceptionBean()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getMessage

          +
          public java.lang.String getMessage()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setMessage

          +
          public void setMessage(java.lang.String message)
          +
          +
          Parameters:
          +
          message - the value for the message property
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
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    Skip navigation links
    + + + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServices.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServices.html new file mode 100644 index 0000000..513571f --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServices.html @@ -0,0 +1,237 @@ + + + + + +TestAllServices + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
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      • +
    • Method
      • +
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      • +
    • Field | 
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      • +
    +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class TestAllServices

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.TestAllServices
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class TestAllServices
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        TestAllServices() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          TestAllServices

          +
          public TestAllServices()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
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      • +
    • Constr | 
      • +
    • Method
      • +
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      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServicesResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServicesResponse.html new file mode 100644 index 0000000..40b4c41 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestAllServicesResponse.html @@ -0,0 +1,328 @@ + + + + + +TestAllServicesResponse + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class TestAllServicesResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.TestAllServicesResponse
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class TestAllServicesResponse
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          _return

          +
          private java.lang.String _return
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          TestAllServicesResponse

          +
          public TestAllServicesResponse()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
          • +
        +
        • +
      +
      • +
    +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/TestService.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestService.html new file mode 100644 index 0000000..35783f6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestService.html @@ -0,0 +1,328 @@ + + + + + +TestService + + + + + + + + +
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    +
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    compbio.data.msa.jaxws
    +

    Class TestService

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.TestService
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class TestService
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private Servicesarg0 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        TestService() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          TestService

          +
          public TestService()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getArg0

          +
          public Services getArg0()
          +
          +
          Returns:
          +
          returns Services
          +
          +
          • +
        + + + +
          +
        • +

          setArg0

          +
          public void setArg0(Services arg0)
          +
          +
          Parameters:
          +
          arg0 - the value for the arg0 property
          +
          +
          • +
        +
        • +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/TestServiceResponse.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestServiceResponse.html new file mode 100644 index 0000000..e7d6417 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/TestServiceResponse.html @@ -0,0 +1,328 @@ + + + + + +TestServiceResponse + + + + + + + + +
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    + + +
    +
    compbio.data.msa.jaxws
    +

    Class TestServiceResponse

    +
    +
    +
      +
    • java.lang.Object
      • +
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        +
      • compbio.data.msa.jaxws.TestServiceResponse
        • +
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    +
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      +
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      public class TestServiceResponse
+extends java.lang.Object
      +
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        +
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        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.String_return 
        +
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      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReturn() 
        voidsetReturn(java.lang.String _return) 
        +
          +
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          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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        Field Detail

        + + + +
          +
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          _return

          +
          private java.lang.String _return
          +
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        +
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      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          TestServiceResponse

          +
          public TestServiceResponse()
          +
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        +
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      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getReturn

          +
          public java.lang.String getReturn()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setReturn

          +
          public void setReturn(java.lang.String _return)
          +
          +
          Parameters:
          +
          _return - the value for the _return property
          +
          +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html b/website/docs/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html new file mode 100644 index 0000000..339cce1 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html @@ -0,0 +1,331 @@ + + + + + +UnsupportedRuntimeExceptionBean + + + + + + + + +
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    compbio.data.msa.jaxws
    +

    Class UnsupportedRuntimeExceptionBean

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
        • +
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    +
    +
      +
    • +
      +
      +
      public class UnsupportedRuntimeExceptionBean
+extends java.lang.Object
      +
      This class was generated by the JAX-WS RI. + JAX-WS RI 2.2.3-b01- + Generated source version: 2.2.3
      +
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        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmessage 
        +
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        Method Summary

        + + + + + + + + + + + + + + +
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        Modifier and TypeMethod and Description
        java.lang.StringgetMessage() 
        voidsetMessage(java.lang.String message) 
        +
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          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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        Field Detail

        + + + +
          +
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          message

          +
          private java.lang.String message
          +
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        +
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        Constructor Detail

        + + + +
          +
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          UnsupportedRuntimeExceptionBean

          +
          public UnsupportedRuntimeExceptionBean()
          +
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      • + + +

        Method Detail

        + + + +
          +
        • +

          getMessage

          +
          public java.lang.String getMessage()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setMessage

          +
          public void setMessage(java.lang.String message)
          +
          +
          Parameters:
          +
          message - the value for the message property
          +
          +
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    compbio.data.msa.jaxws
    +

    Class WrongParameterExceptionBean

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.msa.jaxws.WrongParameterExceptionBean
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class WrongParameterExceptionBean
+extends java.lang.Object
      +
      This class was generated by the JAX-WS RI. + JAX-WS RI 2.2.3-b01- + Generated source version: 2.2.3
      +
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        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmessage 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetMessage() 
        voidsetMessage(java.lang.String message) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
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        Field Detail

        + + + +
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          message

          +
          private java.lang.String message
          +
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        +
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      + +
        +
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        Constructor Detail

        + + + +
          +
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          WrongParameterExceptionBean

          +
          public WrongParameterExceptionBean()
          +
          • +
        +
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      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getMessage

          +
          public java.lang.String getMessage()
          +
          +
          Returns:
          +
          returns String
          +
          +
          • +
        + + + +
          +
        • +

          setMessage

          +
          public void setMessage(java.lang.String message)
          +
          +
          Parameters:
          +
          message - the value for the message property
          +
          +
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    Classes

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    compbio.data.msa

    +
    +

    Interfaces

    + +

    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/data/msa/package-summary.html b/website/docs/full_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..80a202a --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,202 @@ + + + + + +compbio.data.msa + + + + + + + + +
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    +

    Package compbio.data.msa

    +
    +
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    +
    +

    See: Description

    +
    +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Interface Summary 
      InterfaceDescription
      JABAService +
      This is a marker interface, contains no methods
      +
      JManagement 
      Metadata<T> 
      MsaWS<T> +
      Multiple Sequence Alignment (MSA) Web Services Interface
      +
      RegistryWS +
      JABAWS services registry
      +
      SequenceAnnotation<T> +
      Interface for tools that results to one or more annotation to sequence(s) + + Single, multiple sequences their groups or alignments can be annotated
      +
      +
      • +
    • + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      Category 
      +
      • +
    + + + +

    Package compbio.data.msa Description

    +
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    +
    +
    Version:
    +
    1.0 April 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
    + +
    + + +
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    Hierarchy For Package compbio.data.msa

    +Package Hierarchies: + +
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    • java.lang.Object + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/Alignment.html b/website/docs/full_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..ef4c83d --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,473 @@ + + + + + +Alignment + + + + + + + + +
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    compbio.data.sequence
    +

    Class Alignment

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Alignment
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Alignment
+extends java.lang.Object
      +
      Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. It does not guarantee neither the uniqueness of the names of + sequences nor it guarantees the uniqueness of the sequences.
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      FastaSequence, +AlignmentMetadata
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Alignment

          +
          protected Alignment()
          +
          • +
        + + + +
          +
        • +

          Alignment

          +
          public Alignment(java.util.List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
          +
          +
          Parameters:
          +
          sequences -
          +
          program -
          +
          gapchar -
          +
          +
          • +
        + + + +
          +
        • +

          Alignment

          +
          public Alignment(java.util.List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
          +
          +
          Parameters:
          +
          sequences -
          +
          metadata -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getSequences

          +
          public java.util.List<FastaSequence> getSequences()
          +
          +
          Returns:
          +
          list of FastaSequence records
          +
          +
          • +
        + + + +
          +
        • +

          getSize

          +
          public int getSize()
          +
          +
          Returns:
          +
          a number of sequence in the alignment
          +
          +
          • +
        + + + +
          +
        • +

          getMetadata

          +
          public AlignmentMetadata getMetadata()
          +
          +
          Returns:
          +
          AlignmentMetadata object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          Please note that this implementation does not take the order of sequences + into account!
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/docs/full_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..99fc483 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,393 @@ + + + + + +AlignmentMetadata + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class AlignmentMetadata

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.AlignmentMetadata
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public class AlignmentMetadata
+extends java.lang.Object
      +
      Alignment metadata e.g. method/program being used to generate the alignment + and its parameters
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          program

          +
          private Program program
          +
          • +
        + + + +
          +
        • +

          gapchar

          +
          private char gapchar
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AlignmentMetadata

          +
          private AlignmentMetadata()
          +
          • +
        + + + +
          +
        • +

          AlignmentMetadata

          +
          public AlignmentMetadata(Program program,
+                         char gapchar)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getProgram

          +
          public Program getProgram()
          +
          • +
        + + + +
          +
        • +

          getGapchar

          +
          public char getGapchar()
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/docs/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..1111881 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,488 @@ + + + + + +ClustalAlignmentUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ClustalAlignmentUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ClustalAlignmentUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class ClustalAlignmentUtil
+extends java.lang.Object
      +
      Tools to read and write clustal formated files
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      Petr Troshin based on jimp class
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static chargapchar +
        Dash char to be used as gap char in the alignments
        +
        private static java.util.logging.Loggerlog 
        private static intmaxNameLength 
        private static intminNameHolderLength 
        private static intoneLineAlignmentLength 
        private static java.lang.Stringspacer 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleanisValidClustalFile(java.io.InputStream input) +
        Please note this method closes the input stream provided as a parameter
        +
        static AlignmentreadClustalFile(java.io.File file) 
        static AlignmentreadClustalFile(java.io.InputStream instream) +
        Read Clustal formatted alignment.
        +
        static voidwriteClustalAlignment(java.io.Writer out, + Alignment alignment) +
        Write Clustal formatted alignment Limitations: does not record the + consensus.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final java.util.logging.Logger log
          +
          • +
        + + + +
          +
        • +

          gapchar

          +
          public static final char gapchar
          +
          Dash char to be used as gap char in the alignments
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          minNameHolderLength

          +
          private static final int minNameHolderLength
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          oneLineAlignmentLength

          +
          private static final int oneLineAlignmentLength
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClustalAlignmentUtil

          +
          public ClustalAlignmentUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          readClustalFile

          +
          public static Alignment readClustalFile(java.io.InputStream instream)
+                                 throws java.io.IOException,
+                                        UnknownFileFormatException
          +
          Read Clustal formatted alignment. Limitations: Does not read consensus + + Sequence names as well as the sequences are not guaranteed to be unique!
          +
          +
          Throws:
          +
          {@link - IOException}
          +
          {@link - UnknownFileFormatException}
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          isValidClustalFile

          +
          public static boolean isValidClustalFile(java.io.InputStream input)
          +
          Please note this method closes the input stream provided as a parameter
          +
          +
          Parameters:
          +
          input -
          +
          Returns:
          +
          true if the file is recognised as Clustal formatted alignment, + false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          writeClustalAlignment

          +
          public static void writeClustalAlignment(java.io.Writer out,
+                                         Alignment alignment)
+                                  throws java.io.IOException
          +
          Write Clustal formatted alignment Limitations: does not record the + consensus. Potential bug - records 60 chars length alignment where + Clustal would have recorded 50 chars.
          +
          +
          Parameters:
          +
          out -
          +
          alignment -
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/ConservationMethod.html b/website/docs/full_javadoc/compbio/data/sequence/ConservationMethod.html new file mode 100644 index 0000000..1c29a8a --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/ConservationMethod.html @@ -0,0 +1,551 @@ + + + + + +ConservationMethod + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum ConservationMethod

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<ConservationMethod>
      +
      +
      +
      +
      public enum ConservationMethod
+extends java.lang.Enum<ConservationMethod>
      +
      Enumeration listing of all the supported methods.
      +
      +
      Author:
      +
      Agnieszka Golicz & Peter Troshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static ConservationMethod[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (ConservationMethod c : ConservationMethod.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static ConservationMethod valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/DisemblResult.html b/website/docs/full_javadoc/compbio/data/sequence/DisemblResult.html new file mode 100644 index 0000000..922cc2d --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/DisemblResult.html @@ -0,0 +1,356 @@ + + + + + +DisemblResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum DisemblResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<DisemblResult>
        • +
      • +
          +
        • compbio.data.sequence.DisemblResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<DisemblResult>
      +
      +
      +
      +
       enum DisemblResult
+extends java.lang.Enum<DisemblResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        COILS +
        These contains ranges and scores
        +
        HOTLOOPS 
        REM465 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static DisemblResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static DisemblResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static DisemblResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (DisemblResult c : DisemblResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static DisemblResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/DisorderMethod.html b/website/docs/full_javadoc/compbio/data/sequence/DisorderMethod.html new file mode 100644 index 0000000..f66dd79 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/DisorderMethod.html @@ -0,0 +1,341 @@ + + + + + +DisorderMethod + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum DisorderMethod

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<DisorderMethod>
        • +
      • +
          +
        • compbio.data.sequence.DisorderMethod
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<DisorderMethod>
      +
      +
      +
      +
      public enum DisorderMethod
+extends java.lang.Enum<DisorderMethod>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Disembl 
        JRonn 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static DisorderMethodvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static DisorderMethod[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static DisorderMethod[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (DisorderMethod c : DisorderMethod.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static DisorderMethod valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/FastaReader.html b/website/docs/full_javadoc/compbio/data/sequence/FastaReader.html new file mode 100644 index 0000000..daabb49 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/FastaReader.html @@ -0,0 +1,497 @@ + + + + + +FastaReader + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class FastaReader

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.FastaReader
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.Iterator<FastaSequence>
      +
      +
      +
      +
      public class FastaReader
+extends java.lang.Object
+implements java.util.Iterator<FastaSequence>
      +
      Reads files with FASTA formatted sequences. All the information in the FASTA + header is preserved including trailing white spaces. All the white spaces are + removed from the sequence. + + Examples of the correct input: + + 
      + 
+ >zedpshvyzg
+ GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
+ 
+ >xovkactesa
+ CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
+ FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
+ FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
+ DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
+ 
+ >ntazzewyvv
+ CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
+ EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
+ EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
+   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
+   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
+   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
+ 
+    > 12 d t y wi               k       jbke    
+   KLSHHDCD
+    N
+     H
+     HSKCTEPHCGNSHQMLHRDP
+     CCDQCQSWEAENWCASMRKAILF
+ 
+
      +
      +
      Version:
      +
      1.0 April 2011
      +
      Author:
      +
      Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.StringDELIM +
        Delimiter for the scanner
        +
        private java.util.Scannerinput 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        FastaReader(java.io.InputStream inputStream) +
        This class will not close the incoming stream! So the client should do + so.
        +
        FastaReader(java.lang.String inputFile) +
        Header data can contain non-ASCII symbols and read in UTF8
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        voidclose() +
        Call this method to close the connection to the input file if you want to + free up the resources.
        +
        booleanhasNext()
        FastaSequencenext() +
        Reads the next FastaSequence from the input
        +
        voidremove() +
        Not implemented
        +
        private static FastaSequencetoFastaSequence(java.lang.String singleFastaEntry) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
          +
        • + + +

          Methods inherited from interface java.util.Iterator

          +forEachRemaining
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          input

          +
          private final java.util.Scanner input
          +
          • +
        + + + +
          +
        • +

          DELIM

          +
          private final java.lang.String DELIM
          +
          Delimiter for the scanner
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FastaReader

          +
          public FastaReader(java.lang.String inputFile)
+            throws java.io.FileNotFoundException
          +
          Header data can contain non-ASCII symbols and read in UTF8
          +
          +
          Parameters:
          +
          inputFile - the file containing the list of FASTA formatted sequences to + read from
          +
          Throws:
          +
          java.io.FileNotFoundException - if the input file is not found
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          +
          • +
        + + + +
          +
        • +

          FastaReader

          +
          public FastaReader(java.io.InputStream inputStream)
+            throws java.io.FileNotFoundException
          +
          This class will not close the incoming stream! So the client should do + so.
          +
          +
          Parameters:
          +
          inputStream -
          +
          Throws:
          +
          java.io.FileNotFoundException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          hasNext

          +
          public boolean hasNext()
          +
          +
          Specified by:
          +
          hasNext in interface java.util.Iterator<FastaSequence>
          +
          Throws:
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          +
          • +
        + + + +
          +
        • +

          next

          +
          public FastaSequence next()
          +
          Reads the next FastaSequence from the input
          +
          +
          Specified by:
          +
          next in interface java.util.Iterator<FastaSequence>
          +
          Throws:
          +
          java.lang.AssertionError - if the header or the sequence is missing
          +
          java.lang.IllegalStateException - if the close method was called on this instance
          +
          MismatchException - - if there were no more FastaSequence's.
          +
          +
          • +
        + + + +
          +
        • +

          remove

          +
          public void remove()
          +
          Not implemented
          +
          +
          Specified by:
          +
          remove in interface java.util.Iterator<FastaSequence>
          +
          +
          • +
        + + + +
          +
        • +

          close

          +
          public void close()
          +
          Call this method to close the connection to the input file if you want to + free up the resources. The connection will be closed on the JVM shutdown + if this method was not called explicitly. No further reading on this + instance of the FastaReader will be possible after calling this method.
          +
          • +
        + + + +
          +
        • +

          toFastaSequence

          +
          private static FastaSequence toFastaSequence(java.lang.String singleFastaEntry)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/docs/full_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..539995e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,526 @@ + + + + + +FastaSequence + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class FastaSequence

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.FastaSequence
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public class FastaSequence
+extends java.lang.Object
      +
      A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it stores e.g. it could be nucleotide, + protein or even gapped alignment sequence! The only guarantee it makes is + that the sequence does not contain white space characters e.g. spaces, new + lines etc
      +
      +
      Version:
      +
      1.0 September 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringid +
        Sequence id
        +
        private java.lang.Stringsequence +
        Returns the string representation of sequence
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        FastaSequence() 
        FastaSequence(java.lang.String id, + java.lang.String sequence) +
        Upon construction the any whitespace characters are removed from the + sequence
        +
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          id

          +
          private java.lang.String id
          +
          Sequence id
          +
          • +
        + + + +
          +
        • +

          sequence

          +
          private java.lang.String sequence
          +
          Returns the string representation of sequence
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FastaSequence

          +
          FastaSequence()
          +
          • +
        + + + +
          +
        • +

          FastaSequence

          +
          public FastaSequence(java.lang.String id,
+                     java.lang.String sequence)
          +
          Upon construction the any whitespace characters are removed from the + sequence
          +
          +
          Parameters:
          +
          id -
          +
          sequence -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getId

          +
          public java.lang.String getId()
          +
          Gets the value of id
          +
          +
          Returns:
          +
          the value of id
          +
          +
          • +
        + + + +
          +
        • +

          getSequence

          +
          public java.lang.String getSequence()
          +
          Gets the value of sequence
          +
          +
          Returns:
          +
          the value of sequence
          +
          +
          • +
        + + + +
          +
        • +

          countMatchesInSequence

          +
          public static int countMatchesInSequence(java.lang.String theString,
+                                         java.lang.String theRegExp)
          +
          • +
        + + + +
          +
        • +

          getFormattedFasta

          +
          public java.lang.String getFormattedFasta()
          +
          • +
        + + + +
          +
        • +

          getOnelineFasta

          +
          public java.lang.String getOnelineFasta()
          +
          +
          Returns:
          +
          one line name, next line sequence, no matter what the sequence + length is
          +
          +
          • +
        + + + +
          +
        • +

          getFormatedSequence

          +
          public java.lang.String getFormatedSequence(int width)
          +
          Format sequence per width letter in one string. Without spaces.
          +
          +
          Returns:
          +
          multiple line formated sequence, one line width letters length
          +
          +
          • +
        + + + +
          +
        • +

          getLength

          +
          public int getLength()
          +
          +
          Returns:
          +
          sequence length
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          Same as oneLineFasta
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/GlobProtResult.html b/website/docs/full_javadoc/compbio/data/sequence/GlobProtResult.html new file mode 100644 index 0000000..2109063 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/GlobProtResult.html @@ -0,0 +1,392 @@ + + + + + +GlobProtResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum GlobProtResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<GlobProtResult>
        • +
      • +
          +
        • compbio.data.sequence.GlobProtResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<GlobProtResult>
      +
      +
      +
      +
       enum GlobProtResult
+extends java.lang.Enum<GlobProtResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Disorder +
        This a range with no scores
        +
        Dydx +
        This a score with no range
        +
        GlobDoms +
        This a range with no scores
        +
        RawScore +
        This a score with no range
        +
        SmoothedScore +
        This a score with no range
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static GlobProtResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static GlobProtResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          GlobDoms

          +
          public static final GlobProtResult GlobDoms
          +
          This a range with no scores
          +
          • +
        + + + +
          +
        • +

          Disorder

          +
          public static final GlobProtResult Disorder
          +
          This a range with no scores
          +
          • +
        + + + +
          +
        • +

          Dydx

          +
          public static final GlobProtResult Dydx
          +
          This a score with no range
          +
          • +
        + + + +
          +
        • +

          SmoothedScore

          +
          public static final GlobProtResult SmoothedScore
          +
          This a score with no range
          +
          • +
        + + + +
          +
        • +

          RawScore

          +
          public static final GlobProtResult RawScore
          +
          This a score with no range
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static GlobProtResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (GlobProtResult c : GlobProtResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static GlobProtResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/IUPredResult.html b/website/docs/full_javadoc/compbio/data/sequence/IUPredResult.html new file mode 100644 index 0000000..7b3d586 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/IUPredResult.html @@ -0,0 +1,375 @@ + + + + + +IUPredResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum IUPredResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<IUPredResult>
        • +
      • +
          +
        • compbio.data.sequence.IUPredResult
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<IUPredResult>
      +
      +
      +
      +
       enum IUPredResult
+extends java.lang.Enum<IUPredResult>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Glob +
        Globular domains
        +
        Long +
        Long disorder
        +
        Short +
        Short disorder
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static IUPredResultgetType(java.io.File file) 
        static IUPredResultvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static IUPredResult[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          Short

          +
          public static final IUPredResult Short
          +
          Short disorder
          +
          • +
        + + + +
          +
        • +

          Long

          +
          public static final IUPredResult Long
          +
          Long disorder
          +
          • +
        + + + +
          +
        • +

          Glob

          +
          public static final IUPredResult Glob
          +
          Globular domains
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static IUPredResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (IUPredResult c : IUPredResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static IUPredResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + +
          +
        • +

          getType

          +
          static IUPredResult getType(java.io.File file)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/Program.html b/website/docs/full_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..ef56fc5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,442 @@ + + + + + +Program + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum Program

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<Program>
        • +
      • +
          +
        • compbio.data.sequence.Program
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<Program>
      +
      +
      +
      +
      public enum Program
+extends java.lang.Enum<Program>
      +
      The list of programmes that can produce alignments
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static ProgramvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static Program[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          CLUSTAL

          +
          public static final Program CLUSTAL
          +
          ClustalW
          +
          • +
        + + + +
          +
        • +

          ClustalO

          +
          public static final Program ClustalO
          +
          ClustalO
          +
          • +
        + + + +
          +
        • +

          Mafft

          +
          public static final Program Mafft
          +
          Mafft
          +
          • +
        + + + +
          +
        • +

          Muscle

          +
          public static final Program Muscle
          +
          Muscle
          +
          • +
        + + + +
          +
        • +

          Tcoffee

          +
          public static final Program Tcoffee
          +
          Tcoffee
          +
          • +
        + + + +
          +
        • +

          Probcons

          +
          public static final Program Probcons
          +
          Probcons
          +
          • +
        + + + +
          +
        • +

          MSAprobs

          +
          public static final Program MSAprobs
          +
          MSAprobs
          +
          • +
        + + + +
          +
        • +

          GLprobs

          +
          public static final Program GLprobs
          +
          GLprobs
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static Program[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (Program c : Program.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static Program valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html new file mode 100644 index 0000000..bced2dc --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldLine.html @@ -0,0 +1,477 @@ + + + + + +RNAStructReader.AlifoldLine + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.AlifoldLine

    +
    +
    + +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringregex 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static RNAStructReader.AlifoldLinevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static RNAStructReader.AlifoldLine[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          regex

          +
          java.lang.String regex
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.AlifoldLine[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.AlifoldLine c : RNAStructReader.AlifoldLine.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.AlifoldLine valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html new file mode 100644 index 0000000..ff83650 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.AlifoldResult.html @@ -0,0 +1,417 @@ + + + + + +RNAStructReader.AlifoldResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.AlifoldResult

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.AlifoldResult[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.AlifoldResult c : RNAStructReader.AlifoldResult.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.AlifoldResult valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html new file mode 100644 index 0000000..0dffd8a --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.RNAOut.html @@ -0,0 +1,381 @@ + + + + + +RNAStructReader.RNAOut + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum RNAStructReader.RNAOut

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        ENERGY 
        FREQ 
        OTHER 
        SEQ 
        STRUCT 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static RNAStructReader.RNAOutvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static RNAStructReader.RNAOut[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static RNAStructReader.RNAOut[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (RNAStructReader.RNAOut c : RNAStructReader.RNAOut.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static RNAStructReader.RNAOut valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.html b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.html new file mode 100644 index 0000000..9250156 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/RNAStructReader.html @@ -0,0 +1,647 @@ + + + + + +RNAStructReader + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class RNAStructReader

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.RNAStructReader
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class RNAStructReader
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.StringalignmentP 
        (package private) static java.lang.Stringbracket 
        (package private) static java.lang.StringcentStructP 
        (package private) static java.lang.StringenergyP 
        (package private) static java.lang.StringensembleFreqP 
        (package private) static java.lang.StringfloatP 
        (package private) static java.lang.StringfreeEnergyP 
        (package private) static java.lang.StringfreqP 
        (package private) static java.lang.StringjustStructP 
        (package private) static java.lang.StringMEAStructP 
        (package private) static java.lang.StringmfeStructP 
        (package private) static java.lang.StringnotData 
        (package private) static java.lang.Stringps 
        (package private) static java.lang.StringPStructP 
        (package private) static java.lang.Strings 
        (package private) static java.lang.StringseqP 
        (package private) static java.lang.StringstochBTStructP 
        (package private) static java.lang.StringstructP 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        RNAStructReader() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          s

          +
          static java.lang.String s
          +
          • +
        + + + +
          +
        • +

          bracket

          +
          static java.lang.String bracket
          +
          • +
        + + + +
          +
        • +

          notData

          +
          static java.lang.String notData
          +
          • +
        + + + +
          +
        • +

          seqP

          +
          static java.lang.String seqP
          +
          • +
        + + + +
          +
        • +

          structP

          +
          static java.lang.String structP
          +
          • +
        + + + +
          +
        • +

          floatP

          +
          static java.lang.String floatP
          +
          • +
        + + + +
          +
        • +

          energyP

          +
          static java.lang.String energyP
          +
          • +
        + + + +
          +
        • +

          freqP

          +
          static java.lang.String freqP
          +
          • +
        + + + +
          +
        • +

          ps

          +
          static java.lang.String ps
          +
          • +
        + + + +
          +
        • +

          alignmentP

          +
          static java.lang.String alignmentP
          +
          • +
        + + + +
          +
        • +

          mfeStructP

          +
          static java.lang.String mfeStructP
          +
          • +
        + + + +
          +
        • +

          justStructP

          +
          static java.lang.String justStructP
          +
          • +
        + + + +
          +
        • +

          stochBTStructP

          +
          static java.lang.String stochBTStructP
          +
          • +
        + + + +
          +
        • +

          PStructP

          +
          static java.lang.String PStructP
          +
          • +
        + + + +
          +
        • +

          centStructP

          +
          static java.lang.String centStructP
          +
          • +
        + + + +
          +
        • +

          MEAStructP

          +
          static java.lang.String MEAStructP
          +
          • +
        + + + +
          +
        • +

          freeEnergyP

          +
          static java.lang.String freeEnergyP
          +
          • +
        + + + +
          +
        • +

          ensembleFreqP

          +
          static java.lang.String ensembleFreqP
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RNAStructReader

          +
          public RNAStructReader()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          readRNAStructStream

          +
          public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout)
+                                                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          newSetScore

          +
          private static java.util.TreeSet<Score> newSetScore(java.lang.Enum<?> res,
+                                                    java.util.List<java.lang.Float> scores)
          +
          • +
        + + + +
          +
        • +

          newEmptyScore

          +
          public static java.util.TreeSet<Score> newEmptyScore(java.lang.Enum<?> res)
          +
          • +
        + + + +
          +
        • +

          readRNAStructStream

          +
          public static RNAStructScoreManager readRNAStructStream(java.io.InputStream stdout,
+                                                        java.io.InputStream alifold)
+                                                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/RNAStructScoreManager.html b/website/docs/full_javadoc/compbio/data/sequence/RNAStructScoreManager.html new file mode 100644 index 0000000..a292fc6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/RNAStructScoreManager.html @@ -0,0 +1,392 @@ + + + + + +RNAStructScoreManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class RNAStructScoreManager

    +
    +
    + +
    +
      +
    • +
      +
      +
      public class RNAStructScoreManager
+extends ScoreManager
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RNAStructScoreManager

          +
          private RNAStructScoreManager()
          +
          • +
        + + + +
          +
        • +

          RNAStructScoreManager

          +
          public RNAStructScoreManager(java.util.List<java.lang.String> structs,
+                             java.util.List<java.util.TreeSet<Score>> data)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newInstance

          +
          public static RNAStructScoreManager newInstance(java.util.List<java.lang.String> structs,
+                                                java.util.List<java.util.TreeSet<Score>> data)
          +
          • +
        + + + +
          +
        • +

          getStructs

          +
          public java.util.List<java.lang.String> getStructs()
          +
          • +
        + + + +
          +
        • +

          getData

          +
          public java.util.List<java.util.TreeSet<Score>> getData()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class ScoreManager
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/Range.html b/website/docs/full_javadoc/compbio/data/sequence/Range.html new file mode 100644 index 0000000..85b3f9f --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/Range.html @@ -0,0 +1,410 @@ + + + + + +Range + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class Range

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Range
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Comparable<Range>
      +
      +
      +
      +
      public class Range
+extends java.lang.Object
+implements java.lang.Comparable<Range>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        intfrom 
        intto 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Range() 
         Range(int from, + int to) 
         Range(java.lang.String[] twoElementAr) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intcompareTo(Range o) 
        booleanequals(java.lang.Object obj) 
        inthashCode() 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          from

          +
          public final int from
          +
          • +
        + + + +
          +
        • +

          to

          +
          public final int to
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Range

          +
          private Range()
          +
          • +
        + + + +
          +
        • +

          Range

          +
          public Range(int from,
+             int to)
          +
          • +
        + + + +
          +
        • +

          Range

          +
          public Range(java.lang.String[] twoElementAr)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          compareTo

          +
          public int compareTo(Range o)
          +
          +
          Specified by:
          +
          compareTo in interface java.lang.Comparable<Range>
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/docs/full_javadoc/compbio/data/sequence/SMERFSConstraints.html new file mode 100644 index 0000000..530e45f --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/SMERFSConstraints.html @@ -0,0 +1,440 @@ + + + + + +SMERFSConstraints + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Enum SMERFSConstraints

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<SMERFSConstraints>
        • +
      • +
          +
        • compbio.data.sequence.SMERFSConstraints
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<SMERFSConstraints>
      +
      +
      +
      +
      public enum SMERFSConstraints
+extends java.lang.Enum<SMERFSConstraints>
      +
      Enumeration defining two constraints for SMERFS columns score calculation. + MAX_SCORE gives the highest core of all the windows the column belongs to. + MID_SCORE gives the window score to the column in the middle.
      +
      +
      Author:
      +
      Agnieszka Golicz & Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        MAX_SCORE 
        MID_SCORE 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static SMERFSConstraintsgetSMERFSColumnScore(java.lang.String score) 
        static SMERFSConstraintsvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static SMERFSConstraints[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          DEFAULT_COLUMN_SCORE

          +
          public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
          +
          Default column scoring schema
          +
          • +
        + + + +
          +
        • +

          DEFAULT_WINDOW_SIZE

          +
          public static final int DEFAULT_WINDOW_SIZE
          +
          Default window size value for SMERFS algorithm
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          DEFAULT_GAP_THRESHOLD

          +
          public static final double DEFAULT_GAP_THRESHOLD
          +
          Default gap threshold value for SMERFS algorithm
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static SMERFSConstraints[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (SMERFSConstraints c : SMERFSConstraints.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static SMERFSConstraints valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + +
          +
        • +

          getSMERFSColumnScore

          +
          public static SMERFSConstraints getSMERFSColumnScore(java.lang.String score)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/Score.html b/website/docs/full_javadoc/compbio/data/sequence/Score.html new file mode 100644 index 0000000..3dab5e9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/Score.html @@ -0,0 +1,624 @@ + + + + + +Score + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class Score

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.Score
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Comparable<Score>
      +
      +
      +
      +
      @Immutable
+public class Score
+extends java.lang.Object
+implements java.lang.Comparable<Score>
      +
      A value class for AACon annotation results storage. The objects of this type + are immutable
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.lang.Stringmethod 
        (package private) static java.text.NumberFormatNUMBER_FORMAT 
        private java.util.TreeSet<Range>ranges 
        private java.util.ArrayList<java.lang.Float>scores 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Score() 
         Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores) +
        Instantiate the Score
        +
         Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores, + java.util.TreeSet<Range> ranges) 
         Score(java.lang.Enum<?> method, + float[] scores) 
         Score(java.lang.Enum<?> method, + java.util.TreeSet<Range> ranges) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intcompareTo(Score o) 
        booleanequals(java.lang.Object obj) 
        java.lang.StringgetMethod() +
        Returns the ConservationMethod
        +
        java.util.TreeSet<Range>getRanges() +
        Return Ranges if any Collections.EMPTY_SET otherwise
        +
        java.util.ArrayList<java.lang.Float>getScores() +
        The column scores for the alignment
        +
        inthashCode() 
        voidsetRanges(java.util.TreeSet<Range> ranges) 
        private java.util.ArrayList<java.lang.Float>toList(float[] values) 
        java.lang.StringtoString() 
        static voidwrite(java.util.TreeSet<Score> scores, + java.io.Writer writer) +
        Outputs the List of Score objects into the Output stream.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          NUMBER_FORMAT

          +
          static final java.text.NumberFormat NUMBER_FORMAT
          +
          • +
        + + + +
          +
        • +

          method

          +
          private final java.lang.String method
          +
          • +
        + + + +
          +
        • +

          ranges

          +
          private java.util.TreeSet<Range> ranges
          +
          • +
        + + + +
          +
        • +

          scores

          +
          private java.util.ArrayList<java.lang.Float> scores
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Score

          +
          private Score()
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.Float> scores)
          +
          Instantiate the Score
          +
          +
          Parameters:
          +
          method - the ConservationMethod with which scores were + calculated
          +
          scores - the actual conservation values for each column of the + alignment
          +
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.Float> scores,
+             java.util.TreeSet<Range> ranges)
          +
          +
          Parameters:
          +
          method - the ConservationMethod with which scores were + calculated
          +
          scores - the actual conservation values for each column of the + alignment
          +
          ranges - The set of ranges i.e. parts of the sequence with specific + function, usually can be calculated based on scores
          +
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             java.util.TreeSet<Range> ranges)
          +
          • +
        + + + +
          +
        • +

          Score

          +
          public Score(java.lang.Enum<?> method,
+             float[] scores)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toList

          +
          private java.util.ArrayList<java.lang.Float> toList(float[] values)
          +
          • +
        + + + +
          +
        • +

          getMethod

          +
          public java.lang.String getMethod()
          +
          Returns the ConservationMethod
          +
          +
          Returns:
          +
          the ConservationMethod
          +
          +
          • +
        + + + +
          +
        • +

          getScores

          +
          public java.util.ArrayList<java.lang.Float> getScores()
          +
          The column scores for the alignment
          +
          +
          Returns:
          +
          the column scores for the alignment
          +
          +
          • +
        + + + +
          +
        • +

          getRanges

          +
          public java.util.TreeSet<Range> getRanges()
          +
          Return Ranges if any Collections.EMPTY_SET otherwise
          +
          +
          Returns:
          +
          ordered set of Range
          +
          +
          • +
        + + + +
          +
        • +

          setRanges

          +
          public void setRanges(java.util.TreeSet<Range> ranges)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          write

          +
          public static void write(java.util.TreeSet<Score> scores,
+                         java.io.Writer writer)
+                  throws java.io.IOException
          +
          Outputs the List of Score objects into the Output stream. The output + format is as follows: + + 
          + 
+ #MethodName [comma separated list of ranges] <space separated list of values>
+ 	  
+ For example:
+ 	 
+ #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
+ #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
+ #COILS 22-33, 44-56 0.121 3.212
+ 
+
          + + The maximum precision for values is 3 digits, but can be less.
          +
          +
          Parameters:
          +
          scores - the list of scores to output
          +
          writer -
          +
          Throws:
          +
          java.io.IOException - if the OutputStream cannot be written into
          +
          java.lang.NullPointerException - if the output stream is null
          +
          +
          • +
        + + + +
          +
        • +

          compareTo

          +
          public int compareTo(Score o)
          +
          +
          Specified by:
          +
          compareTo in interface java.lang.Comparable<Score>
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html b/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html new file mode 100644 index 0000000..344fec9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html @@ -0,0 +1,419 @@ + + + + + +ScoreManager.ScoreHolder + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ScoreManager.ScoreHolder

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ScoreManager.ScoreHolder
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Enclosing class:
      +
      ScoreManager
      +
      +
      +
      +
      public static class ScoreManager.ScoreHolder
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        java.lang.Stringid 
        java.util.TreeSet<Score>scores 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private ScoreHolder() 
        (package private)ScoreHolder(java.lang.String id, + java.util.Set<Score> scores) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          id

          +
          public java.lang.String id
          +
          • +
        + + + +
          +
        • +

          scores

          +
          public java.util.TreeSet<Score> scores
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ScoreHolder

          +
          private ScoreHolder()
          +
          • +
        + + + +
          +
        • +

          ScoreHolder

          +
          ScoreHolder(java.lang.String id,
+            java.util.Set<Score> scores)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          writeOut

          +
          public void writeOut(java.io.Writer writer)
+              throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getScoreByMethod

          +
          public Score getScoreByMethod(java.lang.Enum<?> method)
          +
          • +
        + + + +
          +
        • +

          getScoreByMethod

          +
          public Score getScoreByMethod(java.lang.String method)
          +
          • +
        + + + +
          +
        • +

          getNumberOfScores

          +
          public int getNumberOfScores()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.html b/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.html new file mode 100644 index 0000000..fb9ffe6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/ScoreManager.html @@ -0,0 +1,507 @@ + + + + + +ScoreManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class ScoreManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.ScoreManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Direct Known Subclasses:
      +
      RNAStructScoreManager
      +
      +
      +
      +
      public class ScoreManager
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ScoreManager

          +
          protected ScoreManager()
          +
          • +
        + + + +
          +
        • +

          ScoreManager

          +
          private ScoreManager(java.lang.String id,
+                     java.util.Set<Score> data)
          +
          • +
        + + + +
          +
        • +

          ScoreManager

          +
          private ScoreManager(java.util.Map<java.lang.String,java.util.Set<Score>> data)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newInstance

          +
          public static ScoreManager newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data)
          +
          • +
        + + + +
          +
        • +

          newInstanceSingleScore

          +
          public static ScoreManager newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap)
          +
          • +
        + + + +
          +
        • +

          newInstanceSingleSequence

          +
          public static ScoreManager newInstanceSingleSequence(java.util.Set<Score> data)
          +
          • +
        + + + +
          +
        • +

          asMap

          +
          public java.util.Map<java.lang.String,java.util.TreeSet<Score>> asMap()
          +
          • +
        + + + +
          +
        • +

          asSet

          +
          public java.util.Set<Score> asSet()
          +
          • +
        + + + +
          +
        • +

          getNumberOfSeq

          +
          public int getNumberOfSeq()
          +
          • +
        + + + + + + + +
          +
        • +

          writeOut

          +
          public void writeOut(java.io.Writer outStream)
+              throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/docs/full_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..63d48d6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,1147 @@ + + + + + +SequenceUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class SequenceUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.data.sequence.SequenceUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class SequenceUtil
+extends java.lang.Object
      +
      Utility class for operations on sequences
      +
      +
      Since:
      +
      1.0
      +
      Version:
      +
      2.0 June 2011
      +
      Author:
      +
      Peter Troshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.util.regex.PatternAA +
        Valid Amino acids
        +
        static java.util.regex.PatternAMBIGUOUS_AA +
        Same as AA pattern but with two additional letters - XU
        +
        static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE +
        Ambiguous nucleotide
        +
        static java.util.regex.PatternDIGIT +
        A digit
        +
        private static java.lang.StringJRONN_WRONG_FORMAT_MESSAGE 
        static java.util.regex.PatternNON_AA +
        inversion of AA pattern
        +
        static java.util.regex.PatternNON_NUCLEOTIDE +
        Non nucleotide
        +
        static java.util.regex.PatternNONWORD +
        Non word
        +
        static java.util.regex.PatternNUCLEOTIDE +
        Nucleotides a, t, g, c, u
        +
        static java.util.regex.PatternWHITE_SPACE +
        A whitespace character: [\t\n\x0B\f\r]
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private SequenceUtil() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.StringcleanProteinSequence(java.lang.String sequence) +
        Remove all non AA chars from the sequence
        +
        static java.lang.StringcleanSequence(java.lang.String sequence) +
        Removes all whitespace chars in the sequence string
        +
        static voidcloseSilently(java.util.logging.Logger log, + java.io.Closeable stream) +
        Closes the Closable and logs the exception if any
        +
        private static float[]convertToNumber(java.lang.String[] annotValues) 
        static java.lang.StringdeepCleanSequence(java.lang.String sequence) +
        Removes all special characters and digits as well as whitespace chars + from the sequence
        +
        static booleanisAmbiguosProtein(java.lang.String sequence) +
        Check whether the sequence confirms to amboguous protein sequence
        +
        static booleanisNonAmbNucleotideSequence(java.lang.String sequence) +
        Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
        +
        static booleanisNucleotideSequence(FastaSequence s) 
        static booleanisProteinSequence(java.lang.String sequence) 
        static java.util.List<FastaSequence>openInputStream(java.lang.String inFilePath) +
        Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
        +
        private static java.util.TreeSet<Range>parseIUPredDomains(java.util.Scanner scan) +
        # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
        +
        private static float[]parseIUPredScores(java.util.Scanner scan) 
        private static java.util.TreeSet<Range>parseRanges(java.lang.Enum resultType, + java.lang.String lines) +
        Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
        +
        static java.util.HashSet<Score>readAAConResults(java.io.InputStream results) +
        Read AACon result with no alignment files.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) +
        Reads fasta sequences from inStream into the list of FastaSequence + objects
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
        static voidwriteClustal(java.io.OutputStream outStream, + java.util.List<FastaSequence> sequences, + char gapChar) 
        static voidwriteFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) +
        Writes FastaSequence in the file, each sequence will take one line only
        +
        static voidwriteFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) +
        Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
        +
        static voidwriteFastaKeepTheStream(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          WHITE_SPACE

          +
          public static final java.util.regex.Pattern WHITE_SPACE
          +
          A whitespace character: [\t\n\x0B\f\r]
          +
          • +
        + + + +
          +
        • +

          DIGIT

          +
          public static final java.util.regex.Pattern DIGIT
          +
          A digit
          +
          • +
        + + + +
          +
        • +

          NONWORD

          +
          public static final java.util.regex.Pattern NONWORD
          +
          Non word
          +
          • +
        + + + +
          +
        • +

          AA

          +
          public static final java.util.regex.Pattern AA
          +
          Valid Amino acids
          +
          • +
        + + + +
          +
        • +

          NON_AA

          +
          public static final java.util.regex.Pattern NON_AA
          +
          inversion of AA pattern
          +
          • +
        + + + +
          +
        • +

          AMBIGUOUS_AA

          +
          public static final java.util.regex.Pattern AMBIGUOUS_AA
          +
          Same as AA pattern but with two additional letters - XU
          +
          • +
        + + + +
          +
        • +

          NUCLEOTIDE

          +
          public static final java.util.regex.Pattern NUCLEOTIDE
          +
          Nucleotides a, t, g, c, u
          +
          • +
        + + + +
          +
        • +

          AMBIGUOUS_NUCLEOTIDE

          +
          public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
          +
          Ambiguous nucleotide
          +
          • +
        + + + +
          +
        • +

          NON_NUCLEOTIDE

          +
          public static final java.util.regex.Pattern NON_NUCLEOTIDE
          +
          Non nucleotide
          +
          • +
        + + + +
          +
        • +

          JRONN_WRONG_FORMAT_MESSAGE

          +
          private static final java.lang.String JRONN_WRONG_FORMAT_MESSAGE
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SequenceUtil

          +
          private SequenceUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isNucleotideSequence

          +
          public static boolean isNucleotideSequence(FastaSequence s)
          +
          +
          Returns:
          +
          true is the sequence contains only letters a,c, t, g, u
          +
          +
          • +
        + + + +
          +
        • +

          isNonAmbNucleotideSequence

          +
          public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
          +
          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
          +
          • +
        + + + +
          +
        • +

          cleanSequence

          +
          public static java.lang.String cleanSequence(java.lang.String sequence)
          +
          Removes all whitespace chars in the sequence string
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          cleaned up sequence
          +
          +
          • +
        + + + +
          +
        • +

          deepCleanSequence

          +
          public static java.lang.String deepCleanSequence(java.lang.String sequence)
          +
          Removes all special characters and digits as well as whitespace chars + from the sequence
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          cleaned up sequence
          +
          +
          • +
        + + + +
          +
        • +

          cleanProteinSequence

          +
          public static java.lang.String cleanProteinSequence(java.lang.String sequence)
          +
          Remove all non AA chars from the sequence
          +
          +
          Parameters:
          +
          sequence - the sequence to clean
          +
          Returns:
          +
          cleaned sequence
          +
          +
          • +
        + + + +
          +
        • +

          isProteinSequence

          +
          public static boolean isProteinSequence(java.lang.String sequence)
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          true is the sequence is a protein sequence, false overwise
          +
          +
          • +
        + + + +
          +
        • +

          isAmbiguosProtein

          +
          public static boolean isAmbiguosProtein(java.lang.String sequence)
          +
          Check whether the sequence confirms to amboguous protein sequence
          +
          +
          Parameters:
          +
          sequence -
          +
          Returns:
          +
          return true only if the sequence if ambiguous protein sequence + Return false otherwise. e.g. if the sequence is non-ambiguous + protein or DNA
          +
          +
          • +
        + + + +
          +
        • +

          writeFasta

          +
          public static void writeFasta(java.io.OutputStream outstream,
+                              java.util.List<FastaSequence> sequences,
+                              int width)
+                       throws java.io.IOException
          +
          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
          +
          +
          Parameters:
          +
          outstream -
          +
          sequences -
          +
          width - - the maximum number of characters to write in one line
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeFastaKeepTheStream

          +
          public static void writeFastaKeepTheStream(java.io.OutputStream outstream,
+                                           java.util.List<FastaSequence> sequences,
+                                           int width)
+                                    throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          readFasta

          +
          public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
+                                               throws java.io.IOException
          +
          Reads fasta sequences from inStream into the list of FastaSequence + objects
          +
          +
          Parameters:
          +
          inStream - from
          +
          Returns:
          +
          list of FastaSequence objects
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeFasta

          +
          public static void writeFasta(java.io.OutputStream os,
+                              java.util.List<FastaSequence> sequences)
+                       throws java.io.IOException
          +
          Writes FastaSequence in the file, each sequence will take one line only
          +
          +
          Parameters:
          +
          os -
          +
          sequences -
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          readIUPred

          +
          public static java.util.Map<java.lang.String,Score> readIUPred(java.io.File result)
+                                                        throws java.io.IOException,
+                                                               UnknownFileFormatException
          +
          Read IUPred output
          +
          +
          Parameters:
          +
          result -
          +
          Returns:
          +
          Map key->sequence name, value->Score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          readIUPred

          +
          private static java.util.Map<java.lang.String,Score> readIUPred(java.io.InputStream input,
+                                                                IUPredResult type)
+                                                         throws java.io.IOException,
+                                                                UnknownFileFormatException
          +
          ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
          +
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          parseIUPredDomains

          +
          private static java.util.TreeSet<Range> parseIUPredDomains(java.util.Scanner scan)
          +
          # P53_HUMA + + Number of globular domains: 2 + + globular domain 1. 98 - 269 + + globular domain 2. 431 - 482 + + >P53_HUMA + + meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp
          +
          +
          Parameters:
          +
          scan -
          +
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          readJRonn

          +
          public static java.util.Map<java.lang.String,Score> readJRonn(java.io.InputStream inStream)
+                                                       throws java.io.IOException,
+                                                              UnknownFileFormatException
          +
          Reader for JRonn horizontal file format + + 
          + >Foobar M G D T T A G 0.48 0.42
+ 0.42 0.48 0.52 0.53 0.54
+ 
+ 
          + Where all values are tab delimited
          +
          +
          Parameters:
          +
          inStream - the InputStream connected to the JRonn output file
          +
          Returns:
          +
          Map key=sequence name value=Score
          +
          Throws:
          +
          java.io.IOException - is thrown if the inStream has problems accessing the data
          +
          UnknownFileFormatException - is thrown if the inStream represents an unknown source of + data, i.e. not a JRonn output
          +
          +
          • +
        + + + + + + + +
          +
        • +

          closeSilently

          +
          public static final void closeSilently(java.util.logging.Logger log,
+                                       java.io.Closeable stream)
          +
          Closes the Closable and logs the exception if any
          +
          +
          Parameters:
          +
          log -
          +
          stream -
          +
          +
          • +
        + + + +
          +
        • +

          readDisembl

          +
          public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readDisembl(java.io.InputStream input)
+                                                                            throws java.io.IOException,
+                                                                                   UnknownFileFormatException
          +
          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
          +
          +
          Parameters:
          +
          input - the InputStream
          +
          Returns:
          +
          Map key=sequence name, value=set of score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          parseRanges

          +
          private static java.util.TreeSet<Range> parseRanges(java.lang.Enum resultType,
+                                                    java.lang.String lines)
          +
          Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
          +
          +
          Parameters:
          +
          lines -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          readGlobPlot

          +
          public static java.util.HashMap<java.lang.String,java.util.Set<Score>> readGlobPlot(java.io.InputStream input)
+                                                                             throws java.io.IOException,
+                                                                                    UnknownFileFormatException
          +
          > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
          +
          +
          Parameters:
          +
          input -
          +
          Returns:
          +
          Map key=sequence name, value=set of score
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          readAAConResults

          +
          public static java.util.HashSet<Score> readAAConResults(java.io.InputStream results)
          +
          Read AACon result with no alignment files. This method leaves incoming + InputStream open!
          +
          +
          Parameters:
          +
          results - output file of AAConservation
          +
          Returns:
          +
          Map with keys ConservationMethod -> float[]
          +
          +
          • +
        + + + +
          +
        • +

          openInputStream

          +
          public static java.util.List<FastaSequence> openInputStream(java.lang.String inFilePath)
+                                                     throws java.io.IOException,
+                                                            UnknownFileFormatException
          +
          Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
          +
          +
          Parameters:
          +
          inFilePath - the path to the input file
          +
          Returns:
          +
          the List of FastaSequence objects
          +
          Throws:
          +
          java.io.IOException - if the file denoted by inFilePath cannot be read
          +
          UnknownFileFormatException - if the inFilePath points to the file which format cannot be + recognised
          +
          +
          • +
        + + + +
          +
        • +

          writeClustal

          +
          public static void writeClustal(java.io.OutputStream outStream,
+                                java.util.List<FastaSequence> sequences,
+                                char gapChar)
+                         throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/docs/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..3fe8aea --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,367 @@ + + + + + +UnknownFileFormatException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.data.sequence
    +

    Class UnknownFileFormatException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.data.sequence.UnknownFileFormatException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class UnknownFileFormatException
+extends java.lang.Exception
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.io.Filefile 
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          file

          +
          java.io.File file
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException()
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.io.File file,
+                                  java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.String message,
+                                  java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          UnknownFileFormatException

          +
          public UnknownFileFormatException(java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/docs/full_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..2e1326e --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,479 @@ + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + +
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    Uses of Class
    compbio.data.sequence.IUPredResult

    +
    +
    +
      +
    • + + + + + + + + + + + + +
      Packages that use IUPredResult 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/class-use/RNAStructReader.AlifoldLine.html b/website/docs/full_javadoc/compbio/data/sequence/class-use/RNAStructReader.AlifoldLine.html new file mode 100644 index 0000000..16c8841 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/class-use/RNAStructReader.AlifoldLine.html @@ -0,0 +1,180 @@ + + + + + +Uses of Class compbio.data.sequence.RNAStructReader.AlifoldLine + + + + + + + + +
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    Uses of Class
    compbio.data.sequence.Range

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    • + + + + + + + + + + + + +
      Packages that use Range 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
      +
      • +
    • +
        +
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        Uses of Range in compbio.data.sequence

        + + + + + + + + + + + + +
        Fields in compbio.data.sequence with type parameters of type Range 
        Modifier and TypeField and Description
        private java.util.TreeSet<Range>Score.ranges 
        + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return types with arguments of type Range 
        Modifier and TypeMethod and Description
        java.util.TreeSet<Range>Score.getRanges() +
        Return Ranges if any Collections.EMPTY_SET otherwise
        +
        private static java.util.TreeSet<Range>SequenceUtil.parseIUPredDomains(java.util.Scanner scan) +
        # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
        +
        private static java.util.TreeSet<Range>SequenceUtil.parseRanges(java.lang.Enum resultType, + java.lang.String lines) +
        Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
        +
        + + + + + + + + + + + + +
        Methods in compbio.data.sequence with parameters of type Range 
        Modifier and TypeMethod and Description
        intRange.compareTo(Range o) 
        + + + + + + + + + + + + +
        Method parameters in compbio.data.sequence with type arguments of type Range 
        Modifier and TypeMethod and Description
        voidScore.setRanges(java.util.TreeSet<Range> ranges) 
        + + + + + + + + + + + + + +
        Constructor parameters in compbio.data.sequence with type arguments of type Range 
        Constructor and Description
        Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores, + java.util.TreeSet<Range> ranges) 
        Score(java.lang.Enum<?> method, + java.util.TreeSet<Range> ranges) 
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/class-use/Score.html b/website/docs/full_javadoc/compbio/data/sequence/class-use/Score.html new file mode 100644 index 0000000..1de2989 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/class-use/Score.html @@ -0,0 +1,420 @@ + + + + + +Uses of Class compbio.data.sequence.Score + + + + + + + + +
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    Uses of Class
    compbio.data.sequence.Score

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      Packages that use Score 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
      compbio.runner +
      Utilities commonly used by all runners.
      +
      compbio.runner.disorder 
      +
      • +
    • +
        +
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        Uses of Score in compbio.data.sequence

        + + + + + + + + + + + + +
        Fields in compbio.data.sequence with type parameters of type Score 
        Modifier and TypeField and Description
        java.util.TreeSet<Score>ScoreManager.ScoreHolder.scores 
        + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return Score 
        Modifier and TypeMethod and Description
        ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.Enum<?> method) 
        ScoreScoreManager.ScoreHolder.getScoreByMethod(java.lang.String method) 
        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that return types with arguments of type Score 
        Modifier and TypeMethod and Description
        java.util.Map<java.lang.String,java.util.TreeSet<Score>>ScoreManager.asMap() 
        java.util.Set<Score>ScoreManager.asSet() 
        java.util.List<java.util.TreeSet<Score>>RNAStructScoreManager.getData() 
        static java.util.TreeSet<Score>RNAStructReader.newEmptyScore(java.lang.Enum<?> res) 
        private static java.util.TreeSet<Score>RNAStructReader.newSetScore(java.lang.Enum<?> res, + java.util.List<java.lang.Float> scores) 
        static java.util.HashSet<Score>SequenceUtil.readAAConResults(java.io.InputStream results) +
        Read AACon result with no alignment files.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
        + + + + + + + + + + + + +
        Methods in compbio.data.sequence with parameters of type Score 
        Modifier and TypeMethod and Description
        intScore.compareTo(Score o) 
        + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Method parameters in compbio.data.sequence with type arguments of type Score 
        Modifier and TypeMethod and Description
        static RNAStructScoreManagerRNAStructScoreManager.newInstance(java.util.List<java.lang.String> structs, + java.util.List<java.util.TreeSet<Score>> data) 
        static ScoreManagerScoreManager.newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data) 
        static ScoreManagerScoreManager.newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap) 
        static ScoreManagerScoreManager.newInstanceSingleSequence(java.util.Set<Score> data) 
        static voidScore.write(java.util.TreeSet<Score> scores, + java.io.Writer writer) +
        Outputs the List of Score objects into the Output stream.
        +
        + + + + + + + + + + + + + + + + + + + +
        Constructor parameters in compbio.data.sequence with type arguments of type Score 
        Constructor and Description
        RNAStructScoreManager(java.util.List<java.lang.String> structs, + java.util.List<java.util.TreeSet<Score>> data) 
        ScoreHolder(java.lang.String id, + java.util.Set<Score> scores) 
        ScoreManager(java.util.Map<java.lang.String,java.util.Set<Score>> data) 
        ScoreManager(java.lang.String id, + java.util.Set<Score> data) 
        +
        • +
      • + + +

        Uses of Score in compbio.runner

        + + + + + + + + + + + + + + + + +
        Methods in compbio.runner that return types with arguments of type Score 
        Modifier and TypeMethod and Description
        static java.util.Map<java.lang.String,Score>Util.readJronnFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        static java.util.Map<java.lang.String,Score>RunnerUtil.readJronnFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        +
        • +
      • + + +

        Uses of Score in compbio.runner.disorder

        + + + + + + + + + + + + + + + + +
        Method parameters in compbio.runner.disorder with type arguments of type Score 
        Modifier and TypeMethod and Description
        (package private) voidIUPred.combineScores(java.util.Map<java.lang.String,java.util.Set<Score>> combined, + java.util.Map<java.lang.String,Score> scores) 
        (package private) voidIUPred.combineScores(java.util.Map<java.lang.String,java.util.Set<Score>> combined, + java.util.Map<java.lang.String,Score> scores) 
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/docs/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..06112e2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + +
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    Uses of Class
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    Uses of Class
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    • + + + + + + + + + + + + + + + + +
      Packages that use UnknownFileFormatException 
      PackageDescription
      compbio.data.sequence +
      A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
      +
      compbio.runner +
      Utilities commonly used by all runners.
      +
      +
      • +
    • +
        +
      • + + +

        Uses of UnknownFileFormatException in compbio.data.sequence

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.data.sequence that throw UnknownFileFormatException 
        Modifier and TypeMethod and Description
        private static float[]SequenceUtil.convertToNumber(java.lang.String[] annotValues) 
        static java.util.List<FastaSequence>SequenceUtil.openInputStream(java.lang.String inFilePath) +
        Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
        +
        private static float[]SequenceUtil.parseIUPredScores(java.util.Scanner scan) 
        static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) 
        static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) +
        Read Clustal formatted alignment.
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readDisembl(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.HashMap<java.lang.String,java.util.Set<Score>>SequenceUtil.readGlobPlot(java.io.InputStream input) +
        > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.File result) +
        Read IUPred output
        +
        private static java.util.Map<java.lang.String,Score>SequenceUtil.readIUPred(java.io.InputStream input, + IUPredResult type) +
        ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
        +
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.File result) 
        static java.util.Map<java.lang.String,Score>SequenceUtil.readJRonn(java.io.InputStream inStream) +
        Reader for JRonn horizontal file format
        +
        +
        • +
      • + + +

        Uses of UnknownFileFormatException in compbio.runner

        + + + + + + + + + + + + + + + + + + + + + + + + +
        Methods in compbio.runner that throw UnknownFileFormatException 
        Modifier and TypeMethod and Description
        static AlignmentUtil.readClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        static AlignmentRunnerUtil.readClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        static java.util.Map<java.lang.String,Score>Util.readJronnFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        static java.util.Map<java.lang.String,Score>RunnerUtil.readJronnFile(java.lang.String workDirectory, + java.lang.String clustFile) 
        +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/package-frame.html b/website/docs/full_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..526f9b5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,48 @@ + + + + + +compbio.data.sequence + + + + + +

    compbio.data.sequence

    +
    +

    Classes

    + +

    Enums

    + +

    Exceptions

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/package-summary.html b/website/docs/full_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..66779c8 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,291 @@ + + + + + +compbio.data.sequence + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
    + +
    + + +
    + +
    +

    Package compbio.data.sequence

    +
    +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    +
    +

    See: Description

    +
    +
    + + + + +

    Package compbio.data.sequence Description

    +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services.
    +
    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Petr Troshin
    +
    +
    + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/data/sequence/package-tree.html b/website/docs/full_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..126a630 --- /dev/null +++ b/website/docs/full_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,181 @@ + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + +
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    Hierarchy For Package compbio.data.sequence

    +Package Hierarchies: + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/AsyncExecutor.html b/website/docs/full_javadoc/compbio/engine/AsyncExecutor.html new file mode 100644 index 0000000..ec19ba4 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/AsyncExecutor.html @@ -0,0 +1,360 @@ + + + + + +AsyncExecutor + + + + + + + + +
    + + +
    Skip navigation links
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    + +
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    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
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      • +
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      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.engine
    +

    Interface AsyncExecutor

    +
    +
    +
    +
      +
    • +
      +
      All Known Implementing Classes:
      +
      AsyncClusterRunner, AsyncJobRunner, AsyncLocalRunner
      +
      +
      +
      +
      public interface AsyncExecutor
      +
      An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface. + Implementation agnostic. Executables can be run either locally to the JVM or on the cluster.
      +
      +
      Author:
      +
      pvtroshin + Date October 2009
      +
      +
      • +
    +
    +
    +
      +
    • + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          submitJob

          +
          java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                    throws JobSubmissionException
          +
          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue.
          +
          +
          Returns:
          +
          unique job identifier
          +
          Throws:
          +
          JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
          +
          +
          • +
        + + + +
          +
        • +

          getResults

          +
          ConfiguredExecutable<?> getResults(java.lang.String jobId)
+                            throws ResultNotAvailableException
          +
          Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation.
          +
          +
          Parameters:
          +
          jobId - job identifier obtained at the job submission
          +
          Returns:
          +
          ConfiguredExecutable object from which result can be obtained
          +
          Throws:
          +
          ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
          +
          +
          • +
        + + + +
          +
        • +

          getWorkDirectory

          +
          java.lang.String getWorkDirectory(java.lang.String jobId)
          +
          +
          Parameters:
          +
          jobId - unique job identifier
          +
          Returns:
          +
          task working directory
          +
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          boolean cleanup(java.lang.String jobId)
          +
          Remove all files and a job directory for a jobid.
          +
          +
          Parameters:
          +
          jobId -
          +
          Returns:
          +
          true if job directory was successfully removed, false otherwise.
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          boolean cancelJob(java.lang.String jobId)
          +
          Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.
          +
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          JobStatus getJobStatus(java.lang.String jobId)
          +
          Query the status of the job
          +
          +
          Parameters:
          +
          String - jobId - unique job identifier
          +
          Returns:
          +
          The JobStatus object representing the status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/Cleaner.html b/website/docs/full_javadoc/compbio/engine/Cleaner.html new file mode 100644 index 0000000..bc2c8a9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/Cleaner.html @@ -0,0 +1,361 @@ + + + + + +Cleaner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class Cleaner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.Cleaner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Cleaner
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Cleaner() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleandeleteAllFiles(java.lang.String directory) 
        static booleandeleteDirectory(java.lang.String directory) 
        static booleandeleteFiles(ConfiguredExecutable<?> exec) +
        This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty)
        +
        (package private) static booleanremoveFile(java.lang.String filename) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Cleaner

          +
          public Cleaner()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          deleteFiles

          +
          public static boolean deleteFiles(ConfiguredExecutable<?> exec)
          +
          This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty)
          +
          +
          Parameters:
          +
          workDirectory -
          +
          files -
          +
          Returns:
          +
          This method returns true if all files specified by List files + were successfully removed, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          removeFile

          +
          static boolean removeFile(java.lang.String filename)
          +
          • +
        + + + +
          +
        • +

          deleteAllFiles

          +
          public static boolean deleteAllFiles(java.lang.String directory)
          +
          • +
        + + + +
          +
        • +

          deleteDirectory

          +
          public static boolean deleteDirectory(java.lang.String directory)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/ClusterJobId.html b/website/docs/full_javadoc/compbio/engine/ClusterJobId.html new file mode 100644 index 0000000..4875bb3 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/ClusterJobId.html @@ -0,0 +1,342 @@ + + + + + +ClusterJobId + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class ClusterJobId

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.ClusterJobId
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public class ClusterJobId
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.StringjobId 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ClusterJobId(java.lang.String jobId) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleanequals(java.lang.Object obj) 
        java.lang.StringgetJobId() 
        inthashCode() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobId

          +
          final java.lang.String jobId
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClusterJobId

          +
          public ClusterJobId(java.lang.String jobId)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/Configurator.html b/website/docs/full_javadoc/compbio/engine/Configurator.html new file mode 100644 index 0000000..cef2617 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/Configurator.html @@ -0,0 +1,630 @@ + + + + + +Configurator + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class Configurator

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.Configurator
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Configurator
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/FilePuller.html b/website/docs/full_javadoc/compbio/engine/FilePuller.html new file mode 100644 index 0000000..c858a76 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/FilePuller.html @@ -0,0 +1,718 @@ + + + + + +FilePuller + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class FilePuller

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.FilePuller
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Comparable<java.util.concurrent.Delayed>, java.util.concurrent.Delayed
      +
      +
      +
      +
      public class FilePuller
+extends java.lang.Object
+implements java.util.concurrent.Delayed
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) intchunkSize 
        private static longdefaultDelay 
        (package private) longdelay 
        private java.io.Filefile 
        private longlastAccessTime 
        private static org.apache.log4j.Loggerlog 
        private compbio.util.FileWatcherwatcher 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private FilePuller(java.lang.String file) 
        private FilePuller(java.lang.String file, + int size) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        intcompareTo(java.util.concurrent.Delayed o) 
        voiddisconnect() 
        (package private) booleandisconnected() 
        booleanequals(java.lang.Object obj) 
        longgetDelay(java.util.concurrent.TimeUnit unit) 
        (package private) longgetDelayValue(java.util.concurrent.TimeUnit unit) 
        java.lang.StringgetFile() 
        bytegetProgress() 
        inthashCode() 
        booleanhasMoreData() 
        private voidinit() 
        voidinitPull() 
        booleanisFileCreated() 
        static FilePullernewFilePuller(java.lang.String file, + int chunkSize) 
        static FilePullernewProgressPuller(java.lang.String file) +
        Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more.
        +
        ChunkHolderpull(long position) 
        (package private) static java.lang.StringremoveInvalidXMLCharacters(java.lang.String str) +
        This method ensures that the output String has only valid XML unicode + characters as specified by the XML 1.0 standard.
        +
        (package private) voidsetDelay(long delay, + java.util.concurrent.TimeUnit unit) 
        java.lang.StringtoString() 
        voidwaitForFile(long maxWaitSeconds) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          defaultDelay

          +
          private static long defaultDelay
          +
          • +
        + + + +
          +
        • +

          file

          +
          private final java.io.File file
          +
          • +
        + + + +
          +
        • +

          lastAccessTime

          +
          private long lastAccessTime
          +
          • +
        + + + +
          +
        • +

          watcher

          +
          private compbio.util.FileWatcher watcher
          +
          • +
        + + + +
          +
        • +

          chunkSize

          +
          final int chunkSize
          +
          • +
        + + + +
          +
        • +

          delay

          +
          long delay
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          FilePuller

          +
          private FilePuller(java.lang.String file,
+                   int size)
          +
          • +
        + + + +
          +
        • +

          FilePuller

          +
          private FilePuller(java.lang.String file)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newFilePuller

          +
          public static FilePuller newFilePuller(java.lang.String file,
+                                       int chunkSize)
          +
          • +
        + + + +
          +
        • +

          newProgressPuller

          +
          public static FilePuller newProgressPuller(java.lang.String file)
          +
          Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more. Intended to be used in conjunction with a tool + which output progress as a percent value from 0 to 100. In any cases + progress could not be more than the largest byte value 255.
          +
          +
          Parameters:
          +
          file -
          +
          Returns:
          +
          instance
          +
          +
          • +
        + + + +
          +
        • +

          pull

          +
          public ChunkHolder pull(long position)
+                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          removeInvalidXMLCharacters

          +
          static java.lang.String removeInvalidXMLCharacters(java.lang.String str)
          +
          This method ensures that the output String has only valid XML unicode + characters as specified by the XML 1.0 standard. For reference, please + see the standard.
          +
          +
          Parameters:
          +
          The - String whose non-valid characters we want to remove.
          +
          Returns:
          +
          The in String, stripped of non-valid characters.
          +
          +
          • +
        + + + +
          +
        • +

          initPull

          +
          public void initPull()
          +
          • +
        + + + +
          +
        • +

          getFile

          +
          public java.lang.String getFile()
          +
          • +
        + + + +
          +
        • +

          isFileCreated

          +
          public boolean isFileCreated()
          +
          • +
        + + + +
          +
        • +

          waitForFile

          +
          public void waitForFile(long maxWaitSeconds)
          +
          • +
        + + + +
          +
        • +

          hasMoreData

          +
          public boolean hasMoreData()
+                    throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          init

          +
          private void init()
          +
          • +
        + + + +
          +
        • +

          compareTo

          +
          public int compareTo(java.util.concurrent.Delayed o)
          +
          +
          Specified by:
          +
          compareTo in interface java.lang.Comparable<java.util.concurrent.Delayed>
          +
          +
          • +
        + + + +
          +
        • +

          getDelay

          +
          public long getDelay(java.util.concurrent.TimeUnit unit)
          +
          +
          Specified by:
          +
          getDelay in interface java.util.concurrent.Delayed
          +
          +
          • +
        + + + +
          +
        • +

          setDelay

          +
          void setDelay(long delay,
+              java.util.concurrent.TimeUnit unit)
          +
          • +
        + + + +
          +
        • +

          getDelayValue

          +
          long getDelayValue(java.util.concurrent.TimeUnit unit)
          +
          • +
        + + + +
          +
        • +

          disconnect

          +
          public void disconnect()
          +
          • +
        + + + +
          +
        • +

          disconnected

          +
          boolean disconnected()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getProgress

          +
          public byte getProgress()
+                 throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/Job.html b/website/docs/full_javadoc/compbio/engine/Job.html new file mode 100644 index 0000000..ea1665e --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/Job.html @@ -0,0 +1,445 @@ + + + + + +Job + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class Job

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.Job
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public final class Job
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Job

          +
          public Job(java.lang.String taskId,
+           java.lang.String jobId,
+           ConfiguredExecutable<?> cexecutable)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getTaskId

          +
          public java.lang.String getTaskId()
          +
          • +
        + + + + + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getByTaskId

          +
          public static Job getByTaskId(java.lang.String taskId,
+                              java.util.List<Job> jobs)
          +
          • +
        + + + +
          +
        • +

          getByJobId

          +
          public static Job getByJobId(java.lang.String jobId,
+                             java.util.List<Job> jobs)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/LoadBalancer.html b/website/docs/full_javadoc/compbio/engine/LoadBalancer.html new file mode 100644 index 0000000..5079fae --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/LoadBalancer.html @@ -0,0 +1,333 @@ + + + + + +LoadBalancer + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class LoadBalancer

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.LoadBalancer
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class LoadBalancer
+extends java.lang.Object
      +
      This class decides where to execute the job. If the local engine is enabled + in the configuration file and it has free threads and the size of the tasks + permits the local execution, then the local execution will be favoured.
      +
      +
      Version:
      +
      1.0 March 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/ProgressGetter.html b/website/docs/full_javadoc/compbio/engine/ProgressGetter.html new file mode 100644 index 0000000..4cf5d37 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/ProgressGetter.html @@ -0,0 +1,358 @@ + + + + + +ProgressGetter + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class ProgressGetter

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.ProgressGetter
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ProgressGetter
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ProgressGetter() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static bytegetProgress(java.lang.String progressFile) 
        (package private) static bytegetProgress(java.lang.String progressFile, + long delay, + java.util.concurrent.TimeUnit unit) 
        static ChunkHolderpull(java.lang.String file, + long position) 
        (package private) static ChunkHolderpull(java.lang.String file, + long position, + long delay, + java.util.concurrent.TimeUnit unit) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ProgressGetter

          +
          public ProgressGetter()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          pull

          +
          static final ChunkHolder pull(java.lang.String file,
+                              long position,
+                              long delay,
+                              java.util.concurrent.TimeUnit unit)
          +
          • +
        + + + +
          +
        • +

          pull

          +
          public static final ChunkHolder pull(java.lang.String file,
+                                     long position)
          +
          • +
        + + + +
          +
        • +

          getProgress

          +
          static byte getProgress(java.lang.String progressFile,
+                        long delay,
+                        java.util.concurrent.TimeUnit unit)
          +
          • +
        + + + +
          +
        • +

          getProgress

          +
          public static final byte getProgress(java.lang.String progressFile)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/PulledFileCache.html b/website/docs/full_javadoc/compbio/engine/PulledFileCache.html new file mode 100644 index 0000000..f048c2f --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/PulledFileCache.html @@ -0,0 +1,395 @@ + + + + + +PulledFileCache + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class PulledFileCache

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.PulledFileCache
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class PulledFileCache
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static java.util.Queue<FilePuller>CACHE 
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        PulledFileCache() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static voidclear() 
        static FilePullerget(java.lang.String fileName) 
        (package private) static intgetSize() 
        (package private) static voidprint() 
        static booleanput(FilePuller fpuller) +
        This method allows duplicates to be added.
        +
        private static voidsweep() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          CACHE

          +
          private static final java.util.Queue<FilePuller> CACHE
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PulledFileCache

          +
          public PulledFileCache()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          get

          +
          public static FilePuller get(java.lang.String fileName)
          +
          • +
        + + + +
          +
        • +

          put

          +
          public static boolean put(FilePuller fpuller)
          +
          This method allows duplicates to be added. This is a responsibility of + the called to ensure this will not happen!
          +
          +
          Parameters:
          +
          fpuller -
          +
          Returns:
          +
          true if the same filepooler is already in cache
          +
          +
          • +
        + + + +
          +
        • +

          sweep

          +
          private static void sweep()
          +
          • +
        + + + +
          +
        • +

          getSize

          +
          static int getSize()
          +
          • +
        + + + +
          +
        • +

          clear

          +
          static void clear()
          +
          • +
        + + + +
          +
        • +

          print

          +
          static void print()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/SubmissionManager.html b/website/docs/full_javadoc/compbio/engine/SubmissionManager.html new file mode 100644 index 0000000..c27b5ce --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/SubmissionManager.html @@ -0,0 +1,368 @@ + + + + + +SubmissionManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine
    +

    Class SubmissionManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.SubmissionManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class SubmissionManager
+extends java.lang.Object
      +
      Submit jobs for execution
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          submittedTasks

          +
          static final java.util.Map<java.lang.String,java.util.concurrent.Future<ConfiguredExecutable<?>>> submittedTasks
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SubmissionManager

          +
          private SubmissionManager()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/SyncExecutor.html b/website/docs/full_javadoc/compbio/engine/SyncExecutor.html new file mode 100644 index 0000000..e8a4783 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/SyncExecutor.html @@ -0,0 +1,342 @@ + + + + + +SyncExecutor + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.engine
    +

    Interface SyncExecutor

    +
    +
    +
    +
      +
    • +
      +
      All Known Implementing Classes:
      +
      ClusterRunner, JobRunner, LocalRunner
      +
      +
      +
      +
      public interface SyncExecutor
      +
      Synchronous executor, is an engine to run the Executable synchronously.
      +
      +
      Author:
      +
      pvtroshin + Date October 2009
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          cleanup

          +
          boolean cleanup()
          +
          Clean up after the job
          +
          +
          Returns:
          +
          true if all the files created by this job have been removed successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          waitForResult

          +
          ConfiguredExecutable<?> waitForResult()
+                               throws JobExecutionException
          +
          Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe
          +
          +
          Returns:
          +
          object from wich the result can be obtained
          +
          Throws:
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          getWorkDirectory

          +
          java.lang.String getWorkDirectory()
          +
          +
          Returns:
          +
          working directory if the task
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          boolean cancelJob()
          +
          Stops running job. + Clean up is not performed.
          +
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          JobStatus getJobStatus()
          +
          Query the status of the job by its id.
          +
          +
          Returns:
          +
          - JobStatus
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/class-use/AsyncExecutor.html b/website/docs/full_javadoc/compbio/engine/class-use/AsyncExecutor.html new file mode 100644 index 0000000..f45efab --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/class-use/AsyncExecutor.html @@ -0,0 +1,247 @@ + + + + + +Uses of Interface compbio.engine.AsyncExecutor + + + + + + + + +
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    Uses of Interface
    compbio.engine.AsyncExecutor

    +
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/class-use/Cleaner.html b/website/docs/full_javadoc/compbio/engine/class-use/Cleaner.html new file mode 100644 index 0000000..7f24e58 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/class-use/Cleaner.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.engine.Cleaner + + + + + + + + +
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    Uses of Class
    compbio.engine.Cleaner

    +
    +
    No usage of compbio.engine.Cleaner
    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/class-use/ClusterJobId.html b/website/docs/full_javadoc/compbio/engine/class-use/ClusterJobId.html new file mode 100644 index 0000000..0cb4e77 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/class-use/ClusterJobId.html @@ -0,0 +1,216 @@ + + + + + +Uses of Class compbio.engine.ClusterJobId + + + + + + + + +
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    Uses of Class
    compbio.engine.ClusterJobId

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    compbio.engine.client
    +

    Class CommandBuilder.Parameter

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.CommandBuilder.Parameter
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Enclosing class:
      +
      CommandBuilder<T>
      +
      +
      +
      +
      static class CommandBuilder.Parameter
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static intFIRST 
        private static intLAST 
        (package private) java.lang.Stringname 
        private intposition 
        (package private) java.lang.Stringvalue 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        Parameter() 
        Parameter(java.lang.String name) 
        Parameter(java.lang.String name, + java.lang.String value) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleanequals(java.lang.Object obj) 
        inthashCode() 
        (package private) booleanisFirst() 
        (package private) booleanisLast() 
        (package private) voidsetAtPosition(int position) 
        (package private) voidsetFirst() 
        (package private) voidsetLast() 
        (package private) java.lang.StringtoCommand(java.lang.String separator) 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + + + + + +
          +
        • +

          position

          +
          private int position
          +
          • +
        + + + +
          +
        • +

          name

          +
          java.lang.String name
          +
          • +
        + + + +
          +
        • +

          value

          +
          java.lang.String value
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Parameter

          +
          Parameter()
          +
          • +
        + + + +
          +
        • +

          Parameter

          +
          Parameter(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          Parameter

          +
          Parameter(java.lang.String name,
+          java.lang.String value)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          setLast

          +
          void setLast()
          +
          • +
        + + + +
          +
        • +

          setFirst

          +
          void setFirst()
          +
          • +
        + + + +
          +
        • +

          setAtPosition

          +
          void setAtPosition(int position)
          +
          • +
        + + + +
          +
        • +

          isLast

          +
          boolean isLast()
          +
          • +
        + + + +
          +
        • +

          isFirst

          +
          boolean isFirst()
          +
          • +
        + + + +
          +
        • +

          toCommand

          +
          java.lang.String toCommand(java.lang.String separator)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
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    Skip navigation links
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/CommandBuilder.html b/website/docs/full_javadoc/compbio/engine/client/CommandBuilder.html new file mode 100644 index 0000000..ded98c6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/CommandBuilder.html @@ -0,0 +1,707 @@ + + + + + +CommandBuilder + + + + + + + + +
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    +
    compbio.engine.client
    +

    Class CommandBuilder<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.CommandBuilder<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class CommandBuilder<T>
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + + + + + +
          +
        • +

          nameValueSeparator

          +
          java.lang.String nameValueSeparator
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CommandBuilder

          +
          private CommandBuilder()
          +
          • +
        + + + +
          +
        • +

          CommandBuilder

          +
          public CommandBuilder(java.lang.String nameValueSeparator)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          addParams

          +
          public void addParams(java.util.List<java.lang.String> params)
          +
          • +
        + + + +
          +
        • +

          setParams

          +
          public void setParams(java.util.List<java.lang.String> params)
          +
          • +
        + + + + + + + +
          +
        • +

          isCombinedValue

          +
          boolean isCombinedValue(java.lang.String param)
          +
          • +
        + + + +
          +
        • +

          hasParam

          +
          public boolean hasParam(java.lang.String paramName)
          +
          • +
        + + + +
          +
        • +

          getName

          +
          java.lang.String getName(java.lang.String param)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          java.lang.String getValue(java.lang.String param)
          +
          • +
        + + + +
          +
        • +

          setFirst

          +
          public boolean setFirst(java.lang.String param)
          +
          • +
        + + + +
          +
        • +

          setParam

          +
          public boolean setParam(java.lang.String param)
          +
          • +
        + + + + + + + +
          +
        • +

          setLast

          +
          public boolean setLast(java.lang.String paramName)
          +
          • +
        + + + +
          +
        • +

          setLast

          +
          public boolean setLast(java.lang.String paramName,
+                       java.lang.String paramValue)
          +
          • +
        + + + +
          +
        • +

          getParamValue

          +
          public java.lang.String getParamValue(java.lang.String paramName)
          +
          • +
        + + + +
          +
        • +

          removeParam

          +
          public boolean removeParam(java.lang.String paramName)
          +
          • +
        + + + +
          +
        • +

          setParam

          +
          public boolean setParam(java.lang.String paramName,
+                        java.lang.String paramValue)
          +
          • +
        + + + +
          +
        • +

          getCommands

          +
          public java.util.List<java.lang.String> getCommands()
          +
          • +
        + + + +
          +
        • +

          getCommandString

          +
          public java.lang.String getCommandString()
          +
          • +
        + + + +
          +
        • +

          parameterToString

          +
          java.util.List<java.lang.String> parameterToString(java.util.List<CommandBuilder.Parameter> parameters)
          +
          • +
        + + + +
          +
        • +

          newCommandBuilder

          +
          public static <T> CommandBuilder<T> newCommandBuilder(java.util.List<? extends Option<T>> arguments,
+                                                      java.lang.String nameValueSeparator)
          +
          This produces the same result as getCommands method. The only difference + is that it accepts a List of Options as an input
          +
          +
          Parameters:
          +
          arguments -
          +
          Returns:
          +
          the instance of the CommandBuilder
          +
          +
          • +
        + + + +
          +
        • +

          size

          +
          public int size()
          +
          • +
        + + + +
          +
        • +

          isWhiteSpaceSeparator

          +
          boolean isWhiteSpaceSeparator()
          +
          • +
        + + + + + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/docs/full_javadoc/compbio/engine/client/ConfExecutable.html new file mode 100644 index 0000000..7fec7fa --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/ConfExecutable.html @@ -0,0 +1,982 @@ + + + + + +ConfExecutable + + + + + + + + +
    + + +
    Skip navigation links
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    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class ConfExecutable<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.ConfExecutable<T>
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
    + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/ConfiguredExecutable.html b/website/docs/full_javadoc/compbio/engine/client/ConfiguredExecutable.html new file mode 100644 index 0000000..f6d07fb --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/ConfiguredExecutable.html @@ -0,0 +1,415 @@ + + + + + +ConfiguredExecutable + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Interface ConfiguredExecutable<T>

    +
    +
    +
    + +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/EngineUtil.html b/website/docs/full_javadoc/compbio/engine/client/EngineUtil.html new file mode 100644 index 0000000..1801a41 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/EngineUtil.html @@ -0,0 +1,576 @@ + + + + + +EngineUtil + + + + + + + + +
    + + +
    Skip navigation links
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    +
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    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class EngineUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.EngineUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class EngineUtil
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        private static compbio.util.PropertyHelperph 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        EngineUtil() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.StringconvertToAbsolute(java.lang.String relativePath) 
        static java.lang.StringgetCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) 
        static java.lang.StringgetExecProperty(java.lang.String propertySpec, + java.lang.Class<?> clazz) 
        static java.lang.StringgetExecProperty(java.lang.String propertySpec, + Executable<?> exec) 
        static java.lang.StringgetFullPath(java.lang.String workDirectory, + java.lang.String fileName) 
        static java.lang.StringgetJava() +
        Returns the absolute path to the Java executable from JAVA_HOME
        +
        static <T> LimitsManager<T>getLimits(java.lang.Class<T> clazz) +
        For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
        +
        static Executable.ExecProvidergetSupportedRuntimes(java.lang.Class<?> clazz) 
        static booleanisJavaLibrary(java.lang.Class<?> clazz) +
        Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
        +
        static booleanisMarked(java.lang.String workDirectory, + JobStatus marker) 
        static booleanisValidJobId(java.lang.String key) 
        static ConfiguredExecutable<?>loadExecutable(java.lang.String taskId) 
        static java.util.Map<java.lang.String,java.lang.String>mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, + java.util.Map<java.lang.String,java.lang.String> variables) 
        static voidwriteFile(java.lang.String workDirectory, + java.lang.String fileAndEventName, + java.lang.String content, + boolean override) 
        static booleanwriteMarker(java.lang.String workDirectory, + JobStatus fileType) 
        static voidwriteStatFile(java.lang.String workDirectory, + java.lang.String fileAndEventName) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          ph

          +
          private static final compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          EngineUtil

          +
          public EngineUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isValidJobId

          +
          public static boolean isValidJobId(java.lang.String key)
          +
          • +
        + + + +
          +
        • +

          writeStatFile

          +
          public static void writeStatFile(java.lang.String workDirectory,
+                                 java.lang.String fileAndEventName)
          +
          • +
        + + + +
          +
        • +

          writeFile

          +
          public static void writeFile(java.lang.String workDirectory,
+                             java.lang.String fileAndEventName,
+                             java.lang.String content,
+                             boolean override)
          +
          • +
        + + + +
          +
        • +

          writeMarker

          +
          public static final boolean writeMarker(java.lang.String workDirectory,
+                                        JobStatus fileType)
          +
          • +
        + + + +
          +
        • +

          isMarked

          +
          public static boolean isMarked(java.lang.String workDirectory,
+                               JobStatus marker)
          +
          • +
        + + + +
          +
        • +

          mergeEnvVariables

          +
          public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
+                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)
          +
          • +
        + + + +
          +
        • +

          convertToAbsolute

          +
          public static java.lang.String convertToAbsolute(java.lang.String relativePath)
          +
          • +
        + + + +
          +
        • +

          getExecProperty

          +
          public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               Executable<?> exec)
          +
          • +
        + + + +
          +
        • +

          getExecProperty

          +
          public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               java.lang.Class<?> clazz)
          +
          • +
        + + + +
          +
        • +

          getFullPath

          +
          public static java.lang.String getFullPath(java.lang.String workDirectory,
+                                           java.lang.String fileName)
          +
          • +
        + + + +
          +
        • +

          getCommand

          +
          public static java.lang.String getCommand(Executable.ExecProvider provider,
+                                          java.lang.Class<?> clazz)
          +
          • +
        + + + +
          +
        • +

          isJavaLibrary

          +
          public static boolean isJavaLibrary(java.lang.Class<?> clazz)
          +
          Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
          +
          +
          Parameters:
          +
          clazz -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          getJava

          +
          public static java.lang.String getJava()
          +
          Returns the absolute path to the Java executable from JAVA_HOME
          +
          +
          Returns:
          +
          returns the absolute path to the Java executable from JAVA_HOME
          +
          +
          • +
        + + + +
          +
        • +

          getSupportedRuntimes

          +
          public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)
          +
          • +
        + + + + + + + +
          +
        • +

          getLimits

          +
          public static <T> LimitsManager<T> getLimits(java.lang.Class<T> clazz)
          +
          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
          +
          +
          Parameters:
          +
          rconfig -
          +
          Returns:
          +
          public static List toOptionString(RunnerConfig + rconfig) { String option = ""; List options = new + ArrayList(); for (Parameter par : + rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) + { option = par.getOptionName(); } else { option = + par.getOptionName() + "=" + par.getPossibleValues().get(0); } // + separate options options.add(option); } return options; }
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/docs/full_javadoc/compbio/engine/client/EnvVariableProcessor.html new file mode 100644 index 0000000..4ae3f36 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/EnvVariableProcessor.html @@ -0,0 +1,481 @@ + + + + + +EnvVariableProcessor + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class EnvVariableProcessor

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.EnvVariableProcessor
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class EnvVariableProcessor
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static java.lang.Stringfasta4mafft 
        private static java.lang.Stringiupred_path 
        private static org.apache.log4j.Loggerlog 
        private static java.lang.Stringmafft_binaries 
        private static java.lang.StringNEXT_ENV_PROPERTY_DELIMITER 
        static java.lang.StringPATH +
        Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable
        +
        private static java.lang.StringPROP_NAME_VALUE_SEPARATOR 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static booleancontainsMultipleVariables(java.lang.String property) 
        (package private) static java.lang.String[]getEnvVariableList(java.lang.String property) 
        (package private) static java.lang.StringgetEnvVariableName(java.lang.String property) 
        static java.util.Map<java.lang.String,java.lang.String>getEnvVariables(java.lang.String property, + java.lang.Class<?> clazz) 
        (package private) static java.lang.StringgetEnvVariableValue(java.lang.String property) 
        (package private) static booleanisValidEnvVariableProperty(java.lang.String property) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          PATH

          +
          public static final java.lang.String PATH
          +
          Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          PROP_NAME_VALUE_SEPARATOR

          +
          private static final java.lang.String PROP_NAME_VALUE_SEPARATOR
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          NEXT_ENV_PROPERTY_DELIMITER

          +
          private static final java.lang.String NEXT_ENV_PROPERTY_DELIMITER
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          mafft_binaries

          +
          private static final java.lang.String mafft_binaries
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          fasta4mafft

          +
          private static final java.lang.String fasta4mafft
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          iupred_path

          +
          private static final java.lang.String iupred_path
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          EnvVariableProcessor

          +
          public EnvVariableProcessor()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          containsMultipleVariables

          +
          static boolean containsMultipleVariables(java.lang.String property)
          +
          • +
        + + + +
          +
        • +

          getEnvVariableList

          +
          static java.lang.String[] getEnvVariableList(java.lang.String property)
          +
          • +
        + + + +
          +
        • +

          getEnvVariableName

          +
          static java.lang.String getEnvVariableName(java.lang.String property)
          +
          • +
        + + + +
          +
        • +

          getEnvVariableValue

          +
          static java.lang.String getEnvVariableValue(java.lang.String property)
          +
          • +
        + + + +
          +
        • +

          isValidEnvVariableProperty

          +
          static boolean isValidEnvVariableProperty(java.lang.String property)
          +
          • +
        + + + +
          +
        • +

          getEnvVariables

          +
          public static java.util.Map<java.lang.String,java.lang.String> getEnvVariables(java.lang.String property,
+                                                                               java.lang.Class<?> clazz)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/docs/full_javadoc/compbio/engine/client/Executable.ExecProvider.html new file mode 100644 index 0000000..1fbd779 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/Executable.ExecProvider.html @@ -0,0 +1,357 @@ + + + + + +Executable.ExecProvider + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Enum Executable.ExecProvider

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Any 
        Cluster 
        Local 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static Executable.ExecProvidervalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static Executable.ExecProvider[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static Executable.ExecProvider[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (Executable.ExecProvider c : Executable.ExecProvider.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static Executable.ExecProvider valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/Executable.html b/website/docs/full_javadoc/compbio/engine/client/Executable.html new file mode 100644 index 0000000..6f871b9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/Executable.html @@ -0,0 +1,405 @@ + + + + + +Executable + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Interface Executable<T>

    +
    +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          addParameters

          +
          Executable<T> addParameters(java.util.List<java.lang.String> parameters)
          +
          Adds parameter to the list of parameters for a native executable
          +
          +
          Parameters:
          +
          parameters -
          +
          Returns:
          +
          this Executable
          +
          +
          • +
        + + + +
          +
        • +

          getCreatedFiles

          +
          @Deprecated
+java.util.List<java.lang.String> getCreatedFiles()
          +
          Deprecated. 
          +
          • +
        + + + +
          +
        • +

          getInput

          +
          java.lang.String getInput()
          +
          • +
        + + + +
          +
        • +

          getOutput

          +
          java.lang.String getOutput()
          +
          • +
        + + + +
          +
        • +

          getError

          +
          java.lang.String getError()
          +
          • +
        + + + + + + + + + + + + + + + +
          +
        • +

          getLimit

          +
          Limit<T> getLimit(java.lang.String presetName)
          +
          • +
        + + + + + + + +
          +
        • +

          getClusterJobSettings

          +
          java.lang.String getClusterJobSettings()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/PathValidator.html b/website/docs/full_javadoc/compbio/engine/client/PathValidator.html new file mode 100644 index 0000000..3b865b1 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/PathValidator.html @@ -0,0 +1,366 @@ + + + + + +PathValidator + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class PathValidator

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.PathValidator
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class PathValidator
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        PathValidator() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleanisAbsolutePath(java.lang.String path) +
        Whether a certain path is absolute or not is operation system dependent!
        +
        static booleanisValidDirectory(java.lang.String directory) 
        static booleanisValidExecutable(java.lang.String command) 
        static voidvalidateDirectory(java.lang.String workDirectory) 
        static voidvalidateExecutable(java.lang.String command) 
        static voidvalidatePathNames(java.util.List<java.lang.String> filenames, + java.lang.String type) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PathValidator

          +
          public PathValidator()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isValidExecutable

          +
          public static boolean isValidExecutable(java.lang.String command)
          +
          • +
        + + + +
          +
        • +

          validateExecutable

          +
          public static void validateExecutable(java.lang.String command)
+                               throws java.lang.IllegalArgumentException
          +
          +
          Throws:
          +
          java.lang.IllegalArgumentException
          +
          +
          • +
        + + + +
          +
        • +

          isValidDirectory

          +
          public static boolean isValidDirectory(java.lang.String directory)
          +
          • +
        + + + +
          +
        • +

          validatePathNames

          +
          public static void validatePathNames(java.util.List<java.lang.String> filenames,
+                                     java.lang.String type)
+                              throws java.lang.IllegalArgumentException
          +
          +
          Parameters:
          +
          filenames -
          +
          type - - merely a string to be added to error message to explain what + type of files are lacking
          +
          Throws:
          +
          java.lang.IllegalArgumentException
          +
          +
          • +
        + + + +
          +
        • +

          isAbsolutePath

          +
          public static boolean isAbsolutePath(java.lang.String path)
          +
          Whether a certain path is absolute or not is operation system dependent!
          +
          +
          Parameters:
          +
          path -
          +
          Returns:
          +
          true is the path is absolute, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          validateDirectory

          +
          public static void validateDirectory(java.lang.String workDirectory)
+                              throws java.lang.IllegalArgumentException
          +
          +
          Throws:
          +
          java.lang.IllegalArgumentException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/docs/full_javadoc/compbio/engine/client/PipedExecutable.html new file mode 100644 index 0000000..79b185c --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/PipedExecutable.html @@ -0,0 +1,230 @@ + + + + + +PipedExecutable + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Interface PipedExecutable<T>

    +
    +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T -
      +
      +
      +
      All Superinterfaces:
      +
      Executable<T>
      +
      +
      +
      All Known Subinterfaces:
      +
      ConfiguredExecutable<T>
      +
      +
      +
      All Known Implementing Classes:
      +
      ConfExecutable, Disembl, GlobPlot, GLprobs, Mafft, MSAprobs, Probcons, RNAalifold, Tcoffee
      +
      +
      +
      +
      public interface PipedExecutable<T>
+extends Executable<T>
      +
      This is a marker interface to indicate that the output of the process must be + captured. It is in generally better for the process to manage its own + streams, but some executables are not capable of this thus require different + handling
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/docs/full_javadoc/compbio/engine/client/RunConfiguration.html new file mode 100644 index 0000000..3790ce3 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/RunConfiguration.html @@ -0,0 +1,661 @@ + + + + + +RunConfiguration + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class RunConfiguration

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.RunConfiguration
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class RunConfiguration
+extends java.lang.Object
      +
      Value class for persisting ConfExecutable instances
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          rconfigFile

          +
          public static final java.lang.String rconfigFile
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          taskId

          +
          java.lang.String taskId
          +
          Task ID (is a part of workDirectory but extracting it from there could be + tricky)
          +
          • +
        + + + +
          +
        • +

          workDirectory

          +
          java.lang.String workDirectory
          +
          Working directory
          +
          • +
        + + + + + + + +
          +
        • +

          error

          +
          private java.lang.String error
          +
          Input option
          +
          • +
        + + + +
          +
        • +

          output

          +
          private java.lang.String output
          +
          Output
          +
          • +
        + + + +
          +
        • +

          input

          +
          private java.lang.String input
          +
          Input
          +
          • +
        + + + +
          +
        • +

          runnerClassName

          +
          java.lang.String runnerClassName
          +
          Runner class name
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RunConfiguration

          +
          public RunConfiguration()
          +
          • +
        + + + +
          +
        • +

          RunConfiguration

          +
          public RunConfiguration(ConfExecutable<?> cexec)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          write

          +
          public static boolean write(RunConfiguration rconf)
+                     throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          load

          +
          public static RunConfiguration load(java.io.InputStream input)
+                             throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          setOutput

          +
          public void setOutput(java.lang.String output)
          +
          • +
        + + + + + + + +
          +
        • +

          setParameters

          +
          public void setParameters(CommandBuilder<?> parameters)
          +
          • +
        + + + +
          +
        • +

          getOutput

          +
          public java.lang.String getOutput()
          +
          • +
        + + + +
          +
        • +

          setError

          +
          public void setError(java.lang.String error)
          +
          • +
        + + + +
          +
        • +

          getError

          +
          public java.lang.String getError()
          +
          • +
        + + + +
          +
        • +

          getInput

          +
          public java.lang.String getInput()
          +
          • +
        + + + +
          +
        • +

          setInput

          +
          public void setInput(java.lang.String input)
          +
          • +
        + + + +
          +
        • +

          getRunnerClassName

          +
          public java.lang.String getRunnerClassName()
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          strEquals

          +
          private boolean strEquals(java.lang.String value,
+                          java.lang.String other)
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/docs/full_javadoc/compbio/engine/client/SkeletalExecutable.html new file mode 100644 index 0000000..a98edbd --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/SkeletalExecutable.html @@ -0,0 +1,897 @@ + + + + + +SkeletalExecutable + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class SkeletalExecutable<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.SkeletalExecutable<T>
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          ph

          +
          protected static final compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + + + + + + + + + + + + + + + + + +
          +
        • +

          inputFile

          +
          protected java.lang.String inputFile
          +
          • +
        + + + +
          +
        • +

          outputFile

          +
          protected java.lang.String outputFile
          +
          • +
        + + + +
          +
        • +

          errorFile

          +
          protected java.lang.String errorFile
          +
          • +
        + + + +
          +
        • +

          isInputSet

          +
          private boolean isInputSet
          +
          • +
        + + + +
          +
        • +

          isOutputSet

          +
          private boolean isOutputSet
          +
          • +
        + + + +
          +
        • +

          isErrorSet

          +
          private boolean isErrorSet
          +
          • +
        + + + +
          +
        • +

          cbuilder

          +
          protected CommandBuilder<T> cbuilder
          +
          This has to allow duplicate parameters as different options may have the + same value e.g. Muscle -weight1 clustalw -weight2 clustalw
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SkeletalExecutable

          +
          public SkeletalExecutable()
          +
          • +
        + + + +
          +
        • +

          SkeletalExecutable

          +
          public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + + + + + + + + + + + + + +
          +
        • +

          addParameters

          +
          public Executable<T> addParameters(java.util.List<java.lang.String> parameters)
          +
          Description copied from interface: Executable
          +
          Adds parameter to the list of parameters for a native executable
          +
          +
          Specified by:
          +
          addParameters in interface Executable<T>
          +
          Returns:
          +
          this Executable
          +
          +
          • +
        + + + +
          +
        • +

          setParameter

          +
          public Executable<T> setParameter(java.lang.String parameter)
          +
          • +
        + + + +
          +
        • +

          paramValueUpdater

          +
          void paramValueUpdater()
          +
          This is a generic method of changing values of the parameters with + properties + + This method iterates via commands for an executable finding matches from + the Executable.properties file and replacing values in CommandBuilder + with a combination of value from CommandBuilder to merge path from + properties
          +
          • +
        + + + +
          +
        • +

          getCreatedFiles

          +
          public java.util.List<java.lang.String> getCreatedFiles()
          +
          This method cannot really tell whether the files has actually been + created or not. It must be overridden as required.
          +
          +
          Specified by:
          +
          getCreatedFiles in interface Executable<T>
          +
          See Also:
          +
          Executable.getCreatedFiles()
          +
          +
          • +
        + + + +
          +
        • +

          getInput

          +
          public java.lang.String getInput()
          +
          +
          Specified by:
          +
          getInput in interface Executable<T>
          +
          +
          • +
        + + + +
          +
        • +

          isInputSet

          +
          protected boolean isInputSet()
          +
          • +
        + + + +
          +
        • +

          isOutputSet

          +
          protected boolean isOutputSet()
          +
          • +
        + + + +
          +
        • +

          isErrorSet

          +
          protected boolean isErrorSet()
          +
          • +
        + + + +
          +
        • +

          getOutput

          +
          public java.lang.String getOutput()
          +
          +
          Specified by:
          +
          getOutput in interface Executable<T>
          +
          +
          • +
        + + + +
          +
        • +

          getError

          +
          public java.lang.String getError()
          +
          +
          Specified by:
          +
          getError in interface Executable<T>
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + + + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getClusterCpuNum

          +
          public static int getClusterCpuNum(java.lang.Class<? extends Executable<?>> type)
          +
          +
          Returns:
          +
          number of cpus to use on the cluster or 0 if the value is undefined
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<T> getLimit(java.lang.String presetName)
          +
          +
          Specified by:
          +
          getLimit in interface Executable<T>
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getType

          +
          public abstract java.lang.Class<T> getType()
          +
          +
          Returns:
          +
          subclasses must return their type
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/client/Util.html b/website/docs/full_javadoc/compbio/engine/client/Util.html new file mode 100644 index 0000000..b81f59c --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/client/Util.html @@ -0,0 +1,576 @@ + + + + + +Util + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.client
    +

    Class Util

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.client.Util
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class Util
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        private static compbio.util.PropertyHelperph 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Util() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.StringconvertToAbsolute(java.lang.String relativePath) 
        static java.lang.StringgetCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) 
        static java.lang.StringgetExecProperty(java.lang.String propertySpec, + java.lang.Class<?> clazz) 
        static java.lang.StringgetExecProperty(java.lang.String propertySpec, + Executable<?> exec) 
        static java.lang.StringgetFullPath(java.lang.String workDirectory, + java.lang.String fileName) 
        static java.lang.StringgetJava() +
        Returns the absolute path to the Java executable from JAVA_HOME
        +
        static <T> LimitsManager<T>getLimits(java.lang.Class<T> clazz) +
        For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
        +
        static Executable.ExecProvidergetSupportedRuntimes(java.lang.Class<?> clazz) 
        static booleanisJavaLibrary(java.lang.Class<?> clazz) +
        Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
        +
        static booleanisMarked(java.lang.String workDirectory, + JobStatus marker) 
        static booleanisValidJobId(java.lang.String key) 
        static ConfiguredExecutable<?>loadExecutable(java.lang.String taskId) 
        static java.util.Map<java.lang.String,java.lang.String>mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, + java.util.Map<java.lang.String,java.lang.String> variables) 
        static voidwriteFile(java.lang.String workDirectory, + java.lang.String fileAndEventName, + java.lang.String content, + boolean override) 
        static booleanwriteMarker(java.lang.String workDirectory, + JobStatus fileType) 
        static voidwriteStatFile(java.lang.String workDirectory, + java.lang.String fileAndEventName) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          ph

          +
          private static final compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Util

          +
          public Util()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isValidJobId

          +
          public static boolean isValidJobId(java.lang.String key)
          +
          • +
        + + + +
          +
        • +

          writeStatFile

          +
          public static void writeStatFile(java.lang.String workDirectory,
+                                 java.lang.String fileAndEventName)
          +
          • +
        + + + +
          +
        • +

          writeFile

          +
          public static void writeFile(java.lang.String workDirectory,
+                             java.lang.String fileAndEventName,
+                             java.lang.String content,
+                             boolean override)
          +
          • +
        + + + +
          +
        • +

          writeMarker

          +
          public static final boolean writeMarker(java.lang.String workDirectory,
+                                        JobStatus fileType)
          +
          • +
        + + + +
          +
        • +

          isMarked

          +
          public static boolean isMarked(java.lang.String workDirectory,
+                               JobStatus marker)
          +
          • +
        + + + +
          +
        • +

          mergeEnvVariables

          +
          public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
+                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)
          +
          • +
        + + + +
          +
        • +

          convertToAbsolute

          +
          public static java.lang.String convertToAbsolute(java.lang.String relativePath)
          +
          • +
        + + + +
          +
        • +

          getExecProperty

          +
          public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               Executable<?> exec)
          +
          • +
        + + + +
          +
        • +

          getExecProperty

          +
          public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               java.lang.Class<?> clazz)
          +
          • +
        + + + +
          +
        • +

          getFullPath

          +
          public static java.lang.String getFullPath(java.lang.String workDirectory,
+                                           java.lang.String fileName)
          +
          • +
        + + + +
          +
        • +

          getCommand

          +
          public static java.lang.String getCommand(Executable.ExecProvider provider,
+                                          java.lang.Class<?> clazz)
          +
          • +
        + + + +
          +
        • +

          isJavaLibrary

          +
          public static boolean isJavaLibrary(java.lang.Class<?> clazz)
          +
          Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
          +
          +
          Parameters:
          +
          clazz -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          getJava

          +
          public static java.lang.String getJava()
          +
          Returns the absolute path to the Java executable from JAVA_HOME
          +
          +
          Returns:
          +
          returns the absolute path to the Java executable from JAVA_HOME
          +
          +
          • +
        + + + +
          +
        • +

          getSupportedRuntimes

          +
          public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)
          +
          • +
        + + + + + + + +
          +
        • +

          getLimits

          +
          public static <T> LimitsManager<T> getLimits(java.lang.Class<T> clazz)
          +
          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
          +
          +
          Parameters:
          +
          rconfig -
          +
          Returns:
          +
          public static List toOptionString(RunnerConfig + rconfig) { String option = ""; List options = new + ArrayList(); for (Parameter par : + rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) + { option = par.getOptionName(); } else { option = + par.getOptionName() + "=" + par.getPossibleValues().get(0); } // + separate options options.add(option); } return options; }
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    compbio.engine.client

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    Interfaces

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    Package compbio.engine.client

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    Hierarchy For Package compbio.engine.client

    +Package Hierarchies: + +
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    +

    Class Hierarchy

    + +

    Interface Hierarchy

    + +

    Enum Hierarchy

    +
      +
    • java.lang.Object +
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    compbio.engine.cluster.drmaa
    +

    Class AsyncClusterRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.AsyncClusterRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      AsyncExecutor
      +
      +
      +
      +
      public class AsyncClusterRunner
+extends java.lang.Object
+implements AsyncExecutor
      +
      Single cluster job runner class
      +
      +
      Version:
      +
      1.0 August 2009 + + TODO after call to submitJob() no setters really work as the job + template gets deleted, this needs to be taken into account in this + class design!
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AsyncClusterRunner() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleancancelJob(java.lang.String jobId) +
        Stop running job.
        +
        booleancleanup(java.lang.String jobId) +
        Remove all files and a job directory for a jobid.
        +
        JobStatusgetJobStatus(java.lang.String jobId) +
        Query the status of the job
        +
        ConfiguredExecutable<?>getResults(java.lang.String jobId) +
        Retrieve the results of the job.
        +
        java.lang.StringgetWorkDirectory(java.lang.String jobId) 
        java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) +
        Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AsyncClusterRunner

          +
          public AsyncClusterRunner()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          submitJob

          +
          public java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
          +
          Description copied from interface: AsyncExecutor
          +
          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue.
          +
          +
          Specified by:
          +
          submitJob in interface AsyncExecutor
          +
          Returns:
          +
          unique job identifier
          +
          Throws:
          +
          JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.
          +
          +
          Specified by:
          +
          cancelJob in interface AsyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Query the status of the job
          +
          +
          Specified by:
          +
          getJobStatus in interface AsyncExecutor
          +
          Returns:
          +
          The JobStatus object representing the status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Remove all files and a job directory for a jobid.
          +
          +
          Specified by:
          +
          cleanup in interface AsyncExecutor
          +
          Returns:
          +
          true if job directory was successfully removed, false otherwise.
          +
          +
          • +
        + + + +
          +
        • +

          getResults

          +
          public ConfiguredExecutable<?> getResults(java.lang.String jobId)
+                                   throws ResultNotAvailableException
          +
          Description copied from interface: AsyncExecutor
          +
          Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation.
          +
          +
          Specified by:
          +
          getResults in interface AsyncExecutor
          +
          Parameters:
          +
          jobId - job identifier obtained at the job submission
          +
          Returns:
          +
          ConfiguredExecutable object from which result can be obtained
          +
          Throws:
          +
          ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
          +
          +
          • +
        + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory(java.lang.String jobId)
          +
          +
          Specified by:
          +
          getWorkDirectory in interface AsyncExecutor
          +
          Parameters:
          +
          jobId - unique job identifier
          +
          Returns:
          +
          task working directory
          +
          +
          • +
        +
        • +
      +
      • +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html new file mode 100644 index 0000000..9e47918 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html @@ -0,0 +1,465 @@ + + + + + +AsyncJobRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class AsyncJobRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.AsyncJobRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      AsyncExecutor
      +
      +
      +
      +
      public class AsyncJobRunner
+extends java.lang.Object
+implements AsyncExecutor
      +
      Single cluster job runner class
      +
      +
      Version:
      +
      1.0 August 2009 + + TODO after call to submitJob() no setters really work as the job + template gets deleted, this needs to be taken into account in this + class design!
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AsyncJobRunner() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleancancelJob(java.lang.String jobId) +
        Stop running job.
        +
        booleancleanup(java.lang.String jobId) +
        Remove all files and a job directory for a jobid.
        +
        JobStatusgetJobStatus(java.lang.String jobId) +
        This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
        +
        ConfiguredExecutable<?>getResults(java.lang.String jobId) +
        Retrieve the results of the job.
        +
        java.lang.StringgetWorkDirectory(java.lang.String jobId) 
        java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) +
        Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AsyncJobRunner

          +
          public AsyncJobRunner()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          submitJob

          +
          public java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
          +
          Description copied from interface: AsyncExecutor
          +
          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue.
          +
          +
          Specified by:
          +
          submitJob in interface AsyncExecutor
          +
          Returns:
          +
          unique job identifier
          +
          Throws:
          +
          JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.
          +
          +
          Specified by:
          +
          cancelJob in interface AsyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed. Cancelled jobs needs to be + tracked manually!
          +
          +
          Specified by:
          +
          getJobStatus in interface AsyncExecutor
          +
          Returns:
          +
          The JobStatus object representing the status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Remove all files and a job directory for a jobid.
          +
          +
          Specified by:
          +
          cleanup in interface AsyncExecutor
          +
          Returns:
          +
          true if job directory was successfully removed, false otherwise.
          +
          +
          • +
        + + + +
          +
        • +

          getResults

          +
          public ConfiguredExecutable<?> getResults(java.lang.String jobId)
+                                   throws ResultNotAvailableException
          +
          Description copied from interface: AsyncExecutor
          +
          Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation.
          +
          +
          Specified by:
          +
          getResults in interface AsyncExecutor
          +
          Parameters:
          +
          jobId - job identifier obtained at the job submission
          +
          Returns:
          +
          ConfiguredExecutable object from which result can be obtained
          +
          Throws:
          +
          ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
          +
          +
          • +
        + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory(java.lang.String jobId)
          +
          +
          Specified by:
          +
          getWorkDirectory in interface AsyncExecutor
          +
          Parameters:
          +
          jobId - unique job identifier
          +
          Returns:
          +
          task working directory
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterEngineUtil.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterEngineUtil.html new file mode 100644 index 0000000..967aa88 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterEngineUtil.html @@ -0,0 +1,342 @@ + + + + + +ClusterEngineUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class ClusterEngineUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.ClusterEngineUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ClusterEngineUtil
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.text.NumberFormatCLUSTER_STAT_IN_SEC 
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ClusterEngineUtil() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleancancelJob(java.lang.String jobId, + ClusterSession csession) 
        static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, + java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          CLUSTER_STAT_IN_SEC

          +
          public static final java.text.NumberFormat CLUSTER_STAT_IN_SEC
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClusterEngineUtil

          +
          public ClusterEngineUtil()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterRunner.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterRunner.html new file mode 100644 index 0000000..2198db5 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterRunner.html @@ -0,0 +1,752 @@ + + + + + +ClusterRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class ClusterRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.ClusterRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      SyncExecutor
      +
      +
      +
      +
      public class ClusterRunner
+extends java.lang.Object
+implements SyncExecutor
      +
      Single cluster job runner class
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobtempl

          +
          final org.ggf.drmaa.JobTemplate jobtempl
          +
          • +
        + + + + + + + +
          +
        • +

          session

          +
          static org.ggf.drmaa.Session session
          +
          • +
        + + + +
          +
        • +

          log

          +
          static final org.apache.log4j.Logger log
          +
          • +
        + + + + + + + +
          +
        • +

          workDirectory

          +
          private final java.lang.String workDirectory
          +
          • +
        + + + +
          +
        • +

          jobId

          +
          java.lang.String jobId
          +
          • +
        +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          setPipes

          +
          void setPipes(ConfiguredExecutable<?> executable)
+       throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          setNativeSpecs

          +
          void setNativeSpecs(Executable<?> executable)
+             throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          setEmail

          +
          void setEmail(java.lang.String email)
          +
          • +
        + + + +
          +
        • +

          setJobName

          +
          void setJobName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setJobEnvironmentVariables

          +
          void setJobEnvironmentVariables(java.util.Map<java.lang.String,java.lang.String> env_variables)
          +
          • +
        + + + +
          +
        • +

          makeLocalPath

          +
          private static java.lang.String makeLocalPath(java.lang.String path)
          +
          • +
        + + + +
          +
        • +

          deepClean

          +
          public boolean deepClean()
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          static JobStatus getJobStatus(java.lang.String jobId)
          +
          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed. Cancelled jobs needs to be + tracked manually!
          +
          • +
        + + + +
          +
        • +

          getRecordedJobStatus

          +
          static JobStatus getRecordedJobStatus(java.lang.String jobId)
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup()
          +
          Description copied from interface: SyncExecutor
          +
          Clean up after the job
          +
          +
          Specified by:
          +
          cleanup in interface SyncExecutor
          +
          Returns:
          +
          true if all the files created by this job have been removed successfully, false otherwise
          +
          +
          • +
        + + + + + + + +
          +
        • +

          cancelJob

          +
          boolean cancelJob(java.lang.String jobId)
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob()
          +
          Description copied from interface: SyncExecutor
          +
          Stops running job. + Clean up is not performed.
          +
          +
          Specified by:
          +
          cancelJob in interface SyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory()
          +
          +
          Specified by:
          +
          getWorkDirectory in interface SyncExecutor
          +
          Returns:
          +
          working directory if the task
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getJobInfo

          +
          public org.ggf.drmaa.JobInfo getJobInfo()
+                                 throws JobExecutionException
          +
          This method will block before the calculation has completed and then + return the object containing a job execution statistics
          +
          +
          Returns:
          +
          Throws:
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          waitForResult

          +
          public ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
          +
          Description copied from interface: SyncExecutor
          +
          Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe
          +
          +
          Specified by:
          +
          waitForResult in interface SyncExecutor
          +
          Returns:
          +
          object from wich the result can be obtained
          +
          Throws:
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus()
          +
          Description copied from interface: SyncExecutor
          +
          Query the status of the job by its id.
          +
          +
          Specified by:
          +
          getJobStatus in interface SyncExecutor
          +
          Returns:
          +
          - JobStatus
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html new file mode 100644 index 0000000..67afff4 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html @@ -0,0 +1,643 @@ + + + + + +ClusterSession + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class ClusterSession

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.ClusterSession
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class ClusterSession
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          ph

          +
          private static final compbio.util.PropertyHelper ph
          +
          • +
        + + + + + + + +
          +
        • +

          jobs

          +
          static final java.util.List<Job> jobs
          +
          • +
        + + + +
          +
        • +

          open

          +
          private static boolean open
          +
          • +
        + + + + + + + +
          +
        • +

          session

          +
          private final org.ggf.drmaa.Session session
          +
          • +
        + + + +
          +
        • +

          sContact

          +
          private final java.lang.String sContact
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClusterSession

          +
          private ClusterSession()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getSession

          +
          public org.ggf.drmaa.Session getSession()
          +
          • +
        + + + +
          +
        • +

          close

          +
          public void close()
          +
          • +
        + + + + + + + +
          +
        • +

          removeJob

          +
          public void removeJob(java.lang.String taskId)
          +
          • +
        + + + +
          +
        • +

          waitForJob

          +
          public org.ggf.drmaa.JobInfo waitForJob(java.lang.String taskId)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getClusterJobId

          +
          public static ClusterJobId getClusterJobId(java.lang.String taskId)
+                                    throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          waitForJob

          +
          public org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId,
+                                        long waitingTime)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          removeJobFromListbyTaskId

          +
          private static void removeJobFromListbyTaskId(java.lang.String taskId)
          +
          • +
        + + + + + + + +
          +
        • +

          getStatistics

          +
          public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
+                                      throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          logStatistics

          +
          static void logStatistics(org.ggf.drmaa.JobInfo status)
+                   throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public int getJobStatus(ClusterJobId jobId)
+                 throws org.ggf.drmaa.DrmaaException,
+                        org.ggf.drmaa.InvalidJobException
          +
          Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed.
          +
          +
          Throws:
          +
          org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it + will throw this exception for all finished or cancelled jobs
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          @Deprecated
+public static java.lang.String getJobStatus(int status)
+                                                 throws org.ggf.drmaa.DrmaaException
          +
          Deprecated. 
          +
          Method for getting jobs status by quering the cluster, It returns status + in therms of a Sessions, not a JobStatus Should only be used for testing!
          +
          +
          Parameters:
          +
          status -
          +
          Returns:
          +
          job status
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html new file mode 100644 index 0000000..17817e8 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html @@ -0,0 +1,342 @@ + + + + + +ClusterUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class ClusterUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.ClusterUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ClusterUtil
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.text.NumberFormatCLUSTER_STAT_IN_SEC 
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ClusterUtil() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleancancelJob(java.lang.String jobId, + ClusterSession csession) 
        static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, + java.lang.String jobId) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          CLUSTER_STAT_IN_SEC

          +
          public static final java.text.NumberFormat CLUSTER_STAT_IN_SEC
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClusterUtil

          +
          public ClusterUtil()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html new file mode 100644 index 0000000..04f41fe --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html @@ -0,0 +1,752 @@ + + + + + +JobRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class JobRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.JobRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      SyncExecutor
      +
      +
      +
      +
      public class JobRunner
+extends java.lang.Object
+implements SyncExecutor
      +
      Single cluster job runner class
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          jobtempl

          +
          final org.ggf.drmaa.JobTemplate jobtempl
          +
          • +
        + + + + + + + +
          +
        • +

          session

          +
          static org.ggf.drmaa.Session session
          +
          • +
        + + + +
          +
        • +

          log

          +
          static final org.apache.log4j.Logger log
          +
          • +
        + + + + + + + +
          +
        • +

          workDirectory

          +
          private final java.lang.String workDirectory
          +
          • +
        + + + +
          +
        • +

          jobId

          +
          java.lang.String jobId
          +
          • +
        +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          setPipes

          +
          void setPipes(ConfiguredExecutable<?> executable)
+       throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          setNativeSpecs

          +
          void setNativeSpecs(Executable<?> executable)
+             throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          setEmail

          +
          void setEmail(java.lang.String email)
          +
          • +
        + + + +
          +
        • +

          setJobName

          +
          void setJobName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setJobEnvironmentVariables

          +
          void setJobEnvironmentVariables(java.util.Map<java.lang.String,java.lang.String> env_variables)
          +
          • +
        + + + +
          +
        • +

          makeLocalPath

          +
          private static java.lang.String makeLocalPath(java.lang.String path)
          +
          • +
        + + + +
          +
        • +

          deepClean

          +
          public boolean deepClean()
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          static JobStatus getJobStatus(java.lang.String jobId)
          +
          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed. Cancelled jobs needs to be + tracked manually!
          +
          • +
        + + + +
          +
        • +

          getRecordedJobStatus

          +
          static JobStatus getRecordedJobStatus(java.lang.String jobId)
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup()
          +
          Description copied from interface: SyncExecutor
          +
          Clean up after the job
          +
          +
          Specified by:
          +
          cleanup in interface SyncExecutor
          +
          Returns:
          +
          true if all the files created by this job have been removed successfully, false otherwise
          +
          +
          • +
        + + + + + + + +
          +
        • +

          cancelJob

          +
          boolean cancelJob(java.lang.String jobId)
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob()
          +
          Description copied from interface: SyncExecutor
          +
          Stops running job. + Clean up is not performed.
          +
          +
          Specified by:
          +
          cancelJob in interface SyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory()
          +
          +
          Specified by:
          +
          getWorkDirectory in interface SyncExecutor
          +
          Returns:
          +
          working directory if the task
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getJobInfo

          +
          public org.ggf.drmaa.JobInfo getJobInfo()
+                                 throws JobExecutionException
          +
          This method will block before the calculation has completed and then + return the object containing a job execution statistics
          +
          +
          Returns:
          +
          Throws:
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          waitForResult

          +
          public ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
          +
          Description copied from interface: SyncExecutor
          +
          Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe
          +
          +
          Specified by:
          +
          waitForResult in interface SyncExecutor
          +
          Returns:
          +
          object from wich the result can be obtained
          +
          Throws:
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus()
          +
          Description copied from interface: SyncExecutor
          +
          Query the status of the job by its id.
          +
          +
          Specified by:
          +
          getJobStatus in interface SyncExecutor
          +
          Returns:
          +
          - JobStatus
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html new file mode 100644 index 0000000..bc1d055 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html @@ -0,0 +1,977 @@ + + + + + +StatisticManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.cluster.drmaa
    +

    Class StatisticManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.cluster.drmaa.StatisticManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class StatisticManager
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringacct_cpu 
        (package private) java.lang.Stringacct_io 
        (package private) java.lang.Stringacct_iow 
        (package private) java.lang.Stringacct_maxvmem 
        (package private) java.lang.Stringacct_mem 
        (package private) java.lang.Stringcpu 
        (package private) java.lang.Stringend_time 
        (package private) java.lang.Stringexit_status 
        (package private) java.lang.Stringio 
        (package private) java.lang.Stringiow 
        (package private) org.ggf.drmaa.JobInfojobinfo 
        (package private) java.lang.Stringmaxvmem 
        private static java.lang.StringnewLine 
        (package private) java.lang.Stringpriority 
        (package private) java.lang.Stringru_stime 
        (package private) java.lang.Stringru_utime 
        (package private) java.lang.Stringru_wallclock 
        (package private) java.lang.Stringsignal +
        see man 5 accounting on sun grid engine installed workstation see also + man 2 getrusage
        +
        (package private) java.lang.Stringstart_time 
        (package private) java.lang.Stringsubmission_time 
        private java.util.Map<java.lang.String,java.lang.String>usage 
        (package private) java.lang.Stringvmem 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        StatisticManager(org.ggf.drmaa.JobInfo status) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          usage

          +
          private final java.util.Map<java.lang.String,java.lang.String> usage
          +
          • +
        + + + +
          +
        • +

          jobinfo

          +
          final org.ggf.drmaa.JobInfo jobinfo
          +
          • +
        + + + +
          +
        • +

          newLine

          +
          private static java.lang.String newLine
          +
          • +
        + + + +
          +
        • +

          signal

          +
          java.lang.String signal
          +
          see man 5 accounting on sun grid engine installed workstation see also + man 2 getrusage
          +
          • +
        + + + +
          +
        • +

          submission_time

          +
          java.lang.String submission_time
          +
          • +
        + + + +
          +
        • +

          vmem

          +
          java.lang.String vmem
          +
          • +
        + + + +
          +
        • +

          maxvmem

          +
          java.lang.String maxvmem
          +
          • +
        + + + +
          +
        • +

          ru_stime

          +
          java.lang.String ru_stime
          +
          • +
        + + + +
          +
        • +

          ru_utime

          +
          java.lang.String ru_utime
          +
          • +
        + + + +
          +
        • +

          ru_wallclock

          +
          java.lang.String ru_wallclock
          +
          • +
        + + + +
          +
        • +

          end_time

          +
          java.lang.String end_time
          +
          • +
        + + + +
          +
        • +

          start_time

          +
          java.lang.String start_time
          +
          • +
        + + + +
          +
        • +

          iow

          +
          java.lang.String iow
          +
          • +
        + + + +
          +
        • +

          cpu

          +
          java.lang.String cpu
          +
          • +
        + + + +
          +
        • +

          io

          +
          java.lang.String io
          +
          • +
        + + + +
          +
        • +

          priority

          +
          java.lang.String priority
          +
          • +
        + + + +
          +
        • +

          exit_status

          +
          java.lang.String exit_status
          +
          • +
        + + + +
          +
        • +

          acct_cpu

          +
          java.lang.String acct_cpu
          +
          • +
        + + + +
          +
        • +

          acct_mem

          +
          java.lang.String acct_mem
          +
          • +
        + + + +
          +
        • +

          acct_iow

          +
          java.lang.String acct_iow
          +
          • +
        + + + +
          +
        • +

          acct_io

          +
          java.lang.String acct_io
          +
          • +
        + + + +
          +
        • +

          acct_maxvmem

          +
          java.lang.String acct_maxvmem
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StatisticManager

          +
          public StatisticManager(org.ggf.drmaa.JobInfo status)
+                 throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getJobId

          +
          public java.lang.String getJobId()
+                          throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          hasExited

          +
          public boolean hasExited()
+                  throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          hasSignaled

          +
          public boolean hasSignaled()
+                    throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          hasDump

          +
          public boolean hasDump()
+                throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          termSignal

          +
          public java.lang.String termSignal()
+                            throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          wasAborted

          +
          public boolean wasAborted()
+                   throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          getSubmissionTime

          +
          public java.lang.String getSubmissionTime()
          +
          • +
        + + + +
          +
        • +

          getVMem

          +
          public java.lang.String getVMem()
          +
          • +
        + + + +
          +
        • +

          getMaxVMem

          +
          public java.lang.String getMaxVMem()
          +
          • +
        + + + +
          +
        • +

          getUsedSysTime

          +
          public java.lang.String getUsedSysTime()
          +
          • +
        + + + +
          +
        • +

          getUsedUserTime

          +
          public java.lang.String getUsedUserTime()
          +
          • +
        + + + +
          +
        • +

          getCalculationTime

          +
          public java.lang.String getCalculationTime()
          +
          • +
        + + + +
          +
        • +

          getEndTime

          +
          public java.lang.String getEndTime()
          +
          • +
        + + + +
          +
        • +

          getStartTime

          +
          public java.lang.String getStartTime()
          +
          • +
        + + + +
          +
        • +

          getIOWait

          +
          public java.lang.String getIOWait()
          +
          • +
        + + + +
          +
        • +

          getCPUUsageTime

          +
          public java.lang.String getCPUUsageTime()
          +
          • +
        + + + +
          +
        • +

          getDataTransfered

          +
          public java.lang.String getDataTransfered()
          +
          • +
        + + + +
          +
        • +

          getJobPriority

          +
          public java.lang.String getJobPriority()
          +
          • +
        + + + +
          +
        • +

          getExitStatus

          +
          public java.lang.String getExitStatus()
          +
          • +
        + + + +
          +
        • +

          getAllStats

          +
          public java.lang.String getAllStats()
+                             throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          getExecutionStat

          +
          public java.lang.String getExecutionStat()
+                                  throws org.ggf.drmaa.DrmaaException
          +
          +
          Throws:
          +
          org.ggf.drmaa.DrmaaException
          +
          +
          • +
        + + + +
          +
        • +

          getMemoryStat

          +
          public java.lang.String getMemoryStat()
          +
          • +
        + + + +
          +
        • +

          getCPUTimeStat

          +
          public java.lang.String getCPUTimeStat()
          +
          • +
        + + + +
          +
        • +

          getTimeStat

          +
          public java.lang.String getTimeStat()
          +
          • +
        + + + +
          +
        • +

          getRawUsage

          +
          public java.util.Map<java.lang.String,java.lang.String> getRawUsage()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          formatTime

          +
          java.lang.String formatTime(java.lang.String time)
          +
          Convert grid engine time format End time: 1250701672.0000 to a readable + time representation as defined in Util.dataf
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncClusterRunner.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncClusterRunner.html new file mode 100644 index 0000000..88ff0cd --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncClusterRunner.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.engine.cluster.drmaa.AsyncClusterRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
    • Prev
      • +
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      • +
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    + +
    +

    Uses of Class
    compbio.engine.cluster.drmaa.AsyncClusterRunner

    +
    +
    No usage of compbio.engine.cluster.drmaa.AsyncClusterRunner
    + +
    + + +
    Skip navigation links
    + + + + +
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      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html new file mode 100644 index 0000000..4e74648 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.engine.cluster.drmaa.AsyncJobRunner + + + + + + + + +
    + + +
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    Uses of Class
    compbio.engine.cluster.drmaa.AsyncJobRunner

    +
    +
    No usage of compbio.engine.cluster.drmaa.AsyncJobRunner
    + +
    + + +
    Skip navigation links
    + + + + +
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    compbio.engine.cluster.drmaa

    +
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    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html new file mode 100644 index 0000000..e5902d9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html @@ -0,0 +1,178 @@ + + + + + +compbio.engine.cluster.drmaa + + + + + + + + +
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    Package compbio.engine.cluster.drmaa

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    Hierarchy For Package compbio.engine.cluster.drmaa

    +Package Hierarchies: + +
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    Class Hierarchy

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    compbio.engine.conf
    +

    Class DirectoryManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.conf.DirectoryManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class DirectoryManager
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.lang.StringDELIM 
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        DirectoryManager() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.Class<Executable<?>>getClass(java.lang.String taskId) 
        (package private) static longgetNonRepeatableNumber() 
        static java.lang.StringgetTaskDirectory(java.lang.Class<?> clazz) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + + +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          DirectoryManager

          +
          public DirectoryManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getTaskDirectory

          +
          public static java.lang.String getTaskDirectory(java.lang.Class<?> clazz)
          +
          • +
        + + + +
          +
        • +

          getNonRepeatableNumber

          +
          static long getNonRepeatableNumber()
          +
          • +
        + + + +
          +
        • +

          getClass

          +
          public static java.lang.Class<Executable<?>> getClass(java.lang.String taskId)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/conf/PropertyHelperManager.html b/website/docs/full_javadoc/compbio/engine/conf/PropertyHelperManager.html new file mode 100644 index 0000000..51bee19 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/conf/PropertyHelperManager.html @@ -0,0 +1,430 @@ + + + + + +PropertyHelperManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.conf
    +

    Class PropertyHelperManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.conf.PropertyHelperManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class PropertyHelperManager
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static java.lang.StringconfDir 
        private static org.apache.log4j.Loggerlog 
        private static compbio.util.PropertyHelperph 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static booleangetBooleanProperty(java.lang.String propValue) 
        static intgetIntProperty(java.lang.String propValue) 
        static java.lang.StringgetLocalPath() +
        Method return the absolute path to the project root directory.
        +
        static compbio.util.PropertyHelpergetPropertyHelper() +
        Ways to fix path problem: + 1) find a path to WEB-INF directory based on the path to a known class.
        +
        (package private) static java.io.FilegetResourceFromClasspath(java.lang.String resourceName) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          ph

          +
          private static compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          confDir

          +
          public static final java.lang.String confDir
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PropertyHelperManager

          +
          public PropertyHelperManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPropertyHelper

          +
          public static compbio.util.PropertyHelper getPropertyHelper()
          +
          Ways to fix path problem: + 1) find a path to WEB-INF directory based on the path to a known class. + Then prepend this absolute path to the rest of paths + pros: no input from user + cons: relocation of the source may cause problems + + 2) Require users to add configuration directories to the class + path and then load entries from it. + pros: + cons: Many paths needs to be added. Put significant burden on the user. + Hard to tell web appl server to add these entries to its class path. + + 3) Ask for project source directory explicitly in the configuration. + pros: + cons: similar to 1, but this initial configuration file must reside in + well known location! Why ask users what can be found automatically? + + 4) Have everything in the location already in class path for tomcat. + pros: + cons: only classes and lib/*.jar are added, Eclipse will remove non + classses from classes dir. + + Try 1 - succeed.
          +
          +
          Returns:
          +
          an instance
          +
          +
          • +
        + + + +
          +
        • +

          getResourceFromClasspath

          +
          static java.io.File getResourceFromClasspath(java.lang.String resourceName)
          +
          • +
        + + + +
          +
        • +

          getLocalPath

          +
          public static java.lang.String getLocalPath()
          +
          Method return the absolute path to the project root directory. It assumes + the following structure of the project: + project-root: + conf/settings + binaries + WEB-INF/classes/compbio/engine/conf/PropertyHelperManager.class + If the structure changes it must be reflected in this method
          +
          +
          Returns:
          +
          the local path
          +
          Throws:
          +
          java.lang.RuntimeException - if cannot determine the local path
          +
          +
          • +
        + + + +
          +
        • +

          getIntProperty

          +
          public static int getIntProperty(java.lang.String propValue)
          +
          • +
        + + + +
          +
        • +

          getBooleanProperty

          +
          public static boolean getBooleanProperty(java.lang.String propValue)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
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    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html b/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html new file mode 100644 index 0000000..4a042f8 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.MySchemaOutputResolver.html @@ -0,0 +1,340 @@ + + + + + +RunnerConfigMarshaller.MySchemaOutputResolver + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.conf
    +

    Class RunnerConfigMarshaller.MySchemaOutputResolver

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.xml.bind.SchemaOutputResolver
        • +
      • +
          +
        • compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Enclosing class:
      +
      RunnerConfigMarshaller<T>
      +
      +
      +
      +
      static class RunnerConfigMarshaller.MySchemaOutputResolver
+extends javax.xml.bind.SchemaOutputResolver
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringdir 
        (package private) java.lang.Stringsname 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        MySchemaOutputResolver(java.lang.String directory, + java.lang.String suggestedFileName) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        javax.xml.transform.ResultcreateOutput(java.lang.String namespaceUri, + java.lang.String suggestedFileName) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          dir

          +
          final java.lang.String dir
          +
          • +
        + + + +
          +
        • +

          sname

          +
          final java.lang.String sname
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MySchemaOutputResolver

          +
          public MySchemaOutputResolver(java.lang.String directory,
+                              java.lang.String suggestedFileName)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          createOutput

          +
          public javax.xml.transform.Result createOutput(java.lang.String namespaceUri,
+                                               java.lang.String suggestedFileName)
+                                        throws java.io.IOException
          +
          +
          Specified by:
          +
          createOutput in class javax.xml.bind.SchemaOutputResolver
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html new file mode 100644 index 0000000..1c58634 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html @@ -0,0 +1,564 @@ + + + + + +RunnerConfigMarshaller + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.conf
    +

    Class RunnerConfigMarshaller<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.conf.RunnerConfigMarshaller<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class RunnerConfigMarshaller<T>
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private javax.xml.bind.JAXBContextctx 
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        RunnerConfigMarshaller(java.lang.Class<?> rootClass) 
        RunnerConfigMarshaller(java.lang.Class<?> rootClass, + java.lang.Class<?>... classes) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) voidgenerateSchema(java.lang.String directoryForSchema, + java.lang.String schemaName) 
        static javax.xml.validation.SchemagetSchema(java.lang.String schemafile) 
        static javax.xml.validation.ValidatorgetValidator(javax.xml.validation.Schema schema) 
        static javax.xml.validation.ValidatorgetValidator(java.lang.String schemafile) 
        <V> Vread(java.io.InputStream instream, + java.lang.Class<V> resultElemType) 
        <V> Vread(java.io.InputStream instream, + java.lang.Class<V> resultElemType, + java.lang.Class<?>... classes) 
        <V> VreadAndValidate(java.io.InputStream document, + java.lang.Class<V> resultElemType) 
        static booleanvalidate(javax.xml.validation.Validator validator, + java.lang.String document) 
        voidwrite(java.lang.Object xmlRootElement, + java.io.OutputStream out) 
        voidwriteAndValidate(java.lang.Object xmlRootElement, + java.lang.String schemafile, + java.io.OutputStream out) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          ctx

          +
          private final javax.xml.bind.JAXBContext ctx
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RunnerConfigMarshaller

          +
          public RunnerConfigMarshaller(java.lang.Class<?> rootClass)
+                       throws javax.xml.bind.JAXBException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          +
          • +
        + + + +
          +
        • +

          RunnerConfigMarshaller

          +
          public RunnerConfigMarshaller(java.lang.Class<?> rootClass,
+                              java.lang.Class<?>... classes)
+                       throws javax.xml.bind.JAXBException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          write

          +
          public void write(java.lang.Object xmlRootElement,
+                  java.io.OutputStream out)
+           throws javax.xml.bind.JAXBException,
+                  java.io.IOException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeAndValidate

          +
          public void writeAndValidate(java.lang.Object xmlRootElement,
+                             java.lang.String schemafile,
+                             java.io.OutputStream out)
+                      throws javax.xml.bind.JAXBException,
+                             java.io.IOException,
+                             org.xml.sax.SAXException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          java.io.IOException
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          generateSchema

          +
          void generateSchema(java.lang.String directoryForSchema,
+                    java.lang.String schemaName)
+             throws javax.xml.bind.JAXBException,
+                    java.io.IOException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getSchema

          +
          public static javax.xml.validation.Schema getSchema(java.lang.String schemafile)
+                                             throws org.xml.sax.SAXException
          +
          +
          Throws:
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          getValidator

          +
          public static javax.xml.validation.Validator getValidator(java.lang.String schemafile)
+                                                   throws org.xml.sax.SAXException
          +
          +
          Returns:
          +
          validator instance
          +
          Throws:
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          getValidator

          +
          public static javax.xml.validation.Validator getValidator(javax.xml.validation.Schema schema)
+                                                   throws org.xml.sax.SAXException
          +
          +
          Throws:
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public static boolean validate(javax.xml.validation.Validator validator,
+                               java.lang.String document)
+                        throws java.io.IOException,
+                               org.xml.sax.SAXException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          readAndValidate

          +
          public <V> V readAndValidate(java.io.InputStream document,
+                             java.lang.Class<V> resultElemType)
+                      throws javax.xml.bind.JAXBException,
+                             java.io.IOException,
+                             org.xml.sax.SAXException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          java.io.IOException
          +
          org.xml.sax.SAXException
          +
          +
          • +
        + + + +
          +
        • +

          read

          +
          public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType)
+           throws javax.xml.bind.JAXBException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          +
          • +
        + + + +
          +
        • +

          read

          +
          public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType,
+                  java.lang.Class<?>... classes)
+           throws javax.xml.bind.JAXBException
          +
          +
          Throws:
          +
          javax.xml.bind.JAXBException
          +
          +
          • +
        +
        • +
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      • +
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    Skip navigation links
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    +
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    compbio.engine.conf

    +
    +

    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/engine/conf/package-summary.html b/website/docs/full_javadoc/compbio/engine/conf/package-summary.html new file mode 100644 index 0000000..23c9832 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/conf/package-summary.html @@ -0,0 +1,154 @@ + + + + + +compbio.engine.conf + + + + + + + + +
    + + +
    Skip navigation links
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    +
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    + +
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    +

    Package compbio.engine.conf

    +
    +
    + +
    + +
    + + +
    Skip navigation links
    + + + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/conf/package-tree.html b/website/docs/full_javadoc/compbio/engine/conf/package-tree.html new file mode 100644 index 0000000..8a39e7e --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/conf/package-tree.html @@ -0,0 +1,144 @@ + + + + + +compbio.engine.conf Class Hierarchy + + + + + + + + +
    + + +
    Skip navigation links
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    + +
    +

    Hierarchy For Package compbio.engine.conf

    +Package Hierarchies: + +
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    +

    Class Hierarchy

    + +
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    Skip navigation links
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    compbio.engine.conf

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    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/AsyncLocalRunner.html b/website/docs/full_javadoc/compbio/engine/local/AsyncLocalRunner.html new file mode 100644 index 0000000..5972d90 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/AsyncLocalRunner.html @@ -0,0 +1,454 @@ + + + + + +AsyncLocalRunner + + + + + + + + +
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    Skip navigation links
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    +
    compbio.engine.local
    +

    Class AsyncLocalRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.local.AsyncLocalRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      AsyncExecutor
      +
      +
      +
      +
      public final class AsyncLocalRunner
+extends java.lang.Object
+implements AsyncExecutor
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AsyncLocalRunner() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        booleancancelJob(java.lang.String jobId) +
        Stop running job.
        +
        booleancleanup(java.lang.String jobId) +
        Remove all files and a job directory for a jobid.
        +
        JobStatusgetJobStatus(java.lang.String jobId) +
        Query the status of the job
        +
        ConfiguredExecutable<?>getResults(java.lang.String taskId) +
        Retrieve the results of the job.
        +
        java.lang.StringgetWorkDirectory(java.lang.String jobId) 
        java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) +
        Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AsyncLocalRunner

          +
          public AsyncLocalRunner()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory(java.lang.String jobId)
          +
          +
          Specified by:
          +
          getWorkDirectory in interface AsyncExecutor
          +
          Parameters:
          +
          jobId - unique job identifier
          +
          Returns:
          +
          task working directory
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Stop running job. Please not that this method does not guarantee to remove the job directory and files in it.
          +
          +
          Specified by:
          +
          cancelJob in interface AsyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Query the status of the job
          +
          +
          Specified by:
          +
          getJobStatus in interface AsyncExecutor
          +
          Returns:
          +
          The JobStatus object representing the status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          submitJob

          +
          public java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
          +
          Description copied from interface: AsyncExecutor
          +
          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue.
          +
          +
          Specified by:
          +
          submitJob in interface AsyncExecutor
          +
          Returns:
          +
          unique job identifier
          +
          Throws:
          +
          JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
          +
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup(java.lang.String jobId)
          +
          Description copied from interface: AsyncExecutor
          +
          Remove all files and a job directory for a jobid.
          +
          +
          Specified by:
          +
          cleanup in interface AsyncExecutor
          +
          Parameters:
          +
          jobId -
          +
          Returns:
          +
          true if all files were removed, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getResults

          +
          public ConfiguredExecutable<?> getResults(java.lang.String taskId)
+                                   throws ResultNotAvailableException
          +
          Description copied from interface: AsyncExecutor
          +
          Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation.
          +
          +
          Specified by:
          +
          getResults in interface AsyncExecutor
          +
          Parameters:
          +
          taskId - job identifier obtained at the job submission
          +
          Returns:
          +
          ConfiguredExecutable object from which result can be obtained
          +
          Throws:
          +
          ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/ExecutableWrapper.html b/website/docs/full_javadoc/compbio/engine/local/ExecutableWrapper.html new file mode 100644 index 0000000..18a274e --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/ExecutableWrapper.html @@ -0,0 +1,473 @@ + + + + + +ExecutableWrapper + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Class ExecutableWrapper

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.local.ExecutableWrapper
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.concurrent.Callable<ConfiguredExecutable<?>>
      +
      +
      +
      +
      @Immutable
+public final class ExecutableWrapper
+extends java.lang.Object
+implements java.util.concurrent.Callable<ConfiguredExecutable<?>>
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private ConfiguredExecutable<?>confExec 
        private static java.util.concurrent.ExecutorServicees 
        private static org.apache.log4j.Loggerlog 
        private java.lang.ProcessBuilderpbuilder 
        static java.lang.StringPROC_ERR_FILE 
        static java.lang.StringPROC_IN_FILE 
        static java.lang.StringPROC_OUT_FILE 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        ConfiguredExecutable<?>call() +
        It is vital that output and error streams are captured immediately for + this call() to succeed.
        +
        private java.lang.StringgetError() 
        private java.lang.StringgetOutput() 
        static voidshutdownService() +
        Stops internal executor service which captures streams of native + executables.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          PROC_IN_FILE

          +
          public static final java.lang.String PROC_IN_FILE
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          PROC_OUT_FILE

          +
          public static final java.lang.String PROC_OUT_FILE
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          PROC_ERR_FILE

          +
          public static final java.lang.String PROC_ERR_FILE
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          es

          +
          private static java.util.concurrent.ExecutorService es
          +
          • +
        + + + + + + + +
          +
        • +

          pbuilder

          +
          private final java.lang.ProcessBuilder pbuilder
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          shutdownService

          +
          public static final void shutdownService()
          +
          Stops internal executor service which captures streams of native + executables. This method is intended for stopping service if deployed in + the web application content. There is NO NEED of using this method + otherwise as the executor service is taken care of internally.
          +
          • +
        + + + +
          +
        • +

          call

          +
          public ConfiguredExecutable<?> call()
+                             throws java.io.IOException
          +
          It is vital that output and error streams are captured immediately for + this call() to succeed. Thus each instance if ExecutableWrapper has 2 its + own thread ready to capture the output. If executor could not execute + capture immediately this could lead to the call method to stale, as + execution could not proceed without output being captured. Every call to + call() method will use 2 threads
          +
          +
          Specified by:
          +
          call in interface java.util.concurrent.Callable<ConfiguredExecutable<?>>
          +
          Throws:
          +
          JobSubmissionException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getOutput

          +
          private java.lang.String getOutput()
          +
          • +
        + + + +
          +
        • +

          getError

          +
          private java.lang.String getError()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/docs/full_javadoc/compbio/engine/local/LocalEngineUtil.html new file mode 100644 index 0000000..0a04a78 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/LocalEngineUtil.html @@ -0,0 +1,389 @@ + + + + + +LocalEngineUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Class LocalEngineUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.local.LocalEngineUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class LocalEngineUtil
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LocalEngineUtil

          +
          public LocalEngineUtil()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/docs/full_javadoc/compbio/engine/local/LocalExecutorService.html new file mode 100644 index 0000000..54c45d2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/LocalExecutorService.html @@ -0,0 +1,548 @@ + + + + + +LocalExecutorService + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Class LocalExecutorService

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.util.concurrent.AbstractExecutorService
        • +
      • +
          +
        • java.util.concurrent.ThreadPoolExecutor
          • +
        • +
            +
          • compbio.engine.local.LocalExecutorService
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.concurrent.Executor, java.util.concurrent.ExecutorService
      +
      +
      +
      +
      public final class LocalExecutorService
+extends java.util.concurrent.ThreadPoolExecutor
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Nested Class Summary

        +
          +
        • + + +

          Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor

          +java.util.concurrent.ThreadPoolExecutor.AbortPolicy, java.util.concurrent.ThreadPoolExecutor.CallerRunsPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardOldestPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardPolicy
          • +
        +
        • +
      + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static LocalExecutorServiceINSTANCE 
        private static org.apache.log4j.Loggerlog 
        private java.util.concurrent.atomic.AtomicLongnumTasks 
        private java.lang.ThreadLocal<java.lang.Long>startTime 
        private static java.lang.StringthreadNumPropName 
        private java.util.concurrent.atomic.AtomicLongtotalTime 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private LocalExecutorService(int corePoolSize, + int maximumPoolSize, + long keepAliveTime, + java.util.concurrent.TimeUnit unit, + java.util.concurrent.BlockingQueue<java.lang.Runnable> workQueue) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voidafterExecute(java.lang.Runnable r, + java.lang.Throwable t) 
        protected voidbeforeExecute(java.lang.Thread t, + java.lang.Runnable r) 
        booleancanAcceptMoreWork() +
        If the Executor queue is empty
        +
        static LocalExecutorServicegetExecutor() +
        This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally
        +
        private static LocalExecutorServiceinit() 
        static voidshutDown() +
        This stops all executing processes via interruption.
        +
        protected voidterminated() 
        +
          +
        • + + +

          Methods inherited from class java.util.concurrent.ThreadPoolExecutor

          +allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, finalize, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.util.concurrent.AbstractExecutorService

          +invokeAll, invokeAll, invokeAny, invokeAny, newTaskFor, newTaskFor, submit, submit, submit
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          threadNumPropName

          +
          private static final java.lang.String threadNumPropName
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + + + + + +
          +
        • +

          startTime

          +
          private final java.lang.ThreadLocal<java.lang.Long> startTime
          +
          • +
        + + + +
          +
        • +

          numTasks

          +
          private final java.util.concurrent.atomic.AtomicLong numTasks
          +
          • +
        + + + +
          +
        • +

          totalTime

          +
          private final java.util.concurrent.atomic.AtomicLong totalTime
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LocalExecutorService

          +
          private LocalExecutorService(int corePoolSize,
+                             int maximumPoolSize,
+                             long keepAliveTime,
+                             java.util.concurrent.TimeUnit unit,
+                             java.util.concurrent.BlockingQueue<java.lang.Runnable> workQueue)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getExecutor

          +
          public static LocalExecutorService getExecutor()
          +
          This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally
          +
          +
          Returns:
          +
          the instance
          +
          +
          • +
        + + + + + + + +
          +
        • +

          shutDown

          +
          public static void shutDown()
          +
          This stops all executing processes via interruption. Thus it is vital + that all processes that use this service respond to interruption + + Stops internal executor service which captures streams of native + executables. This method is intended for stopping service if deployed in + the web application context. There is NO NEED of using this method + otherwise as the executor service is taken care of internally.
          +
          • +
        + + + +
          +
        • +

          canAcceptMoreWork

          +
          public boolean canAcceptMoreWork()
          +
          If the Executor queue is empty
          +
          +
          Returns:
          +
          true is not all threads are busy, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          beforeExecute

          +
          protected void beforeExecute(java.lang.Thread t,
+                             java.lang.Runnable r)
          +
          +
          Overrides:
          +
          beforeExecute in class java.util.concurrent.ThreadPoolExecutor
          +
          +
          • +
        + + + +
          +
        • +

          afterExecute

          +
          protected void afterExecute(java.lang.Runnable r,
+                            java.lang.Throwable t)
          +
          +
          Overrides:
          +
          afterExecute in class java.util.concurrent.ThreadPoolExecutor
          +
          +
          • +
        + + + +
          +
        • +

          terminated

          +
          protected void terminated()
          +
          +
          Overrides:
          +
          terminated in class java.util.concurrent.ThreadPoolExecutor
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/LocalRunner.html b/website/docs/full_javadoc/compbio/engine/local/LocalRunner.html new file mode 100644 index 0000000..6cd1e10 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/LocalRunner.html @@ -0,0 +1,506 @@ + + + + + +LocalRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Class LocalRunner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.local.LocalRunner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      SyncExecutor
      +
      +
      +
      +
      public final class LocalRunner
+extends java.lang.Object
+implements SyncExecutor
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          executor

          +
          private final java.util.concurrent.ExecutorService executor
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          workDirectory

          +
          private final java.lang.String workDirectory
          +
          • +
        +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getWorkDirectory

          +
          public java.lang.String getWorkDirectory()
          +
          +
          Specified by:
          +
          getWorkDirectory in interface SyncExecutor
          +
          Returns:
          +
          working directory if the task
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob()
          +
          Description copied from interface: SyncExecutor
          +
          Stops running job. + Clean up is not performed.
          +
          +
          Specified by:
          +
          cancelJob in interface SyncExecutor
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + + + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus()
          +
          Description copied from interface: SyncExecutor
          +
          Query the status of the job by its id.
          +
          +
          Specified by:
          +
          getJobStatus in interface SyncExecutor
          +
          Returns:
          +
          - JobStatus
          +
          +
          • +
        + + + + + + + +
          +
        • +

          waitForResult

          +
          public ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
          +
          Description copied from interface: SyncExecutor
          +
          Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe
          +
          +
          Specified by:
          +
          waitForResult in interface SyncExecutor
          +
          Returns:
          +
          object from wich the result can be obtained
          +
          Throws:
          +
          java.util.concurrent.CancellationException
          +
          JobExecutionException
          +
          +
          • +
        + + + +
          +
        • +

          cleanup

          +
          public boolean cleanup()
          +
          Description copied from interface: SyncExecutor
          +
          Clean up after the job
          +
          +
          Specified by:
          +
          cleanup in interface SyncExecutor
          +
          Returns:
          +
          true if all the files created by this job have been removed successfully, false otherwise
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.OutputType.html b/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.OutputType.html new file mode 100644 index 0000000..e3a1380 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.OutputType.html @@ -0,0 +1,345 @@ + + + + + +StreamGobbler.OutputType + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Enum StreamGobbler.OutputType

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        ERROR 
        OUTPUT 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static StreamGobbler.OutputTypevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static StreamGobbler.OutputType[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static StreamGobbler.OutputType[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (StreamGobbler.OutputType c : StreamGobbler.OutputType.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static StreamGobbler.OutputType valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.html new file mode 100644 index 0000000..0f6bdde --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/StreamGobbler.html @@ -0,0 +1,392 @@ + + + + + +StreamGobbler + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.engine.local
    +

    Class StreamGobbler

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.engine.local.StreamGobbler
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Runnable
      +
      +
      +
      +
      @ThreadSafe
+public class StreamGobbler
+extends java.lang.Object
+implements java.lang.Runnable
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Nested Class Summary

        + + + + + + + + + + +
        Nested Classes 
        Modifier and TypeClass and Description
        (package private) static class StreamGobbler.OutputType 
        +
        • +
      + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.io.InputStreamis 
        private static org.apache.log4j.Loggerlog 
        private java.io.OutputStreamos 
        private StreamGobbler.OutputTypetype 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        private static voidcloseSilently(java.io.Closeable stream) 
        voidrun() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          is

          +
          private final java.io.InputStream is
          +
          • +
        + + + +
          +
        • +

          os

          +
          private final java.io.OutputStream os
          +
          • +
        + + + + +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StreamGobbler

          +
          StreamGobbler(java.io.InputStream is,
+              java.io.OutputStream os,
+              StreamGobbler.OutputType type)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          run

          +
          public void run()
          +
          +
          Specified by:
          +
          run in interface java.lang.Runnable
          +
          +
          • +
        + + + +
          +
        • +

          closeSilently

          +
          private static void closeSilently(java.io.Closeable stream)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/docs/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html new file mode 100644 index 0000000..9336655 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.engine.local.AsyncLocalRunner + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
    • Prev
      • +
    • Next
      • +
    + + +
    + +
    + + +
    + +
    +

    Uses of Class
    compbio.engine.local.AsyncLocalRunner

    +
    +
    No usage of compbio.engine.local.AsyncLocalRunner
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
    • Prev
      • +
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    compbio.engine.local

    +
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    Classes

    + +

    Enums

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    Hierarchy For Package compbio.engine.local

    +Package Hierarchies: + +
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    Class Hierarchy

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    Enum Hierarchy

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    • java.lang.Object +
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    compbio.engine

    +
    +

    Interfaces

    + +

    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/engine/package-summary.html b/website/docs/full_javadoc/compbio/engine/package-summary.html new file mode 100644 index 0000000..d9c3156 --- /dev/null +++ b/website/docs/full_javadoc/compbio/engine/package-summary.html @@ -0,0 +1,202 @@ + + + + + +compbio.engine + + + + + + + + +
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    Package compbio.engine

    +
    +
    +
      +
    • + + + + + + + + + + + + + + + + +
      Interface Summary 
      InterfaceDescription
      AsyncExecutor +
      An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
      +
      SyncExecutor +
      Synchronous executor, is an engine to run the Executable synchronously.
      +
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      Cleaner 
      ClusterJobId 
      Configurator 
      FilePuller 
      Job 
      LoadBalancer +
      This class decides where to execute the job.
      +
      ProgressGetter 
      PulledFileCache 
      SubmissionManager +
      Submit jobs for execution
      +
      +
      • +
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    + +
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    Hierarchy For Package compbio.engine

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    + + +
    Skip navigation links
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    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
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      +
    • Detail: 
      • +
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      • +
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    + + +
    +
    compbio.metadata
    +

    Interface Argument<T>

    +
    +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      All Known Implementing Classes:
      +
      Option, Parameter
      +
      +
      +
      +
      public interface Argument<T>
      +
      An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
      +
      +
      Author:
      +
      pvtroshin + + Date December 2009
      +
      See Also:
      +
      Parameter, +Option
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFurtherDetails

          +
          java.lang.String getFurtherDetails()
          +
          • +
        + + + +
          +
        • +

          getDefaultValue

          +
          java.lang.String getDefaultValue()
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          java.lang.String getDescription()
          +
          • +
        + + + +
          +
        • +

          getName

          +
          java.lang.String getName()
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          java.util.List<java.lang.String> getPossibleValues()
          +
          +
          Returns:
          +
          List of values allowed for an Argument
          +
          +
          • +
        + + + +
          +
        • +

          setValue

          +
          void setValue(java.lang.String defaultValue)
+       throws WrongParameterException
          +
          Set default values for the parameter or an option
          +
          +
          Parameters:
          +
          defaultValue - the value to be set
          +
          Throws:
          +
          WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
          +
          See Also:
          +
          ValueConstrain
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
      +
    • Detail: 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/ChunkHolder.html b/website/docs/full_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..bbdb508 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,409 @@ + + + + + +ChunkHolder + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ChunkHolder

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.ChunkHolder
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ChunkHolder
+extends java.lang.Object
      +
      Represents a chunk of a string data together with the position in a file for + the next read operation.
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringchunk 
        (package private) longposition 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private ChunkHolder() 
         ChunkHolder(java.lang.String chunk, + long position) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          chunk

          +
          java.lang.String chunk
          +
          • +
        + + + +
          +
        • +

          position

          +
          long position
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ChunkHolder

          +
          private ChunkHolder()
          +
          • +
        + + + +
          +
        • +

          ChunkHolder

          +
          public ChunkHolder(java.lang.String chunk,
+                   long position)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getChunk

          +
          public java.lang.String getChunk()
          +
          • +
        + + + +
          +
        • +

          getNextPosition

          +
          public long getNextPosition()
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        +
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    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/JobExecutionException.html b/website/docs/full_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..276782a --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,337 @@ + + + + + +JobExecutionException + + + + + + + + +
    + + +
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    +
    compbio.metadata
    +

    Class JobExecutionException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.JobExecutionException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class JobExecutionException
+extends java.lang.Exception
      +
      JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          JobExecutionException

          +
          public JobExecutionException(java.lang.String message,
+                             java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
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    Skip navigation links
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/JobStatus.html b/website/docs/full_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..7575a8d --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,462 @@ + + + + + +JobStatus + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Enum JobStatus

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<JobStatus>
        • +
      • +
          +
        • compbio.metadata.JobStatus
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<JobStatus>
      +
      +
      +
      +
      public enum JobStatus
+extends java.lang.Enum<JobStatus>
      +
      The status of the job.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        CANCELLED +
        Jobs that has been cancelled
        +
        COLLECTED +
        Results has been collected
        +
        FAILED +
        Failed jobs
        +
        FINISHED +
        Finished jobs
        +
        PENDING +
        Jobs which are in the queue and awaiting execution reported for cluster + jobs only
        +
        RUNNING +
        Jobs that are running
        +
        STARTED +
        Job calculation has been started.
        +
        SUBMITTED +
        Job has been submitted.
        +
        UNDEFINED +
        Represents jobs with unknown status
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static JobStatusvalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static JobStatus[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          PENDING

          +
          public static final JobStatus PENDING
          +
          Jobs which are in the queue and awaiting execution reported for cluster + jobs only
          +
          • +
        + + + +
          +
        • +

          RUNNING

          +
          public static final JobStatus RUNNING
          +
          Jobs that are running
          +
          • +
        + + + +
          +
        • +

          CANCELLED

          +
          public static final JobStatus CANCELLED
          +
          Jobs that has been cancelled
          +
          • +
        + + + +
          +
        • +

          FINISHED

          +
          public static final JobStatus FINISHED
          +
          Finished jobs
          +
          • +
        + + + +
          +
        • +

          FAILED

          +
          public static final JobStatus FAILED
          +
          Failed jobs
          +
          • +
        + + + +
          +
        • +

          UNDEFINED

          +
          public static final JobStatus UNDEFINED
          +
          Represents jobs with unknown status
          +
          • +
        + + + +
          +
        • +

          STARTED

          +
          public static final JobStatus STARTED
          +
          Job calculation has been started. First status reported by the local + engine
          +
          • +
        + + + +
          +
        • +

          SUBMITTED

          +
          public static final JobStatus SUBMITTED
          +
          Job has been submitted. This status is only set for cluster jobs
          +
          • +
        + + + +
          +
        • +

          COLLECTED

          +
          public static final JobStatus COLLECTED
          +
          Results has been collected
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static JobStatus[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (JobStatus c : JobStatus.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static JobStatus valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/docs/full_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..b051784 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,339 @@ + + + + + +JobSubmissionException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class JobSubmissionException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.JobSubmissionException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      Direct Known Subclasses:
      +
      LimitExceededException, UnsupportedRuntimeException
      +
      +
      +
      +
      public class JobSubmissionException
+extends java.lang.Exception
      +
      Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException. If + this exception is thrown the task has not been calculated
      +
      +
      Author:
      +
      pvtroshin + + Date December 2009
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          JobSubmissionException

          +
          public JobSubmissionException(java.lang.String message,
+                              java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/Limit.html b/website/docs/full_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..9974e32 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,594 @@ + + + + + +Limit + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Limit<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Limit<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - the type of an executable for which this limit is defined.
      +
      +
      +
      +
      public class Limit<T>
+extends java.lang.Object
      +
      A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. Also contains static method for determining the + number of sequence and their average length in the List
      +
      +
      Version:
      +
      1.0 January 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      LimitsManager
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) booleanisDefault 
        private java.lang.Stringpreset 
        private intseqLength 
        private intseqNumber 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private Limit() 
         Limit(int seqNumber, + int seqLength, + java.lang.String preset) +
        Instantiate the limit
        +
         Limit(int seqNumber, + int seqLength, + java.lang.String preset, + boolean isDefault) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          preset

          +
          private java.lang.String preset
          +
          • +
        + + + +
          +
        • +

          seqNumber

          +
          private int seqNumber
          +
          • +
        + + + +
          +
        • +

          seqLength

          +
          private int seqLength
          +
          • +
        + + + +
          +
        • +

          isDefault

          +
          boolean isDefault
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Limit

          +
          private Limit()
          +
          • +
        + + + +
          +
        • +

          Limit

          +
          public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset)
          +
          Instantiate the limit
          +
          +
          Parameters:
          +
          seqNumber - the maximum number of sequences allowed for calculation. + Required
          +
          seqLength - the average length of the sequence, optional
          +
          preset - the name of preset if any, optional
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
          +
          +
          • +
        + + + +
          +
        • +

          Limit

          +
          public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset,
+             boolean isDefault)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPreset

          +
          public java.lang.String getPreset()
          +
          • +
        + + + +
          +
        • +

          getAvgSeqLength

          +
          public int getAvgSeqLength()
          +
          +
          Returns:
          +
          the allowed average sequence length
          +
          +
          • +
        + + + +
          +
        • +

          getSeqNumber

          +
          public int getSeqNumber()
          +
          +
          Returns:
          +
          the maximum number of sequences allowed
          +
          +
          • +
        + + + +
          +
        • +

          isDefault

          +
          public boolean isDefault()
          +
          +
          Returns:
          +
          true is this is a default limit to be used, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          numberOfLetters

          +
          long numberOfLetters()
          +
          • +
        + + + +
          +
        • +

          isExceeded

          +
          public boolean isExceeded(java.util.List<FastaSequence> data)
          +
          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
          +
          +
          Parameters:
          +
          data - the dataset to measure
          +
          Returns:
          +
          true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise. First check the number of sequences + in the dataset and if it exceeds the limit return true + irrespective of the average length. If the number of sequences in + the dataset is less than the limit and average length is defined, + then check whether the total number of letters (number of + sequence multiplied by the average sequence length) is greater + then the total number of letters in the dataset. Returns true if + the total number of letters in the dataset is greater than the + limit, false otherwise.
          +
          +
          • +
        + + + +
          +
        • +

          getAvgSequenceLength

          +
          public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
          +
          Calculates an average sequence length of the dataset
          +
          +
          Parameters:
          +
          data -
          +
          Returns:
          +
          an average sequence length in the input dataset
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/LimitExceededException.html b/website/docs/full_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..1adabba --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,454 @@ + + + + + +LimitExceededException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class LimitExceededException

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class LimitExceededException
+extends JobSubmissionException
      +
      This exception is thrown if the task larger in size that the limit that + applies to the calculation.
      +
      +
      Version:
      +
      1.0 February 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Limit, +Serialized Form
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          numberOfSequencesAllowed

          +
          int numberOfSequencesAllowed
          +
          • +
        + + + +
          +
        • +

          actualNumberofSequences

          +
          int actualNumberofSequences
          +
          • +
        + + + +
          +
        • +

          aSequenceLenghtAllowed

          +
          int aSequenceLenghtAllowed
          +
          • +
        + + + +
          +
        • +

          aSequenceLenghtActual

          +
          int aSequenceLenghtActual
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LimitExceededException

          +
          public LimitExceededException(java.lang.String message)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getNumberOfSequencesAllowed

          +
          public int getNumberOfSequencesAllowed()
          +
          • +
        + + + +
          +
        • +

          getActualNumberofSequences

          +
          public int getActualNumberofSequences()
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtAllowed

          +
          public int getSequenceLenghtAllowed()
          +
          • +
        + + + +
          +
        • +

          getSequenceLenghtActual

          +
          public int getSequenceLenghtActual()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/LimitsManager.html b/website/docs/full_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..3fbb1ad --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,427 @@ + + + + + +LimitsManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class LimitsManager<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.LimitsManager<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      +
      public class LimitsManager<T>
+extends java.lang.Object
      +
      A collection of Limits
      +
      +
      Version:
      +
      1.0 January 2010
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Limit
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          java.lang.String runnerClassName
          +
          • +
        + + + +
          +
        • +

          limit

          +
          java.util.List<Limit<T>> limit
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          LimitsManager

          +
          public LimitsManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getLimits

          +
          public java.util.List<Limit<T>> getLimits()
          +
          +
          Returns:
          +
          all limits defined for an executable T
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getLimitByName

          +
          public Limit<T> getLimitByName(java.lang.String presetName)
          +
          +
          Parameters:
          +
          presetName -
          +
          Returns:
          +
          Limit defined for the executable T and presetName. If no limit is + defined for the presetName then default Limit is returned. If + presetName is empty or null than the default Limit will be + returned. If not limit defined for the type T than NULL will be + returned
          +
          +
          • +
        + + + +
          +
        • +

          getDefaultLimit

          +
          public Limit<T> getDefaultLimit()
          +
          +
          Returns:
          +
          the default Limit for an executable type T
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate(PresetManager<T> presets)
+              throws javax.xml.bind.ValidationException
          +
          Validate Limits
          +
          +
          Parameters:
          +
          presets -
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if any of the Limit defined is found to be invalid. That is + when + + 1) No default limit is defined + + 2) More than 1 default limit is defined + + 3) Limit's preset name does not match any presets for type T
          +
          See Also:
          +
          Limit, +Preset
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/Option.html b/website/docs/full_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..0a5a74b --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/Option.html @@ -0,0 +1,831 @@ + + + + + +Option + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Option<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Option<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of executable
      +
      +
      +
      All Implemented Interfaces:
      +
      Argument<T>
      +
      +
      +
      Direct Known Subclasses:
      +
      Parameter
      +
      +
      +
      +
      public class Option<T>
+extends java.lang.Object
+implements Argument<T>
      +
      Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.net.URLbasicURL 
        protected java.lang.StringdefaultValue 
        protected java.lang.Stringdescription 
        protected java.lang.StringfurtherDetails 
        protected booleanisRequired 
        protected java.lang.Stringname 
        (package private) java.util.Set<java.lang.String>optionNames 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        Option() 
        Option(java.lang.String name, + java.lang.String description) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) +
        Adds an option to the optionName list
        +
        booleanequals(java.lang.Object obj) 
        java.net.URLgetBasicURL() 
        java.lang.StringgetDefaultValue() +
        A default value of the option.
        +
        java.lang.StringgetDescription() +
        A long description of the Option
        +
        java.lang.StringgetFurtherDetails() +
        The URL where further details about the option can be found
        +
        java.lang.StringgetName() +
        Human readable name of the option
        +
        java.util.List<java.lang.String>getOptionNames() 
        java.util.List<java.lang.String>getPossibleValues() +
        List of possible optionNames
        +
        inthashCode() 
        booleanisRequired() +
        Flag that indicated that this option must be specified in the command + line for an executable to run
        +
        voidsetBasicURL(java.net.URL url) 
        voidsetDefaultValue(java.lang.String defaultVal) +
        Sets one of the values defined in optionList as default.
        +
        voidsetDescription(java.lang.String description) 
        voidsetFurtherDetails(java.lang.String furtherDetails) 
        voidsetName(java.lang.String name) 
        voidsetOptionNames(java.util.Set<java.lang.String> optionNames) 
        voidsetRequired(boolean isRequired) 
        voidsetValue(java.lang.String dValue) +
        Set default values for the parameter or an option
        +
        java.lang.StringtoCommand(java.lang.String nameValueSeparator) +
        Convert the option to the command string.
        +
        java.lang.StringtoString() 
        (package private) voidvalidate() +
        Validate the option
        +
        (package private) static booleanvalueExist(java.lang.String testValue, + java.util.List<java.lang.String> values) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          description

          +
          protected java.lang.String description
          +
          • +
        + + + +
          +
        • +

          optionNames

          +
          java.util.Set<java.lang.String> optionNames
          +
          • +
        + + + +
          +
        • +

          name

          +
          protected java.lang.String name
          +
          • +
        + + + +
          +
        • +

          isRequired

          +
          protected boolean isRequired
          +
          • +
        + + + +
          +
        • +

          furtherDetails

          +
          protected java.lang.String furtherDetails
          +
          • +
        + + + +
          +
        • +

          defaultValue

          +
          protected java.lang.String defaultValue
          +
          • +
        + + + +
          +
        • +

          basicURL

          +
          private java.net.URL basicURL
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Option

          +
          Option()
          +
          • +
        + + + +
          +
        • +

          Option

          +
          public Option(java.lang.String name,
+              java.lang.String description)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getName

          +
          public java.lang.String getName()
          +
          Human readable name of the option
          +
          +
          Specified by:
          +
          getName in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setName

          +
          public void setName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setBasicURL

          +
          public void setBasicURL(java.net.URL url)
          +
          • +
        + + + +
          +
        • +

          getBasicURL

          +
          public java.net.URL getBasicURL()
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          public java.lang.String getDescription()
          +
          A long description of the Option
          +
          +
          Specified by:
          +
          getDescription in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setDescription

          +
          public void setDescription(java.lang.String description)
          +
          • +
        + + + +
          +
        • +

          getFurtherDetails

          +
          public java.lang.String getFurtherDetails()
          +
          The URL where further details about the option can be found
          +
          +
          Specified by:
          +
          getFurtherDetails in interface Argument<T>
          +
          Throws:
          +
          java.net.MalformedURLException
          +
          +
          • +
        + + + +
          +
        • +

          setFurtherDetails

          +
          public void setFurtherDetails(java.lang.String furtherDetails)
          +
          • +
        + + + +
          +
        • +

          getDefaultValue

          +
          public java.lang.String getDefaultValue()
          +
          A default value of the option. Defaults to command line argument name + e.g. -auto
          +
          +
          Specified by:
          +
          getDefaultValue in interface Argument<T>
          +
          +
          • +
        + + + +
          +
        • +

          setDefaultValue

          +
          public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
          +
          Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception
          +
          +
          Parameters:
          +
          defaultVal -
          +
          Throws:
          +
          WrongParameterException - is thrown if the defaultValue is not found in optionList
          +
          +
          • +
        + + + +
          +
        • +

          valueExist

          +
          static boolean valueExist(java.lang.String testValue,
+                          java.util.List<java.lang.String> values)
          +
          • +
        + + + +
          +
        • +

          isRequired

          +
          public boolean isRequired()
          +
          Flag that indicated that this option must be specified in the command + line for an executable to run
          +
          +
          Returns:
          +
          true is the option is required, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          setRequired

          +
          public void setRequired(boolean isRequired)
          +
          • +
        + + + +
          +
        • +

          getOptionNames

          +
          public java.util.List<java.lang.String> getOptionNames()
          +
          +
          Returns:
          +
          List of option names
          +
          +
          • +
        + + + +
          +
        • +

          setOptionNames

          +
          public void setOptionNames(java.util.Set<java.lang.String> optionNames)
          +
          • +
        + + + +
          +
        • +

          addOptionNames

          +
          public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
          +
          Adds an option to the optionName list
          +
          +
          Parameters:
          +
          value -
          +
          Returns:
          +
          modified optionName list
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toCommand

          +
          public java.lang.String toCommand(java.lang.String nameValueSeparator)
          +
          Convert the option to the command string.
          +
          +
          Returns:
          +
          If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          public java.util.List<java.lang.String> getPossibleValues()
          +
          List of possible optionNames
          +
          +
          Specified by:
          +
          getPossibleValues in interface Argument<T>
          +
          Returns:
          +
          List of values allowed for an Argument
          +
          +
          • +
        + + + +
          +
        • +

          setValue

          +
          public void setValue(java.lang.String dValue)
+              throws WrongParameterException
          +
          Description copied from interface: Argument
          +
          Set default values for the parameter or an option
          +
          +
          Specified by:
          +
          setValue in interface Argument<T>
          +
          Parameters:
          +
          dValue - the value to be set
          +
          Throws:
          +
          WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
          +
          See Also:
          +
          ValueConstrain
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Validate the option
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - is the option is invalid. This happens if option does not + have a default value but have multiple option names, or no + option names is defined
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/Parameter.html b/website/docs/full_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..a1db650 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,655 @@ + + + + + +Parameter + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Parameter<T>

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Argument<T>
      +
      +
      +
      +
      public class Parameter<T>
+extends Option<T>
      +
      A single value containing an option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues
      +
      +
      Version:
      +
      1.0 November 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Option, +Argument
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          possibleValues

          +
          java.util.Set<java.lang.String> possibleValues
          +
          • +
        + + + + +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Parameter

          +
          private Parameter()
          +
          • +
        + + + +
          +
        • +

          Parameter

          +
          public Parameter(java.lang.String name,
+                 java.lang.String description)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          setValidValue

          +
          public void setValidValue(ValueConstrain validValue)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          toCommand

          +
          public java.lang.String toCommand(java.lang.String nameValueSeparator)
          +
          Description copied from class: Option
          +
          Convert the option to the command string.
          +
          +
          Overrides:
          +
          toCommand in class Option<T>
          +
          Returns:
          +
          If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          getPossibleValues

          +
          public java.util.List<java.lang.String> getPossibleValues()
          +
          List is more convenient to work with
          +
          +
          Specified by:
          +
          getPossibleValues in interface Argument<T>
          +
          Overrides:
          +
          getPossibleValues in class Option<T>
          +
          Returns:
          +
          List of String
          +
          +
          • +
        + + + +
          +
        • +

          setPossibleValues

          +
          public void setPossibleValues(java.util.Set<java.lang.String> possibleValues)
          +
          • +
        + + + +
          +
        • +

          addPossibleValues

          +
          public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          setOptionNames

          +
          public void setOptionNames(java.util.Set<java.lang.String> optionName)
          +
          +
          Overrides:
          +
          setOptionNames in class Option<T>
          +
          +
          • +
        + + + +
          +
        • +

          addOptionNames

          +
          public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
          +
          Description copied from class: Option
          +
          Adds an option to the optionName list
          +
          +
          Overrides:
          +
          addOptionNames in class Option<T>
          +
          Returns:
          +
          modified optionName list
          +
          +
          • +
        + + + +
          +
        • +

          getOptionName

          +
          public java.lang.String getOptionName()
          +
          • +
        + + + +
          +
        • +

          setOptionName

          +
          public void setOptionName(java.lang.String optionName)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          java.lang.String getValue()
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Description copied from class: Option
          +
          Validate the option
          +
          +
          Overrides:
          +
          validate in class Option<T>
          +
          Throws:
          +
          javax.xml.bind.ValidationException - is the option is invalid. This happens if option does not + have a default value but have multiple option names, or no + option names is defined
          +
          +
          • +
        + + + +
          +
        • +

          isValidValue

          +
          boolean isValidValue(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          setDefaultValue

          +
          public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
          +
          Description copied from class: Option
          +
          Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception
          +
          +
          Overrides:
          +
          setDefaultValue in class Option<T>
          +
          Throws:
          +
          WrongParameterException - is thrown if the defaultValue is not found in optionList
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/Preset.html b/website/docs/full_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..7191230 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,557 @@ + + + + + +Preset + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class Preset<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.Preset<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - executable type
      +
      +
      +
      +
      public class Preset<T>
+extends java.lang.Object
      +
      Collection of Options and Parameters with their values
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Option, +Parameter
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringdescription 
        (package private) java.lang.Stringname 
        (package private) java.util.List<java.lang.String>option 
        private static java.lang.StringSPACE 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Preset() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) booleancontainValue(java.lang.String option) 
        booleanequals(java.lang.Object obj) 
        java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) +
        Converts list of options as String to type Option
        +
        java.lang.StringgetDescription() 
        java.lang.StringgetName() 
        (package private) java.lang.StringgetName(java.lang.String option) 
        java.util.List<java.lang.String>getOptions() 
        (package private) java.lang.StringgetValue(java.lang.String option) 
        inthashCode() 
        voidsetDescription(java.lang.String description) 
        voidsetName(java.lang.String name) 
        voidsetOptions(java.util.List<java.lang.String> option) 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          name

          +
          java.lang.String name
          +
          • +
        + + + +
          +
        • +

          description

          +
          java.lang.String description
          +
          • +
        + + + +
          +
        • +

          option

          +
          java.util.List<java.lang.String> option
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Preset

          +
          public Preset()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<java.lang.String> option)
          +
          • +
        + + + +
          +
        • +

          setName

          +
          public void setName(java.lang.String name)
          +
          • +
        + + + +
          +
        • +

          setDescription

          +
          public void setDescription(java.lang.String description)
          +
          • +
        + + + +
          +
        • +

          getOptions

          +
          public java.util.List<java.lang.String> getOptions()
          +
          +
          Returns:
          +
          a List of Options as a String
          +
          +
          • +
        + + + +
          +
        • +

          getName

          +
          public java.lang.String getName()
          +
          +
          Returns:
          +
          - name of the Preset
          +
          +
          • +
        + + + +
          +
        • +

          getDescription

          +
          public java.lang.String getDescription()
          +
          +
          Returns:
          +
          - a long description of the Preset
          +
          +
          • +
        + + + + + + + +
          +
        • +

          containValue

          +
          boolean containValue(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          getName

          +
          java.lang.String getName(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          java.lang.String getValue(java.lang.String option)
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/PresetManager.html b/website/docs/full_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..ff4ceb7 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,513 @@ + + + + + +PresetManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class PresetManager<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.PresetManager<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of executable.
      +
      +
      +
      +
      public class PresetManager<T>
+extends java.lang.Object
      +
      Collection of presets and methods to manipulate them @see Preset
      +
      +
      Version:
      +
      1.0 December 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          java.lang.String runnerClassName
          +
          • +
        + + + +
          +
        • +

          preset

          +
          java.util.List<Preset<T>> preset
          +
          • +
        + + + +
          +
        • +

          LOCAL_ENGINE_LIMIT_PRESET

          +
          public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          PresetManager

          +
          public PresetManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getPresets

          +
          public java.util.List<Preset<T>> getPresets()
          +
          • +
        + + + +
          +
        • +

          setPresets

          +
          public void setPresets(java.util.List<Preset<T>> presets)
          +
          • +
        + + + +
          +
        • +

          getRunnerClassName

          +
          public java.lang.String getRunnerClassName()
          +
          +
          Returns:
          +
          fully qualified class name of type T
          +
          +
          • +
        + + + +
          +
        • +

          setRunnerClassName

          +
          public void setRunnerClassName(java.lang.String runnerClassName)
          +
          • +
        + + + +
          +
        • +

          getPresetByName

          +
          public Preset<T> getPresetByName(java.lang.String presetName)
          +
          +
          Parameters:
          +
          presetName -
          +
          Returns:
          +
          preset by its name, null if no preset found
          +
          +
          • +
        + + + +
          +
        • +

          isComposite

          +
          boolean isComposite(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          containsValue

          +
          boolean containsValue(java.util.List<java.lang.String> values,
+                      java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          isNumeric

          +
          boolean isNumeric(java.lang.String value)
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate(RunnerConfig<T> options)
+              throws javax.xml.bind.ValidationException
          +
          Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly!
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if preset is found to be invalid.
          +
          +
          • +
        + + + +
          +
        • +

          getArgument

          +
          Argument<T> getArgument(RunnerConfig<T> options,
+                        java.lang.String optionName)
+                 throws javax.xml.bind.ValidationException
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/docs/full_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..cbfe7b1 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,338 @@ + + + + + +ResultNotAvailableException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ResultNotAvailableException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.ResultNotAvailableException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class ResultNotAvailableException
+extends java.lang.Exception
      +
      ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides lower level exceptions + like DrmaaException
      +
      +
      Author:
      +
      pvtroshin + + Date October 2009
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          ResultNotAvailableException

          +
          public ResultNotAvailableException(java.lang.String message,
+                                   java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/RunnerConfig.html b/website/docs/full_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..d8f7dee --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,790 @@ + + + + + +RunnerConfig + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class RunnerConfig<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.RunnerConfig<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Type Parameters:
      +
      T - type of an Executable
      +
      +
      +
      +
      @NotThreadSafe
+public class RunnerConfig<T>
+extends java.lang.Object
      +
      The list of Parameters and Options supported by executable. + The lists is defined in and loaded from Parameters.xml file.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.util.List<Option<T>>arguments 
        (package private) java.util.List<Option<T>>options 
        (package private) java.util.List<Parameter<T>>parameters 
        (package private) java.lang.StringprmSeparator 
        private java.lang.StringrunnerClassName +
        The class name of a runnable e.g.
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        RunnerConfig() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          runnerClassName

          +
          private java.lang.String runnerClassName
          +
          The class name of a runnable e.g. T
          +
          • +
        + + + +
          +
        • +

          options

          +
          java.util.List<Option<T>> options
          +
          • +
        + + + +
          +
        • +

          prmSeparator

          +
          java.lang.String prmSeparator
          +
          • +
        + + + +
          +
        • +

          parameters

          +
          java.util.List<Parameter<T>> parameters
          +
          • +
        + + + +
          +
        • +

          arguments

          +
          java.util.List<Option<T>> arguments
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RunnerConfig

          +
          public RunnerConfig()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          getOptions

          +
          public java.util.List<Option<T>> getOptions()
          +
          Returns the list of the Options supported by the executable of type T
          +
          +
          Returns:
          +
          list of Option supported by type T
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          addParameter

          +
          public void addParameter(Parameter<T> param)
          +
          Adds parameter to the internal parameter list
          +
          +
          Parameters:
          +
          param - the Parameter to add
          +
          See Also:
          +
          Parameter
          +
          +
          • +
        + + + +
          +
        • +

          addOption

          +
          public void addOption(Option<T> option)
          +
          Adds Option to the internal list of options
          +
          +
          Parameters:
          +
          option - the Option to add
          +
          +
          • +
        + + + +
          +
        • +

          getArguments

          +
          public java.util.List<Option<T>> getArguments()
          +
          Returns list of Parameter and Option supported by current + runner
          +
          +
          Returns:
          +
          list of Option and Parameter supported by type T
          +
          +
          • +
        + + + +
          +
        • +

          getPrmSeparator

          +
          public java.lang.String getPrmSeparator()
          +
          +
          Returns:
          +
          name value separator character
          +
          +
          • +
        + + + +
          +
        • +

          setPrmSeparator

          +
          public void setPrmSeparator(java.lang.String prmSeparator)
          +
          Sets name value separator character
          +
          +
          Parameters:
          +
          prmSeparator - the separator char
          +
          +
          • +
        + + + +
          +
        • +

          setOptions

          +
          public void setOptions(java.util.List<Option<T>> parameters)
          +
          Adds the list of options or parameters to the internal list of options
          +
          +
          Parameters:
          +
          parameters - the list of parameters to add
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerClassName

          +
          public java.lang.String getRunnerClassName()
          +
          +
          Returns:
          +
          fully qualified class name for type T
          +
          +
          • +
        + + + +
          +
        • +

          setRunnerClassName

          +
          public void setRunnerClassName(java.lang.String runnerClassName)
          +
          Set the name of a runner class
          +
          +
          Parameters:
          +
          runnerClassName - the name of the executable wrapping class
          +
          +
          • +
        + + + +
          +
        • +

          setParameters

          +
          public void setParameters(java.util.List<Parameter<T>> parameters)
          +
          Sets the list of parameters as internal list
          +
          +
          Parameters:
          +
          parameters - the list of parameters
          +
          +
          • +
        + + + +
          +
        • +

          getParameters

          +
          public java.util.List<Parameter<T>> getParameters()
          +
          Returns the list of parameters supported executable of type T. Where + Parameter is an Option with value.
          +
          +
          Returns:
          +
          List of Parameter supported by type T.
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getArgument

          +
          public Option<T> getArgument(java.lang.String name)
          +
          Returns the argument by its name if found, NULL otherwise. Where the + Argument is a common interface for Option and Parameter + therefore this method can return either. If you need to retrieve the + Option by its optionNames use @link + getArgumentByOptionName(String) method. The + difference between option name and optionName is explained by the + following example: + + 
          + Sequence type
+         
+         --nuc - Assume the sequences are nucleotide.
+         --amino - Assume the sequences are amino acid. 
+         --amino
+         --nuc
+         --auto
+
          + + In the example, the "Sequence type" is a name whereas --amino, --nuc and + --auto are all optionNames. This dichotomy only manifests in + Option never in Parameters as the latter can + only have single element
          +
          +
          Parameters:
          +
          name - the Parameter of Option name
          +
          Returns:
          +
          Argument
          +
          +
          • +
        + + + +
          +
        • +

          removeArgument

          +
          public boolean removeArgument(java.lang.String name)
          +
          Removes the argument Argument if found. Where Argument is either + Option or Parameter.
          +
          +
          Parameters:
          +
          name - of the argument
          +
          Returns:
          +
          true if argument was removed, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getArgumentByOptionName

          +
          public Option<T> getArgumentByOptionName(java.lang.String optionName)
          +
          Returns the argument by option name, NULL if the argument is not found
          +
          +
          Parameters:
          +
          optionName - - the optionName. This is not the same as an Option name. + + For example: + + 
          +            Output sequences order
+                          --inputorder - Output order: same as input. 
+                           --reorder - Output order: aligned. Default: same as input
+                          --inputorder
+                          --reorder
+
          + + The name of the option in the example is + "Output sequences order" whereas optionNames are + "--inputorder" and "--reorder". If you need to retrieve the + Option or Parameter by its names use + getArgument(String) method
          +
          Returns:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          removeArgumentByOptionName

          +
          public boolean removeArgumentByOptionName(java.lang.String optionName)
          +
          Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
          +
          +
          Parameters:
          +
          optionName - the optionName of the option, do not confuse with the name!
          +
          Returns:
          +
          true if argument with optionName exists and was removed, false + otherwise
          +
          See Also:
          +
          for destinctions + between optionNames and the name of the Option
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          public void validate()
+              throws javax.xml.bind.ValidationException
          +
          Validate the value of the argument. Checks whether the argument value is + in the valid values range.
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - if any of the arguments found invalid which is when +
          +
        • Parameter value outside ValueConstrain boundary
          • +
        • Parameter name is not listed in possible values
          • +
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/docs/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..64d0f5d --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,326 @@ + + + + + +UnsupportedRuntimeException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class UnsupportedRuntimeException

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class UnsupportedRuntimeException
+extends JobSubmissionException
      +
      Indicates that the server could not execute native executables. e.g. If Mafft + (unix executable) is asked to be run on Windows. In context of JABAWS this + exception indicates that the service is deployed but is not able to run.
      +
      +
      Author:
      +
      pvtroshin + + Date February 2010
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          UnsupportedRuntimeException

          +
          public UnsupportedRuntimeException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          UnsupportedRuntimeException

          +
          public UnsupportedRuntimeException(java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/docs/full_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..4941508 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,345 @@ + + + + + +ValueConstrain.Type + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
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    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Enum ValueConstrain.Type

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        Float 
        Integer 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static ValueConstrain.TypevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static ValueConstrain.Type[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static ValueConstrain.Type[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (ValueConstrain.Type c : ValueConstrain.Type.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static ValueConstrain.Type valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/ValueConstrain.html b/website/docs/full_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..7738acb --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,545 @@ + + + + + +ValueConstrain + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class ValueConstrain

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.metadata.ValueConstrain
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ValueConstrain
+extends java.lang.Object
      +
      The type and the lower and upper boundaries for numerical value.
      +
      +
      Version:
      +
      1.0 November 2009
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Nested Class Summary

        + + + + + + + + + + +
        Nested Classes 
        Modifier and TypeClass and Description
        static class ValueConstrain.Type 
        +
        • +
      + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringmax 
        (package private) java.lang.Stringmin 
        (package private) ValueConstrain.Typetype 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ValueConstrain() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) voidcheckValue(java.lang.String value) +
        Validate that the value is within the constrain boundaries
        +
        booleanequals(java.lang.Object obj) 
        java.lang.NumbergetMax() 
        java.lang.NumbergetMin() 
        ValueConstrain.TypegetType() 
        inthashCode() 
        (package private) booleanhasMaxValue() 
        (package private) booleanhasMinValue() 
        voidsetMax(java.lang.String max) 
        voidsetMin(java.lang.String min) 
        voidsetType(ValueConstrain.Type type) 
        java.lang.StringtoString() 
        (package private) voidvalidate() +
        Validate the ValueConstrain object.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, finalize, getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ValueConstrain

          +
          public ValueConstrain()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + + + + + +
          +
        • +

          getMax

          +
          public java.lang.Number getMax()
          +
          • +
        + + + +
          +
        • +

          setMax

          +
          public void setMax(java.lang.String max)
          +
          • +
        + + + +
          +
        • +

          getMin

          +
          public java.lang.Number getMin()
          +
          • +
        + + + +
          +
        • +

          setMin

          +
          public void setMin(java.lang.String min)
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hasMinValue

          +
          boolean hasMinValue()
          +
          • +
        + + + +
          +
        • +

          hasMaxValue

          +
          boolean hasMaxValue()
          +
          • +
        + + + +
          +
        • +

          checkValue

          +
          void checkValue(java.lang.String value)
          +
          Validate that the value is within the constrain boundaries
          +
          +
          Parameters:
          +
          value -
          +
          Throws:
          +
          java.lang.IndexOutOfBoundsException - when the value is outside the defined boundaries
          +
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
+       throws javax.xml.bind.ValidationException
          +
          Validate the ValueConstrain object. For the ValueConstrain object the + type and at least one boundary has to be defined
          +
          +
          Throws:
          +
          javax.xml.bind.ValidationException - - if the type or no boundaries are defined
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
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    Skip navigation links
    + + + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/WrongParameterException.html b/website/docs/full_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..1f714fb --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,350 @@ + + + + + +WrongParameterException + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.metadata
    +

    Class WrongParameterException

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Throwable
        • +
      • +
          +
        • java.lang.Exception
          • +
        • +
            +
          • compbio.metadata.WrongParameterException
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable
      +
      +
      +
      +
      public class WrongParameterException
+extends java.lang.Exception
      +
      WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
      +
      +
      Version:
      +
      1.0 October 2009
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static longserialVersionUID +
        Default stable serial for serialization
        +
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Throwable

          +addSuppressed, fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, getSuppressed, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          serialVersionUID

          +
          private static final long serialVersionUID
          +
          Default stable serial for serialization
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(Option<?> option)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.String message)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.Throwable cause)
          +
          • +
        + + + +
          +
        • +

          WrongParameterException

          +
          public WrongParameterException(java.lang.String message,
+                               java.lang.Throwable cause)
          +
          • +
        +
        • +
      +
      • +
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    compbio.metadata.Argument

    +
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    +
      +
    • + + + + + + + + + + + + +
      Packages that use Argument 
      PackageDescription
      compbio.metadata +
      A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
      +
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    compbio.metadata

    +
    +

    Interfaces

    + +

    Classes

    + +

    Enums

    + +

    Exceptions

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/metadata/package-summary.html b/website/docs/full_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..1396133 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,304 @@ + + + + + +compbio.metadata + + + + + + + + +
    + + +
    Skip navigation links
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    +

    Package compbio.metadata

    +
    +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    +
    +

    See: Description

    +
    +
    +
      +
    • + + + + + + + + + + + + +
      Interface Summary 
      InterfaceDescription
      Argument<T> +
      An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
      +
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      ChunkHolder +
      Represents a chunk of a string data together with the position in a file for + the next read operation.
      +
      Limit<T> +
      A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
      +
      LimitsManager<T> +
      A collection of Limits
      +
      Option<T> +
      Command line option/flag or multiple exclusive options with no value.
      +
      Parameter<T> +
      A single value containing an option supported by the web service e.g.
      +
      Preset<T> +
      Collection of Options and Parameters with their values
      +
      PresetManager<T> +
      Collection of presets and methods to manipulate them @see Preset
      +
      RunnerConfig<T> +
      The list of Parameters and Options supported by executable.
      +
      ValueConstrain +
      The type and the lower and upper boundaries for numerical value.
      +
      +
      • +
    • + + + + + + + + + + + + + + + + +
      Enum Summary 
      EnumDescription
      JobStatus +
      The status of the job.
      +
      ValueConstrain.Type 
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Exception Summary 
      ExceptionDescription
      JobExecutionException +
      JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
      +
      JobSubmissionException +
      Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
      +
      LimitExceededException +
      This exception is thrown if the task larger in size that the limit that + applies to the calculation.
      +
      ResultNotAvailableException +
      ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
      +
      UnsupportedRuntimeException +
      Indicates that the server could not execute native executables.
      +
      WrongParameterException +
      WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
      +
      +
      • +
    + + + +

    Package compbio.metadata Description

    +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS)
    +
    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
    + +
    + + +
    Skip navigation links
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    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/metadata/package-tree.html b/website/docs/full_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..0138647 --- /dev/null +++ b/website/docs/full_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,182 @@ + + + + + +compbio.metadata Class Hierarchy + + + + + + + + +
    + + +
    Skip navigation links
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    + + +
    + +
    +

    Hierarchy For Package compbio.metadata

    +Package Hierarchies: + +
    +
    +

    Class Hierarchy

    + +

    Interface Hierarchy

    + +

    Enum Hierarchy

    +
      +
    • java.lang.Object +
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    compbio.runner
    +

    Class OptionCombinator

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.runner.OptionCombinator
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      @Immutable
+public final class OptionCombinator
+extends java.lang.Object
      +
      This class solve the following problems. Given the RunnerConfig + + 1) generate a valid option string with all options and parameters in it + + 2) Permute all possible combinations of options order and parameters values
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          rand

          +
          private static final java.util.Random rand
          +
          • +
        + + + + +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          optionsToCommandString

          +
          public java.util.List<java.lang.String> optionsToCommandString(java.util.List<Option<?>> options)
          +
          • +
        + + + +
          +
        • +

          getOptionsAtRandom

          +
          public java.util.List<java.lang.String> getOptionsAtRandom()
          +
          • +
        + + + +
          +
        • +

          getAllOptions

          +
          public java.util.List<Option<?>> getAllOptions()
          +
          • +
        + + + +
          +
        • +

          optionToCommandString

          +
          static java.lang.String optionToCommandString(Option<?> option)
          +
          • +
        + + + +
          +
        • +

          getAllParameters

          +
          public java.util.List<Parameter<?>> getAllParameters()
          +
          • +
        + + + +
          +
        • +

          argumentsToCommandString

          +
          public java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments)
          +
          • +
        + + + +
          +
        • +

          argumentsToCommandString

          +
          public static java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments,
+                                                                        RunnerConfig<? extends Executable<?>> rconfig)
          +
          • +
        + + + +
          +
        • +

          parametersToCommandString

          +
          public java.util.List<java.lang.String> parametersToCommandString(java.util.List<Parameter<?>> orderedList,
+                                                                  java.util.Map<Parameter<?>,java.lang.String> prmValue)
          +
          • +
        + + + +
          +
        • +

          getAllConstrainedParametersWithBorderValues

          +
          public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithBorderValues(boolean minValue)
          +
          • +
        + + + +
          +
        • +

          getAllConstrainedParametersWithRandomValues

          +
          public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithRandomValues()
          +
          • +
        + + + +
          +
        • +

          getLowBorderValue

          +
          java.lang.String getLowBorderValue(Parameter<?> param)
          +
          • +
        + + + +
          +
        • +

          getUpperBorderValue

          +
          java.lang.String getUpperBorderValue(Parameter<?> param)
          +
          • +
        + + + +
          +
        • +

          getRandomValue

          +
          java.lang.String getRandomValue(Parameter<?> param)
          +
          • +
        + + + +
          +
        • +

          getValue

          +
          static java.lang.String getValue(Parameter<?> param)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/RunnerUtil.html b/website/docs/full_javadoc/compbio/runner/RunnerUtil.html new file mode 100644 index 0000000..cf64c50 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/RunnerUtil.html @@ -0,0 +1,436 @@ + + + + + +RunnerUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.runner
    +

    Class RunnerUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.runner.RunnerUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class RunnerUtil
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          public static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RunnerUtil

          +
          public RunnerUtil()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + + +
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    + + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/Util.html b/website/docs/full_javadoc/compbio/runner/Util.html new file mode 100644 index 0000000..a6b6e39 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/Util.html @@ -0,0 +1,422 @@ + + + + + +Util + + + + + + + + +
    + + +
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    + + +
    + + +
    + + +
    +
    compbio.runner
    +

    Class Util

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.runner.Util
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class Util
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        static org.apache.log4j.Loggerlog 
        private static compbio.util.PropertyHelperph 
        static java.lang.StringSPACE 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Util() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          public static org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          ph

          +
          private static final compbio.util.PropertyHelper ph
          +
          • +
        + + + + +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Util

          +
          public Util()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/runner/class-use/OptionCombinator.html b/website/docs/full_javadoc/compbio/runner/class-use/OptionCombinator.html new file mode 100644 index 0000000..044ed32 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/class-use/OptionCombinator.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.runner.OptionCombinator + + + + + + + + +
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    +
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    No usage of compbio.runner.OptionCombinator
    + +
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    compbio.runner.conservation
    +

    Class AACon

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Executable<AACon>
      +
      +
      +
      +
      public class AACon
+extends SkeletalExecutable<AACon>
      +
      Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
      +
      +
      Author:
      +
      pvtroshin
      +
      +
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    compbio.runner.conservation

    +
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    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/runner/conservation/package-summary.html b/website/docs/full_javadoc/compbio/runner/conservation/package-summary.html new file mode 100644 index 0000000..70e61fa --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/conservation/package-summary.html @@ -0,0 +1,146 @@ + + + + + +compbio.runner.conservation + + + + + + + + +
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    Package compbio.runner.conservation

    +
    +
    +
      +
    • + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      AACon +
      Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
      +
      +
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    Hierarchy For Package compbio.runner.conservation

    +Package Hierarchies: + +
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    Class Hierarchy

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    compbio.runner.disorder
    +

    Class Disembl

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Executable<Disembl>, PipedExecutable<Disembl>
      +
      +
      +
      +
      public class Disembl
+extends SkeletalExecutable<Disembl>
+implements PipedExecutable<Disembl>
      +
      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops + fold_rem465 sequence_file print + + 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' + + This version of DisEMBL is 1.4 (latest available for download in Feb 2011) + capable of outputting raw values + + The values of the parameters are hard coded in DisEMBL.py script. + smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4 + fold_rem465=1.2 + + Changing these values are not recommended by developers, apart from smoothing + window. However, 5 orders of magnitude changes in this parameter does not + change the output so allowing this change also seems pointless. Finally, the + binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to + these values, so changing them can lead to problems. + + + This is not a standard DisEMBL! The script has been modified!
      +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/GlobPlot.html b/website/docs/full_javadoc/compbio/runner/disorder/GlobPlot.html new file mode 100644 index 0000000..b240683 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/GlobPlot.html @@ -0,0 +1,409 @@ + + + + + +GlobPlot + + + + + + + + +
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    compbio.runner.disorder
    +

    Class GlobPlot

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Executable<GlobPlot>, PipedExecutable<GlobPlot>
      +
      +
      +
      +
      public class GlobPlot
+extends SkeletalExecutable<GlobPlot>
+implements PipedExecutable<GlobPlot>
      +
      ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5. + + Changing these values are not recommended by developers, apart from smoothing + window. However, the binary, GlobPlot depends on - Tisean which is not happy + with arbitrary changes to these values, so changing them can lead to + problems. May be we can offer preset? + + This is not a standard GlobPlot! The script has been modified!
      +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/IUPred.html b/website/docs/full_javadoc/compbio/runner/disorder/IUPred.html new file mode 100644 index 0000000..03599b8 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/IUPred.html @@ -0,0 +1,505 @@ + + + + + +IUPred + + + + + + + + +
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    +
    compbio.runner.disorder
    +

    Class IUPred

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Executable<IUPred>
      +
      +
      +
      +
      public class IUPred
+extends SkeletalExecutable<IUPred>
      +
      iupred sequenceFile + + Maximum sequence length is 40000 chars. Single string length max is a 1000 + chars!
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/Jronn.html b/website/docs/full_javadoc/compbio/runner/disorder/Jronn.html new file mode 100644 index 0000000..9423657 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/Jronn.html @@ -0,0 +1,555 @@ + + + + + +Jronn + + + + + + + + +
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    compbio.runner.disorder
    +

    Class Jronn

    +
    +
    + +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      Executable<Jronn>
      +
      +
      +
      +
      public class Jronn
+extends SkeletalExecutable<Jronn>
      +
      Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
      +
      +
      Author:
      +
      pvtroshin
      +
      +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/class-use/Disembl.html b/website/docs/full_javadoc/compbio/runner/disorder/class-use/Disembl.html new file mode 100644 index 0000000..9cdb7df --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/class-use/Disembl.html @@ -0,0 +1,205 @@ + + + + + +Uses of Class compbio.runner.disorder.Disembl + + + + + + + + +
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    compbio.runner.disorder

    +
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    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/package-summary.html b/website/docs/full_javadoc/compbio/runner/disorder/package-summary.html new file mode 100644 index 0000000..aafce25 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/package-summary.html @@ -0,0 +1,179 @@ + + + + + +compbio.runner.disorder + + + + + + + + +
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    Package compbio.runner.disorder

    +
    +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      Disembl +
      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops + fold_rem465 sequence_file print + + 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' + + This version of DisEMBL is 1.4 (latest available for download in Feb 2011) + capable of outputting raw values + + The values of the parameters are hard coded in DisEMBL.py script.
      +
      GlobPlot +
      ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5.
      +
      IUPred +
      iupred sequenceFile + + Maximum sequence length is 40000 chars.
      +
      Jronn +
      Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
      +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/package-tree.html b/website/docs/full_javadoc/compbio/runner/disorder/package-tree.html new file mode 100644 index 0000000..8c5f815 --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/package-tree.html @@ -0,0 +1,144 @@ + + + + + +compbio.runner.disorder Class Hierarchy + + + + + + + + +
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    Hierarchy For Package compbio.runner.disorder

    +Package Hierarchies: + +
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    Class Hierarchy

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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/disorder/package-use.html b/website/docs/full_javadoc/compbio/runner/disorder/package-use.html new file mode 100644 index 0000000..0bdc6cb --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/disorder/package-use.html @@ -0,0 +1,237 @@ + + + + + +Uses of Package compbio.runner.disorder + + + + + + + + +
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    compbio.runner.disorder

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    • + + + + + + + + + + + + + + + + +
      Packages that use compbio.runner.disorder 
      PackageDescription
      compbio.runner.disorder 
      compbio.ws.server 
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + +
      Classes in compbio.runner.disorder used by compbio.runner.disorder 
      Class and Description
      Disembl +
      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops + fold_rem465 sequence_file print + + 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' + + This version of DisEMBL is 1.4 (latest available for download in Feb 2011) + capable of outputting raw values + + The values of the parameters are hard coded in DisEMBL.py script.
      +
      GlobPlot +
      ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5.
      +
      IUPred +
      iupred sequenceFile + + Maximum sequence length is 40000 chars.
      +
      Jronn +
      Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
      +
      +
      • +
    • + + + + + + + + + + + + + + + + + + +
      Classes in compbio.runner.disorder used by compbio.ws.server 
      Class and Description
      Disembl +
      DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops + fold_rem465 sequence_file print + + 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' + + This version of DisEMBL is 1.4 (latest available for download in Feb 2011) + capable of outputting raw values + + The values of the parameters are hard coded in DisEMBL.py script.
      +
      GlobPlot +
      ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5.
      +
      IUPred +
      iupred sequenceFile + + Maximum sequence length is 40000 chars.
      +
      +
      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/runner/msa/ClustalO.html b/website/docs/full_javadoc/compbio/runner/msa/ClustalO.html new file mode 100644 index 0000000..375149d --- /dev/null +++ b/website/docs/full_javadoc/compbio/runner/msa/ClustalO.html @@ -0,0 +1,540 @@ + + + + + +ClustalO + + + + + + + + +
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    compbio.runner.msa
    +

    Class ClustalO

    +
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    compbio.runner.msa

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    Package compbio.runner.msa

    +
    +
    Wrappers for native executables for multiple sequence alignment (msa)
    +
    +

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    +
    + + + + +

    Package compbio.runner.msa Description

    +
    Wrappers for native executables for multiple sequence alignment (msa)
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    +
    Author:
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    Petr Troshin + + Date January 2010
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    Package compbio.runner

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    Utilities commonly used by all runners.
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      Class Summary 
      ClassDescription
      OptionCombinator +
      This class solve the following problems.
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      RunnerUtil 
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    Package compbio.runner Description

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    Utilities commonly used by all runners.
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    Petr Troshin + + Date January 2010
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    Package compbio.runner.structure

    +
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      Class Summary 
      ClassDescription
      RNAalifold 
      +
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    Hierarchy For Package compbio.runner.structure

    +Package Hierarchies: + +
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    Class Hierarchy

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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/DirCleaner.html b/website/docs/full_javadoc/compbio/stat/collector/DirCleaner.html new file mode 100644 index 0000000..d40674f --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/DirCleaner.html @@ -0,0 +1,444 @@ + + + + + +DirCleaner + + + + + + + + +
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    compbio.stat.collector
    +

    Class DirCleaner

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.DirCleaner
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Runnable
      +
      +
      +
      +
      public class DirCleaner
+extends java.lang.Object
+implements java.lang.Runnable
      +
      Number of runs of each WS = number of folders with name + + Number of successful runs = all runs with no result file + + Per period of time = limit per file creating time Runtime (avg/max) = + + started time - finished time + + Task & result size = result.size + + Abandoned runs - not collected runs + + Cancelled runs - cancelled + + Cluster vs local runs + + Reasons for failure = look in the err out? + + Metadata required: + + work directory for local and cluster tasks = from Helper or cmd parameter. WS + names - enumeration. Status file names and content.
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.io.FileFilterdirectories 
        private intLifeSpanInHours 
        private static org.apache.log4j.Loggerlog 
        (package private) static intUNDEFINED 
        private java.io.FileworkDirectory 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        DirCleaner(java.lang.String workDirectory, + int LifeSpanInHours) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          workDirectory

          +
          private final java.io.File workDirectory
          +
          • +
        + + + +
          +
        • +

          LifeSpanInHours

          +
          private final int LifeSpanInHours
          +
          • +
        + + + +
          +
        • +

          directories

          +
          static java.io.FileFilter directories
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          DirCleaner

          +
          public DirCleaner(java.lang.String workDirectory,
+                  int LifeSpanInHours)
          +
          +
          Parameters:
          +
          workDirectory -
          +
          timeOutInHours -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          hasCompleted

          +
          boolean hasCompleted(JobDirectory jd)
          +
          • +
        + + + +
          +
        • +

          livesOverLifeSpan

          +
          boolean livesOverLifeSpan(JobDirectory jd)
          +
          • +
        + + + +
          +
        • +

          doCleaning

          +
          void doCleaning()
          +
          • +
        + + + +
          +
        • +

          run

          +
          public void run()
          +
          +
          Specified by:
          +
          run in interface java.lang.Runnable
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/ExecutionStatCollector.html b/website/docs/full_javadoc/compbio/stat/collector/ExecutionStatCollector.html new file mode 100644 index 0000000..dee3d20 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/ExecutionStatCollector.html @@ -0,0 +1,530 @@ + + + + + +ExecutionStatCollector + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class ExecutionStatCollector

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.ExecutionStatCollector
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.lang.Runnable
      +
      +
      +
      +
      public class ExecutionStatCollector
+extends java.lang.Object
+implements java.lang.Runnable
      +
      Class assumptions: + 1. Number of runs of each WS = number of folders with name + 2. Number of successful runs = all runs with no result file + 3. Per period of time = limit per file creating time + 4. Runtime (avg/max) = finish time - start time + 5. Task & result size = result.size + + Abandoned runs - not collected runs + + Cancelled runs - cancelled + + Cluster vs local runs + + Reasons for failure = look in the err out? + + + Metadata required: + + work directory for local and cluster tasks = from Helper or cmd parameter. WS + names - enumeration. Status file names and content.
      +
      +
      Author:
      +
      Peter Troshin, Alexander Sherstnev
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.text.SimpleDateFormatDF 
        (package private) static java.io.FileFilterdirectories 
        private static org.apache.log4j.Loggerlog 
        private java.util.List<JobStat>stats 
        private inttimeOutInHours +
        Consider the job that has been working for longer than timeOutInHours + completed, whatever the outcome
        +
        (package private) static intUNDEFINED 
        private java.io.FileworkingDirectory 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ExecutionStatCollector(java.lang.String workingDirectory, + int timeOutInHours) +
        List subdirectories in the job directory
        +
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          DF

          +
          static java.text.SimpleDateFormat DF
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          workingDirectory

          +
          private final java.io.File workingDirectory
          +
          • +
        + + + +
          +
        • +

          stats

          +
          private final java.util.List<JobStat> stats
          +
          • +
        + + + +
          +
        • +

          timeOutInHours

          +
          private final int timeOutInHours
          +
          Consider the job that has been working for longer than timeOutInHours + completed, whatever the outcome
          +
          • +
        + + + +
          +
        • +

          directories

          +
          static java.io.FileFilter directories
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ExecutionStatCollector

          +
          public ExecutionStatCollector(java.lang.String workingDirectory,
+                              int timeOutInHours)
          +
          List subdirectories in the job directory
          +
          +
          Parameters:
          +
          workingDirectory -
          +
          timeOutInHours -
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          hasCompleted

          +
          boolean hasCompleted(JobDirectory jd)
          +
          • +
        + + + + + + + + + + + +
          +
        • +

          writeStatToDB

          +
          void writeStatToDB()
+            throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
+                 throws java.io.IOException,
+                        java.sql.SQLException
          +
          Not in use
          +
          +
          Throws:
          +
          java.io.IOException
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          collectStatistics

          +
          void collectStatistics()
          +
          • +
        + + + +
          +
        • +

          run

          +
          public void run()
          +
          +
          Specified by:
          +
          run in interface java.lang.Runnable
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/InputFilter.html b/website/docs/full_javadoc/compbio/stat/collector/InputFilter.html new file mode 100644 index 0000000..b0a73f0 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/InputFilter.html @@ -0,0 +1,345 @@ + + + + + +InputFilter + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class InputFilter

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.InputFilter
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class InputFilter
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        InputFilter() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static booleanaccept(java.io.File input) +
        Accepts input as valid unless it is a test input
        +
        private static booleancompareClustalLines(java.io.File input, + java.lang.String[] reference) 
        private static booleancompareLines(java.io.File input, + java.lang.String[] reference) 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          InputFilter

          +
          public InputFilter()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          accept

          +
          static boolean accept(java.io.File input)
          +
          Accepts input as valid unless it is a test input
          +
          +
          Parameters:
          +
          input -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          compareLines

          +
          private static boolean compareLines(java.io.File input,
+                                    java.lang.String[] reference)
          +
          • +
        + + + +
          +
        • +

          compareClustalLines

          +
          private static boolean compareClustalLines(java.io.File input,
+                                           java.lang.String[] reference)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/JobDirectory.html b/website/docs/full_javadoc/compbio/stat/collector/JobDirectory.html new file mode 100644 index 0000000..ac8ad2c --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/JobDirectory.html @@ -0,0 +1,505 @@ + + + + + +JobDirectory + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class JobDirectory

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.JobDirectory
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class JobDirectory
+extends java.lang.Object
      +
      +
      Author:
      +
      Alexander Sherstnev
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.util.Map<java.lang.String,java.io.File>files 
        (package private) java.io.Filejobdir 
        private static org.apache.log4j.Loggerlog 
        (package private) static intUNDEFINED 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        JobDirectory(java.io.File directory) 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          jobdir

          +
          java.io.File jobdir
          +
          • +
        + + + +
          +
        • +

          files

          +
          java.util.Map<java.lang.String,java.io.File> files
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobDirectory

          +
          JobDirectory(java.io.File directory)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          hasStatus

          +
          boolean hasStatus(JobStatus status)
          +
          • +
        + + + +
          +
        • +

          isCollected

          +
          boolean isCollected()
          +
          • +
        + + + +
          +
        • +

          isCancelled

          +
          boolean isCancelled()
          +
          • +
        + + + +
          +
        • +

          getStartTime

          +
          long getStartTime()
          +
          • +
        + + + +
          +
        • +

          getClusterJobID

          +
          java.lang.String getClusterJobID()
          +
          • +
        + + + +
          +
        • +

          getFinishedTime

          +
          long getFinishedTime()
          +
          • +
        + + + +
          +
        • +

          getService

          +
          private Services getService()
          +
          • +
        + + + +
          +
        • +

          getResultSize

          +
          long getResultSize()
          +
          • +
        + + + +
          +
        • +

          getInputSize

          +
          long getInputSize()
          +
          • +
        + + + +
          +
        • +

          getJobStat

          +
          JobStat getJobStat()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/JobStat.html b/website/docs/full_javadoc/compbio/stat/collector/JobStat.html new file mode 100644 index 0000000..ce172b9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/JobStat.html @@ -0,0 +1,866 @@ + + + + + +JobStat + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class JobStat

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.JobStat
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class JobStat
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          RUNTIME

          +
          static final java.util.Comparator<JobStat> RUNTIME
          +
          • +
        + + + +
          +
        • +

          STARTTIME

          +
          static final java.util.Comparator<JobStat> STARTTIME
          +
          • +
        + + + +
          +
        • +

          RESULTSIZE

          +
          static final java.util.Comparator<JobStat> RESULTSIZE
          +
          • +
        + + + +
          +
        • +

          DATE_TIME

          +
          private static java.text.DateFormat DATE_TIME
          +
          • +
        + + + + + + + +
          +
        • +

          clusterJobId

          +
          java.lang.String clusterJobId
          +
          • +
        + + + +
          +
        • +

          jobname

          +
          java.lang.String jobname
          +
          • +
        + + + +
          +
        • +

          start

          +
          long start
          +
          • +
        + + + +
          +
        • +

          finish

          +
          long finish
          +
          • +
        + + + +
          +
        • +

          inputSize

          +
          long inputSize
          +
          • +
        + + + +
          +
        • +

          resultSize

          +
          long resultSize
          +
          • +
        + + + +
          +
        • +

          isCollected

          +
          boolean isCollected
          +
          • +
        + + + +
          +
        • +

          isCancelled

          +
          boolean isCancelled
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JobStat

          +
          private JobStat(Services webService,
+                java.lang.String clusterJobId,
+                java.lang.String jobname,
+                long start,
+                long finish,
+                long inputSize,
+                long resultSize,
+                boolean isCancelled,
+                boolean isCollected)
          +
          • +
        + + + +
          +
        • +

          JobStat

          +
          private JobStat(java.lang.String jobId)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          newInstance

          +
          public static JobStat newInstance(Services webService,
+                                  java.lang.String clusterJobId,
+                                  java.lang.String jobname,
+                                  long start,
+                                  long finish,
+                                  long inputSize,
+                                  long resultSize,
+                                  boolean isCancelled,
+                                  boolean isCollected)
          +
          • +
        + + + +
          +
        • +

          newInstance

          +
          public static JobStat newInstance(Services webService,
+                                  java.lang.String clusterJobId,
+                                  java.lang.String jobname,
+                                  java.sql.Timestamp start,
+                                  java.sql.Timestamp finish,
+                                  long inputSize,
+                                  long resultSize,
+                                  boolean isCancelled,
+                                  boolean isCollected)
          +
          • +
        + + + +
          +
        • +

          validate

          +
          void validate()
          +
          • +
        + + + +
          +
        • +

          newIncompleteStat

          +
          public static JobStat newIncompleteStat(java.lang.String jobname)
          +
          • +
        + + + +
          +
        • +

          isClusterJob

          +
          public boolean isClusterJob()
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getRuntime

          +
          public int getRuntime()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getJobReport

          +
          java.lang.String getJobReport()
          +
          • +
        + + + +
          +
        • +

          getJobReportTabulated

          +
          java.lang.String getJobReportTabulated()
          +
          Header Job Started Finished Runtime Input Result
          +
          • +
        + + + +
          +
        • +

          getWebService

          +
          public Services getWebService()
          +
          • +
        + + + +
          +
        • +

          getClusterJobId

          +
          public java.lang.String getClusterJobId()
          +
          • +
        + + + +
          +
        • +

          getJobname

          +
          public java.lang.String getJobname()
          +
          • +
        + + + +
          +
        • +

          getEscJobname

          +
          public java.lang.String getEscJobname()
          +
          • +
        + + + +
          +
        • +

          getStart

          +
          public java.lang.String getStart()
          +
          • +
        + + + +
          +
        • +

          getNumericalStart

          +
          public long getNumericalStart()
          +
          • +
        + + + +
          +
        • +

          getNumericalFinish

          +
          public long getNumericalFinish()
          +
          • +
        + + + +
          +
        • +

          getFinish

          +
          public java.lang.String getFinish()
          +
          • +
        + + + +
          +
        • +

          getInputSize

          +
          public long getInputSize()
          +
          • +
        + + + +
          +
        • +

          getResultSize

          +
          public long getResultSize()
          +
          • +
        + + + +
          +
        • +

          hasResult

          +
          public boolean hasResult()
          +
          • +
        + + + +
          +
        • +

          hasStarted

          +
          public boolean hasStarted()
          +
          • +
        + + + +
          +
        • +

          getIsCollected

          +
          public boolean getIsCollected()
          +
          • +
        + + + +
          +
        • +

          getIsCancelled

          +
          public boolean getIsCancelled()
          +
          • +
        + + + +
          +
        • +

          getIsFinished

          +
          public boolean getIsFinished()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/StatDB.html b/website/docs/full_javadoc/compbio/stat/collector/StatDB.html new file mode 100644 index 0000000..e3be39a --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/StatDB.html @@ -0,0 +1,689 @@ + + + + + +StatDB + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class StatDB

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.StatDB
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class StatDB
+extends java.lang.Object
      +
      The database must be stored in the application root directory and called + "ExecutionStatistic"
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.sql.Connectionconn 
        private static java.lang.Stringdriver 
        private static org.apache.log4j.Loggerlog 
        private static java.lang.Stringprotocol 
        private static java.lang.StringstatDBName 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + +
        Constructors 
        Constructor and Description
        StatDB() 
        StatDB(boolean ignored) +
        Connect to test database
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static voidclearStatTable() 
        private voidcreateStatTable() +
        rs.getBoolean(i) will return true for any non-zero value and false for 0 + on SMALLINT data column.
        +
        intgetAbandonedCount(java.sql.Timestamp from, + java.sql.Timestamp to) 
        intgetCancelledCount(java.sql.Timestamp from, + java.sql.Timestamp to) 
        private static java.sql.ConnectiongetDBConnection() 
        java.util.DategetEarliestRecord() 
        intgetIncompleteCount(java.sql.Timestamp from, + java.sql.Timestamp to) 
        private intgetIntResult(java.sql.Timestamp from, + java.sql.Timestamp to, + java.lang.String query) 
        private static java.sql.ConnectiongetTestDBConnection() 
        intgetTotalJobsCount(java.sql.Timestamp from, + java.sql.Timestamp to) 
        (package private) voidinsertData(java.util.Set<JobStat> jobstatus) 
        static voidmain(java.lang.String[] args) 
        java.util.List<JobStat>readData(java.sql.Timestamp from, + java.sql.Timestamp to, + Services wservice, + java.lang.Boolean clusterOnly) 
        voidremoveRecordedJobs(java.util.Set<JobStat> fsJobs) +
        Removes the job if + + 1) It has already been recorded + + 2) It has not completed and did not timeout - this is to prevent + recording the information on the incomplete jobs.
        +
        static voidshutdownDBServer() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + + + + + +
          +
        • +

          statDBName

          +
          private static final java.lang.String statDBName
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          conn

          +
          static java.sql.Connection conn
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StatDB

          +
          public StatDB()
+       throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          StatDB

          +
          StatDB(boolean ignored)
+throws java.sql.SQLException
          +
          Connect to test database
          +
          +
          Parameters:
          +
          ignored -
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getDBConnection

          +
          private static java.sql.Connection getDBConnection()
+                                            throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getTestDBConnection

          +
          private static java.sql.Connection getTestDBConnection()
+                                                throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          createStatTable

          +
          private void createStatTable()
+                      throws java.sql.SQLException
          +
          rs.getBoolean(i) will return true for any non-zero value and false for 0 + on SMALLINT data column.
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          clearStatTable

          +
          static void clearStatTable()
+                    throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          insertData

          +
          void insertData(java.util.Set<JobStat> jobstatus)
+         throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getEarliestRecord

          +
          public java.util.Date getEarliestRecord()
+                                 throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getTotalJobsCount

          +
          public int getTotalJobsCount(java.sql.Timestamp from,
+                             java.sql.Timestamp to)
+                      throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getCancelledCount

          +
          public int getCancelledCount(java.sql.Timestamp from,
+                             java.sql.Timestamp to)
+                      throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getAbandonedCount

          +
          public int getAbandonedCount(java.sql.Timestamp from,
+                             java.sql.Timestamp to)
+                      throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getIncompleteCount

          +
          public int getIncompleteCount(java.sql.Timestamp from,
+                              java.sql.Timestamp to)
+                       throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getIntResult

          +
          private int getIntResult(java.sql.Timestamp from,
+                         java.sql.Timestamp to,
+                         java.lang.String query)
+                  throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          readData

          +
          public java.util.List<JobStat> readData(java.sql.Timestamp from,
+                                        java.sql.Timestamp to,
+                                        Services wservice,
+                                        java.lang.Boolean clusterOnly)
+                                 throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          removeRecordedJobs

          +
          public void removeRecordedJobs(java.util.Set<JobStat> fsJobs)
+                        throws java.sql.SQLException
          +
          Removes the job if + + 1) It has already been recorded + + 2) It has not completed and did not timeout - this is to prevent + recording the information on the incomplete jobs.
          +
          +
          Parameters:
          +
          fsJobs -
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          shutdownDBServer

          +
          public static final void shutdownDBServer()
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/StatProcessor.html b/website/docs/full_javadoc/compbio/stat/collector/StatProcessor.html new file mode 100644 index 0000000..286a626 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/StatProcessor.html @@ -0,0 +1,516 @@ + + + + + +StatProcessor + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.collector
    +

    Class StatProcessor

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.collector.StatProcessor
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class StatProcessor
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          stats

          +
          java.util.List<JobStat> stats
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StatProcessor

          +
          public StatProcessor(java.util.List<JobStat> stats)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getClusterJobs

          +
          public java.util.List<JobStat> getClusterJobs()
          +
          • +
        + + + +
          +
        • +

          getLocalJobs

          +
          public java.util.List<JobStat> getLocalJobs()
          +
          • +
        + + + +
          +
        • +

          getJobSubset

          +
          private java.util.List<JobStat> getJobSubset(boolean cluster)
          +
          • +
        + + + +
          +
        • +

          getAbandonedJobs

          +
          public java.util.List<JobStat> getAbandonedJobs()
          +
          Not collected. Excludes all cancelled jobs, and jobs with no results as + these are reported separately.
          +
          • +
        + + + +
          +
        • +

          getFailedJobs

          +
          public java.util.List<JobStat> getFailedJobs()
          +
          Started & finished but did not produce result
          +
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          getCancelledJobs

          +
          public java.util.List<JobStat> getCancelledJobs()
          +
          • +
        + + + +
          +
        • +

          sortByRuntime

          +
          public java.util.List<JobStat> sortByRuntime()
          +
          • +
        + + + +
          +
        • +

          sortByStartTime

          +
          public java.util.List<JobStat> sortByStartTime()
          +
          • +
        + + + +
          +
        • +

          sortByResultSize

          +
          public java.util.List<JobStat> sortByResultSize()
          +
          • +
        + + + +
          +
        • +

          getJobNumber

          +
          public int getJobNumber()
          +
          • +
        + + + +
          +
        • +

          getJobs

          +
          public java.util.List<JobStat> getJobs()
          +
          • +
        + + + + + + + +
          +
        • +

          getTotalRuntime

          +
          public long getTotalRuntime()
          +
          • +
        + + + +
          +
        • +

          getIncompleteJobs

          +
          public java.util.List<JobStat> getIncompleteJobs()
          +
          • +
        + + + +
          +
        • +

          reportStat

          +
          public java.lang.String reportStat()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/class-use/DirCleaner.html b/website/docs/full_javadoc/compbio/stat/collector/class-use/DirCleaner.html new file mode 100644 index 0000000..4fd01e2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/class-use/DirCleaner.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.collector.DirCleaner + + + + + + + + +
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    Uses of Class
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    +
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    Uses of Class
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    +
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    No usage of compbio.stat.collector.ExecutionStatCollector
    + +
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    compbio.stat.collector.JobStat

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    Uses of Class
    compbio.stat.collector.StatDB

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    + +
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    Uses of Class
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/package-frame.html b/website/docs/full_javadoc/compbio/stat/collector/package-frame.html new file mode 100644 index 0000000..c230de4 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/package-frame.html @@ -0,0 +1,26 @@ + + + + + +compbio.stat.collector + + + + + +

    compbio.stat.collector

    +
    +

    Classes

    + +
    + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/package-summary.html b/website/docs/full_javadoc/compbio/stat/collector/package-summary.html new file mode 100644 index 0000000..da6cf3a --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/package-summary.html @@ -0,0 +1,194 @@ + + + + + +compbio.stat.collector + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    +

    Package compbio.stat.collector

    +
    +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      DirCleaner +
      Number of runs of each WS = number of folders with name + + Number of successful runs = all runs with no result file + + Per period of time = limit per file creating time Runtime (avg/max) = + + started time - finished time + + Task & result size = result.size + + Abandoned runs - not collected runs + + Cancelled runs - cancelled + + Cluster vs local runs + + Reasons for failure = look in the err out? + + Metadata required: + + work directory for local and cluster tasks = from Helper or cmd parameter.
      +
      ExecutionStatCollector +
      Class assumptions: + 1.
      +
      InputFilter 
      JobDirectory 
      JobStat 
      StatDB +
      The database must be stored in the application root directory and called + "ExecutionStatistic"
      +
      StatProcessor 
      +
      • +
    +
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/package-tree.html b/website/docs/full_javadoc/compbio/stat/collector/package-tree.html new file mode 100644 index 0000000..fc17e59 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/package-tree.html @@ -0,0 +1,143 @@ + + + + + +compbio.stat.collector Class Hierarchy + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    +

    Hierarchy For Package compbio.stat.collector

    +Package Hierarchies: + +
    +
    +

    Class Hierarchy

    + +
    + +
    + + +
    Skip navigation links
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/collector/package-use.html b/website/docs/full_javadoc/compbio/stat/collector/package-use.html new file mode 100644 index 0000000..aa459d6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/collector/package-use.html @@ -0,0 +1,182 @@ + + + + + +Uses of Package compbio.stat.collector + + + + + + + + +
    + + +
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    Uses of Package
    compbio.stat.collector

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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/AnnualStat.html b/website/docs/full_javadoc/compbio/stat/servlet/AnnualStat.html new file mode 100644 index 0000000..3e601e9 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/AnnualStat.html @@ -0,0 +1,327 @@ + + + + + +AnnualStat + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class AnnualStat

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.AnnualStat
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class AnnualStat
+extends javax.servlet.http.HttpServlet
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AnnualStat() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        (package private) static booleanisAdmin(javax.servlet.http.HttpServletRequest request) 
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doHead, doOptions, doPost, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AnnualStat

          +
          public AnnualStat()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          isAdmin

          +
          static boolean isAdmin(javax.servlet.http.HttpServletRequest request)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/DisplayStat.html b/website/docs/full_javadoc/compbio/stat/servlet/DisplayStat.html new file mode 100644 index 0000000..32369fb --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/DisplayStat.html @@ -0,0 +1,350 @@ + + + + + +DisplayStat + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class DisplayStat

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.DisplayStat
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class DisplayStat
+extends javax.servlet.http.HttpServlet
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        DisplayStat() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doHead, doOptions, doPost, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          DisplayStat

          +
          public DisplayStat()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/DownloadRedirector.html b/website/docs/full_javadoc/compbio/stat/servlet/DownloadRedirector.html new file mode 100644 index 0000000..96e32dd --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/DownloadRedirector.html @@ -0,0 +1,338 @@ + + + + + +DownloadRedirector + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class DownloadRedirector

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.DownloadRedirector
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class DownloadRedirector
+extends javax.servlet.http.HttpServlet
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        DownloadRedirector() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        protected voiddoPost(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doHead, doOptions, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          DownloadRedirector

          +
          public DownloadRedirector()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          doPost

          +
          protected void doPost(javax.servlet.http.HttpServletRequest req,
+                      javax.servlet.http.HttpServletResponse resp)
+               throws javax.servlet.ServletException,
+                      java.io.IOException
          +
          +
          Overrides:
          +
          doPost in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/HttpCodeResponseServiceStatus.html b/website/docs/full_javadoc/compbio/stat/servlet/HttpCodeResponseServiceStatus.html new file mode 100644 index 0000000..1622e3f --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/HttpCodeResponseServiceStatus.html @@ -0,0 +1,383 @@ + + + + + +HttpCodeResponseServiceStatus + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class HttpCodeResponseServiceStatus

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.HttpCodeResponseServiceStatus
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class HttpCodeResponseServiceStatus
+extends javax.servlet.http.HttpServlet
      +
      This servlet checks the webservice coming as pathinfo and returns http code + as a reply. If the web service functions correctly then OK (200) is returned. + otherwise Service unavailable (503). When the webservice is not recognised + unknown service error (400) is sent as a response. + + If no pathinfo is specified all web services are checked and OK is returned + only if all webservices are functioning.
      +
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + + + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        protected voiddoHead(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doOptions, doPost, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          HttpCodeResponseServiceStatus

          +
          public HttpCodeResponseServiceStatus()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          doHead

          +
          protected void doHead(javax.servlet.http.HttpServletRequest req,
+                      javax.servlet.http.HttpServletResponse resp)
+               throws javax.servlet.ServletException,
+                      java.io.IOException
          +
          +
          Overrides:
          +
          doHead in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/Joblist.html b/website/docs/full_javadoc/compbio/stat/servlet/Joblist.html new file mode 100644 index 0000000..292f06b --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/Joblist.html @@ -0,0 +1,445 @@ + + + + + +Joblist + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class Joblist

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.Joblist
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class Joblist
+extends javax.servlet.http.HttpServlet
      +
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.StringJT_ABANDONED 
        (package private) static java.lang.StringJT_ALL 
        (package private) static java.lang.StringJT_CANCELLED 
        (package private) static java.lang.StringJT_FAILED 
        (package private) static java.lang.StringJT_INCOMPLETE 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Joblist() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) +
        Input: + + ws=${ws.key} + + where=everywhere cluster local + + type=cancelled all incomplete + + from=${startDate} + + to=${stopDate}
        +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doHead, doOptions, doPost, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Joblist

          +
          public Joblist()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          Input: + + ws=${ws.key} + + where=everywhere cluster local + + type=cancelled all incomplete + + from=${startDate} + + to=${stopDate}
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/ServiceStatus.html b/website/docs/full_javadoc/compbio/stat/servlet/ServiceStatus.html new file mode 100644 index 0000000..dfc7699 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/ServiceStatus.html @@ -0,0 +1,386 @@ + + + + + +ServiceStatus + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class ServiceStatus

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • javax.servlet.GenericServlet
        • +
      • +
          +
        • javax.servlet.http.HttpServlet
          • +
        • +
            +
          • compbio.stat.servlet.ServiceStatus
            • +
          +
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
      +
      +
      +
      +
      public class ServiceStatus
+extends javax.servlet.http.HttpServlet
      +
      Use cases: +
      +
    • Test web services and display results on the web page
      • +
      +
      +
      Author:
      +
      pvtroshin
      +
      See Also:
      +
      Serialized Form
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        ServiceStatus() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        protected voiddoGet(javax.servlet.http.HttpServletRequest req, + javax.servlet.http.HttpServletResponse resp) 
        private java.util.List<java.lang.String>getEndPoints() 
        +
          +
        • + + +

          Methods inherited from class javax.servlet.http.HttpServlet

          +doDelete, doHead, doOptions, doPost, doPut, doTrace, getLastModified, service, service
          • +
        +
          +
        • + + +

          Methods inherited from class javax.servlet.GenericServlet

          +destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ServiceStatus

          +
          public ServiceStatus()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getEndPoints

          +
          private java.util.List<java.lang.String> getEndPoints()
+                                               throws javax.management.MalformedObjectNameException,
+                                                      java.lang.NullPointerException,
+                                                      java.net.UnknownHostException,
+                                                      javax.management.AttributeNotFoundException,
+                                                      javax.management.InstanceNotFoundException,
+                                                      javax.management.MBeanException,
+                                                      javax.management.ReflectionException
          +
          +
          Throws:
          +
          javax.management.MalformedObjectNameException
          +
          java.lang.NullPointerException
          +
          java.net.UnknownHostException
          +
          javax.management.AttributeNotFoundException
          +
          javax.management.InstanceNotFoundException
          +
          javax.management.MBeanException
          +
          javax.management.ReflectionException
          +
          +
          • +
        + + + +
          +
        • +

          doGet

          +
          protected void doGet(javax.servlet.http.HttpServletRequest req,
+                     javax.servlet.http.HttpServletResponse resp)
+              throws javax.servlet.ServletException,
+                     java.io.IOException
          +
          +
          Overrides:
          +
          doGet in class javax.servlet.http.HttpServlet
          +
          Throws:
          +
          javax.servlet.ServletException
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/ServiceTestResult.html b/website/docs/full_javadoc/compbio/stat/servlet/ServiceTestResult.html new file mode 100644 index 0000000..79f9e1c --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/ServiceTestResult.html @@ -0,0 +1,494 @@ + + + + + +ServiceTestResult + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class ServiceTestResult

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.servlet.ServiceTestResult
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ServiceTestResult
+extends java.lang.Object
      +
      Value class for test results. Two ServiceTestResult are considered equals if + their services are equals.
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) java.lang.Stringdetails 
        (package private) booleanfailed 
        (package private) java.lang.Stringgroup 
        (package private) java.lang.Stringreference 
        (package private) Servicesservice 
        (package private) java.lang.Stringversion 
        +
        • +
      + + + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          service

          +
          final Services service
          +
          • +
        + + + +
          +
        • +

          failed

          +
          boolean failed
          +
          • +
        + + + +
          +
        • +

          details

          +
          java.lang.String details
          +
          • +
        + + + +
          +
        • +

          group

          +
          java.lang.String group
          +
          • +
        + + + +
          +
        • +

          version

          +
          java.lang.String version
          +
          • +
        + + + +
          +
        • +

          reference

          +
          java.lang.String reference
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ServiceTestResult

          +
          public ServiceTestResult(Services service)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getService

          +
          public Services getService()
          +
          • +
        + + + +
          +
        • +

          getStatus

          +
          public boolean getStatus()
          +
          • +
        + + + +
          +
        • +

          getDetails

          +
          public java.lang.String getDetails()
          +
          • +
        + + + +
          +
        • +

          getGroup

          +
          public java.lang.String getGroup()
          +
          • +
        + + + +
          +
        • +

          getVersion

          +
          public java.lang.String getVersion()
          +
          • +
        + + + +
          +
        • +

          getReference

          +
          public java.lang.String getReference()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/StatisticCollector.html b/website/docs/full_javadoc/compbio/stat/servlet/StatisticCollector.html new file mode 100644 index 0000000..e3c81cc --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/StatisticCollector.html @@ -0,0 +1,528 @@ + + + + + +StatisticCollector + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet
    +

    Class StatisticCollector

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.servlet.StatisticCollector
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.EventListener, javax.servlet.ServletContextListener
      +
      +
      +
      +
      public class StatisticCollector
+extends java.lang.Object
+implements javax.servlet.ServletContextListener
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          ph

          +
          static compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          log

          +
          private final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          localcf

          +
          private java.util.concurrent.ScheduledFuture<?> localcf
          +
          • +
        + + + +
          +
        • +

          clustercf

          +
          private java.util.concurrent.ScheduledFuture<?> clustercf
          +
          • +
        + + + +
          +
        • +

          executor

          +
          private java.util.concurrent.ScheduledExecutorService executor
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StatisticCollector

          +
          public StatisticCollector()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          contextDestroyed

          +
          public void contextDestroyed(javax.servlet.ServletContextEvent arg0)
          +
          +
          Specified by:
          +
          contextDestroyed in interface javax.servlet.ServletContextListener
          +
          +
          • +
        + + + +
          +
        • +

          contextInitialized

          +
          public void contextInitialized(javax.servlet.ServletContextEvent arg0)
          +
          +
          Specified by:
          +
          contextInitialized in interface javax.servlet.ServletContextListener
          +
          +
          • +
        + + + +
          +
        • +

          getClusterJobDir

          +
          static java.lang.String getClusterJobDir()
          +
          • +
        + + + +
          +
        • +

          getClusterJobTimeOut

          +
          static int getClusterJobTimeOut()
          +
          • +
        + + + +
          +
        • +

          getLocalJobTimeOut

          +
          static int getLocalJobTimeOut()
          +
          • +
        + + + +
          +
        • +

          getLocalJobDir

          +
          static java.lang.String getLocalJobDir()
          +
          • +
        + + + +
          +
        • +

          getStringProperty

          +
          private static java.lang.String getStringProperty(java.lang.String propName)
          +
          • +
        + + + +
          +
        • +

          getIntProperty

          +
          private static int getIntProperty(java.lang.String propValue)
          +
          • +
        + + + +
          +
        • +

          collectClusterStats

          +
          static boolean collectClusterStats()
          +
          • +
        + + + +
          +
        • +

          collectLocalStats

          +
          static boolean collectLocalStats()
          +
          • +
        + + + +
          +
        • +

          updateClusterStatsFrequency

          +
          static int updateClusterStatsFrequency()
          +
          • +
        + + + +
          +
        • +

          updateLocalStatsFrequency

          +
          static int updateLocalStatsFrequency()
          +
          • +
        + + + +
          +
        • +

          getBooleanProperty

          +
          private static boolean getBooleanProperty(java.lang.String propValue)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html b/website/docs/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html new file mode 100644 index 0000000..f66a139 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.servlet.AnnualStat + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
    • Prev
      • +
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      • +
    + + +
    + +
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    + +
    +

    Uses of Class
    compbio.stat.servlet.AnnualStat

    +
    +
    No usage of compbio.stat.servlet.AnnualStat
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
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      • +
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      • +
    + + +
    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/class-use/DisplayStat.html b/website/docs/full_javadoc/compbio/stat/servlet/class-use/DisplayStat.html new file mode 100644 index 0000000..fd05441 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/class-use/DisplayStat.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.servlet.DisplayStat + + + + + + + + +
    + + +
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    +

    Uses of Class
    compbio.stat.servlet.DisplayStat

    +
    +
    No usage of compbio.stat.servlet.DisplayStat
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    +
      +
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      • +
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      • +
    + + +
    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/class-use/DownloadRedirector.html b/website/docs/full_javadoc/compbio/stat/servlet/class-use/DownloadRedirector.html new file mode 100644 index 0000000..8ac1b6c --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/class-use/DownloadRedirector.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.servlet.DownloadRedirector + + + + + + + + +
    + + +
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    +

    Uses of Class
    compbio.stat.servlet.DownloadRedirector

    +
    +
    No usage of compbio.stat.servlet.DownloadRedirector
    + +
    + + +
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    + + + + +
    +
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      • +
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/class-use/HttpCodeResponseServiceStatus.html b/website/docs/full_javadoc/compbio/stat/servlet/class-use/HttpCodeResponseServiceStatus.html new file mode 100644 index 0000000..1b21d23 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/class-use/HttpCodeResponseServiceStatus.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.servlet.HttpCodeResponseServiceStatus + + + + + + + + +
    + + +
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    Uses of Class
    compbio.stat.servlet.HttpCodeResponseServiceStatus

    +
    +
    No usage of compbio.stat.servlet.HttpCodeResponseServiceStatus
    + +
    + + +
    Skip navigation links
    + + + + +
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      +
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      • +
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    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/class-use/Joblist.html b/website/docs/full_javadoc/compbio/stat/servlet/class-use/Joblist.html new file mode 100644 index 0000000..82b9582 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/class-use/Joblist.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.stat.servlet.Joblist + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    +
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    Uses of Class
    compbio.stat.servlet.Joblist

    +
    +
    No usage of compbio.stat.servlet.Joblist
    + +
    + + +
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    + + + + +
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    compbio.stat.servlet.util
    +

    Enum StatCollection.Stattype

    +
    +
    +
      +
    • java.lang.Object
      • +
    • + +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<StatCollection.Stattype>
      +
      +
      +
      Enclosing class:
      +
      StatCollection
      +
      +
      +
      +
      public static enum StatCollection.Stattype
+extends java.lang.Enum<StatCollection.Stattype>
      +
      Total number of requests + + incomplete abandoned cancelled
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Summary

        + + + + + + + + + + + + + + +
        Enum Constants 
        Enum Constant and Description
        ALL 
        CLUSTER 
        LOCAL 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static StatCollection.StattypevalueOf(java.lang.String name) +
        Returns the enum constant of this type with the specified name.
        +
        static StatCollection.Stattype[]values() +
        Returns an array containing the constants of this enum type, in +the order they are declared.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Enum

          +clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
          • +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +getClass, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static StatCollection.Stattype[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (StatCollection.Stattype c : StatCollection.Stattype.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static StatCollection.Stattype valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
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    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/util/StatCollection.html b/website/docs/full_javadoc/compbio/stat/servlet/util/StatCollection.html new file mode 100644 index 0000000..f59933d --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/util/StatCollection.html @@ -0,0 +1,522 @@ + + + + + +StatCollection + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet.util
    +

    Class StatCollection

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.servlet.util.StatCollection
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class StatCollection
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          StatCollection

          +
          public StatCollection()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + + + + + + + + + +
          +
        • +

          getStats

          +
          public static java.util.Map<java.util.Date,Totals> getStats(int monthsToReport)
+                                                     throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getStats

          +
          public static java.util.Map<java.util.Date,Totals> getStats(java.util.Date fromDate)
+                                                     throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          getJobCounts

          +
          private static Totals getJobCounts(java.util.Date from,
+                                   java.util.Date to)
+                            throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          newStatCollecton

          +
          public static StatCollection newStatCollecton(java.util.Date startDate,
+                                              java.util.Date endDate)
+                                       throws java.sql.SQLException
          +
          +
          Throws:
          +
          java.sql.SQLException
          +
          +
          • +
        + + + +
          +
        • +

          hashCode

          +
          public int hashCode()
          +
          +
          Overrides:
          +
          hashCode in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          equals

          +
          public boolean equals(java.lang.Object obj)
          +
          +
          Overrides:
          +
          equals in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/stat/servlet/util/Totals.html b/website/docs/full_javadoc/compbio/stat/servlet/util/Totals.html new file mode 100644 index 0000000..19ead10 --- /dev/null +++ b/website/docs/full_javadoc/compbio/stat/servlet/util/Totals.html @@ -0,0 +1,437 @@ + + + + + +Totals + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.stat.servlet.util
    +

    Class Totals

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.stat.servlet.util.Totals
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Totals
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          total

          +
          int total
          +
          • +
        + + + +
          +
        • +

          incomplete

          +
          int incomplete
          +
          • +
        + + + +
          +
        • +

          abandoned

          +
          int abandoned
          +
          • +
        + + + +
          +
        • +

          cancelled

          +
          int cancelled
          +
          • +
        + + + +
          +
        • +

          failed

          +
          int failed
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Totals

          +
          public Totals()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getTotal

          +
          public int getTotal()
          +
          • +
        + + + +
          +
        • +

          getIncomplete

          +
          public int getIncomplete()
          +
          • +
        + + + +
          +
        • +

          getAbandoned

          +
          public int getAbandoned()
          +
          • +
        + + + +
          +
        • +

          getCancelled

          +
          public int getCancelled()
          +
          • +
        + + + +
          +
        • +

          getFailed

          +
          public int getFailed()
          +
          • +
        + + + +
          +
        • +

          sumOfTotals

          +
          public static Totals sumOfTotals(java.util.Map<java.util.Date,Totals> stat)
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
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    + + +
    Skip navigation links
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    Package compbio.stat.servlet.util

    +
    +
    +
      +
    • + + + + + + + + + + + + + + + + +
      Class Summary 
      ClassDescription
      StatCollection 
      Totals 
      +
      • +
    • + + + + + + + + + + + + +
      Enum Summary 
      EnumDescription
      StatCollection.Stattype +
      Total number of requests + + incomplete abandoned cancelled
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    + + +
    +
    compbio.ws.client
    +

    Class AAConClient

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.AAConClient
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class AAConClient
+extends java.lang.Object
      +
      A command line client for AACon web service
      +
      +
      Version:
      +
      1.0
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.Stringhostname +
        Web service host
        +
        private static java.util.logging.Loggerlog +
        Use java.util.Logger instead of log4j logger to reduce the size of the + client package
        +
        (package private) static java.lang.StringQUALIFIED_SERVICE_NAME +
        The fully qualified web service namespace
        +
        (package private) static java.lang.StringserviceName +
        Web service name
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        AAConClient(java.lang.String[] cmd) +
        Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static ScoreManageranalize(java.io.File file, + SequenceAnnotation<AAConWS> wsproxy, + Preset<AAConWS> preset, + java.util.List<Option<AAConWS>> customOptions) +
        Calculate conservation for sequences loaded from the file
        +
        static SequenceAnnotation<AAConWS>connect() +
        Connects to a AACon web service by the host and the service name
        +
        static voidmain(java.lang.String[] args) +
        Starts command line client, if no parameters are supplied prints help.
        +
        (package private) static voidprintUsage(int exitStatus) +
        Prints AAConClient usage information to standard out
        +
        (package private) static voidwriteOut(java.io.Writer writer, + ScoreManager result) +
        Outputs AAcon results into the file represented by the outStream
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final java.util.logging.Logger log
          +
          Use java.util.Logger instead of log4j logger to reduce the size of the + client package
          +
          • +
        + + + +
          +
        • +

          QUALIFIED_SERVICE_NAME

          +
          static final java.lang.String QUALIFIED_SERVICE_NAME
          +
          The fully qualified web service namespace
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          hostname

          +
          static final java.lang.String hostname
          +
          Web service host
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          serviceName

          +
          static final java.lang.String serviceName
          +
          Web service name
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AAConClient

          +
          AAConClient(java.lang.String[] cmd)
+     throws java.io.IOException
          +
          Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Throws:
          +
          java.io.IOException - if the system cannot read/write from/into the file system
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          writeOut

          +
          static void writeOut(java.io.Writer writer,
+                     ScoreManager result)
          +
          Outputs AAcon results into the file represented by the outStream
          +
          +
          Parameters:
          +
          outStream -
          +
          result - the AACon scores to output
          +
          +
          • +
        + + + +
          +
        • +

          connect

          +
          public static SequenceAnnotation<AAConWS> connect()
+                                           throws javax.xml.ws.WebServiceException
          +
          Connects to a AACon web service by the host and the service name
          +
          +
          Returns:
          +
          AlignmentAnnotation
          +
          Throws:
          +
          javax.xml.ws.WebServiceException - if cannot connect to a web service
          +
          +
          • +
        + + + +
          +
        • +

          analize

          +
          static ScoreManager analize(java.io.File file,
+                            SequenceAnnotation<AAConWS> wsproxy,
+                            Preset<AAConWS> preset,
+                            java.util.List<Option<AAConWS>> customOptions)
          +
          Calculate conservation for sequences loaded from the file
          +
          +
          Parameters:
          +
          wsproxy - a web service proxy
          +
          file - the file to read the results from
          +
          preset - Preset to use optional
          +
          customOptions - the list of options
          +
          Returns:
          +
          Set the conservation scores
          +
          Throws:
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          printUsage

          +
          static void printUsage(int exitStatus)
          +
          Prints AAConClient usage information to standard out
          +
          +
          Parameters:
          +
          exitStatus -
          +
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          Starts command line client, if no parameters are supplied prints help.
          +
          +
          Parameters:
          +
          args - Usage: ACTION [OPTIONS] + + -i= - full path to fasta or Clustal formatted + alignment file + + -parameters - lists parameters supported by web service + + -presets - lists presets supported by web service + + -limits - lists web services limits. Please note that if input + file is specified other actions are ignored + + OPTIONS: (only for use with -i action): + + -r= - name of the preset to use + + -o= - full path to the file where to write results + -f= - the name of the file with the list + of parameters to use. Please note that -r and -f options + cannot be used together. Conservation is calculated with + either a preset or parameters from the file, but not both!
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/CmdHelper.html b/website/docs/full_javadoc/compbio/ws/client/CmdHelper.html new file mode 100644 index 0000000..51f7d2f --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/CmdHelper.html @@ -0,0 +1,457 @@ + + + + + +CmdHelper + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class CmdHelper

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.CmdHelper
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      class CmdHelper
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        CmdHelper() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        static java.lang.StringgetHost(java.lang.String[] cmd) +
        Extracts host name from the command line
        +
        (package private) static java.lang.StringgetPresetName(java.lang.String[] cmd) +
        Extracts preset name from the command line is any
        +
        static java.lang.StringgetServiceName(java.lang.String[] cmd) +
        Extracts service name from the command line
        +
        (package private) static booleankeyFound(java.lang.String[] cmd, + java.lang.String key) +
        Checks whether the key is in the command line
        +
        (package private) static booleanlistLimits(java.lang.String[] cmd) +
        Checks whether limitList parameter is in the command line
        +
        (package private) static booleanlistParameters(java.lang.String[] cmd) +
        Searches the command line keys in the array of parameters
        +
        (package private) static booleanlistPresets(java.lang.String[] cmd) +
        Check whether presetList is set in the command line
        +
        (package private) static booleanlistServices(java.lang.String[] cmd) +
        list available services
        +
        (package private) static booleantestService(java.lang.String[] cmd) +
        tests service
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          CmdHelper

          +
          CmdHelper()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          listPresets

          +
          static boolean listPresets(java.lang.String[] cmd)
          +
          Check whether presetList is set in the command line
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Returns:
          +
          true if presetList is found, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          listLimits

          +
          static boolean listLimits(java.lang.String[] cmd)
          +
          Checks whether limitList parameter is in the command line
          +
          +
          Parameters:
          +
          cmd - - command line options
          +
          Returns:
          +
          true if it is, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          listServices

          +
          static boolean listServices(java.lang.String[] cmd)
          +
          list available services
          +
          +
          Parameters:
          +
          cmd -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          testService

          +
          static boolean testService(java.lang.String[] cmd)
          +
          tests service
          +
          +
          Parameters:
          +
          cmd -
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          keyFound

          +
          static boolean keyFound(java.lang.String[] cmd,
+                        java.lang.String key)
          +
          Checks whether the key is in the command line
          +
          +
          Parameters:
          +
          cmd -
          +
          key -
          +
          Returns:
          +
          true if it is, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getPresetName

          +
          static java.lang.String getPresetName(java.lang.String[] cmd)
          +
          Extracts preset name from the command line is any
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Returns:
          +
          presetName or null if no presets is defined
          +
          +
          • +
        + + + +
          +
        • +

          getServiceName

          +
          public static java.lang.String getServiceName(java.lang.String[] cmd)
          +
          Extracts service name from the command line
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Returns:
          +
          service name or null if it is not defined
          +
          +
          • +
        + + + +
          +
        • +

          getHost

          +
          public static java.lang.String getHost(java.lang.String[] cmd)
          +
          Extracts host name from the command line
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Returns:
          +
          host name or null if it is not defined
          +
          +
          • +
        + + + +
          +
        • +

          listParameters

          +
          static boolean listParameters(java.lang.String[] cmd)
          +
          Searches the command line keys in the array of parameters
          +
          +
          Parameters:
          +
          cmd - command line options
          +
          Returns:
          +
          true is the list of Parameters is requested, false otherwise
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/Constraints.html b/website/docs/full_javadoc/compbio/ws/client/Constraints.html new file mode 100644 index 0000000..3d13611 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/Constraints.html @@ -0,0 +1,515 @@ + + + + + +Constraints + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class Constraints

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.Constraints
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      class Constraints
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.Stringhelp_text 
        (package private) static java.lang.Stringhostkey 
        (package private) static java.lang.Stringinputkey 
        (package private) static java.lang.StringlimitList 
        (package private) static java.lang.StringlistServices 
        (package private) static java.lang.StringlistServicesOld 
        (package private) static java.lang.Stringoutputkey 
        (package private) static java.lang.Stringparameterkey 
        (package private) static java.lang.StringparamFile 
        (package private) static java.lang.StringparamList 
        (package private) static java.lang.Stringpresetkey 
        (package private) static java.lang.StringpresetList 
        (package private) static java.lang.Stringpseparator 
        (package private) static java.lang.Stringservicekey 
        (package private) static java.lang.StringtestKey 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Constraints() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/IOHelper.html b/website/docs/full_javadoc/compbio/ws/client/IOHelper.html new file mode 100644 index 0000000..72044d6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/IOHelper.html @@ -0,0 +1,375 @@ + + + + + +IOHelper + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class IOHelper

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.IOHelper
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class IOHelper
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        IOHelper() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static java.io.FilegetFile(java.lang.String[] cmd, + java.lang.String key, + boolean mustExist) +
        Checks -i options and return the File if one was provided, null otherwise
        +
        (package private) static java.io.WritergetWriter(java.io.File file) 
        (package private) static java.util.List<java.lang.String>loadParameters(java.io.File paramsfile) +
        Load parameters from file
        +
        (package private) static voidwriteOut(java.io.Writer writer, + Alignment align) +
        Outputs clustal formatted alignment into the file represented by the + outStream
        +
        (package private) static voidwriteOut(java.io.Writer writer, + ScoreManager results) +
        Outputs AAcon results into the file represented by the outStream
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          IOHelper

          +
          public IOHelper()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getFile

          +
          static java.io.File getFile(java.lang.String[] cmd,
+                            java.lang.String key,
+                            boolean mustExist)
+                     throws java.io.IOException
          +
          Checks -i options and return the File if one was provided, null otherwise
          +
          +
          Parameters:
          +
          cmd -
          +
          key -
          +
          mustExist -
          +
          Returns:
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          loadParameters

          +
          static java.util.List<java.lang.String> loadParameters(java.io.File paramsfile)
+                                                throws java.io.IOException
          +
          Load parameters from file
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          getWriter

          +
          static java.io.Writer getWriter(java.io.File file)
+                         throws java.io.IOException
          +
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          writeOut

          +
          static void writeOut(java.io.Writer writer,
+                     Alignment align)
          +
          Outputs clustal formatted alignment into the file represented by the + outStream
          +
          +
          Parameters:
          +
          outStream -
          +
          align - the alignment to output
          +
          +
          • +
        + + + +
          +
        • +

          writeOut

          +
          static void writeOut(java.io.Writer writer,
+                     ScoreManager results)
          +
          Outputs AAcon results into the file represented by the outStream
          +
          +
          Parameters:
          +
          outStream -
          +
          result - the AACon scores to output
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/Jws2Client.html b/website/docs/full_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..5c8a3f0 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,602 @@ + + + + + +Jws2Client + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class Jws2Client

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.Jws2Client
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class Jws2Client
+extends java.lang.Object
      +
      A command line client for JAva Bioinformatics Analysis Web Services
      +
      +
      Version:
      +
      1.0
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static java.util.logging.Loggerlog +
        Use java.util.Logger instead of log4j logger to reduce the size of the client package
        +
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        Jws2Client(java.lang.String[] cmd) +
        Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
        +
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static <T> Alignmentalign(java.io.File file, + MsaWS<T> msaws, + Preset<T> preset, + java.util.List<Option<T>> customOptions) +
        Align sequences from the file using MsaWS
        +
        (package private) static <T> ScoreManageranalize(java.io.File file, + SequenceAnnotation<T> wsproxy, + Preset<T> preset, + java.util.List<Option<T>> customOptions) +
        Calculate conservation for sequences loaded from the file
        +
        (package private) static <T> ScoreManageranalize(java.util.List<FastaSequence> fastalist, + SequenceAnnotation<T> wsproxy, + Preset<T> preset, + java.util.List<Option<T>> customOptions) +
        Calculate conservation for sequences loaded from a FASTA record list structure
        +
        static JABAServiceconnect(java.lang.String host, + Services service) +
        Connects to a web service by the host and the service name web service type
        +
        static RegistryWSconnectToRegistry(java.lang.String host) +
        Get a connection of JABAWS registry
        +
        private static voidlistAllServices(java.lang.String hostname) 
        static voidmain(java.lang.String[] args) +
        Starts command line client, if no parameter are supported print help.
        +
        static voidtestService(java.lang.String hostname, + Services service, + java.io.PrintWriter writer) +
        Asks registry to test the service on the host hostname
        +
        static booleanvalidURL(java.lang.String urlstr) +
        Attempt to construct the URL object from the string
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static final java.util.logging.Logger log
          +
          Use java.util.Logger instead of log4j logger to reduce the size of the client package
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          Jws2Client

          +
          Jws2Client(java.lang.String[] cmd)
+    throws java.io.IOException
          +
          Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          cmd - command line options
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          validURL

          +
          public static boolean validURL(java.lang.String urlstr)
          +
          Attempt to construct the URL object from the string
          +
          +
          Parameters:
          +
          urlstr -
          +
          Returns:
          +
          true if it succeed false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          connect

          +
          public static JABAService connect(java.lang.String host,
+                                  Services service)
+                           throws javax.xml.ws.WebServiceException,
+                                  java.net.ConnectException
          +
          Connects to a web service by the host and the service name web service type
          +
          +
          Parameters:
          +
          host - the fully qualified name of JABAWS server including JABAWS + context name e.g + http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
          +
          service - the name of the JABAWS service to connect to
          +
          Returns:
          +
          JABAService
          +
          Throws:
          +
          javax.xml.ws.WebServiceException
          +
          java.net.ConnectException - if fails to connect to the service on the host
          +
          +
          • +
        + + + +
          +
        • +

          connectToRegistry

          +
          public static RegistryWS connectToRegistry(java.lang.String host)
+                                    throws javax.xml.ws.WebServiceException,
+                                           java.net.ConnectException
          +
          Get a connection of JABAWS registry
          +
          +
          Parameters:
          +
          host - the fully qualified name of JABAWS server including JABAWS + context name e.g + http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
          +
          Returns:
          +
          compbio.data.msa.RegistryWS - instance of a RegistryWS web + service
          +
          Throws:
          +
          javax.xml.ws.WebServiceException
          +
          java.net.ConnectException
          +
          +
          • +
        + + + +
          +
        • +

          testService

          +
          public static void testService(java.lang.String hostname,
+                               Services service,
+                               java.io.PrintWriter writer)
+                        throws java.net.ConnectException,
+                               javax.xml.ws.WebServiceException
          +
          Asks registry to test the service on the host hostname
          +
          +
          Parameters:
          +
          hostname -
          +
          service -
          +
          writer -
          +
          Throws:
          +
          java.net.ConnectException
          +
          javax.xml.ws.WebServiceException
          +
          +
          • +
        + + + +
          +
        • +

          listAllServices

          +
          private static void listAllServices(java.lang.String hostname)
+                             throws javax.xml.ws.WebServiceException,
+                                    java.io.IOException
          +
          +
          Throws:
          +
          javax.xml.ws.WebServiceException
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          analize

          +
          static <T> ScoreManager analize(java.util.List<FastaSequence> fastalist,
+                                SequenceAnnotation<T> wsproxy,
+                                Preset<T> preset,
+                                java.util.List<Option<T>> customOptions)
          +
          Calculate conservation for sequences loaded from a FASTA record list structure
          +
          +
          Parameters:
          +
          fastalist - the list of FASTA records
          +
          wsproxy - a web service proxy
          +
          preset - Preset to use optional
          +
          customOptions - the list of options
          +
          Returns:
          +
          Set the conservation scores
          +
          Throws:
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          analize

          +
          static <T> ScoreManager analize(java.io.File file,
+                                SequenceAnnotation<T> wsproxy,
+                                Preset<T> preset,
+                                java.util.List<Option<T>> customOptions)
          +
          Calculate conservation for sequences loaded from the file
          +
          +
          Parameters:
          +
          wsproxy - a web service proxy
          +
          file - the file to read the results from
          +
          preset - Preset to use optional
          +
          customOptions - the list of options
          +
          Returns:
          +
          Set the conservation scores
          +
          Throws:
          +
          java.io.IOException
          +
          UnknownFileFormatException
          +
          +
          • +
        + + + +
          +
        • +

          align

          +
          static <T> Alignment align(java.io.File file,
+                           MsaWS<T> msaws,
+                           Preset<T> preset,
+                           java.util.List<Option<T>> customOptions)
          +
          Align sequences from the file using MsaWS
          +
          +
          Type Parameters:
          +
          T - web service type e.g. Clustal
          +
          Parameters:
          +
          file - to write the resulting alignment to
          +
          msaws - MsaWS required
          +
          preset - Preset to use optional
          +
          customOptions - file which contains new line separated list of options
          +
          Returns:
          +
          Alignment
          +
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          Starts command line client, if no parameter are supported print help. Two + parameters are required for successful call the JWS2 host name and a + service name.
          +
          +
          Parameters:
          +
          args - Usage: -h=host_and_context + -s=serviceName ACTION [OPTIONS] + + -h= - a full URL to the JWS2 web server + including context path e.g. http://10.31.1.159:8080/ws + + -s= - one of [MafftWS, MuscleWS, ClustalWS, + TcoffeeWS, ProbconsWS] ACTIONS: + + -i= - full path to fasta formatted sequence file, + from which to align sequences + + -parameters - lists parameters supported by web service + + -presets - lists presets supported by web service + + -limits - lists web services limits Please note that if input + file is specified other actions are ignored + + OPTIONS: (only for use with -i action): + + -r= - name of the preset to use + + -o= - full path to the file where to write an + alignment -f= - the name of the file with + the list of parameters to use. Please note that -r and -f + options cannot be used together. Alignment is done with either + preset or a parameters from the file, but not both!
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/MetadataHelper.html b/website/docs/full_javadoc/compbio/ws/client/MetadataHelper.html new file mode 100644 index 0000000..fe9951d --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/MetadataHelper.html @@ -0,0 +1,459 @@ + + + + + +MetadataHelper + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class MetadataHelper

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.MetadataHelper
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class MetadataHelper
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        MetadataHelper() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        All Methods Static Methods Concrete Methods 
        Modifier and TypeMethod and Description
        (package private) static <T> java.util.List<Limit<T>>getLimits(Metadata<T> msaws) +
        Returns a list of limits supported by web service Each limit correspond + to a particular preset.
        +
        (package private) static <T> java.util.List<Option<T>>getParametersList(Metadata<T> msaws) +
        Returns a list of options supported by web service
        +
        (package private) static <T> java.util.List<Option<T>>getParametersList(Metadata<T> msaws, + java.lang.String host) +
        Returns a list of options supported by web service
        +
        (package private) static java.lang.StringgetParamName(java.lang.String fullName) 
        (package private) static java.lang.StringgetParamValue(java.lang.String fullName) 
        (package private) static <T> Preset<T>getPreset(Metadata<T> msaws, + java.lang.String presetName) +
        Returns Preset by its name
        +
        (package private) static <T> PresetManager<T>getPresetList(Metadata<T> msaws) +
        Returns an objects from which the list of presets supported by web + service can be obtained
        +
        (package private) static booleanisParameter(java.lang.String param) 
        (package private) static <T> java.util.List<Option<T>>processParameters(java.util.List<java.lang.String> params, + RunnerConfig<T> options) +
        Converts options supplied via parameters file into Option objects
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MetadataHelper

          +
          public MetadataHelper()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getParametersList

          +
          static <T> java.util.List<Option<T>> getParametersList(Metadata<T> msaws)
          +
          Returns a list of options supported by web service
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          msaws - web service proxy
          +
          Returns:
          +
          List of options supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getParametersList

          +
          static <T> java.util.List<Option<T>> getParametersList(Metadata<T> msaws,
+                                                       java.lang.String host)
+                                                throws java.net.MalformedURLException
          +
          Returns a list of options supported by web service
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          msaws - web service proxy
          +
          host - the server URL, as a string
          +
          Returns:
          +
          List of options supported by a web service
          +
          Throws:
          +
          java.net.MalformedURLException
          +
          +
          • +
        + + + +
          +
        • +

          getPresetList

          +
          static <T> PresetManager<T> getPresetList(Metadata<T> msaws)
          +
          Returns an objects from which the list of presets supported by web + service can be obtained
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          msaws - web service proxy
          +
          Returns:
          +
          PresetManager, object which operates on presets
          +
          +
          • +
        + + + +
          +
        • +

          getLimits

          +
          static <T> java.util.List<Limit<T>> getLimits(Metadata<T> msaws)
          +
          Returns a list of limits supported by web service Each limit correspond + to a particular preset.
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          msaws - web service proxy
          +
          Returns:
          +
          List of limits supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getPreset

          +
          static <T> Preset<T> getPreset(Metadata<T> msaws,
+                               java.lang.String presetName)
          +
          Returns Preset by its name
          +
          +
          Type Parameters:
          +
          T -
          +
          Parameters:
          +
          msaws -
          +
          presetName -
          +
          Returns:
          +
          Return a Preset by its optionName
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          processParameters

          +
          static <T> java.util.List<Option<T>> processParameters(java.util.List<java.lang.String> params,
+                                                       RunnerConfig<T> options)
          +
          Converts options supplied via parameters file into Option objects
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          params -
          +
          options -
          +
          Returns:
          +
          List of Options of type T
          +
          +
          • +
        + + + +
          +
        • +

          getParamName

          +
          static java.lang.String getParamName(java.lang.String fullName)
          +
          • +
        + + + +
          +
        • +

          getParamValue

          +
          static java.lang.String getParamValue(java.lang.String fullName)
          +
          • +
        + + + +
          +
        • +

          isParameter

          +
          static boolean isParameter(java.lang.String param)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/Services.ServiceInfo.html b/website/docs/full_javadoc/compbio/ws/client/Services.ServiceInfo.html new file mode 100644 index 0000000..7784341 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/Services.ServiceInfo.html @@ -0,0 +1,418 @@ + + + + + +Services.ServiceInfo + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class Services.ServiceInfo

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.Services.ServiceInfo
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Enclosing class:
      +
      Services
      +
      +
      +
      +
      static class Services.ServiceInfo
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        (package private) static java.lang.Stringline_delimiter 
        (package private) java.lang.Stringmoreinfo 
        (package private) java.lang.Stringreference 
        (package private) Servicesservice 
        (package private) java.lang.Stringversion 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + + + + + + + +
        Constructors 
        ModifierConstructor and Description
        private ServiceInfo() 
        private ServiceInfo(Services service, + java.lang.String reference, + java.lang.String version, + java.lang.String moreinfo) 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        java.lang.StringgetReference() 
        java.lang.StringgetVersion() 
        java.lang.StringtoString() 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          reference

          +
          java.lang.String reference
          +
          • +
        + + + +
          +
        • +

          version

          +
          java.lang.String version
          +
          • +
        + + + +
          +
        • +

          moreinfo

          +
          java.lang.String moreinfo
          +
          • +
        + + + +
          +
        • +

          line_delimiter

          +
          static final java.lang.String line_delimiter
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ServiceInfo

          +
          private ServiceInfo()
          +
          • +
        + + + +
          +
        • +

          ServiceInfo

          +
          private ServiceInfo(Services service,
+                    java.lang.String reference,
+                    java.lang.String version,
+                    java.lang.String moreinfo)
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          toString

          +
          public java.lang.String toString()
          +
          +
          Overrides:
          +
          toString in class java.lang.Object
          +
          +
          • +
        + + + +
          +
        • +

          getReference

          +
          public java.lang.String getReference()
          +
          • +
        + + + +
          +
        • +

          getVersion

          +
          public java.lang.String getVersion()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/Services.html b/website/docs/full_javadoc/compbio/ws/client/Services.html new file mode 100644 index 0000000..90b34ef --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/Services.html @@ -0,0 +1,868 @@ + + + + + +Services + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Enum Services

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • java.lang.Enum<Services>
        • +
      • +
          +
        • compbio.ws.client.Services
          • +
        +
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.io.Serializable, java.lang.Comparable<Services>
      +
      +
      +
      +
      public enum Services
+extends java.lang.Enum<Services>
      +
      List of web services currently supported by JABAWS version 2.1
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Enum Constant Detail

        + + + +
          +
        • +

          MafftWS

          +
          public static final Services MafftWS
          +
          • +
        + + + +
          +
        • +

          MuscleWS

          +
          public static final Services MuscleWS
          +
          • +
        + + + +
          +
        • +

          ClustalWS

          +
          public static final Services ClustalWS
          +
          • +
        + + + +
          +
        • +

          ClustalOWS

          +
          public static final Services ClustalOWS
          +
          • +
        + + + +
          +
        • +

          TcoffeeWS

          +
          public static final Services TcoffeeWS
          +
          • +
        + + + +
          +
        • +

          ProbconsWS

          +
          public static final Services ProbconsWS
          +
          • +
        + + + +
          +
        • +

          MSAprobsWS

          +
          public static final Services MSAprobsWS
          +
          • +
        + + + +
          +
        • +

          GLprobsWS

          +
          public static final Services GLprobsWS
          +
          • +
        + + + +
          +
        • +

          AAConWS

          +
          public static final Services AAConWS
          +
          • +
        + + + +
          +
        • +

          JronnWS

          +
          public static final Services JronnWS
          +
          • +
        + + + +
          +
        • +

          DisemblWS

          +
          public static final Services DisemblWS
          +
          • +
        + + + +
          +
        • +

          GlobPlotWS

          +
          public static final Services GlobPlotWS
          +
          • +
        + + + +
          +
        • +

          IUPredWS

          +
          public static final Services IUPredWS
          +
          • +
        + + + +
          +
        • +

          RNAalifoldWS

          +
          public static final Services RNAalifoldWS
          +
          • +
        +
        • +
      + + + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          values

          +
          public static Services[] values()
          +
          Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
          +for (Services c : Services.values())
+    System.out.println(c);
+
          +
          +
          Returns:
          +
          an array containing the constants of this enum type, in the order they are declared
          +
          +
          • +
        + + + +
          +
        • +

          valueOf

          +
          public static Services valueOf(java.lang.String name)
          +
          Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.)
          +
          +
          Parameters:
          +
          name - the name of the enum constant to be returned.
          +
          Returns:
          +
          the enum constant with the specified name
          +
          Throws:
          +
          java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
          +
          java.lang.NullPointerException - if the argument is null
          +
          +
          • +
        + + + +
          +
        • +

          getService

          +
          public static Services getService(java.lang.String servName)
          +
          • +
        + + + +
          +
        • +

          getService

          +
          javax.xml.ws.Service getService(java.net.URL url,
+                                java.lang.String sqname)
          +
          • +
        + + + +
          +
        • +

          getJabawsVersion

          +
          public java.lang.String getJabawsVersion()
          +
          • +
        + + + +
          +
        • +

          toString

          +
          public static java.lang.String toString(java.util.Set<Services> services)
          +
          • +
        + + + +
          +
        • +

          getServiceType

          +
          java.lang.Class<? extends JABAService> getServiceType()
          +
          • +
        + + + +
          +
        • +

          getServiceNamespace

          +
          java.lang.String getServiceNamespace()
          +
          • +
        + + + +
          +
        • +

          getInterface

          +
          JABAService getInterface(javax.xml.ws.Service service)
          +
          • +
        + + + +
          +
        • +

          getServiceInfo

          +
          public java.lang.String getServiceInfo()
          +
          • +
        + + + +
          +
        • +

          getServiceReference

          +
          public java.lang.String getServiceReference()
          +
          • +
        + + + +
          +
        • +

          getServiceVersion

          +
          public java.lang.String getServiceVersion()
          +
          • +
        + + + +
          +
        • +

          getServiceGroup

          +
          public java.lang.String getServiceGroup()
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/ServicesUtil.html b/website/docs/full_javadoc/compbio/ws/client/ServicesUtil.html new file mode 100644 index 0000000..c22023e --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/ServicesUtil.html @@ -0,0 +1,336 @@ + + + + + +ServicesUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class ServicesUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.ServicesUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class ServicesUtil
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ServicesUtil

          +
          public ServicesUtil()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          getServiceByRunner

          +
          public static Services getServiceByRunner(java.lang.Class<? extends Executable> class1)
          +
          • +
        + + + +
          +
        • +

          getServiceImpl

          +
          private static java.lang.Class<? extends Executable<?>> getServiceImpl(Services service)
          +
          • +
        + + + +
          +
        • +

          getRunnerByJobDirectory

          +
          public static java.lang.Class<? extends Executable<?>> getRunnerByJobDirectory(java.io.File jobdir)
          +
          • +
        + + + +
          +
        • +

          getRunnerNameByJobDirectory

          +
          private static java.lang.String getRunnerNameByJobDirectory(java.io.File jobdir)
          +
          • +
        + + + +
          +
        • +

          getServiceByJobDirectory

          +
          public static Services getServiceByJobDirectory(java.io.File jobdir)
          +
          • +
        + + + +
          +
        • +

          getServiceByRunnerName

          +
          private static Services getServiceByRunnerName(java.lang.String name)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/WSTester.html b/website/docs/full_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..8e08071 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,825 @@ + + + + + +WSTester + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.client
    +

    Class WSTester

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.client.WSTester
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class WSTester
+extends java.lang.Object
      +
      Class for testing web services
      +
      +
      Version:
      +
      1.5 February 2013
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          fastaInput2records

          +
          public static final java.lang.String fastaInput2records
          +
          Test sequences to be used as input for WS
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          fastaInput1record

          +
          public static final java.lang.String fastaInput1record
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          fastaAlignment

          +
          public static final java.lang.String fastaAlignment
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          fastaRNAAlignment

          +
          public static final java.lang.String fastaRNAAlignment
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          clustalRNAAlignment

          +
          public static final java.lang.String clustalRNAAlignment
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          FAILED

          +
          private static final java.lang.String FAILED
          +
          Status strings
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + + + + + +
          +
        • +

          UNSUPPORTED

          +
          private static final java.lang.String UNSUPPORTED
          +
          +
          See Also:
          +
          Constant Field Values
          +
          +
          • +
        + + + +
          +
        • +

          writer

          +
          private final java.io.PrintWriter writer
          +
          • +
        + + + +
          +
        • +

          hostname

          +
          private final java.lang.String hostname
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          WSTester

          +
          public WSTester(java.lang.String hostname,
+                java.io.PrintWriter writer)
          +
          Construct an instance of JABAWS tester
          +
          +
          Parameters:
          +
          hostname - - fully qualified host and context name of JABAWS e.g. + http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
          +
          writer - a PrintWriter instance to writer test log to.
          +
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          loadSeqs

          +
          private static java.util.List<FastaSequence> loadSeqs(int nLines)
          +
          Converting input to a form accepted by WS
          +
          +
          Returns:
          +
          List of FastaSequence records
          +
          +
          • +
        + + + +
          +
        • +

          loadAlignment

          +
          private static java.util.List<FastaSequence> loadAlignment()
          +
          Converting input to a form accepted by WS
          +
          +
          Returns:
          +
          List of FastaSequence records
          +
          +
          • +
        + + + +
          +
        • +

          loadRNAAlignment

          +
          private static java.util.List<FastaSequence> loadRNAAlignment()
          +
          Converting input to a form accepted by WS
          +
          +
          Returns:
          +
          List of FastaSequence records with aligned RNA sequences
          +
          +
          • +
        + + + +
          +
        • +

          printUsage

          +
          static void printUsage()
          +
          Prints usage
          +
          • +
        + + + + + + + +
          +
        • +

          testMsaWS

          +
          private <T> boolean testMsaWS(MsaWS<T> msaws,
+                              Services service)
+                       throws java.lang.Exception
          +
          +
          Throws:
          +
          java.lang.Exception
          +
          +
          • +
        + + + +
          +
        • +

          checkService

          +
          private <T> boolean checkService(JABAService wservice,
+                                 Services service)
          +
          Call most of web services functions and check the output
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          msaws -
          +
          Throws:
          +
          UnsupportedRuntimeException - is thrown if the connection to a web service was made, but + the web service is not functional. e.g. when native + executable does not exists for a server platform
          +
          +
          • +
        + + + +
          +
        • +

          testSequenceAnnotationWS

          +
          private <T> boolean testSequenceAnnotationWS(SequenceAnnotation<T> wservice,
+                                             Services service)
+                                      throws java.lang.Exception
          +
          +
          Throws:
          +
          java.lang.Exception
          +
          +
          • +
        + + + +
          +
        • +

          testDefaultAnalyse

          +
          private <T> boolean testDefaultAnalyse(java.util.List<FastaSequence> fastalist,
+                                       SequenceAnnotation<T> wsproxy,
+                                       Preset<T> preset,
+                                       java.util.List<Option<T>> customOptions)
+                                throws java.lang.Exception
          +
          +
          Throws:
          +
          java.lang.Exception
          +
          +
          • +
        + + + +
          +
        • +

          reportException

          +
          private void reportException(java.lang.Exception e)
          +
          • +
        + + + + + + + +
          +
        • +

          testDefaultAlignment

          +
          private <T> boolean testDefaultAlignment(MsaWS<T> msaws,
+                                         Services service)
+                                  throws java.lang.Exception
          +
          Align using default settings
          +
          +
          Type Parameters:
          +
          T -
          +
          Parameters:
          +
          msaws -
          +
          Throws:
          +
          UnsupportedRuntimeException
          +
          java.lang.Exception
          +
          +
          • +
        + + + +
          +
        • +

          main

          +
          public static <T> void main(java.lang.String[] args)
+                     throws java.io.IOException
          +
          Test JWS2 web services
          +
          +
          Type Parameters:
          +
          T - web service type
          +
          Parameters:
          +
          args - -h= + + -s= which is optional. If service name is not + provided then all known JWS2 web services are tested
          +
          Throws:
          +
          java.io.IOException
          +
          +
          • +
        + + + +
          +
        • +

          connect

          +
          private JABAService connect(java.lang.String host,
+                            Services service)
+                     throws javax.xml.ws.WebServiceException,
+                            java.net.ConnectException
          +
          Connects to a web service by the host and the service name web service type
          +
          +
          Parameters:
          +
          host - the fully qualified name of JABAWS server including JABAWS + context name e.g + http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
          +
          service - the name of the JABAWS service to connect to
          +
          Returns:
          +
          JABAService
          +
          Throws:
          +
          javax.xml.ws.WebServiceException
          +
          java.net.ConnectException - if fails to connect to the service on the host
          +
          +
          • +
        + + + +
          +
        • +

          checkService

          +
          public boolean checkService(Services service)
+                     throws java.net.ConnectException,
+                            javax.xml.ws.WebServiceException
          +
          Test JABA web service
          +
          +
          Parameters:
          +
          service - the service to test
          +
          Returns:
          +
          true if the service works as expected, false otherwise
          +
          Throws:
          +
          javax.xml.ws.WebServiceException
          +
          java.net.ConnectException
          +
          +
          • +
        + + + +
          +
        • +

          reportResults

          +
          private void reportResults(Services serv,
+                           boolean succeed)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/client/class-use/AAConClient.html b/website/docs/full_javadoc/compbio/ws/client/class-use/AAConClient.html new file mode 100644 index 0000000..30e92a3 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/class-use/AAConClient.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.ws.client.AAConClient + + + + + + + + +
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    +
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    + +
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    compbio.ws.client

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    Classes

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    + + diff --git a/website/docs/full_javadoc/compbio/ws/client/package-summary.html b/website/docs/full_javadoc/compbio/ws/client/package-summary.html new file mode 100644 index 0000000..f6b989b --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/client/package-summary.html @@ -0,0 +1,214 @@ + + + + + +compbio.ws.client + + + + + + + + +
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    Package compbio.ws.client

    +
    +
    A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    +
    +

    See: Description

    +
    +
    + + + + +

    Package compbio.ws.client Description

    +
    A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    +
    +
    Version:
    +
    1.0 April 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
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    Hierarchy For Package compbio.ws.client

    +Package Hierarchies: + +
    +
    +

    Class Hierarchy

    + +

    Enum Hierarchy

    +
      +
    • java.lang.Object +
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    +
    compbio.ws.server
    +

    Class AAConWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          AAConWS

          +
          public AAConWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          analize

          +
          public java.lang.String analize(java.util.List<FastaSequence> sequences)
+                         throws UnsupportedRuntimeException,
+                                LimitExceededException,
+                                JobSubmissionException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences. The actual analysis algorithm is defined by the + type T. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          analize in interface SequenceAnnotation<AACon>
          +
          Overrides:
          +
          analize in class SequenceAnnotationService<AACon>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          +
          • +
        + + + +
          +
        • +

          customAnalize

          +
          public java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
+                                      java.util.List<Option<AACon>> options)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to custom settings defined in options + list. The actual analysis algorithm is defined by the type T. Default + Limit is used to decide whether the calculation will be permitted or + denied
          +
          +
          Specified by:
          +
          customAnalize in interface SequenceAnnotation<AACon>
          +
          Overrides:
          +
          customAnalize in class SequenceAnnotationService<AACon>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          presetAnalize

          +
          public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                                      Preset<AACon> preset)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAnalize in interface SequenceAnnotation<AACon>
          +
          Overrides:
          +
          presetAnalize in class SequenceAnnotationService<AACon>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          +
          • +
        + + + + +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/ClustalOWS.html b/website/docs/full_javadoc/compbio/ws/server/ClustalOWS.html new file mode 100644 index 0000000..f6b3bf2 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/ClustalOWS.html @@ -0,0 +1,736 @@ + + + + + +ClustalOWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class ClustalOWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.ClustalOWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClustalOWS

          +
          public ClustalOWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<ClustalO>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<ClustalO> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<ClustalO>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<ClustalO>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<ClustalO>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<ClustalO> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<ClustalO>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<ClustalO>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<ClustalO> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<ClustalO>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<ClustalO> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<ClustalO>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/ClustalWS.html b/website/docs/full_javadoc/compbio/ws/server/ClustalWS.html new file mode 100644 index 0000000..ed8fe8d --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/ClustalWS.html @@ -0,0 +1,736 @@ + + + + + +ClustalWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class ClustalWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.ClustalWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ClustalWS

          +
          public ClustalWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<ClustalW>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<ClustalW> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<ClustalW>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<ClustalW>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<ClustalW>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<ClustalW> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<ClustalW>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<ClustalW>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<ClustalW> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<ClustalW>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<ClustalW> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<ClustalW>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/DisemblWS.html b/website/docs/full_javadoc/compbio/ws/server/DisemblWS.html new file mode 100644 index 0000000..02152f1 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/DisemblWS.html @@ -0,0 +1,470 @@ + + + + + +DisemblWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class DisemblWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          DisemblWS

          +
          public DisemblWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          customAnalize

          +
          public java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
+                                      java.util.List<Option<Disembl>> options)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to custom settings defined in options + list. The actual analysis algorithm is defined by the type T. Default + Limit is used to decide whether the calculation will be permitted or + denied
          +
          +
          Specified by:
          +
          customAnalize in interface SequenceAnnotation<Disembl>
          +
          Overrides:
          +
          customAnalize in class SequenceAnnotationService<Disembl>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          presetAnalize

          +
          public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                                      Preset<Disembl> preset)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAnalize in interface SequenceAnnotation<Disembl>
          +
          Overrides:
          +
          presetAnalize in class SequenceAnnotationService<Disembl>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/GAUtils.html b/website/docs/full_javadoc/compbio/ws/server/GAUtils.html new file mode 100644 index 0000000..38fc527 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/GAUtils.html @@ -0,0 +1,443 @@ + + + + + +GAUtils + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class GAUtils

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.GAUtils
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public class GAUtils
+extends java.lang.Object
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private static compbio.stat.ga.AnalyticsConfigDataconfig 
        (package private) static booleanIS_GA_ENABLED 
        private static org.apache.log4j.Loggerlog 
        (package private) static compbio.util.PropertyHelperPROP_HELPER 
        private static java.lang.StringSERVER_ADDRESS 
        private static compbio.stat.ga.GoogleAnalyticsTrackerTRACKER 
        (package private) static java.lang.StringVERSION_TYPE 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        GAUtils() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + + + + + +
          +
        • +

          log

          +
          private static final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          PROP_HELPER

          +
          static compbio.util.PropertyHelper PROP_HELPER
          +
          • +
        + + + +
          +
        • +

          config

          +
          private static compbio.stat.ga.AnalyticsConfigData config
          +
          • +
        + + + +
          +
        • +

          TRACKER

          +
          private static compbio.stat.ga.GoogleAnalyticsTracker TRACKER
          +
          • +
        + + + +
          +
        • +

          IS_GA_ENABLED

          +
          static final boolean IS_GA_ENABLED
          +
          • +
        + + + +
          +
        • +

          SERVER_ADDRESS

          +
          private static java.lang.String SERVER_ADDRESS
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GAUtils

          +
          public GAUtils()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          isGoogleAnalyticsEnabled

          +
          private static boolean isGoogleAnalyticsEnabled()
          +
          • +
        + + + +
          +
        • +

          getServerIP

          +
          private static java.lang.String getServerIP()
          +
          • +
        + + + +
          +
        • +

          anonymizeIP

          +
          private static boolean anonymizeIP()
          +
          • +
        + + + +
          +
        • +

          reportUsage

          +
          static void reportUsage(Services service)
          +
          • +
        + + + +
          +
        • +

          reportUsage

          +
          static void reportUsage(Services service,
+                        java.lang.String CLIENT_ADDRESS)
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/GLprobsWS.html b/website/docs/full_javadoc/compbio/ws/server/GLprobsWS.html new file mode 100644 index 0000000..97122dd --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/GLprobsWS.html @@ -0,0 +1,723 @@ + + + + + +GLprobsWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class GLprobsWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.GLprobsWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GLprobsWS

          +
          public GLprobsWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<GLprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<GLprobs>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<GLprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<GLprobs> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<GLprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<GLprobs>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<GLprobs> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<GLprobs>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<GLprobs> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<GLprobs>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<GLprobs> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<GLprobs>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/GenericMetadataService.html b/website/docs/full_javadoc/compbio/ws/server/GenericMetadataService.html new file mode 100644 index 0000000..46497c6 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/GenericMetadataService.html @@ -0,0 +1,473 @@ + + + + + +GenericMetadataService + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class GenericMetadataService<T>

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.GenericMetadataService<T>
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Direct Known Subclasses:
      +
      SequenceAnnotationService
      +
      +
      +
      +
      public abstract class GenericMetadataService<T>
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/GlobPlotWS.html b/website/docs/full_javadoc/compbio/ws/server/GlobPlotWS.html new file mode 100644 index 0000000..c8d7922 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/GlobPlotWS.html @@ -0,0 +1,470 @@ + + + + + +GlobPlotWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class GlobPlotWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          GlobPlotWS

          +
          public GlobPlotWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          customAnalize

          +
          public java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
+                                      java.util.List<Option<GlobPlot>> options)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to custom settings defined in options + list. The actual analysis algorithm is defined by the type T. Default + Limit is used to decide whether the calculation will be permitted or + denied
          +
          +
          Specified by:
          +
          customAnalize in interface SequenceAnnotation<GlobPlot>
          +
          Overrides:
          +
          customAnalize in class SequenceAnnotationService<GlobPlot>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          presetAnalize

          +
          public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                                      Preset<GlobPlot> preset)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAnalize in interface SequenceAnnotation<GlobPlot>
          +
          Overrides:
          +
          presetAnalize in class SequenceAnnotationService<GlobPlot>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/IUPredWS.html b/website/docs/full_javadoc/compbio/ws/server/IUPredWS.html new file mode 100644 index 0000000..95f2d03 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/IUPredWS.html @@ -0,0 +1,410 @@ + + + + + +IUPredWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class IUPredWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          IUPredWS

          +
          public IUPredWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          presetAnalize

          +
          public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                                      Preset<IUPred> preset)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAnalize in interface SequenceAnnotation<IUPred>
          +
          Overrides:
          +
          presetAnalize in class SequenceAnnotationService<IUPred>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/JronnWS.html b/website/docs/full_javadoc/compbio/ws/server/JronnWS.html new file mode 100644 index 0000000..66dab46 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/JronnWS.html @@ -0,0 +1,383 @@ + + + + + +JronnWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class JronnWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          JronnWS

          +
          public JronnWS()
          +
          • +
        +
        • +
      + + +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/MSAprobsWS.html b/website/docs/full_javadoc/compbio/ws/server/MSAprobsWS.html new file mode 100644 index 0000000..c232d25 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/MSAprobsWS.html @@ -0,0 +1,723 @@ + + + + + +MSAprobsWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class MSAprobsWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.MSAprobsWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MSAprobsWS

          +
          public MSAprobsWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<MSAprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<MSAprobs>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<MSAprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<MSAprobs> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<MSAprobs>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<MSAprobs>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<MSAprobs> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<MSAprobs>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<MSAprobs> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<MSAprobs>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<MSAprobs> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<MSAprobs>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/MafftWS.html b/website/docs/full_javadoc/compbio/ws/server/MafftWS.html new file mode 100644 index 0000000..2d07e92 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/MafftWS.html @@ -0,0 +1,736 @@ + + + + + +MafftWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class MafftWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.MafftWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MafftWS

          +
          public MafftWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<Mafft>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Mafft>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<Mafft>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Mafft> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<Mafft>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<Mafft>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<Mafft> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<Mafft>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<Mafft> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<Mafft>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<Mafft> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<Mafft>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/MainManager.html b/website/docs/full_javadoc/compbio/ws/server/MainManager.html new file mode 100644 index 0000000..0860693 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/MainManager.html @@ -0,0 +1,420 @@ + + + + + +MainManager + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class MainManager

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.MainManager
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.EventListener, javax.servlet.ServletContextListener
      +
      +
      +
      +
      public class MainManager
+extends java.lang.Object
+implements javax.servlet.ServletContextListener
      +
      Two tasks: + 1. Switch off engines if JABAWS web application is un-deployed, or web server is shutdown + 2. delete old job directories
      +
      +
      Version:
      +
      2.0
      +
      Author:
      +
      Peter Troshin, Alexander Sherstnev
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + + + + + + + + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private java.util.concurrent.ScheduledFuture<?>clustercl 
        private java.util.concurrent.ScheduledExecutorServiceexecutor 
        private java.util.concurrent.ScheduledFuture<?>localcl 
        private org.apache.log4j.Loggerlog 
        (package private) static compbio.util.PropertyHelperph 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        MainManager() 
        +
        • +
      + + +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private final org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          ph

          +
          static compbio.util.PropertyHelper ph
          +
          • +
        + + + +
          +
        • +

          localcl

          +
          private java.util.concurrent.ScheduledFuture<?> localcl
          +
          • +
        + + + +
          +
        • +

          clustercl

          +
          private java.util.concurrent.ScheduledFuture<?> clustercl
          +
          • +
        + + + +
          +
        • +

          executor

          +
          private java.util.concurrent.ScheduledExecutorService executor
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MainManager

          +
          public MainManager()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          contextDestroyed

          +
          public void contextDestroyed(javax.servlet.ServletContextEvent ignored)
          +
          +
          Specified by:
          +
          contextDestroyed in interface javax.servlet.ServletContextListener
          +
          +
          • +
        + + + +
          +
        • +

          contextInitialized

          +
          public void contextInitialized(javax.servlet.ServletContextEvent arg0)
          +
          +
          Specified by:
          +
          contextInitialized in interface javax.servlet.ServletContextListener
          +
          +
          • +
        + + + +
          +
        • +

          getClusterJobDir

          +
          static java.lang.String getClusterJobDir()
          +
          • +
        + + + +
          +
        • +

          getLocalJobDir

          +
          static java.lang.String getLocalJobDir()
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/MuscleWS.html b/website/docs/full_javadoc/compbio/ws/server/MuscleWS.html new file mode 100644 index 0000000..9aaa6cc --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/MuscleWS.html @@ -0,0 +1,736 @@ + + + + + +MuscleWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class MuscleWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.MuscleWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          MuscleWS

          +
          public MuscleWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<Muscle>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Muscle>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<Muscle>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Muscle> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<Muscle>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<Muscle>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<Muscle> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<Muscle>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<Muscle> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<Muscle>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<Muscle> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<Muscle>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/docs/full_javadoc/compbio/ws/server/ProbconsWS.html new file mode 100644 index 0000000..3147b84 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/ProbconsWS.html @@ -0,0 +1,723 @@ + + + + + +ProbconsWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class ProbconsWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.ProbconsWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          ProbconsWS

          +
          public ProbconsWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<Probcons>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Probcons>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<Probcons>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Probcons> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<Probcons>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<Probcons>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<Probcons> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<Probcons>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<Probcons> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<Probcons>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<Probcons> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<Probcons>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/RNAalifoldWS.html b/website/docs/full_javadoc/compbio/ws/server/RNAalifoldWS.html new file mode 100644 index 0000000..2d677ee --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/RNAalifoldWS.html @@ -0,0 +1,522 @@ + + + + + +RNAalifoldWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class RNAalifoldWS

    +
    +
    + +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RNAalifoldWS

          +
          public RNAalifoldWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          analize

          +
          public java.lang.String analize(java.util.List<FastaSequence> sequences)
+                         throws UnsupportedRuntimeException,
+                                LimitExceededException,
+                                JobSubmissionException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences. The actual analysis algorithm is defined by the + type T. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          analize in interface SequenceAnnotation<RNAalifold>
          +
          Overrides:
          +
          analize in class SequenceAnnotationService<RNAalifold>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          +
          • +
        + + + +
          +
        • +

          customAnalize

          +
          public java.lang.String customAnalize(java.util.List<FastaSequence> sequences,
+                                      java.util.List<Option<RNAalifold>> options)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to custom settings defined in options + list. The actual analysis algorithm is defined by the type T. Default + Limit is used to decide whether the calculation will be permitted or + denied
          +
          +
          Specified by:
          +
          customAnalize in interface SequenceAnnotation<RNAalifold>
          +
          Overrides:
          +
          customAnalize in class SequenceAnnotationService<RNAalifold>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Option
          +
          +
          • +
        + + + +
          +
        • +

          presetAnalize

          +
          public java.lang.String presetAnalize(java.util.List<FastaSequence> sequences,
+                                      Preset<RNAalifold> preset)
+                               throws UnsupportedRuntimeException,
+                                      LimitExceededException,
+                                      JobSubmissionException,
+                                      WrongParameterException
          +
          Description copied from interface: SequenceAnnotation
          +
          Analyse the sequences according to the preset settings. The actual + analysis algorithm is defined by the type T. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAnalize in interface SequenceAnnotation<RNAalifold>
          +
          Overrides:
          +
          presetAnalize in class SequenceAnnotationService<RNAalifold>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/RegistryWS.html b/website/docs/full_javadoc/compbio/ws/server/RegistryWS.html new file mode 100644 index 0000000..387732c --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/RegistryWS.html @@ -0,0 +1,620 @@ + + + + + +RegistryWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class RegistryWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.RegistryWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          wsContext

          +
          javax.xml.ws.WebServiceContext wsContext
          +
          • +
        + + + +
          +
        • +

          log

          +
          private static org.apache.log4j.Logger log
          +
          • +
        + + + +
          +
        • +

          operating

          +
          private static final java.util.Map<Services,java.util.Date> operating
          +
          Stores tested and passed (the test) services and their testing time
          +
          • +
        + + + +
          +
        • +

          nonoperating

          +
          private static final java.util.Map<Services,java.util.Date> nonoperating
          +
          • +
        + + + +
          +
        • +

          allTested

          +
          private static boolean allTested
          +
          Indicate whether the services were tested at all
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          RegistryWS

          +
          public RegistryWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + + + + + +
          +
        • +

          init

          +
          private void init()
          +
          • +
        + + + +
          +
        • +

          timeToTest

          +
          private boolean timeToTest()
          +
          • +
        + + + +
          +
        • +

          getLongestUntestedServiceTime

          +
          private int getLongestUntestedServiceTime()
          +
          Return time in seconds for the test for the oldest unchecked service
          +
          +
          Returns:
          +
          +
          • +
        + + + +
          +
        • +

          getLastTested

          +
          public int getLastTested(Services service)
          +
          Description copied from interface: RegistryWS
          +
          Number of seconds since the last test. Returns 0 if the service was not + tested or tested less then a one second ago.
          +
          +
          Specified by:
          +
          getLastTested in interface RegistryWS
          +
          Returns:
          +
          when last time tested
          +
          +
          • +
        + + + +
          +
        • +

          getLastTestedOn

          +
          public java.util.Date getLastTestedOn(Services service)
          +
          Can potentially return null if the service has not been tested yet.
          +
          +
          Specified by:
          +
          getLastTestedOn in interface RegistryWS
          +
          Returns:
          +
          the Date and time on which the service was last tested
          +
          +
          • +
        + + + +
          +
        • +

          testAllServices

          +
          public java.lang.String testAllServices()
          +
          TODO improve reporting. stop testing service on unsupported runtime env + exception
          +
          +
          Specified by:
          +
          testAllServices in interface RegistryWS
          +
          Returns:
          +
          the test log
          +
          +
          • +
        + + + +
          +
        • +

          getServicePath

          +
          private java.lang.String getServicePath()
          +
          • +
        + + + +
          +
        • +

          testService

          +
          public java.lang.String testService(Services service)
          +
          Description copied from interface: RegistryWS
          +
          Test a particular service
          +
          +
          Specified by:
          +
          testService in interface RegistryWS
          +
          Returns:
          +
          the testing log
          +
          +
          • +
        + + + +
          +
        • +

          isOperating

          +
          public boolean isOperating(Services service)
          +
          Description copied from interface: RegistryWS
          +
          Check whether a particular web service is working on this server
          +
          +
          Specified by:
          +
          isOperating in interface RegistryWS
          +
          Returns:
          +
          true if the service was functioning in time of last testing.
          +
          +
          • +
        + + + +
          +
        • +

          getServiceDescription

          +
          public java.lang.String getServiceDescription(Services service)
          +
          Description copied from interface: RegistryWS
          +
          Gives the description of the service.
          +
          +
          Specified by:
          +
          getServiceDescription in interface RegistryWS
          +
          Returns:
          +
          String, plain text or html formatted piece, but NOT a full html + document
          +
          +
          • +
        + + + +
          +
        • +

          getServiceCategories

          +
          public java.util.Set<Category> getServiceCategories()
          +
          Description copied from interface: RegistryWS
          +
          Gets the list of services per category. ServiceClassifier has the method + that returns Map>
          +
          +
          Specified by:
          +
          getServiceCategories in interface RegistryWS
          +
          Returns:
          +
          ServiceClassifier the object to represent relation between + Services and Categories
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/SequenceAnnotationService.html b/website/docs/full_javadoc/compbio/ws/server/SequenceAnnotationService.html new file mode 100644 index 0000000..868baa3 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/SequenceAnnotationService.html @@ -0,0 +1,396 @@ + + + + + +SequenceAnnotationService + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class SequenceAnnotationService<T>

    +
    +
    + +
    + +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/SetExecutableFlag.html b/website/docs/full_javadoc/compbio/ws/server/SetExecutableFlag.html new file mode 100644 index 0000000..73db21a --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/SetExecutableFlag.html @@ -0,0 +1,345 @@ + + + + + +SetExecutableFlag + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class SetExecutableFlag

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.SetExecutableFlag
        • +
      +
      • +
    +
    +
      +
    • +
      +
      All Implemented Interfaces:
      +
      java.util.EventListener, javax.servlet.ServletContextListener
      +
      +
      +
      +
      public class SetExecutableFlag
+extends java.lang.Object
+implements javax.servlet.ServletContextListener
      +
      Run setexecflag.sh script if executable flag is not set
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Summary

        + + + + + + + + + + +
        Fields 
        Modifier and TypeField and Description
        private org.apache.log4j.Loggerlog 
        +
        • +
      + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        SetExecutableFlag() 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + + + + + +
        All Methods Instance Methods Concrete Methods 
        Modifier and TypeMethod and Description
        voidcontextDestroyed(javax.servlet.ServletContextEvent arg0) 
        voidcontextInitialized(javax.servlet.ServletContextEvent arg0) +
        This listener is designed to run only once when the web application is + deployed to set executable flag for binaries.
        +
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Field Detail

        + + + +
          +
        • +

          log

          +
          private final org.apache.log4j.Logger log
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SetExecutableFlag

          +
          public SetExecutableFlag()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          contextDestroyed

          +
          public void contextDestroyed(javax.servlet.ServletContextEvent arg0)
          +
          +
          Specified by:
          +
          contextDestroyed in interface javax.servlet.ServletContextListener
          +
          +
          • +
        + + + +
          +
        • +

          contextInitialized

          +
          public void contextInitialized(javax.servlet.ServletContextEvent arg0)
          +
          This listener is designed to run only once when the web application is + deployed to set executable flag for binaries.
          +
          +
          Specified by:
          +
          contextInitialized in interface javax.servlet.ServletContextListener
          +
          Parameters:
          +
          arg0 - - ignored
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/docs/full_javadoc/compbio/ws/server/SimpleWSPublisher.html new file mode 100644 index 0000000..b4c519b --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/SimpleWSPublisher.html @@ -0,0 +1,287 @@ + + + + + +SimpleWSPublisher + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class SimpleWSPublisher

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.SimpleWSPublisher
        • +
      +
      • +
    +
    +
      +
    • +
      +
      Deprecated.
      +
      +
      @Deprecated
+public class SimpleWSPublisher
+extends java.lang.Object
      +
      This class publish a web service. This is not a production implementation. + Should be used only for during development and testing
      +
      +
      Author:
      +
      pvtroshin
      +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Summary

        + + + + + + + + +
        Constructors 
        Constructor and Description
        SimpleWSPublisher(java.lang.Object exec, + java.lang.String context) +
        Deprecated. 
        + 
        +
        • +
      + +
        +
      • + + +

        Method Summary

        + + + + + + + + + + +
        All Methods Static Methods Concrete Methods Deprecated Methods 
        Modifier and TypeMethod and Description
        static voidmain(java.lang.String[] args) +
        Deprecated. 
        + 
        +
          +
        • + + +

          Methods inherited from class java.lang.Object

          +clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
          • +
        +
        • +
      +
      • +
    +
    +
    +
      +
    • + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          SimpleWSPublisher

          +
          public SimpleWSPublisher(java.lang.Object exec,
+                         java.lang.String context)
          +
          Deprecated. 
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          main

          +
          public static void main(java.lang.String[] args)
          +
          Deprecated. 
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/docs/full_javadoc/compbio/ws/server/TcoffeeWS.html new file mode 100644 index 0000000..3f2a022 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/TcoffeeWS.html @@ -0,0 +1,736 @@ + + + + + +TcoffeeWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class TcoffeeWS

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.TcoffeeWS
        • +
      +
      • +
    +
    + +
    +
    + +
    +
    +
      +
    • + + + +
        +
      • + + +

        Constructor Detail

        + + + +
          +
        • +

          TcoffeeWS

          +
          public TcoffeeWS()
          +
          • +
        +
        • +
      + +
        +
      • + + +

        Method Detail

        + + + +
          +
        • +

          align

          +
          public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown.
          +
          +
          Specified by:
          +
          align in interface MsaWS<Tcoffee>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The program does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          customAlign

          +
          public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Tcoffee>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with options.
          +
          +
          Specified by:
          +
          customAlign in interface MsaWS<Tcoffee>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          options - A list of Options
          +
          Returns:
          +
          jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Default Limit is used to decide whether the calculation will be + permitted or denied
          +
          +
          • +
        + + + +
          +
        • +

          presetAlign

          +
          public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Tcoffee> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
          +
          Description copied from interface: MsaWS
          +
          Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used.
          +
          +
          Specified by:
          +
          presetAlign in interface MsaWS<Tcoffee>
          +
          Parameters:
          +
          sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
          +
          preset - A list of Options
          +
          Returns:
          +
          String - jobId - unique identifier for the job
          +
          Throws:
          +
          JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception.
          +
          UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called
          +
          LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
          +
          WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option.
          +
          See Also:
          +
          Preset
          +
          +
          • +
        + + + +
          +
        • +

          getResult

          +
          public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
          +
          Description copied from interface: MsaWS
          +
          Return the result of the job. This method waits for the job + jobId to complete before return.
          +
          +
          Specified by:
          +
          getResult in interface MsaWS<Tcoffee>
          +
          Parameters:
          +
          jobId - a unique job identifier
          +
          Returns:
          +
          Alignment
          +
          Throws:
          +
          ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
          +
          +
          • +
        + + + +
          +
        • +

          getLimit

          +
          public Limit<Tcoffee> getLimit(java.lang.String presetName)
          +
          Description copied from interface: Metadata
          +
          Get a Limit for a preset.
          +
          +
          Specified by:
          +
          getLimit in interface Metadata<Tcoffee>
          +
          Parameters:
          +
          presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned
          +
          Returns:
          +
          Limit
          +
          +
          • +
        + + + + + + + +
          +
        • +

          pullExecStatistics

          +
          public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
          +
          Description copied from interface: JManagement
          +
          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file.
          +
          +
          Specified by:
          +
          pullExecStatistics in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          position - - next position within the file to read
          +
          Returns:
          +
          ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read
          +
          See Also:
          +
          ChunkHolder
          +
          +
          • +
        + + + +
          +
        • +

          cancelJob

          +
          public boolean cancelJob(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Stop running the job jobId but leave its output untouched
          +
          +
          Specified by:
          +
          cancelJob in interface JManagement
          +
          Returns:
          +
          true if job was cancelled successfully, false otherwise
          +
          +
          • +
        + + + +
          +
        • +

          getJobStatus

          +
          public JobStatus getJobStatus(java.lang.String jobId)
          +
          Description copied from interface: JManagement
          +
          Return the status of the job.
          +
          +
          Specified by:
          +
          getJobStatus in interface JManagement
          +
          Parameters:
          +
          jobId - - unique job identifier
          +
          Returns:
          +
          JobStatus - status of the job
          +
          See Also:
          +
          JobStatus
          +
          +
          • +
        + + + +
          +
        • +

          getPresets

          +
          public PresetManager<Tcoffee> getPresets()
          +
          Description copied from interface: Metadata
          +
          Get presets supported by a web service
          +
          +
          Specified by:
          +
          getPresets in interface Metadata<Tcoffee>
          +
          Returns:
          +
          PresetManager the object contains information about presets + supported by a web service
          +
          +
          • +
        + + + +
          +
        • +

          getRunnerOptions

          +
          public RunnerConfig<Tcoffee> getRunnerOptions()
          +
          Description copied from interface: Metadata
          +
          Get options supported by a web service
          +
          +
          Specified by:
          +
          getRunnerOptions in interface Metadata<Tcoffee>
          +
          Returns:
          +
          RunnerConfig the list of options and parameters supported by a + web service.
          +
          +
          • +
        +
        • +
      +
      • +
    +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    + + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/WSUtil.html b/website/docs/full_javadoc/compbio/ws/server/WSUtil.html new file mode 100644 index 0000000..d8cf9fd --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/WSUtil.html @@ -0,0 +1,509 @@ + + + + + +WSUtil + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + +
    +
    compbio.ws.server
    +

    Class WSUtil

    +
    +
    +
      +
    • java.lang.Object
      • +
    • +
        +
      • compbio.ws.server.WSUtil
        • +
      +
      • +
    +
    +
      +
    • +
      +
      +
      public final class WSUtil
+extends java.lang.Object
      +
      • +
    +
    +
    + +
    +
    + +
    +
    + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    +
    +
      +
    • Summary: 
      • +
    • Nested | 
      • +
    • Field | 
      • +
    • Constr | 
      • +
    • Method
      • +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/class-use/AAConWS.html b/website/docs/full_javadoc/compbio/ws/server/class-use/AAConWS.html new file mode 100644 index 0000000..6f79b76 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/class-use/AAConWS.html @@ -0,0 +1,205 @@ + + + + + +Uses of Class compbio.ws.server.AAConWS + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
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      +
    • Prev
      • +
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    + +
    +

    Uses of Class
    compbio.ws.server.AAConWS

    +
    +
    + +
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    + + +
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      • +
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    + +
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    + + + diff --git a/website/docs/full_javadoc/compbio/ws/server/class-use/ClustalOWS.html b/website/docs/full_javadoc/compbio/ws/server/class-use/ClustalOWS.html new file mode 100644 index 0000000..1098af7 --- /dev/null +++ b/website/docs/full_javadoc/compbio/ws/server/class-use/ClustalOWS.html @@ -0,0 +1,124 @@ + + + + + +Uses of Class compbio.ws.server.ClustalOWS + + + + + + + + +
    + + +
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    +

    Uses of Class
    compbio.ws.server.ClustalOWS

    +
    +
    No usage of compbio.ws.server.ClustalOWS
    + +
    + + +
    Skip navigation links
    + + + + +
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    compbio.ws.server

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    Classes

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    + +
    +

    Constant Field Values

    +

    Contents

    + +
    +
    + + +

    compbio.data.*

    + +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.data.sequence.ClustalAlignmentUtil 
      Modifier and TypeConstant FieldValue
      + +public static final chargapchar45
      + +private static final intmaxNameLength30
      + +private static final intminNameHolderLength10
      + +private static final intoneLineAlignmentLength60
      + +private static final java.lang.Stringspacer" "
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.FastaReader 
      Modifier and TypeConstant FieldValue
      + +private final java.lang.StringDELIM">"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.ScoreManager 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringSINGLE_ENTRY_KEY"Alignment"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.SequenceUtil 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringJRONN_WRONG_FORMAT_MESSAGE"Jronn file must be in the following format:\n>sequence_name\n M\tV\tS\n0.43\t0.22\t0.65\nWhere first line is the sequence name,\nsecond line is the tab delimited sequence,\nthird line contains tab delimited disorder prediction values.\nNo lines are allowed between these three. Additionally, the number of sequence residues must be equal to the number of the disorder values."
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.data.sequence.SMERFSConstraints 
      Modifier and TypeConstant FieldValue
      + +public static final doubleDEFAULT_GAP_THRESHOLD0.1
      + +public static final intDEFAULT_WINDOW_SIZE7
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.data.sequence.UnknownFileFormatException 
      Modifier and TypeConstant FieldValue
      + +private static final longserialVersionUID196629543695636854L
      +
      • +
    + + + +

    compbio.engine.*

    +
      +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.engine.client.compbio.engine.client.CommandBuilder.Parameter 
      Modifier and TypeConstant FieldValue
      + +private static final intFIRST-200
      + +private static final intLAST-100
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.engine.client.ConfExecutable<T> 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringCLUSTER_TASK_ID_PREFIX"@"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.engine.client.EnvVariableProcessor 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.Stringfasta4mafft"FASTA_4_MAFFT"
      + +private static final java.lang.Stringiupred_path"IUPred_PATH"
      + +private static final java.lang.Stringmafft_binaries"MAFFT_BINARIES"
      + +private static final java.lang.StringNEXT_ENV_PROPERTY_DELIMITER";"
      + +public static final java.lang.StringPATH"PATH"
      + +private static final java.lang.StringPROP_NAME_VALUE_SEPARATOR"#"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.engine.client.RunConfiguration 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringrconfigFile"RunnerConfig.xml"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.engine.client.SkeletalExecutable<T> 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringERROR"error.txt"
      + +public static final java.lang.StringINPUT"input.txt"
      + +public static final java.lang.StringOUTPUT"result.txt"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + +
      compbio.engine.cluster.drmaa.ClusterSession 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringJOBID"JOBID"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + +
      compbio.engine.conf.DirectoryManager 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringDELIM"#"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.engine.local.ExecutableWrapper 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringPROC_ERR_FILE"procError.txt"
      + +public static final java.lang.StringPROC_IN_FILE"procInput.txt"
      + +public static final java.lang.StringPROC_OUT_FILE"procOutput.txt"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.engine.local.LocalExecutorService 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringthreadNumPropName"engine.local.thread.number"
      +
      • +
    + + + +

    compbio.metadata.*

    + + + + +

    compbio.runner.*

    +
      +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.OptionCombinator 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringMAXVALUE"100"
      + +private static final java.lang.StringMINVALUE"-100"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.runner.Util 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringSPACE" "
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.runner.conservation.AACon 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
      + +private final java.lang.StringncorePrm"-t="
      + +public static final java.lang.StringSTAT_FILE"stat.txt"
      +
      • +
    + +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.ClustalO 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringEXEC_STAT_FILE"stat.log"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
      + +private static final java.lang.StringncorePrm"--threads"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.ClustalW 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringEXEC_STAT_FILE"stat.log"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
      + +private static final java.lang.StringTREE_FILE_EXT".dnd"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.GLprobs 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringANNOTATION"annotation.txt"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.Mafft 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      + +private final java.lang.StringMATRIX_PAR_NAME"--aamatrix"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.MSAprobs 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringANNOTATION"annotation.txt"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.Muscle 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringEXEC_STAT_FILE"stat.log"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.Probcons 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.StringANNOTATION"annotation.txt"
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      +
      • +
    • + + + + + + + + + + + + + + + + + + + +
      compbio.runner.msa.Tcoffee 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
      + +private static final java.lang.StringncorePrm"-n_core"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + +
      compbio.runner.structure.RNAalifold 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
      +
      • +
    + + + +

    compbio.stat.*

    +
      +
    • + + + + + + + + + + + + + + +
      compbio.stat.collector.DirCleaner 
      Modifier and TypeConstant FieldValue
      + +static final intUNDEFINED-1
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.stat.collector.ExecutionStatCollector 
      Modifier and TypeConstant FieldValue
      + +static final intUNDEFINED-1
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.stat.collector.JobDirectory 
      Modifier and TypeConstant FieldValue
      + +static final intUNDEFINED-1
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.stat.collector.StatDB 
      Modifier and TypeConstant FieldValue
      + +private static final java.lang.Stringdriver"org.apache.derby.jdbc.EmbeddedDriver"
      + +private static final java.lang.Stringprotocol"jdbc:derby:"
      + +private static final java.lang.StringstatDBName"ExecutionStatistic"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.stat.servlet.Joblist 
      Modifier and TypeConstant FieldValue
      + +static final java.lang.StringJT_ABANDONED"abandoned"
      + +static final java.lang.StringJT_ALL"all"
      + +static final java.lang.StringJT_CANCELLED"cancelled"
      + +static final java.lang.StringJT_FAILED"failed"
      + +static final java.lang.StringJT_INCOMPLETE"incomplete"
      +
      • +
    + + + +

    compbio.ws.*

    +
      +
    • + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.ws.client.AAConClient 
      Modifier and TypeConstant FieldValue
      + +static final java.lang.Stringhostname"http://www.compbio.dundee.ac.uk/aacon"
      + +static final java.lang.StringQUALIFIED_SERVICE_NAME"http://msa.data.compbio/01/12/2010/"
      + +static final java.lang.StringserviceName"AAConWS"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.ws.client.compbio.ws.client.Constraints 
      Modifier and TypeConstant FieldValue
      + +static final java.lang.Stringhelp_text"\r\nUsage: java -jar <JAR file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n\r\n -h=<host_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n -s=<ServiceName> - a name of servise (the full list can be obtain with the option -list)\r\n <serviceName> is required for all ACTIONS except -list\r\n\r\nACTIONS: \r\n -i=<inputFile> - defines an input file. For most services this is a FASTA file with initial sequences\r\n -list - lists all available web services\r\n -test - tests functioning of <ServiceName> \r\n -parameters - lists parameters supported by <ServiceName>\r\n -presets - lists presets supported by <ServiceName>\r\n -limits - lists limits of <ServiceName>\r\n\r\nN.B. If an input file is specified with -i other actions are ignored!\r\n\r\nOPTIONS (used with the -i action only):\r\n -r=<presetName> - name of the preset to use\r\n -o=<outputFile> - file with output results\r\n -f=<paramFile> - file with the list of parameters to use.\r\n\r\nPlease note that -r and -f options cannot be used together. \r\nAlignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\nEXAMPLES: \r\n<THECLIENT> is java -jar <JAR file name>\r\n\r\n1) List all available services on the host:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n\r\n2) Test Clustal web service:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n\r\n3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n into the output.txt:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n\r\n4) Calculate disorder with Disembl take input from input.txt with output results\r\n to be printed out to the standard output:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n\r\n5) List all parameters available for AAconWS service:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n\r\n6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n from input.txt and report the scores to the standard output:\r\n <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n\r\n Where the content of prm.txt file is -m=LANDGRAF\r\nN.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n"
      + +static final java.lang.Stringhostkey"-h"
      + +static final java.lang.Stringinputkey"-i"
      + +static final java.lang.StringlimitList"-limits"
      + +static final java.lang.StringlistServices"-list"
      + +static final java.lang.StringlistServicesOld"-list_services"
      + +static final java.lang.Stringoutputkey"-o"
      + +static final java.lang.Stringparameterkey"-p"
      + +static final java.lang.StringparamFile"-f"
      + +static final java.lang.StringparamList"-parameters"
      + +static final java.lang.Stringpresetkey"-r"
      + +static final java.lang.StringpresetList"-presets"
      + +static final java.lang.Stringpseparator"="
      + +static final java.lang.Stringservicekey"-s"
      + +static final java.lang.StringtestKey"-test"
      +
      • +
    • + + + + + + + + + + + + + + +
      compbio.ws.client.compbio.ws.client.Services.ServiceInfo 
      Modifier and TypeConstant FieldValue
      + +static final java.lang.Stringline_delimiter"\n"
      +
      • +
    • + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
      compbio.ws.client.WSTester 
      Modifier and TypeConstant FieldValue
      + +public static final java.lang.StringclustalRNAAlignment"CLUSTAL\nFoo C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGA\nBar G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGA\nFoo UGGUUG----GCAAC\nBar U-UACGAUUAACCAC"
      + +private static final java.lang.StringFAILED"FAILED"
      + +public static final java.lang.StringfastaAlignment">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
      + +public static final java.lang.StringfastaInput1record">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"
      + +public static final java.lang.StringfastaInput2records">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"
      + +public static final java.lang.StringfastaRNAAlignment">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n>Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n"
      + +private static final java.lang.StringOK"OK"
      + +private static final java.lang.StringUNSUPPORTED"UNSUPPORTED"
      +
      • +
    +
      +
    • + + + + + + + + + + + + + + +
      compbio.ws.server.GAUtils 
      Modifier and TypeConstant FieldValue
      + +static final java.lang.StringVERSION_TYPE"WAR"
      +
      • +
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    Deprecated API

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    How This API Document Is Organized

    +
    This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.
    +
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      Overview

      +

      The Overview page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.

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      Package

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      +

      Each documented package, class and interface has its own Use page. This page describes what packages, classes, methods, constructors and fields use any part of the given class or package. Given a class or interface A, its Use page includes subclasses of A, fields declared as A, methods that return A, and methods and constructors with parameters of type A. You can access this page by first going to the package, class or interface, then clicking on the "Use" link in the navigation bar.

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      +

      The Deprecated API page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.

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      Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.

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      Constant Field Values

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      The Constant Field Values page lists the static final fields and their values.

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    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    A

    +
    +
    AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Valid Amino acids
    +
    +
    AACon - Class in compbio.runner.conservation
    +
    +
    Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    +
    +
    AACon() - Constructor for class compbio.runner.conservation.AACon
    +
     
    +
    AACON_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    AAConClient - Class in compbio.ws.client
    +
    +
    A command line client for AACon web service
    +
    +
    AAConClient(String[]) - Constructor for class compbio.ws.client.AAConClient
    +
    +
    Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
    +
    +
    aaconOptions - Variable in class compbio.ws.server.GenericMetadataService
    +
     
    +
    aaconPresets - Variable in class compbio.ws.server.GenericMetadataService
    +
     
    +
    AAConWS - Class in compbio.ws.server
    +
     
    +
    AAConWS() - Constructor for class compbio.ws.server.AAConWS
    +
     
    +
    abandoned - Variable in class compbio.stat.servlet.util.Totals
    +
     
    +
    accept(File) - Static method in class compbio.stat.collector.InputFilter
    +
    +
    Accepts input as valid unless it is a test input
    +
    +
    acct_cpu - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    acct_io - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    acct_iow - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    acct_maxvmem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    acct_mem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    actualNumberofSequences - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    actualNumberofSequences - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    addJob(String, ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    addOption(Option<T>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds Option to the internal list of options
    +
    +
    addOptionNames(String...) - Method in class compbio.metadata.Option
    +
    +
    Adds an option to the optionName list
    +
    +
    addOptionNames(String...) - Method in class compbio.metadata.Parameter
    +
     
    +
    addParameter(Parameter<T>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds parameter to the internal parameter list
    +
    +
    addParameters(List<String>) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    addParameters(List<String>) - Method in interface compbio.engine.client.Executable
    +
    +
    Adds parameter to the list of parameters for a native executable
    +
    +
    addParameters(List<String>) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    addParameters(List<String>) - Method in class compbio.runner.msa.Mafft
    +
    +
    Mafft input must always be the last parameter!
    +
    +
    addParams(List<String>) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    addPossibleValues(String...) - Method in class compbio.metadata.Parameter
    +
     
    +
    addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - Static method in class compbio.engine.SubmissionManager
    +
     
    +
    afterExecute(Runnable, Throwable) - Method in class compbio.engine.local.LocalExecutorService
    +
     
    +
    AlifoldLine(String) - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
     
    +
    AlifoldResult() - Constructor for enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
     
    +
    Align - Class in compbio.data.msa.jaxws
    +
     
    +
    Align() - Constructor for class compbio.data.msa.jaxws.Align
    +
     
    +
    align(List<FastaSequence>) - Method in interface compbio.data.msa.MsaWS
    +
    +
    Align a list of sequences with default settings.
    +
    +
    align(File, MsaWS<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Align sequences from the file using MsaWS
    +
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    align(List<FastaSequence>) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    alignment - Variable in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    alignment - Variable in class compbio.data.msa.jaxws.Fold
    +
     
    +
    alignment - Variable in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    Alignment - Class in compbio.data.sequence
    +
    +
    Multiple sequence alignment.
    +
    +
    Alignment() - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    Alignment(List<FastaSequence>, AlignmentMetadata) - Constructor for class compbio.data.sequence.Alignment
    +
     
    +
    AlignmentMetadata - Class in compbio.data.sequence
    +
    +
    Alignment metadata e.g.
    +
    +
    AlignmentMetadata() - Constructor for class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    AlignmentMetadata(Program, char) - Constructor for class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    alignmentP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    AlignResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    AlignResponse() - Constructor for class compbio.data.msa.jaxws.AlignResponse
    +
     
    +
    allStat - Variable in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    allTested - Static variable in class compbio.ws.server.RegistryWS
    +
    +
    Indicate whether the services were tested at all
    +
    +
    AMBIGUOUS_AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Same as AA pattern but with two additional letters - XU
    +
    +
    AMBIGUOUS_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Ambiguous nucleotide
    +
    +
    Analize - Class in compbio.data.msa.jaxws
    +
     
    +
    Analize() - Constructor for class compbio.data.msa.jaxws.Analize
    +
     
    +
    analize(List<FastaSequence>) - Method in interface compbio.data.msa.SequenceAnnotation
    +
    +
    Analyse the sequences.
    +
    +
    analize(File, SequenceAnnotation<AAConWS>, Preset<AAConWS>, List<Option<AAConWS>>) - Static method in class compbio.ws.client.AAConClient
    +
    +
    Calculate conservation for sequences loaded from the file
    +
    +
    analize(List<FastaSequence>, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Calculate conservation for sequences loaded from a FASTA record list structure
    +
    +
    analize(File, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Calculate conservation for sequences loaded from the file
    +
    +
    analize(List<FastaSequence>) - Method in class compbio.ws.server.AAConWS
    +
     
    +
    analize(List<FastaSequence>) - Method in class compbio.ws.server.RNAalifoldWS
    +
     
    +
    analize(List<FastaSequence>) - Method in class compbio.ws.server.SequenceAnnotationService
    +
     
    +
    analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    AnalizeResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    AnalizeResponse() - Constructor for class compbio.data.msa.jaxws.AnalizeResponse
    +
     
    +
    ANNOTATION - Static variable in class compbio.runner.msa.GLprobs
    +
     
    +
    ANNOTATION - Static variable in class compbio.runner.msa.MSAprobs
    +
     
    +
    ANNOTATION - Static variable in class compbio.runner.msa.Probcons
    +
     
    +
    AnnualStat - Class in compbio.stat.servlet
    +
     
    +
    AnnualStat() - Constructor for class compbio.stat.servlet.AnnualStat
    +
     
    +
    anonymizeIP() - Static method in class compbio.ws.server.GAUtils
    +
     
    +
    arg0 - Variable in class compbio.data.msa.jaxws.GetLastTested
    +
     
    +
    arg0 - Variable in class compbio.data.msa.jaxws.GetLastTestedOn
    +
     
    +
    arg0 - Variable in class compbio.data.msa.jaxws.GetServiceDescription
    +
     
    +
    arg0 - Variable in class compbio.data.msa.jaxws.IsOperating
    +
     
    +
    arg0 - Variable in class compbio.data.msa.jaxws.TestService
    +
     
    +
    Argument<T> - Interface in compbio.metadata
    +
    +
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +
    +
    arguments - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    argumentsToCommandString(List<? extends Option<?>>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - Static method in class compbio.runner.OptionCombinator
    +
     
    +
    aSequenceLenghtActual - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    aSequenceLenghtAllowed - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    asMap() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    asSet() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    AsyncClusterRunner - Class in compbio.engine.cluster.drmaa
    +
    +
    Single cluster job runner class
    +
    +
    AsyncClusterRunner() - Constructor for class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    AsyncExecutor - Interface in compbio.engine
    +
    +
    An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    +
    +
    AsyncJobRunner - Class in compbio.engine.cluster.drmaa
    +
    +
    Single cluster job runner class
    +
    +
    AsyncJobRunner() - Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    AsyncLocalRunner - Class in compbio.engine.local
    +
     
    +
    AsyncLocalRunner() - Constructor for class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    autoOption - Static variable in class compbio.runner.msa.Mafft
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-10.html b/website/docs/full_javadoc/index-files/index-10.html new file mode 100644 index 0000000..49c65ae --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-10.html @@ -0,0 +1,262 @@ + + + + + +J-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    J

    +
    +
    JABAService - Interface in compbio.data.msa
    +
    +
    This is a marker interface, contains no methods
    +
    +
    JABAWS_VERSION - Static variable in interface compbio.data.msa.JABAService
    +
     
    +
    JManagement - Interface in compbio.data.msa
    +
     
    +
    Job - Class in compbio.engine
    +
     
    +
    Job(String, String, ConfiguredExecutable<?>) - Constructor for class compbio.engine.Job
    +
     
    +
    jobdir - Variable in class compbio.stat.collector.JobDirectory
    +
     
    +
    JobDirectory - Class in compbio.stat.collector
    +
     
    +
    JobDirectory(File) - Constructor for class compbio.stat.collector.JobDirectory
    +
     
    +
    JobExecutionException - Exception in compbio.metadata
    +
    +
    JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    +
    +
    JobExecutionException(String) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    JobExecutionException(Throwable) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    JobExecutionException(String, Throwable) - Constructor for exception compbio.metadata.JobExecutionException
    +
     
    +
    jobId - Variable in class compbio.data.msa.jaxws.CancelJob
    +
     
    +
    jobId - Variable in class compbio.data.msa.jaxws.GetAnnotation
    +
     
    +
    jobId - Variable in class compbio.data.msa.jaxws.GetJobStatus
    +
     
    +
    jobId - Variable in class compbio.data.msa.jaxws.GetResult
    +
     
    +
    jobId - Variable in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    jobId - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    JOBID - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    jobId - Variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    jobId - Variable in class compbio.engine.ClusterJobId
    +
     
    +
    jobId - Variable in class compbio.engine.Job
    +
     
    +
    jobinfo - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    Joblist - Class in compbio.stat.servlet
    +
     
    +
    Joblist() - Constructor for class compbio.stat.servlet.Joblist
    +
     
    +
    jobname - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    JobRunner - Class in compbio.engine.cluster.drmaa
    +
    +
    Single cluster job runner class
    +
    +
    JobRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    jobs - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    JobStat - Class in compbio.stat.collector
    +
     
    +
    JobStat(Services, String, String, long, long, long, long, boolean, boolean) - Constructor for class compbio.stat.collector.JobStat
    +
     
    +
    JobStat(String) - Constructor for class compbio.stat.collector.JobStat
    +
     
    +
    JobStatus - Enum in compbio.metadata
    +
    +
    The status of the job.
    +
    +
    JobStatus() - Constructor for enum compbio.metadata.JobStatus
    +
     
    +
    JobSubmissionException - Exception in compbio.metadata
    +
    +
    Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    +
    +
    JobSubmissionException(String) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JobSubmissionException(Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JobSubmissionException(String, Throwable) - Constructor for exception compbio.metadata.JobSubmissionException
    +
     
    +
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    +
    +
    This class was generated by the JAX-WS RI.
    +
    +
    JobSubmissionExceptionBean() - Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean
    +
     
    +
    jobtempl - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    jobtempl - Variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    Jronn - Class in compbio.runner.disorder
    +
    +
    Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    +
    +
    Jronn() - Constructor for class compbio.runner.disorder.Jronn
    +
     
    +
    JRONN_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    JRONN_WRONG_FORMAT_MESSAGE - Static variable in class compbio.data.sequence.SequenceUtil
    +
     
    +
    JronnWS - Class in compbio.ws.server
    +
     
    +
    JronnWS() - Constructor for class compbio.ws.server.JronnWS
    +
     
    +
    JT_ABANDONED - Static variable in class compbio.stat.servlet.Joblist
    +
     
    +
    JT_ALL - Static variable in class compbio.stat.servlet.Joblist
    +
     
    +
    JT_CANCELLED - Static variable in class compbio.stat.servlet.Joblist
    +
     
    +
    JT_FAILED - Static variable in class compbio.stat.servlet.Joblist
    +
     
    +
    JT_INCOMPLETE - Static variable in class compbio.stat.servlet.Joblist
    +
     
    +
    justStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    Jws2Client - Class in compbio.ws.client
    +
    +
    A command line client for JAva Bioinformatics Analysis Web Services
    +
    +
    Jws2Client(String[]) - Constructor for class compbio.ws.client.Jws2Client
    +
    +
    Connects to the service and do the job as requested, if something goes + wrong reports or/and prints usage help.
    +
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-11.html b/website/docs/full_javadoc/index-files/index-11.html new file mode 100644 index 0000000..9c6350b --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-11.html @@ -0,0 +1,151 @@ + + + + + +K-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    K

    +
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.conservation.AACon
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.ClustalO
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.ClustalW
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.GLprobs
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.Mafft
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.MSAprobs
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.Muscle
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.Probcons
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.msa.Tcoffee
    +
     
    +
    KEY_VALUE_SEPARATOR - Static variable in class compbio.runner.structure.RNAalifold
    +
     
    +
    keyFound(String[], String) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Checks whether the key is in the command line
    +
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-12.html b/website/docs/full_javadoc/index-files/index-12.html new file mode 100644 index 0000000..7f2ef0b --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-12.html @@ -0,0 +1,448 @@ + + + + + +L-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    L

    +
    +
    LAST - Static variable in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    lastAccessTime - Variable in class compbio.engine.FilePuller
    +
     
    +
    launderThrowable(Throwable) - Static method in class compbio.engine.local.LocalEngineUtil
    +
    +
    Coerce an unchecked Throwable to a RuntimeException or Error
    +
    +
    LifeSpanInHours - Variable in class compbio.stat.collector.DirCleaner
    +
     
    +
    Limit<T> - Class in compbio.metadata
    +
    +
    A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    +
    +
    Limit() - Constructor for class compbio.metadata.Limit
    +
     
    +
    Limit(int, int, String) - Constructor for class compbio.metadata.Limit
    +
    +
    Instantiate the limit
    +
    +
    Limit(int, int, String, boolean) - Constructor for class compbio.metadata.Limit
    +
     
    +
    limit - Variable in class compbio.metadata.LimitsManager
    +
     
    +
    LimitExceededException - Exception in compbio.metadata
    +
    +
    This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    +
    +
    LimitExceededException(String) - Constructor for exception compbio.metadata.LimitExceededException
    +
     
    +
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    +
    +
    This class was generated by the JAX-WS RI.
    +
    +
    LimitExceededExceptionBean() - Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    limitList - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.ClustalOWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.ClustalWS
    +
     
    +
    limitMan - Variable in class compbio.ws.server.GenericMetadataService
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.GLprobsWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.MafftWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.MSAprobsWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.MuscleWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.ProbconsWS
    +
     
    +
    limitMan - Static variable in class compbio.ws.server.TcoffeeWS
    +
     
    +
    limits - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    LimitsManager<T> - Class in compbio.metadata
    +
    +
    A collection of Limits
    +
    +
    LimitsManager() - Constructor for class compbio.metadata.LimitsManager
    +
     
    +
    line_delimiter - Static variable in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    listAllServices(String) - Static method in class compbio.ws.client.Jws2Client
    +
     
    +
    listLimits(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Checks whether limitList parameter is in the command line
    +
    +
    listParameters(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Searches the command line keys in the array of parameters
    +
    +
    listPresets(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Check whether presetList is set in the command line
    +
    +
    listServices(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    list available services
    +
    +
    listServices - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    listServicesOld - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    livesOverLifeSpan(JobDirectory) - Method in class compbio.stat.collector.DirCleaner
    +
     
    +
    load(InputStream) - Static method in class compbio.engine.client.RunConfiguration
    +
     
    +
    loadAlignment() - Static method in class compbio.ws.client.WSTester
    +
    +
    Converting input to a form accepted by WS
    +
    +
    LoadBalancer - Class in compbio.engine
    +
    +
    This class decides where to execute the job.
    +
    +
    LoadBalancer() - Constructor for class compbio.engine.LoadBalancer
    +
     
    +
    loadExecutable(String) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    loadExecutable(String) - Static method in class compbio.engine.client.Util
    +
     
    +
    loadParameters(File) - Static method in class compbio.ws.client.IOHelper
    +
    +
    Load parameters from file
    +
    +
    loadRNAAlignment() - Static method in class compbio.ws.client.WSTester
    +
    +
    Converting input to a form accepted by WS
    +
    +
    loadRunConfiguration(RunConfiguration) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    loadRunConfiguration(InputStream) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    loadRunConfiguration(InputStream) - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    loadRunConfiguration(RunConfiguration) - Method in interface compbio.engine.client.Executable
    +
     
    +
    loadRunConfiguration(RunConfiguration) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    loadSeqs(int) - Static method in class compbio.ws.client.WSTester
    +
    +
    Converting input to a form accepted by WS
    +
    +
    LOCAL_ENGINE_LIMIT_PRESET - Static variable in class compbio.metadata.PresetManager
    +
     
    +
    LOCAL_WORK_DIRECTORY - Static variable in class compbio.engine.Configurator
    +
     
    +
    localcf - Variable in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    localcl - Variable in class compbio.ws.server.MainManager
    +
     
    +
    LocalEngineUtil - Class in compbio.engine.local
    +
     
    +
    LocalEngineUtil() - Constructor for class compbio.engine.local.LocalEngineUtil
    +
     
    +
    LocalExecutorService - Class in compbio.engine.local
    +
     
    +
    LocalExecutorService(int, int, long, TimeUnit, BlockingQueue<Runnable>) - Constructor for class compbio.engine.local.LocalExecutorService
    +
     
    +
    LocalRunner - Class in compbio.engine.local
    +
     
    +
    LocalRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.local.LocalRunner
    +
     
    +
    localStat - Variable in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    log - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    log - Static variable in class compbio.engine.Cleaner
    +
     
    +
    log - Static variable in class compbio.engine.client.CommandBuilder
    +
     
    +
    log - Static variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    log - Static variable in class compbio.engine.client.EngineUtil
    +
     
    +
    log - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    log - Static variable in class compbio.engine.client.RunConfiguration
    +
     
    +
    log - Static variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    log - Static variable in class compbio.engine.client.Util
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.ClusterEngineUtil
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.ClusterUtil
    +
     
    +
    log - Static variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    log - Static variable in class compbio.engine.conf.DirectoryManager
    +
     
    +
    log - Static variable in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    log - Static variable in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    log - Static variable in class compbio.engine.Configurator
    +
     
    +
    log - Static variable in class compbio.engine.FilePuller
    +
     
    +
    log - Static variable in class compbio.engine.LoadBalancer
    +
     
    +
    log - Static variable in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    log - Static variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    log - Static variable in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    log - Static variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    log - Static variable in class compbio.engine.local.LocalRunner
    +
     
    +
    log - Static variable in class compbio.engine.local.StreamGobbler
    +
     
    +
    log - Static variable in class compbio.engine.ProgressGetter
    +
     
    +
    log - Static variable in class compbio.engine.PulledFileCache
    +
     
    +
    log - Static variable in class compbio.engine.SubmissionManager
    +
     
    +
    log - Static variable in class compbio.runner.conservation.AACon
    +
     
    +
    log - Static variable in class compbio.runner.disorder.Disembl
    +
     
    +
    log - Static variable in class compbio.runner.disorder.GlobPlot
    +
     
    +
    log - Static variable in class compbio.runner.disorder.IUPred
    +
     
    +
    log - Static variable in class compbio.runner.disorder.Jronn
    +
     
    +
    log - Static variable in class compbio.runner.msa.ClustalO
    +
     
    +
    log - Static variable in class compbio.runner.msa.ClustalW
    +
     
    +
    log - Static variable in class compbio.runner.msa.GLprobs
    +
     
    +
    log - Static variable in class compbio.runner.msa.Mafft
    +
     
    +
    log - Static variable in class compbio.runner.msa.MSAprobs
    +
     
    +
    log - Static variable in class compbio.runner.msa.Muscle
    +
     
    +
    log - Static variable in class compbio.runner.msa.Probcons
    +
     
    +
    log - Static variable in class compbio.runner.msa.Tcoffee
    +
     
    +
    log - Static variable in class compbio.runner.OptionCombinator
    +
     
    +
    log - Static variable in class compbio.runner.RunnerUtil
    +
     
    +
    log - Static variable in class compbio.runner.structure.RNAalifold
    +
     
    +
    log - Static variable in class compbio.runner.Util
    +
     
    +
    log - Static variable in class compbio.stat.collector.DirCleaner
    +
     
    +
    log - Static variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    log - Static variable in class compbio.stat.collector.InputFilter
    +
     
    +
    log - Static variable in class compbio.stat.collector.JobDirectory
    +
     
    +
    log - Static variable in class compbio.stat.collector.StatDB
    +
     
    +
    log - Static variable in class compbio.stat.servlet.DisplayStat
    +
     
    +
    log - Static variable in class compbio.stat.servlet.HttpCodeResponseServiceStatus
    +
     
    +
    log - Static variable in class compbio.stat.servlet.ServiceStatus
    +
     
    +
    log - Variable in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    log - Static variable in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    log - Static variable in class compbio.ws.client.AAConClient
    +
    +
    Use java.util.Logger instead of log4j logger to reduce the size of the + client package
    +
    +
    log - Static variable in class compbio.ws.client.Jws2Client
    +
    +
    Use java.util.Logger instead of log4j logger to reduce the size of the client package
    +
    +
    log - Static variable in class compbio.ws.server.AAConWS
    +
     
    +
    log - Static variable in class compbio.ws.server.ClustalOWS
    +
     
    +
    log - Static variable in class compbio.ws.server.ClustalWS
    +
     
    +
    log - Static variable in class compbio.ws.server.DisemblWS
    +
     
    +
    log - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    log - Variable in class compbio.ws.server.GenericMetadataService
    +
     
    +
    log - Static variable in class compbio.ws.server.GlobPlotWS
    +
     
    +
    log - Static variable in class compbio.ws.server.GLprobsWS
    +
     
    +
    log - Static variable in class compbio.ws.server.IUPredWS
    +
     
    +
    log - Static variable in class compbio.ws.server.JronnWS
    +
     
    +
    log - Static variable in class compbio.ws.server.MafftWS
    +
     
    +
    log - Variable in class compbio.ws.server.MainManager
    +
     
    +
    log - Static variable in class compbio.ws.server.MSAprobsWS
    +
     
    +
    log - Static variable in class compbio.ws.server.MuscleWS
    +
     
    +
    log - Static variable in class compbio.ws.server.ProbconsWS
    +
     
    +
    log - Static variable in class compbio.ws.server.RegistryWS
    +
     
    +
    log - Static variable in class compbio.ws.server.RNAalifoldWS
    +
     
    +
    log - Variable in class compbio.ws.server.SetExecutableFlag
    +
     
    +
    log - Static variable in class compbio.ws.server.TcoffeeWS
    +
     
    +
    logStatistics(JobInfo) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    LONG_OUTPUT - Static variable in class compbio.runner.disorder.IUPred
    +
     
    +
    LOOPS_EXPECTATION_THRESHOLD - Variable in class compbio.runner.disorder.Disembl
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-13.html b/website/docs/full_javadoc/index-files/index-13.html new file mode 100644 index 0000000..1af0682 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-13.html @@ -0,0 +1,262 @@ + + + + + +M-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    M

    +
    +
    Mafft - Class in compbio.runner.msa
    +
     
    +
    Mafft() - Constructor for class compbio.runner.msa.Mafft
    +
     
    +
    mafft_binaries - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    MAFFT_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    mafftOptions - Static variable in class compbio.ws.server.MafftWS
    +
     
    +
    mafftPresets - Static variable in class compbio.ws.server.MafftWS
    +
     
    +
    MafftWS - Class in compbio.ws.server
    +
     
    +
    MafftWS() - Constructor for class compbio.ws.server.MafftWS
    +
     
    +
    main(String[]) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    main(String[]) - Static method in class compbio.stat.collector.ExecutionStatCollector
    +
    +
    Not in use
    +
    +
    main(String[]) - Static method in class compbio.stat.collector.StatDB
    +
     
    +
    main(String[]) - Static method in class compbio.ws.client.AAConClient
    +
    +
    Starts command line client, if no parameters are supplied prints help.
    +
    +
    main(String[]) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Starts command line client, if no parameter are supported print help.
    +
    +
    main(String[]) - Static method in enum compbio.ws.client.Services
    +
     
    +
    main(String[]) - Static method in class compbio.ws.client.WSTester
    +
    +
    Test JWS2 web services
    +
    +
    main(String[]) - Static method in class compbio.ws.server.SimpleWSPublisher
    +
    +
    Deprecated.
    + 
    +
    MainManager - Class in compbio.ws.server
    +
    +
    Two tasks: + 1.
    +
    +
    MainManager() - Constructor for class compbio.ws.server.MainManager
    +
     
    +
    makeLocalPath(String) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    makeLocalPath(String) - Static method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    MATRIX_PAR_NAME - Variable in class compbio.runner.msa.Mafft
    +
     
    +
    max - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    maxNameLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    MAXVALUE - Static variable in class compbio.runner.OptionCombinator
    +
     
    +
    maxvmem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    MEAStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    mergeEnvVariables(Map<String, String>, Map<String, String>) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    mergeEnvVariables(Map<String, String>, Map<String, String>) - Static method in class compbio.engine.client.Util
    +
     
    +
    message - Variable in class compbio.data.msa.jaxws.JobSubmissionExceptionBean
    +
     
    +
    message - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    message - Variable in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
    +
     
    +
    message - Variable in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
    +
     
    +
    message - Variable in class compbio.data.msa.jaxws.WrongParameterExceptionBean
    +
     
    +
    Metadata<T> - Interface in compbio.data.msa
    +
     
    +
    metadata - Variable in class compbio.data.sequence.Alignment
    +
     
    +
    MetadataHelper - Class in compbio.ws.client
    +
     
    +
    MetadataHelper() - Constructor for class compbio.ws.client.MetadataHelper
    +
     
    +
    method - Variable in class compbio.data.sequence.Score
    +
     
    +
    mfeStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    min - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    minNameHolderLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    MINVALUE - Static variable in class compbio.runner.OptionCombinator
    +
     
    +
    moreinfo - Variable in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    MSAprobs - Class in compbio.runner.msa
    +
     
    +
    MSAprobs() - Constructor for class compbio.runner.msa.MSAprobs
    +
     
    +
    MSAPROBS_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    MSAprobsOptions - Static variable in class compbio.ws.server.MSAprobsWS
    +
     
    +
    MSAprobsWS - Class in compbio.ws.server
    +
     
    +
    MSAprobsWS() - Constructor for class compbio.ws.server.MSAprobsWS
    +
     
    +
    MsaWS<T> - Interface in compbio.data.msa
    +
    +
    Multiple Sequence Alignment (MSA) Web Services Interface
    +
    +
    Muscle - Class in compbio.runner.msa
    +
     
    +
    Muscle() - Constructor for class compbio.runner.msa.Muscle
    +
    +
    Default options are + + -clwstrict - write output in clustal format
    +
    +
    MUSCLE_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    muscleOptions - Static variable in class compbio.ws.server.MuscleWS
    +
     
    +
    musclePresets - Static variable in class compbio.ws.server.MuscleWS
    +
     
    +
    MuscleWS - Class in compbio.ws.server
    +
     
    +
    MuscleWS() - Constructor for class compbio.ws.server.MuscleWS
    +
     
    +
    MySchemaOutputResolver(String, String) - Constructor for class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-14.html b/website/docs/full_javadoc/index-files/index-14.html new file mode 100644 index 0000000..c887c59 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-14.html @@ -0,0 +1,241 @@ + + + + + +N-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    N

    +
    +
    name - Variable in class compbio.data.msa.Category
    +
     
    +
    name - Variable in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    name - Variable in class compbio.metadata.Option
    +
     
    +
    name - Variable in class compbio.metadata.Preset
    +
     
    +
    nameValueSeparator - Variable in class compbio.engine.client.CommandBuilder
    +
     
    +
    ncoreNumber - Variable in class compbio.runner.conservation.AACon
    +
    +
    Number of cores to use, defaults to 1 for local execution or the value of + "jronn.cluster.cpunum" property for cluster execution
    +
    +
    ncoreNumber - Variable in class compbio.runner.disorder.Jronn
    +
     
    +
    ncoreNumber - Variable in class compbio.runner.msa.ClustalO
    +
    +
    Number of cores to use, defaults to 1 for local execution or the value of + "tcoffee.cluster.cpunum" property for cluster execution
    +
    +
    ncoreNumber - Variable in class compbio.runner.msa.Tcoffee
    +
    +
    Number of cores to use, defaults to 1 for local execution or the value of + "tcoffee.cluster.cpunum" property for cluster execution
    +
    +
    ncorePrm - Variable in class compbio.runner.conservation.AACon
    +
     
    +
    ncorePrm - Variable in class compbio.runner.disorder.Jronn
    +
     
    +
    ncorePrm - Static variable in class compbio.runner.msa.ClustalO
    +
    +
    Number of cores parameter name
    +
    +
    ncorePrm - Static variable in class compbio.runner.msa.Tcoffee
    +
     
    +
    newCommandBuilder(List<? extends Option<T>>, String) - Static method in class compbio.engine.client.CommandBuilder
    +
    +
    This produces the same result as getCommands method.
    +
    +
    newConfExecutable(RunConfiguration) - Static method in class compbio.engine.client.ConfExecutable
    +
     
    +
    newEmptyScore(Enum<?>) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    newFilePuller(String, int) - Static method in class compbio.engine.FilePuller
    +
     
    +
    newIncompleteStat(String) - Static method in class compbio.stat.collector.JobStat
    +
     
    +
    newInstance(List<String>, List<TreeSet<Score>>) - Static method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    newInstance(Map<String, Set<Score>>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newInstance(Services, String, String, long, long, long, long, boolean, boolean) - Static method in class compbio.stat.collector.JobStat
    +
     
    +
    newInstance(Services, String, String, Timestamp, Timestamp, long, long, boolean, boolean) - Static method in class compbio.stat.collector.JobStat
    +
     
    +
    newInstanceSingleScore(Map<String, Score>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newInstanceSingleSequence(Set<Score>) - Static method in class compbio.data.sequence.ScoreManager
    +
     
    +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - Static method in exception compbio.metadata.LimitExceededException
    +
     
    +
    newLine - Static variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    newParameter(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    newProgressPuller(String) - Static method in class compbio.engine.FilePuller
    +
    +
    Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more.
    +
    +
    newSetScore(Enum<?>, List<Float>) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    newStatCollecton(Date, Date) - Static method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    newUnsupportedOutputException() - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    next() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Reads the next FastaSequence from the input
    +
    +
    NEXT_ENV_PROPERTY_DELIMITER - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    NON_AA - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    inversion of AA pattern
    +
    +
    NON_NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Non nucleotide
    +
    +
    nonoperating - Static variable in class compbio.ws.server.RegistryWS
    +
     
    +
    NONWORD - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Non word
    +
    +
    notData - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    NUCLEOTIDE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    Nucleotides a, t, g, c, u
    +
    +
    NUMBER_FORMAT - Static variable in class compbio.data.sequence.Score
    +
     
    +
    numberOfLetters() - Method in class compbio.metadata.Limit
    +
     
    +
    numberOfSequencesAllowed - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    numberOfSequencesAllowed - Variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    numTasks - Variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-15.html b/website/docs/full_javadoc/index-files/index-15.html new file mode 100644 index 0000000..84d6aa4 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-15.html @@ -0,0 +1,186 @@ + + + + + +O-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
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    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    O

    +
    +
    OK - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    oneLineAlignmentLength - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    open - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    openInputStream(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reads and parses Fasta or Clustal formatted file into a list of + FastaSequence objects
    +
    +
    operating - Static variable in class compbio.ws.server.RegistryWS
    +
    +
    Stores tested and passed (the test) services and their testing time
    +
    +
    Option<T> - Class in compbio.metadata
    +
    +
    Command line option/flag or multiple exclusive options with no value.
    +
    +
    Option() - Constructor for class compbio.metadata.Option
    +
     
    +
    Option(String, String) - Constructor for class compbio.metadata.Option
    +
     
    +
    option - Variable in class compbio.metadata.Preset
    +
     
    +
    OptionCombinator - Class in compbio.runner
    +
    +
    This class solve the following problems.
    +
    +
    OptionCombinator(RunnerConfig<? extends Executable<?>>) - Constructor for class compbio.runner.OptionCombinator
    +
     
    +
    optionNames - Variable in class compbio.metadata.Option
    +
     
    +
    options - Variable in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    options - Variable in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    options - Variable in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    options - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    optionsToCommandString(List<Option<?>>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    optionToCommandString(Option<?>) - Static method in class compbio.runner.OptionCombinator
    +
     
    +
    os - Variable in class compbio.engine.local.StreamGobbler
    +
     
    +
    output - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Output
    +
    +
    OUTPUT - Static variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    outputFile - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    outputkey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    OutputType() - Constructor for enum compbio.engine.local.StreamGobbler.OutputType
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-16.html b/website/docs/full_javadoc/index-files/index-16.html new file mode 100644 index 0000000..926fc9a --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-16.html @@ -0,0 +1,447 @@ + + + + + +P-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    P

    +
    +
    Parameter() - Constructor for class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    Parameter(String) - Constructor for class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    Parameter(String, String) - Constructor for class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    Parameter<T> - Class in compbio.metadata
    +
    +
    A single value containing an option supported by the web service e.g.
    +
    +
    Parameter() - Constructor for class compbio.metadata.Parameter
    +
     
    +
    Parameter(String, String) - Constructor for class compbio.metadata.Parameter
    +
     
    +
    parameterkey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    parameters - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Parameters
    +
    +
    parameters - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    parameterToString(List<CommandBuilder.Parameter>) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    paramFile - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    paramList - Variable in class compbio.engine.client.CommandBuilder
    +
     
    +
    paramList - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    paramValueUpdater() - Method in class compbio.engine.client.SkeletalExecutable
    +
    +
    This is a generic method of changing values of the parameters with + properties + + This method iterates via commands for an executable finding matches from + the Executable.properties file and replacing values in CommandBuilder + with a combination of value from CommandBuilder to merge path from + properties
    +
    +
    parseIUPredDomains(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    # P53_HUMA + + Number of globular domains: 2 + + globular domain 1.
    +
    +
    parseIUPredScores(Scanner) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    parseRanges(Enum, String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Parsing: + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343, + 350-391, 429-485, 497-506, 539-547 + + # REM465 355-368 + + # HOTLOOPS 190-204
    +
    +
    PATH - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
    +
    Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable
    +
    +
    PathValidator - Class in compbio.engine.client
    +
     
    +
    PathValidator() - Constructor for class compbio.engine.client.PathValidator
    +
     
    +
    pbuilder - Variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    ph - Static variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    ph - Static variable in class compbio.engine.client.EngineUtil
    +
     
    +
    ph - Static variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    ph - Static variable in class compbio.engine.client.Util
    +
     
    +
    ph - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    ph - Static variable in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    ph - Static variable in class compbio.engine.Configurator
    +
     
    +
    ph - Static variable in class compbio.runner.msa.Tcoffee
    +
     
    +
    ph - Static variable in class compbio.runner.Util
    +
     
    +
    ph - Static variable in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    ph - Static variable in class compbio.ws.server.MainManager
    +
     
    +
    PipedExecutable<T> - Interface in compbio.engine.client
    +
    +
    This is a marker interface to indicate that the output of the process must be + captured.
    +
    +
    position - Variable in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    position - Variable in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    position - Variable in class compbio.metadata.ChunkHolder
    +
     
    +
    possibleValues - Variable in class compbio.metadata.Parameter
    +
     
    +
    preset - Variable in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    preset - Variable in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    preset - Variable in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    preset - Variable in class compbio.metadata.Limit
    +
     
    +
    Preset<T> - Class in compbio.metadata
    +
    +
    Collection of Options and Parameters with their values
    +
    +
    Preset() - Constructor for class compbio.metadata.Preset
    +
     
    +
    preset - Variable in class compbio.metadata.PresetManager
    +
     
    +
    PresetAlign - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetAlign() - Constructor for class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<T>) - Method in interface compbio.data.msa.MsaWS
    +
    +
    Align a list of sequences with preset.
    +
    +
    presetAlign(MsaWS<T>, List<Preset<T>>) - Method in class compbio.ws.client.WSTester
    +
    +
    Calls alignment with preset
    +
    +
    presetAlign(List<FastaSequence>, Preset<ClustalO>) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<ClustalW>) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<GLprobs>) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<Mafft>) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<MSAprobs>) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<Muscle>) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<Probcons>) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    presetAlign(List<FastaSequence>, Preset<Tcoffee>) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    PresetAlignResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetAlignResponse() - Constructor for class compbio.data.msa.jaxws.PresetAlignResponse
    +
     
    +
    PresetAnalize - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetAnalize() - Constructor for class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<T>) - Method in interface compbio.data.msa.SequenceAnnotation
    +
    +
    Analyse the sequences according to the preset settings.
    +
    +
    presetAnalize(List<FastaSequence>, Preset<AACon>) - Method in class compbio.ws.server.AAConWS
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<Disembl>) - Method in class compbio.ws.server.DisemblWS
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<GlobPlot>) - Method in class compbio.ws.server.GlobPlotWS
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<IUPred>) - Method in class compbio.ws.server.IUPredWS
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<RNAalifold>) - Method in class compbio.ws.server.RNAalifoldWS
    +
     
    +
    presetAnalize(List<FastaSequence>, Preset<T>) - Method in class compbio.ws.server.SequenceAnnotationService
    +
     
    +
    PresetAnalizeResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetAnalizeResponse() - Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse
    +
     
    +
    PresetFold - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetFold() - Constructor for class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    PresetFoldResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    PresetFoldResponse() - Constructor for class compbio.data.msa.jaxws.PresetFoldResponse
    +
     
    +
    presetkey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    presetList - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    PresetManager<T> - Class in compbio.metadata
    +
    +
    Collection of presets and methods to manipulate them @see Preset
    +
    +
    PresetManager() - Constructor for class compbio.metadata.PresetManager
    +
     
    +
    presetName - Variable in class compbio.data.msa.jaxws.GetLimit
    +
     
    +
    print() - Static method in class compbio.engine.PulledFileCache
    +
     
    +
    printUsage(int) - Static method in class compbio.ws.client.AAConClient
    +
    +
    Prints AAConClient usage information to standard out
    +
    +
    printUsage() - Static method in class compbio.ws.client.WSTester
    +
    +
    Prints usage
    +
    +
    priority - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    prmSeparator - Variable in class compbio.metadata.RunnerConfig
    +
     
    +
    Probcons - Class in compbio.runner.msa
    +
     
    +
    Probcons() - Constructor for class compbio.runner.msa.Probcons
    +
     
    +
    PROBCONS_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    probconsOptions - Static variable in class compbio.ws.server.ProbconsWS
    +
     
    +
    ProbconsWS - Class in compbio.ws.server
    +
     
    +
    ProbconsWS() - Constructor for class compbio.ws.server.ProbconsWS
    +
     
    +
    PROC_ERR_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    PROC_IN_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    PROC_OUT_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    processParameters(List<String>, RunnerConfig<T>) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Converts options supplied via parameters file into Option objects
    +
    +
    program - Variable in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    Program - Enum in compbio.data.sequence
    +
    +
    The list of programmes that can produce alignments
    +
    +
    Program() - Constructor for enum compbio.data.sequence.Program
    +
     
    +
    ProgressGetter - Class in compbio.engine
    +
     
    +
    ProgressGetter() - Constructor for class compbio.engine.ProgressGetter
    +
     
    +
    PROP_HELPER - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    PROP_NAME_VALUE_SEPARATOR - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    PropertyHelperManager - Class in compbio.engine.conf
    +
     
    +
    PropertyHelperManager() - Constructor for class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    protocol - Static variable in class compbio.stat.collector.StatDB
    +
     
    +
    provider - Variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    ps - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    pseparator - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    PStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    pull(long) - Method in class compbio.engine.FilePuller
    +
     
    +
    pull(String, long, long, TimeUnit) - Static method in class compbio.engine.ProgressGetter
    +
     
    +
    pull(String, long) - Static method in class compbio.engine.ProgressGetter
    +
     
    +
    PulledFileCache - Class in compbio.engine
    +
     
    +
    PulledFileCache() - Constructor for class compbio.engine.PulledFileCache
    +
     
    +
    PullExecStatistics - Class in compbio.data.msa.jaxws
    +
     
    +
    PullExecStatistics() - Constructor for class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    pullExecStatistics(String, long) - Method in interface compbio.data.msa.JManagement
    +
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.AAConWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.GenericMetadataService
    +
    +
    Assume statistics is not supported
    +
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.JronnWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    pullExecStatistics(String, long) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    PullExecStatisticsResponse() - Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse
    +
     
    +
    pullFile(String, long) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    put(FilePuller) - Static method in class compbio.engine.PulledFileCache
    +
    +
    This method allows duplicates to be added.
    +
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-17.html b/website/docs/full_javadoc/index-files/index-17.html new file mode 100644 index 0000000..1c588d3 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-17.html @@ -0,0 +1,131 @@ + + + + + +Q-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    Q

    +
    +
    QUALIFIED_SERVICE_NAME - Static variable in class compbio.ws.client.AAConClient
    +
    +
    The fully qualified web service namespace
    +
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-18.html b/website/docs/full_javadoc/index-files/index-18.html new file mode 100644 index 0000000..c196a6a --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-18.html @@ -0,0 +1,411 @@ + + + + + +R-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    R

    +
    +
    rand - Static variable in class compbio.runner.OptionCombinator
    +
     
    +
    Range - Class in compbio.data.sequence
    +
     
    +
    Range() - Constructor for class compbio.data.sequence.Range
    +
     
    +
    Range(int, int) - Constructor for class compbio.data.sequence.Range
    +
     
    +
    Range(String[]) - Constructor for class compbio.data.sequence.Range
    +
     
    +
    ranges - Variable in class compbio.data.sequence.Score
    +
     
    +
    rconfig - Variable in class compbio.runner.OptionCombinator
    +
     
    +
    rconfigFile - Static variable in class compbio.engine.client.RunConfiguration
    +
     
    +
    read(InputStream, Class<V>) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    read(InputStream, Class<V>, Class<?>...) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    readAAConResults(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Read AACon result with no alignment files.
    +
    +
    readAndValidate(InputStream, Class<V>) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    readClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Read Clustal formatted alignment.
    +
    +
    readClustalFile(File) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    readClustalFile(String, String) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    readClustalFile(String, String) - Static method in class compbio.runner.Util
    +
     
    +
    readData(Timestamp, Timestamp, Services, Boolean) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    readDisembl(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
    +
    +
    readFasta(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reads fasta sequences from inStream into the list of FastaSequence + objects
    +
    +
    readGlobPlot(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    > Foobar_dundeefriends + + # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 + + # REM465 355-368 + + # HOTLOOPS 190-204 + + # RESIDUE COILS REM465 HOTLOOPS + + M 0.86010 0.88512 0.37094 + + T 0.79983 0.85864 0.44331 + + >Next Sequence name
    +
    +
    readIUPred(File) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Read IUPred output
    +
    +
    readIUPred(InputStream, IUPredResult) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    ## Long Disorder + + # P53_HUMAN + + 1 M 0.9943 + + 2 E 0.9917 + + 3 E 0.9879 + + (every line)
    +
    +
    readJRonn(File) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    readJRonn(InputStream) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Reader for JRonn horizontal file format
    +
    +
    readJronnFile(String, String) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    readJronnFile(String, String) - Static method in class compbio.runner.Util
    +
     
    +
    readRNAStruct(String, String) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    readRNAStructStream(InputStream) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    readRNAStructStream(InputStream, InputStream) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    reference - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    reference - Variable in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    regex - Variable in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
     
    +
    RegistryWS - Interface in compbio.data.msa
    +
    +
    JABAWS services registry
    +
    +
    RegistryWS - Class in compbio.ws.server
    +
    +
    JABAWS services registry
    +
    +
    RegistryWS() - Constructor for class compbio.ws.server.RegistryWS
    +
     
    +
    REM_EXPECTATION_THRESHOLD - Variable in class compbio.runner.disorder.Disembl
    +
     
    +
    remove() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Not implemented
    +
    +
    removeArgument(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Removes the argument Argument if found.
    +
    +
    removeArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
    +
    +
    removeFile(String) - Static method in class compbio.engine.Cleaner
    +
     
    +
    removeInvalidXMLCharacters(String) - Static method in class compbio.engine.FilePuller
    +
    +
    This method ensures that the output String has only valid XML unicode + characters as specified by the XML 1.0 standard.
    +
    +
    removeJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    removeJobFromListbyTaskId(String) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    removeParam(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    removeRecordedJobs(Set<JobStat>) - Method in class compbio.stat.collector.StatDB
    +
    +
    Removes the job if + + 1) It has already been recorded + + 2) It has not completed and did not timeout - this is to prevent + recording the information on the incomplete jobs.
    +
    +
    removeTask(ConfiguredExecutable<?>) - Static method in class compbio.engine.SubmissionManager
    +
     
    +
    removeTask(String) - Static method in class compbio.engine.SubmissionManager
    +
     
    +
    reportException(Exception) - Method in class compbio.ws.client.WSTester
    +
     
    +
    reportResults(Services, boolean) - Method in class compbio.ws.client.WSTester
    +
     
    +
    reportStat() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    reportUsage(Services) - Static method in class compbio.ws.server.GAUtils
    +
     
    +
    reportUsage(Services, String) - Static method in class compbio.ws.server.GAUtils
    +
     
    +
    reportUsage(ConfiguredExecutable<T>, Logger) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    ResultNotAvailableException - Exception in compbio.metadata
    +
    +
    ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +
    +
    ResultNotAvailableException(String) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    ResultNotAvailableException(Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    ResultNotAvailableException(String, Throwable) - Constructor for exception compbio.metadata.ResultNotAvailableException
    +
     
    +
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    +
    +
    This class was generated by the JAX-WS RI.
    +
    +
    ResultNotAvailableExceptionBean() - Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
    +
     
    +
    RESULTSIZE - Static variable in class compbio.stat.collector.JobStat
    +
     
    +
    resultSize - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    RNAalifold - Class in compbio.runner.structure
    +
     
    +
    RNAalifold() - Constructor for class compbio.runner.structure.RNAalifold
    +
     
    +
    RNAALIFOLD_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    RNAalifoldWS - Class in compbio.ws.server
    +
     
    +
    RNAalifoldWS() - Constructor for class compbio.ws.server.RNAalifoldWS
    +
     
    +
    RNAOut() - Constructor for enum compbio.data.sequence.RNAStructReader.RNAOut
    +
     
    +
    RNAStructReader - Class in compbio.data.sequence
    +
     
    +
    RNAStructReader() - Constructor for class compbio.data.sequence.RNAStructReader
    +
     
    +
    RNAStructReader.AlifoldLine - Enum in compbio.data.sequence
    +
     
    +
    RNAStructReader.AlifoldResult - Enum in compbio.data.sequence
    +
     
    +
    RNAStructReader.RNAOut - Enum in compbio.data.sequence
    +
     
    +
    RNAStructScoreManager - Class in compbio.data.sequence
    +
     
    +
    RNAStructScoreManager() - Constructor for class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    RNAStructScoreManager(List<String>, List<TreeSet<Score>>) - Constructor for class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    ru_stime - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    ru_utime - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    ru_wallclock - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    run() - Method in class compbio.engine.local.StreamGobbler
    +
     
    +
    run() - Method in class compbio.stat.collector.DirCleaner
    +
     
    +
    run() - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    RunConfiguration - Class in compbio.engine.client
    +
    +
    Value class for persisting ConfExecutable instances
    +
    +
    RunConfiguration() - Constructor for class compbio.engine.client.RunConfiguration
    +
     
    +
    RunConfiguration(ConfExecutable<?>) - Constructor for class compbio.engine.client.RunConfiguration
    +
     
    +
    runnerClassName - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Runner class name
    +
    +
    runnerClassName - Variable in class compbio.metadata.LimitsManager
    +
     
    +
    runnerClassName - Variable in class compbio.metadata.PresetManager
    +
     
    +
    runnerClassName - Variable in class compbio.metadata.RunnerConfig
    +
    +
    The class name of a runnable e.g.
    +
    +
    RunnerConfig<T> - Class in compbio.metadata
    +
    +
    The list of Parameters and Options supported by executable.
    +
    +
    RunnerConfig() - Constructor for class compbio.metadata.RunnerConfig
    +
     
    +
    RunnerConfigMarshaller<T> - Class in compbio.engine.conf
    +
     
    +
    RunnerConfigMarshaller(Class<?>) - Constructor for class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    RunnerConfigMarshaller(Class<?>, Class<?>...) - Constructor for class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    RunnerConfigMarshaller.MySchemaOutputResolver - Class in compbio.engine.conf
    +
     
    +
    RunnerUtil - Class in compbio.runner
    +
     
    +
    RunnerUtil() - Constructor for class compbio.runner.RunnerUtil
    +
     
    +
    RUNTIME - Static variable in class compbio.stat.collector.JobStat
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-19.html b/website/docs/full_javadoc/index-files/index-19.html new file mode 100644 index 0000000..120bb1c --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-19.html @@ -0,0 +1,748 @@ + + + + + +S-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    S

    +
    +
    s - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    saveRunConfiguration() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    saveRunConfiguration() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    sContact - Variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    Score - Class in compbio.data.sequence
    +
    +
    A value class for AACon annotation results storage.
    +
    +
    Score() - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, ArrayList<Float>) - Constructor for class compbio.data.sequence.Score
    +
    +
    Instantiate the Score
    +
    +
    Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, TreeSet<Range>) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    Score(Enum<?>, float[]) - Constructor for class compbio.data.sequence.Score
    +
     
    +
    ScoreHolder() - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    ScoreHolder(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    ScoreManager - Class in compbio.data.sequence
    +
     
    +
    ScoreManager() - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager(String, Set<Score>) - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager(Map<String, Set<Score>>) - Constructor for class compbio.data.sequence.ScoreManager
    +
     
    +
    ScoreManager.ScoreHolder - Class in compbio.data.sequence
    +
     
    +
    scores - Variable in class compbio.data.sequence.Score
    +
     
    +
    scores - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    seqLength - Variable in class compbio.metadata.Limit
    +
     
    +
    seqNumber - Variable in class compbio.metadata.Limit
    +
     
    +
    seqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    seqScores - Variable in class compbio.data.sequence.ScoreManager
    +
     
    +
    sequence - Variable in class compbio.data.sequence.FastaSequence
    +
    +
    Returns the string representation of sequence
    +
    +
    SequenceAnnotation<T> - Interface in compbio.data.msa
    +
    +
    Interface for tools that results to one or more annotation to sequence(s) + + Single, multiple sequences their groups or alignments can be annotated
    +
    +
    SequenceAnnotationService<T> - Class in compbio.ws.server
    +
    +
    Common methods for all SequenceAnnotation web services
    +
    +
    SequenceAnnotationService(SkeletalExecutable<T>, Logger) - Constructor for class compbio.ws.server.SequenceAnnotationService
    +
     
    +
    sequenceLenghtActual - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    sequenceLenghtAllowed - Variable in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    sequences - Variable in class compbio.data.sequence.Alignment
    +
     
    +
    SequenceUtil - Class in compbio.data.sequence
    +
    +
    Utility class for operations on sequences
    +
    +
    SequenceUtil() - Constructor for class compbio.data.sequence.SequenceUtil
    +
     
    +
    serialVersionUID - Static variable in exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.JobExecutionException
    +
    +
    Default stable serial for serialization
    +
    +
    serialVersionUID - Static variable in exception compbio.metadata.JobSubmissionException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.LimitExceededException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.ResultNotAvailableException
    +
    +
    Default stable serial for serialization
    +
    +
    serialVersionUID - Static variable in exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    serialVersionUID - Static variable in exception compbio.metadata.WrongParameterException
    +
    +
    Default stable serial for serialization
    +
    +
    SERVER_ADDRESS - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    service - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    service - Variable in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    SERVICE_NAMESPACE - Static variable in interface compbio.data.msa.JABAService
    +
     
    +
    ServiceInfo() - Constructor for class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    ServiceInfo(Services, String, String, String) - Constructor for class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    servicekey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    serviceName - Static variable in class compbio.ws.client.AAConClient
    +
    +
    Web service name
    +
    +
    services - Variable in class compbio.data.msa.Category
    +
     
    +
    Services - Enum in compbio.ws.client
    +
    +
    List of web services currently supported by JABAWS version 2.1
    +
    +
    Services() - Constructor for enum compbio.ws.client.Services
    +
     
    +
    Services.ServiceInfo - Class in compbio.ws.client
    +
     
    +
    ServiceStatus - Class in compbio.stat.servlet
    +
    +
    Use cases: + + Test web services and display results on the web page +
    +
    +
    ServiceStatus() - Constructor for class compbio.stat.servlet.ServiceStatus
    +
     
    +
    ServicesUtil - Class in compbio.ws.client
    +
     
    +
    ServicesUtil() - Constructor for class compbio.ws.client.ServicesUtil
    +
     
    +
    ServiceTestResult - Class in compbio.stat.servlet
    +
    +
    Value class for test results.
    +
    +
    ServiceTestResult(Services) - Constructor for class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    session - Static variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    session - Variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    session - Static variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setActualNumberofSequences(int) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    setAlignment(Alignment) - Method in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    setAlignment(Alignment) - Method in class compbio.data.msa.jaxws.Fold
    +
     
    +
    setAlignment(Alignment) - Method in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    setArg0(Services) - Method in class compbio.data.msa.jaxws.GetLastTested
    +
     
    +
    setArg0(Services) - Method in class compbio.data.msa.jaxws.GetLastTestedOn
    +
     
    +
    setArg0(Services) - Method in class compbio.data.msa.jaxws.GetServiceDescription
    +
     
    +
    setArg0(Services) - Method in class compbio.data.msa.jaxws.IsOperating
    +
     
    +
    setArg0(Services) - Method in class compbio.data.msa.jaxws.TestService
    +
     
    +
    setAtPosition(int) - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    setBasicURL(URL) - Method in class compbio.metadata.Option
    +
     
    +
    setDefaultValue(String) - Method in class compbio.metadata.Option
    +
    +
    Sets one of the values defined in optionList as default.
    +
    +
    setDefaultValue(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    setDelay(long, TimeUnit) - Method in class compbio.engine.FilePuller
    +
     
    +
    setDescription(String) - Method in class compbio.metadata.Option
    +
     
    +
    setDescription(String) - Method in class compbio.metadata.Preset
    +
     
    +
    setEmail(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    setEmail(String) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setError(String) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    setError(String) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    setExecProvider(Executable.ExecProvider) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    SetExecutableFlag - Class in compbio.ws.server
    +
    +
    Run setexecflag.sh script if executable flag is not set
    +
    +
    SetExecutableFlag() - Constructor for class compbio.ws.server.SetExecutableFlag
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.Align
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.Analize
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    setFastaSequences(List<FastaSequence>) - Method in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    setFirst() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    setFirst(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setFurtherDetails(String) - Method in class compbio.metadata.Option
    +
     
    +
    setInput(String) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    setInput(String) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    setInput(String) - Method in class compbio.runner.conservation.AACon
    +
     
    +
    setInput(String) - Method in class compbio.runner.disorder.Disembl
    +
     
    +
    setInput(String) - Method in class compbio.runner.disorder.GlobPlot
    +
     
    +
    setInput(String) - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    setInput(String) - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.ClustalW
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.GLprobs
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.Mafft
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.MSAprobs
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.Muscle
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.Probcons
    +
     
    +
    setInput(String) - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    setInput(String) - Method in class compbio.runner.structure.RNAalifold
    +
     
    +
    setJobEnvironmentVariables(Map<String, String>) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    setJobEnvironmentVariables(Map<String, String>) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setJobId(String) - Method in class compbio.data.msa.jaxws.CancelJob
    +
     
    +
    setJobId(String) - Method in class compbio.data.msa.jaxws.GetAnnotation
    +
     
    +
    setJobId(String) - Method in class compbio.data.msa.jaxws.GetJobStatus
    +
     
    +
    setJobId(String) - Method in class compbio.data.msa.jaxws.GetResult
    +
     
    +
    setJobId(String) - Method in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    setJobName(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    setJobName(String) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setLast() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    setLast(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setLast(String, String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setMax(String) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setMessage(String) - Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean
    +
     
    +
    setMessage(String) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    setMessage(String) - Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
    +
     
    +
    setMessage(String) - Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
    +
     
    +
    setMessage(String) - Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean
    +
     
    +
    setMin(String) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setName(String) - Method in class compbio.metadata.Option
    +
     
    +
    setName(String) - Method in class compbio.metadata.Preset
    +
     
    +
    setNativeSpecs(Executable<?>) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    setNativeSpecs(Executable<?>) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setNCore(int) - Method in class compbio.runner.conservation.AACon
    +
     
    +
    setNCore(int) - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    setNCore(int) - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    setNCore(int) - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    setNumberOfSequencesAllowed(int) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    setOptionName(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    setOptionNames(Set<String>) - Method in class compbio.metadata.Option
    +
     
    +
    setOptionNames(Set<String>) - Method in class compbio.metadata.Parameter
    +
     
    +
    setOptions(List<Option>) - Method in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    setOptions(List<Option>) - Method in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    setOptions(List<Option>) - Method in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    setOptions(List<String>) - Method in class compbio.metadata.Preset
    +
     
    +
    setOptions(List<Option<T>>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Adds the list of options or parameters to the internal list of options
    +
    +
    setOutput(String) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    setOutput(String) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    setOutput(String) - Method in class compbio.runner.conservation.AACon
    +
     
    +
    setOutput(String) - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    setOutput(String) - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    setOutput(String) - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    setOutput(String) - Method in class compbio.runner.msa.ClustalW
    +
     
    +
    setOutput(String) - Method in class compbio.runner.msa.Muscle
    +
     
    +
    setOutput(String) - Method in class compbio.runner.structure.RNAalifold
    +
     
    +
    setParam(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setParam(CommandBuilder.Parameter) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setParam(String, String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setParameter(String) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    setParameters(CommandBuilder<?>) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    setParameters(List<Parameter<T>>) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Sets the list of parameters as internal list
    +
    +
    setParams(List<String>) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    setPipes(ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    setPipes(ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    setPosition(long) - Method in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    setPossibleValues(Set<String>) - Method in class compbio.metadata.Parameter
    +
     
    +
    setPreset(Preset) - Method in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    setPreset(Preset) - Method in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    setPreset(Preset) - Method in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    setPresetName(String) - Method in class compbio.data.msa.jaxws.GetLimit
    +
     
    +
    setPresets(List<Preset<T>>) - Method in class compbio.metadata.PresetManager
    +
     
    +
    setPrmSeparator(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Sets name value separator character
    +
    +
    setRanges(TreeSet<Range>) - Method in class compbio.data.sequence.Score
    +
     
    +
    setRequired(boolean) - Method in class compbio.metadata.Option
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.AlignResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.AnalizeResponse
    +
     
    +
    setReturn(boolean) - Method in class compbio.data.msa.jaxws.CancelJobResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.CustomAlignResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.CustomAnalizeResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.CustomFoldResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.FoldResponse
    +
     
    +
    setReturn(ScoreManager) - Method in class compbio.data.msa.jaxws.GetAnnotationResponse
    +
     
    +
    setReturn(JobStatus) - Method in class compbio.data.msa.jaxws.GetJobStatusResponse
    +
     
    +
    setReturn(Date) - Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse
    +
     
    +
    setReturn(int) - Method in class compbio.data.msa.jaxws.GetLastTestedResponse
    +
     
    +
    setReturn(Limit) - Method in class compbio.data.msa.jaxws.GetLimitResponse
    +
     
    +
    setReturn(LimitsManager) - Method in class compbio.data.msa.jaxws.GetLimitsResponse
    +
     
    +
    setReturn(Set<Services>) - Method in class compbio.data.msa.jaxws.GetNonoperatedServicesResponse
    +
     
    +
    setReturn(PresetManager) - Method in class compbio.data.msa.jaxws.GetPresetsResponse
    +
     
    +
    setReturn(Alignment) - Method in class compbio.data.msa.jaxws.GetResultResponse
    +
     
    +
    setReturn(RunnerConfig) - Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse
    +
     
    +
    setReturn(Set<Category>) - Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse
    +
     
    +
    setReturn(Set<Services>) - Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse
    +
     
    +
    setReturn(boolean) - Method in class compbio.data.msa.jaxws.IsOperatingResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.PresetAlignResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.PresetAnalizeResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.PresetFoldResponse
    +
     
    +
    setReturn(ChunkHolder) - Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.TestAllServicesResponse
    +
     
    +
    setReturn(String) - Method in class compbio.data.msa.jaxws.TestServiceResponse
    +
     
    +
    setRunnerClassName(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    setRunnerClassName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Set the name of a runner class
    +
    +
    setSequenceLenghtActual(int) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    setSequenceLenghtAllowed(int) - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    setType(ValueConstrain.Type) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    setupWorkDirectory(ConfExecutable<T>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
    +
     
    +
    setValidValue(ValueConstrain) - Method in class compbio.metadata.Parameter
    +
     
    +
    setValue(String) - Method in interface compbio.metadata.Argument
    +
    +
    Set default values for the parameter or an option
    +
    +
    setValue(String) - Method in class compbio.metadata.Option
    +
     
    +
    setWorkDirectory(String) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    setWorkDirectory(String) - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    SHORT_OUTPUT - Static variable in class compbio.runner.disorder.IUPred
    +
     
    +
    shutDown() - Static method in class compbio.engine.local.LocalExecutorService
    +
    +
    This stops all executing processes via interruption.
    +
    +
    shutdownDBServer() - Static method in class compbio.stat.collector.StatDB
    +
     
    +
    shutdownService() - Static method in class compbio.engine.local.ExecutableWrapper
    +
    +
    Stops internal executor service which captures streams of native + executables.
    +
    +
    signal - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
    +
    see man 5 accounting on sun grid engine installed workstation see also + man 2 getrusage
    +
    +
    SimpleWSPublisher - Class in compbio.ws.server
    +
    +
    Deprecated.
    +
    +
    SimpleWSPublisher(Object, String) - Constructor for class compbio.ws.server.SimpleWSPublisher
    +
    +
    Deprecated.
    + 
    +
    SINGLE_ENTRY_KEY - Static variable in class compbio.data.sequence.ScoreManager
    +
     
    +
    size() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    SkeletalExecutable<T> - Class in compbio.engine.client
    +
     
    +
    SkeletalExecutable() - Constructor for class compbio.engine.client.SkeletalExecutable
    +
     
    +
    SkeletalExecutable(String) - Constructor for class compbio.engine.client.SkeletalExecutable
    +
     
    +
    SMERFSConstraints - Enum in compbio.data.sequence
    +
    +
    Enumeration defining two constraints for SMERFS columns score calculation.
    +
    +
    SMERFSConstraints() - Constructor for enum compbio.data.sequence.SMERFSConstraints
    +
     
    +
    sname - Variable in class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
    +
     
    +
    sortByResultSize() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    sortByRuntime() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    sortByStartTime() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    SPACE - Static variable in class compbio.metadata.Preset
    +
     
    +
    SPACE - Static variable in class compbio.runner.Util
    +
     
    +
    spacer - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    start - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    start_time - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    startTime - Variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    STARTTIME - Static variable in class compbio.stat.collector.JobStat
    +
     
    +
    STAT_FILE - Static variable in class compbio.runner.conservation.AACon
    +
     
    +
    STAT_FILE - Static variable in class compbio.runner.disorder.Jronn
    +
     
    +
    StatCollection - Class in compbio.stat.servlet.util
    +
     
    +
    StatCollection() - Constructor for class compbio.stat.servlet.util.StatCollection
    +
     
    +
    StatCollection.Stattype - Enum in compbio.stat.servlet.util
    +
    +
    Total number of requests + + incomplete abandoned cancelled
    +
    +
    StatDB - Class in compbio.stat.collector
    +
    +
    The database must be stored in the application root directory and called + "ExecutionStatistic"
    +
    +
    StatDB() - Constructor for class compbio.stat.collector.StatDB
    +
     
    +
    StatDB(boolean) - Constructor for class compbio.stat.collector.StatDB
    +
    +
    Connect to test database
    +
    +
    statDBName - Static variable in class compbio.stat.collector.StatDB
    +
     
    +
    StatisticCollector - Class in compbio.stat.servlet
    +
     
    +
    StatisticCollector() - Constructor for class compbio.stat.servlet.StatisticCollector
    +
     
    +
    StatisticManager - Class in compbio.engine.cluster.drmaa
    +
     
    +
    StatisticManager(JobInfo) - Constructor for class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    StatProcessor - Class in compbio.stat.collector
    +
     
    +
    StatProcessor(List<JobStat>) - Constructor for class compbio.stat.collector.StatProcessor
    +
     
    +
    stats - Variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    stats - Variable in class compbio.stat.collector.StatProcessor
    +
     
    +
    Stattype() - Constructor for enum compbio.stat.servlet.util.StatCollection.Stattype
    +
     
    +
    stochBTStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    StreamGobbler - Class in compbio.engine.local
    +
     
    +
    StreamGobbler(InputStream, OutputStream, StreamGobbler.OutputType) - Constructor for class compbio.engine.local.StreamGobbler
    +
     
    +
    StreamGobbler.OutputType - Enum in compbio.engine.local
    +
     
    +
    strEquals(String, String) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    structP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    submission_time - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    SubmissionManager - Class in compbio.engine
    +
    +
    Submit jobs for execution
    +
    +
    SubmissionManager() - Constructor for class compbio.engine.SubmissionManager
    +
     
    +
    submitJob(ConfiguredExecutable<?>) - Method in interface compbio.engine.AsyncExecutor
    +
    +
    Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +
    +
    submitJob(ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    submitJob(ConfiguredExecutable<?>) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    submitJob() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    submitJob() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    submitJob(ConfiguredExecutable<?>) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    submittedTasks - Static variable in class compbio.engine.SubmissionManager
    +
     
    +
    sumOfTotals(Map<Date, Totals>) - Static method in class compbio.stat.servlet.util.Totals
    +
     
    +
    sumStats(Map<Services, StatProcessor>) - Static method in class compbio.stat.servlet.util.Totals
    +
     
    +
    sweep() - Static method in class compbio.engine.PulledFileCache
    +
     
    +
    SyncExecutor - Interface in compbio.engine
    +
    +
    Synchronous executor, is an engine to run the Executable synchronously.
    +
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-2.html b/website/docs/full_javadoc/index-files/index-2.html new file mode 100644 index 0000000..985d320 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-2.html @@ -0,0 +1,133 @@ + + + + + +B-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    B

    +
    +
    basicURL - Variable in class compbio.metadata.Option
    +
     
    +
    beforeExecute(Thread, Runnable) - Method in class compbio.engine.local.LocalExecutorService
    +
     
    +
    bracket - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-20.html b/website/docs/full_javadoc/index-files/index-20.html new file mode 100644 index 0000000..549a461 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-20.html @@ -0,0 +1,305 @@ + + + + + +T-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
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    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    T

    +
    +
    taskDirectory - Variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    taskId - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Task ID (is a part of workDirectory but extracting it from there could be + tricky)
    +
    +
    taskId - Variable in class compbio.engine.Job
    +
     
    +
    Tcoffee - Class in compbio.runner.msa
    +
     
    +
    Tcoffee() - Constructor for class compbio.runner.msa.Tcoffee
    +
     
    +
    TCOFFEE_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    tcoffeeOptions - Static variable in class compbio.ws.server.TcoffeeWS
    +
     
    +
    tcoffeePresets - Static variable in class compbio.ws.server.TcoffeeWS
    +
     
    +
    TcoffeeWS - Class in compbio.ws.server
    +
     
    +
    TcoffeeWS() - Constructor for class compbio.ws.server.TcoffeeWS
    +
     
    +
    terminated() - Method in class compbio.engine.local.LocalExecutorService
    +
     
    +
    termSignal() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    TestAllServices - Class in compbio.data.msa.jaxws
    +
     
    +
    TestAllServices() - Constructor for class compbio.data.msa.jaxws.TestAllServices
    +
     
    +
    testAllServices() - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Test all JABAWS services on the server
    +
    +
    testAllServices() - Method in class compbio.ws.server.RegistryWS
    +
    +
    TODO improve reporting.
    +
    +
    TestAllServicesResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    TestAllServicesResponse() - Constructor for class compbio.data.msa.jaxws.TestAllServicesResponse
    +
     
    +
    testDefaultAlignment(MsaWS<T>, Services) - Method in class compbio.ws.client.WSTester
    +
    +
    Align using default settings
    +
    +
    testDefaultAnalyse(List<FastaSequence>, SequenceAnnotation<T>, Preset<T>, List<Option<T>>) - Method in class compbio.ws.client.WSTester
    +
     
    +
    testKey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    testMetadata(Metadata<T>) - Method in class compbio.ws.client.WSTester
    +
     
    +
    testMsaWS(MsaWS<T>, Services) - Method in class compbio.ws.client.WSTester
    +
     
    +
    testSequenceAnnotationWS(SequenceAnnotation<T>, Services) - Method in class compbio.ws.client.WSTester
    +
     
    +
    TestService - Class in compbio.data.msa.jaxws
    +
     
    +
    TestService() - Constructor for class compbio.data.msa.jaxws.TestService
    +
     
    +
    testService(Services) - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Test a particular service
    +
    +
    testService(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    tests service
    +
    +
    testService(String, Services, PrintWriter) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Asks registry to test the service on the host hostname
    +
    +
    testService(Services) - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    TestServiceResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    TestServiceResponse() - Constructor for class compbio.data.msa.jaxws.TestServiceResponse
    +
     
    +
    threadNumPropName - Static variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    timeOutInHours - Variable in class compbio.stat.collector.ExecutionStatCollector
    +
    +
    Consider the job that has been working for longer than timeOutInHours + completed, whatever the outcome
    +
    +
    timeToTest() - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    to - Variable in class compbio.data.sequence.Range
    +
     
    +
    toCommand(String) - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    toCommand(String) - Method in class compbio.metadata.Option
    +
    +
    Convert the option to the command string.
    +
    +
    toCommand(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    toFastaSequence(String) - Static method in class compbio.data.sequence.FastaReader
    +
     
    +
    toList(float[]) - Method in class compbio.data.sequence.Score
    +
     
    +
    toString() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    toString() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Same as oneLineFasta
    +
    +
    toString() - Method in class compbio.data.sequence.Range
    +
     
    +
    toString() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    toString() - Method in class compbio.data.sequence.Score
    +
     
    +
    toString() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    toString() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    toString() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    toString() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    toString() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    toString() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    toString() - Method in class compbio.engine.FilePuller
    +
     
    +
    toString() - Method in class compbio.engine.Job
    +
     
    +
    toString() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    toString() - Method in class compbio.metadata.Limit
    +
     
    +
    toString() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    toString() - Method in class compbio.metadata.Option
    +
     
    +
    toString() - Method in class compbio.metadata.Parameter
    +
     
    +
    toString() - Method in class compbio.metadata.Preset
    +
     
    +
    toString() - Method in class compbio.metadata.PresetManager
    +
     
    +
    toString() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    toString() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    toString() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    toString() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    toString() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    toString() - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    toString() - Method in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    toString(Set<Services>) - Static method in enum compbio.ws.client.Services
    +
     
    +
    total - Variable in class compbio.stat.servlet.util.Totals
    +
     
    +
    Totals - Class in compbio.stat.servlet.util
    +
     
    +
    Totals() - Constructor for class compbio.stat.servlet.util.Totals
    +
     
    +
    totalTime - Variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    TRACKER - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    TREE_FILE_EXT - Static variable in class compbio.runner.msa.ClustalW
    +
     
    +
    type - Variable in class compbio.engine.local.StreamGobbler
    +
     
    +
    type - Variable in class compbio.metadata.ValueConstrain
    +
     
    +
    Type() - Constructor for enum compbio.metadata.ValueConstrain.Type
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-21.html b/website/docs/full_javadoc/index-files/index-21.html new file mode 100644 index 0000000..991436c --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-21.html @@ -0,0 +1,175 @@ + + + + + +U-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    U

    +
    +
    UNDEFINED - Static variable in class compbio.stat.collector.DirCleaner
    +
     
    +
    UNDEFINED - Static variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    UNDEFINED - Static variable in class compbio.stat.collector.JobDirectory
    +
     
    +
    UnknownFileFormatException - Exception in compbio.data.sequence
    +
     
    +
    UnknownFileFormatException() - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(File, Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(String, Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(String) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UnknownFileFormatException(Throwable) - Constructor for exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    UNSUPPORTED - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    UnsupportedRuntimeException - Exception in compbio.metadata
    +
    +
    Indicates that the server could not execute native executables.
    +
    +
    UnsupportedRuntimeException(String) - Constructor for exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    UnsupportedRuntimeException(Throwable) - Constructor for exception compbio.metadata.UnsupportedRuntimeException
    +
     
    +
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    +
    +
    This class was generated by the JAX-WS RI.
    +
    +
    UnsupportedRuntimeExceptionBean() - Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
    +
     
    +
    updateClusterStatsFrequency() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    updateLocalStatsFrequency() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    usage - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    Util - Class in compbio.engine.client
    +
     
    +
    Util() - Constructor for class compbio.engine.client.Util
    +
     
    +
    Util - Class in compbio.runner
    +
     
    +
    Util() - Constructor for class compbio.runner.Util
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-22.html b/website/docs/full_javadoc/index-files/index-22.html new file mode 100644 index 0000000..b1dddd8 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-22.html @@ -0,0 +1,342 @@ + + + + + +V-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    V

    +
    +
    V2_SERVICE_NAMESPACE - Static variable in interface compbio.data.msa.JABAService
    +
     
    +
    V3_SERVICE_NAMESPACE - Static variable in interface compbio.data.msa.JABAService
    +
     
    +
    validate(Validator, String) - Static method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    validate() - Method in class compbio.metadata.Limit
    +
     
    +
    validate(PresetManager<T>) - Method in class compbio.metadata.LimitsManager
    +
    +
    Validate Limits
    +
    +
    validate() - Method in class compbio.metadata.Option
    +
    +
    Validate the option
    +
    +
    validate() - Method in class compbio.metadata.Parameter
    +
     
    +
    validate(RunnerConfig<T>) - Method in class compbio.metadata.PresetManager
    +
    +
    Checks whether preset option and parameter are defined in RunnerConfig + object.
    +
    +
    validate() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Validate the value of the argument.
    +
    +
    validate() - Method in class compbio.metadata.ValueConstrain
    +
    +
    Validate the ValueConstrain object.
    +
    +
    validate() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    validateAAConInput(List<FastaSequence>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    validateDirectory(String) - Static method in class compbio.engine.client.PathValidator
    +
     
    +
    validateExecutable(String) - Static method in class compbio.engine.client.PathValidator
    +
     
    +
    validateFastaInput(List<FastaSequence>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    validateJobId(String) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    validatePathNames(List<String>, String) - Static method in class compbio.engine.client.PathValidator
    +
     
    +
    validURL(String) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Attempt to construct the URL object from the string
    +
    +
    validValue - Variable in class compbio.metadata.Parameter
    +
     
    +
    value - Variable in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    ValueConstrain - Class in compbio.metadata
    +
    +
    The type and the lower and upper boundaries for numerical value.
    +
    +
    ValueConstrain() - Constructor for class compbio.metadata.ValueConstrain
    +
     
    +
    ValueConstrain.Type - Enum in compbio.metadata
    +
     
    +
    valueExist(String, List<String>) - Static method in class compbio.metadata.Option
    +
     
    +
    valueOf(String) - Static method in enum compbio.data.sequence.ConservationMethod
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.DisemblResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.DisorderMethod
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.GlobProtResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.IUPredResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.Program
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.RNAStructReader.RNAOut
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.engine.client.Executable.ExecProvider
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.engine.local.StreamGobbler.OutputType
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.metadata.JobStatus
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.metadata.ValueConstrain.Type
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.stat.servlet.util.StatCollection.Stattype
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    valueOf(String) - Static method in enum compbio.ws.client.Services
    +
    +
    Returns the enum constant of this type with the specified name.
    +
    +
    values() - Static method in enum compbio.data.sequence.ConservationMethod
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.DisemblResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.DisorderMethod
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.GlobProtResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.IUPredResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.Program
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldLine
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.AlifoldResult
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.RNAStructReader.RNAOut
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.engine.client.Executable.ExecProvider
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.engine.local.StreamGobbler.OutputType
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.metadata.JobStatus
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.metadata.ValueConstrain.Type
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.stat.servlet.util.StatCollection.Stattype
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    values() - Static method in enum compbio.ws.client.Services
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared.
    +
    +
    version - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    version - Variable in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    VERSION_TYPE - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    vmem - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-23.html b/website/docs/full_javadoc/index-files/index-23.html new file mode 100644 index 0000000..89cd2b7 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-23.html @@ -0,0 +1,278 @@ + + + + + +W-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    W

    +
    +
    waitForFile(long) - Method in class compbio.engine.FilePuller
    +
     
    +
    waitForJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    waitForJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    waitForJob(String, long) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    waitForJob(String) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    waitForResult(ClusterSession, String) - Static method in class compbio.engine.cluster.drmaa.ClusterEngineUtil
    +
     
    +
    waitForResult() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    waitForResult(ClusterSession, String) - Static method in class compbio.engine.cluster.drmaa.ClusterUtil
    +
     
    +
    waitForResult() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    waitForResult() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    waitForResult() - Method in interface compbio.engine.SyncExecutor
    +
    +
    Call to this method block for as long as it is required for an executable to finish its job.
    +
    +
    wasAborted() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    watcher - Variable in class compbio.engine.FilePuller
    +
     
    +
    webService - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    WHITE_SPACE - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    A whitespace character: [\t\n\x0B\f\r]
    +
    +
    workDirectory - Variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    workDirectory - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Working directory
    +
    +
    workDirectory - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    workDirectory - Variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    workDirectory - Variable in class compbio.engine.local.LocalRunner
    +
     
    +
    workDirectory - Variable in class compbio.stat.collector.DirCleaner
    +
     
    +
    workingDirectory - Variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    write(TreeSet<Score>, Writer) - Static method in class compbio.data.sequence.Score
    +
    +
    Outputs the List of Score objects into the Output stream.
    +
    +
    write(RunConfiguration) - Static method in class compbio.engine.client.RunConfiguration
    +
     
    +
    write(Object, OutputStream) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    writeAndValidate(Object, String, OutputStream) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    writeClustal(OutputStream, List<FastaSequence>, char) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    writeClustalAlignment(Writer, Alignment) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Write Clustal formatted alignment Limitations: does not record the + consensus.
    +
    +
    writeClustalInput(List<FastaSequence>, ConfiguredExecutable<?>, char) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    writeFasta(OutputStream, List<FastaSequence>, int) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +
    +
    writeFasta(OutputStream, List<FastaSequence>) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Writes FastaSequence in the file, each sequence will take one line only
    +
    +
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    writeFile(String, String, String, boolean) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    writeFile(String, String, String, boolean) - Static method in class compbio.engine.client.Util
    +
     
    +
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - Static method in class compbio.runner.Util
    +
     
    +
    writeMarker(String, JobStatus) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    writeMarker(String, JobStatus) - Static method in class compbio.engine.client.Util
    +
     
    +
    writeOut(Writer) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    writeOut(Writer) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    writeOut(Writer, ScoreManager) - Static method in class compbio.ws.client.AAConClient
    +
    +
    Outputs AAcon results into the file represented by the outStream
    +
    +
    writeOut(Writer, Alignment) - Static method in class compbio.ws.client.IOHelper
    +
    +
    Outputs clustal formatted alignment into the file represented by the + outStream
    +
    +
    writeOut(Writer, ScoreManager) - Static method in class compbio.ws.client.IOHelper
    +
    +
    Outputs AAcon results into the file represented by the outStream
    +
    +
    writer - Variable in class compbio.ws.client.WSTester
    +
     
    +
    writeStatFile(String, String) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    writeStatFile(String, String) - Static method in class compbio.engine.client.Util
    +
     
    +
    writeStatToDB() - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    WrongParameterException - Exception in compbio.metadata
    +
    +
    WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +
    +
    WrongParameterException(Option<?>) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(String) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(Throwable) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterException(String, Throwable) - Constructor for exception compbio.metadata.WrongParameterException
    +
     
    +
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    +
    +
    This class was generated by the JAX-WS RI.
    +
    +
    WrongParameterExceptionBean() - Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean
    +
     
    +
    wsContext - Variable in class compbio.ws.server.RegistryWS
    +
     
    +
    WSTester - Class in compbio.ws.client
    +
    +
    Class for testing web services
    +
    +
    WSTester(String, PrintWriter) - Constructor for class compbio.ws.client.WSTester
    +
    +
    Construct an instance of JABAWS tester
    +
    +
    WSUtil - Class in compbio.ws.server
    +
     
    +
    WSUtil() - Constructor for class compbio.ws.server.WSUtil
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-24.html b/website/docs/full_javadoc/index-files/index-24.html new file mode 100644 index 0000000..1be8570 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-24.html @@ -0,0 +1,181 @@ + + + + + +_-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    _

    +
    +
    _return - Variable in class compbio.data.msa.jaxws.AlignResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.AnalizeResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.CancelJobResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.CustomAlignResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.CustomAnalizeResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.CustomFoldResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.FoldResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetAnnotationResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetJobStatusResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetLastTestedOnResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetLastTestedResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetLimitResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetLimitsResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetNonoperatedServicesResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetPresetsResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetResultResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetRunnerOptionsResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetServiceCategoriesResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetServiceDescriptionResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.GetSupportedServicesResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.IsOperatingResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.PresetAlignResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.PresetAnalizeResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.PresetFoldResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.PullExecStatisticsResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.TestAllServicesResponse
    +
     
    +
    _return - Variable in class compbio.data.msa.jaxws.TestServiceResponse
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
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    Skip navigation links
    + + + + +
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    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    C

    +
    +
    CACHE - Static variable in class compbio.engine.PulledFileCache
    +
     
    +
    call() - Method in class compbio.engine.local.ExecutableWrapper
    +
    +
    It is vital that output and error streams are captured immediately for + this call() to succeed.
    +
    +
    canAcceptMoreWork() - Method in class compbio.engine.local.LocalExecutorService
    +
    +
    If the Executor queue is empty
    +
    +
    CancelJob - Class in compbio.data.msa.jaxws
    +
     
    +
    CancelJob() - Constructor for class compbio.data.msa.jaxws.CancelJob
    +
     
    +
    cancelJob(String) - Method in interface compbio.data.msa.JManagement
    +
    +
    Stop running the job jobId but leave its output untouched
    +
    +
    cancelJob(String) - Method in interface compbio.engine.AsyncExecutor
    +
    +
    Stop running job.
    +
    +
    cancelJob(String) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    cancelJob(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    cancelJob(String, ClusterSession) - Static method in class compbio.engine.cluster.drmaa.ClusterEngineUtil
    +
     
    +
    cancelJob(String) - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    cancelJob() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    cancelJob(String, ClusterSession) - Static method in class compbio.engine.cluster.drmaa.ClusterUtil
    +
     
    +
    cancelJob(String) - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    cancelJob() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    cancelJob(String) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    cancelJob(Future<ConfiguredExecutable<?>>, String) - Static method in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    cancelJob() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    cancelJob() - Method in interface compbio.engine.SyncExecutor
    +
    +
    Stops running job.
    +
    +
    cancelJob(String) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    cancelJob(String) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    cancelJob(String) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    CancelJobResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    CancelJobResponse() - Constructor for class compbio.data.msa.jaxws.CancelJobResponse
    +
     
    +
    cancelled - Variable in class compbio.stat.servlet.util.Totals
    +
     
    +
    Category - Class in compbio.data.msa
    +
     
    +
    Category(String, Set<Services>) - Constructor for class compbio.data.msa.Category
    +
     
    +
    Category() - Constructor for class compbio.data.msa.Category
    +
     
    +
    CATEGORY_ALIGNMENT - Static variable in class compbio.data.msa.Category
    +
    +
    All of the Category names
    +
    +
    CATEGORY_CONSERVATION - Static variable in class compbio.data.msa.Category
    +
     
    +
    CATEGORY_DISORDER - Static variable in class compbio.data.msa.Category
    +
     
    +
    CATEGORY_PREDICTION - Static variable in class compbio.data.msa.Category
    +
     
    +
    cbuilder - Variable in class compbio.engine.client.SkeletalExecutable
    +
    +
    This has to allow duplicate parameters as different options may have the + same value e.g.
    +
    +
    centStructP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    cexecutable - Variable in class compbio.engine.Job
    +
     
    +
    checkService(JABAService, Services) - Method in class compbio.ws.client.WSTester
    +
    +
    Call most of web services functions and check the output
    +
    +
    checkService(Services) - Method in class compbio.ws.client.WSTester
    +
    +
    Test JABA web service
    +
    +
    checkValue(String) - Method in class compbio.metadata.ValueConstrain
    +
    +
    Validate that the value is within the constrain boundaries
    +
    +
    chunk - Variable in class compbio.metadata.ChunkHolder
    +
     
    +
    ChunkHolder - Class in compbio.metadata
    +
    +
    Represents a chunk of a string data together with the position in a file for + the next read operation.
    +
    +
    ChunkHolder() - Constructor for class compbio.metadata.ChunkHolder
    +
     
    +
    ChunkHolder(String, long) - Constructor for class compbio.metadata.ChunkHolder
    +
     
    +
    chunkSize - Variable in class compbio.engine.FilePuller
    +
     
    +
    Cleaner - Class in compbio.engine
    +
     
    +
    Cleaner() - Constructor for class compbio.engine.Cleaner
    +
     
    +
    cleanProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Remove all non AA chars from the sequence
    +
    +
    cleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Removes all whitespace chars in the sequence string
    +
    +
    cleanup(String) - Method in interface compbio.engine.AsyncExecutor
    +
    +
    Remove all files and a job directory for a jobid.
    +
    +
    cleanup(String) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    cleanup(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    cleanup() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    cleanup() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    cleanup(String) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    cleanup(ConfiguredExecutable<?>) - Static method in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    cleanup() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    cleanup() - Method in interface compbio.engine.SyncExecutor
    +
    +
    Clean up after the job
    +
    +
    clear() - Static method in class compbio.engine.PulledFileCache
    +
     
    +
    clearStatTable() - Static method in class compbio.stat.collector.StatDB
    +
     
    +
    close() - Method in class compbio.data.sequence.FastaReader
    +
    +
    Call this method to close the connection to the input file if you want to + free up the resources.
    +
    +
    close() - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    closeSilently(Logger, Closeable) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Closes the Closable and logs the exception if any
    +
    +
    closeSilently(Closeable) - Static method in class compbio.engine.local.StreamGobbler
    +
     
    +
    CLUSTAL_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    CLUSTAL_OMEGA_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    +
    +
    Tools to read and write clustal formated files
    +
    +
    ClustalAlignmentUtil() - Constructor for class compbio.data.sequence.ClustalAlignmentUtil
    +
     
    +
    ClustalO - Class in compbio.runner.msa
    +
     
    +
    ClustalO() - Constructor for class compbio.runner.msa.ClustalO
    +
    +
    --threads= Number of processors to use + + -l, --log= Log all non-essential output to this file
    +
    +
    clustalOptions - Static variable in class compbio.ws.server.ClustalOWS
    +
     
    +
    clustalOptions - Static variable in class compbio.ws.server.ClustalWS
    +
     
    +
    ClustalOWS - Class in compbio.ws.server
    +
     
    +
    ClustalOWS() - Constructor for class compbio.ws.server.ClustalOWS
    +
     
    +
    clustalPresets - Static variable in class compbio.ws.server.ClustalOWS
    +
     
    +
    clustalPresets - Static variable in class compbio.ws.server.ClustalWS
    +
     
    +
    clustalRNAAlignment - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    ClustalW - Class in compbio.runner.msa
    +
     
    +
    ClustalW() - Constructor for class compbio.runner.msa.ClustalW
    +
     
    +
    ClustalWS - Class in compbio.ws.server
    +
     
    +
    ClustalWS() - Constructor for class compbio.ws.server.ClustalWS
    +
     
    +
    CLUSTER_STAT_IN_SEC - Static variable in class compbio.engine.cluster.drmaa.ClusterEngineUtil
    +
     
    +
    CLUSTER_STAT_IN_SEC - Static variable in class compbio.engine.cluster.drmaa.ClusterUtil
    +
     
    +
    CLUSTER_TASK_ID_PREFIX - Static variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    CLUSTER_WORK_DIRECTORY - Static variable in class compbio.engine.Configurator
    +
     
    +
    clustercf - Variable in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    clustercl - Variable in class compbio.ws.server.MainManager
    +
     
    +
    ClusterEngineUtil - Class in compbio.engine.cluster.drmaa
    +
     
    +
    ClusterEngineUtil() - Constructor for class compbio.engine.cluster.drmaa.ClusterEngineUtil
    +
     
    +
    ClusterJobId - Class in compbio.engine
    +
     
    +
    ClusterJobId(String) - Constructor for class compbio.engine.ClusterJobId
    +
     
    +
    clusterJobId - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    ClusterRunner - Class in compbio.engine.cluster.drmaa
    +
    +
    Single cluster job runner class
    +
    +
    ClusterRunner(ConfiguredExecutable<?>) - Constructor for class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    ClusterSession - Class in compbio.engine.cluster.drmaa
    +
     
    +
    ClusterSession() - Constructor for class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    clusterStat - Variable in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    ClusterUtil - Class in compbio.engine.cluster.drmaa
    +
     
    +
    ClusterUtil() - Constructor for class compbio.engine.cluster.drmaa.ClusterUtil
    +
     
    +
    clustSession - Static variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    clustSession - Static variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    CmdHelper - Class in compbio.ws.client
    +
     
    +
    CmdHelper() - Constructor for class compbio.ws.client.CmdHelper
    +
     
    +
    COILS_EXPECTATION_THRESHOLD - Variable in class compbio.runner.disorder.Disembl
    +
    +
    For the region to be considered disordered the values must exceed these
    +
    +
    collectClusterStats() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    collectLocalStats() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    collectStatistics() - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    combineScores(Map<String, Set<Score>>, Map<String, Score>) - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    CommandBuilder<T> - Class in compbio.engine.client
    +
     
    +
    CommandBuilder() - Constructor for class compbio.engine.client.CommandBuilder
    +
     
    +
    CommandBuilder(String) - Constructor for class compbio.engine.client.CommandBuilder
    +
     
    +
    CommandBuilder.Parameter - Class in compbio.engine.client
    +
     
    +
    compareClustalLines(File, String[]) - Static method in class compbio.stat.collector.InputFilter
    +
     
    +
    compareLines(File, String[]) - Static method in class compbio.stat.collector.InputFilter
    +
     
    +
    compareTo(Range) - Method in class compbio.data.sequence.Range
    +
     
    +
    compareTo(Score) - Method in class compbio.data.sequence.Score
    +
     
    +
    compareTo(Delayed) - Method in class compbio.engine.FilePuller
    +
     
    +
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
    +
     
    +
    confDir - Static variable in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    confExec - Variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    ConfExecutable<T> - Class in compbio.engine.client
    +
     
    +
    ConfExecutable(Executable<T>, String) - Constructor for class compbio.engine.client.ConfExecutable
    +
     
    +
    ConfExecutable(RunConfiguration) - Constructor for class compbio.engine.client.ConfExecutable
    +
     
    +
    confExecutable - Variable in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    confExecutable - Variable in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    config - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    Configurator - Class in compbio.engine
    +
     
    +
    Configurator() - Constructor for class compbio.engine.Configurator
    +
     
    +
    ConfiguredExecutable<T> - Interface in compbio.engine.client
    +
     
    +
    configureExecutable(Executable<T>) - Static method in class compbio.engine.Configurator
    +
     
    +
    configureExecutable(Executable<T>, List<FastaSequence>) - Static method in class compbio.engine.Configurator
    +
     
    +
    configureExecutable(Executable<T>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
    +
     
    +
    conn - Static variable in class compbio.stat.collector.StatDB
    +
     
    +
    connect() - Static method in class compbio.ws.client.AAConClient
    +
    +
    Connects to a AACon web service by the host and the service name
    +
    +
    connect(String, Services) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Connects to a web service by the host and the service name web service type
    +
    +
    connect(String, Services) - Method in class compbio.ws.client.WSTester
    +
    +
    Connects to a web service by the host and the service name web service type
    +
    +
    connectToRegistry(String) - Static method in class compbio.ws.client.Jws2Client
    +
    +
    Get a connection of JABAWS registry
    +
    +
    ConservationMethod - Enum in compbio.data.sequence
    +
    +
    Enumeration listing of all the supported methods.
    +
    +
    ConservationMethod() - Constructor for enum compbio.data.sequence.ConservationMethod
    +
     
    +
    Constraints - Class in compbio.ws.client
    +
     
    +
    Constraints() - Constructor for class compbio.ws.client.Constraints
    +
     
    +
    containsMultipleVariables(String) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    containsValue(List<String>, String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    containValue(String) - Method in class compbio.metadata.Preset
    +
     
    +
    contextDestroyed(ServletContextEvent) - Method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    contextDestroyed(ServletContextEvent) - Method in class compbio.ws.server.MainManager
    +
     
    +
    contextDestroyed(ServletContextEvent) - Method in class compbio.ws.server.SetExecutableFlag
    +
     
    +
    contextInitialized(ServletContextEvent) - Method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    contextInitialized(ServletContextEvent) - Method in class compbio.ws.server.MainManager
    +
     
    +
    contextInitialized(ServletContextEvent) - Method in class compbio.ws.server.SetExecutableFlag
    +
    +
    This listener is designed to run only once when the web application is + deployed to set executable flag for binaries.
    +
    +
    convertInputNameToTreeName() - Method in class compbio.runner.msa.ClustalW
    +
    +
    Clustal output tree with same name as input file but .dnd extension e.g.
    +
    +
    convertToAbsolute(String) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    convertToAbsolute(String) - Static method in class compbio.engine.client.Util
    +
     
    +
    convertToNumber(String[]) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    copyAndValidateRConfig(RunnerConfig<?>) - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    countMatchesInSequence(String, String) - Static method in class compbio.data.sequence.FastaSequence
    +
     
    +
    cpu - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    createOutput(String, String) - Method in class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
    +
     
    +
    createStatTable() - Method in class compbio.stat.collector.StatDB
    +
    +
    rs.getBoolean(i) will return true for any non-zero value and false for 0 + on SMALLINT data column.
    +
    +
    ctx - Variable in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    CustomAlign - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomAlign() - Constructor for class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<T>>) - Method in interface compbio.data.msa.MsaWS
    +
    +
    Align a list of sequences with options.
    +
    +
    customAlign(List<FastaSequence>, List<Option<ClustalO>>) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<ClustalW>>) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<GLprobs>>) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<Mafft>>) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<MSAprobs>>) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<Muscle>>) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<Probcons>>) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    CustomAlignResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomAlignResponse() - Constructor for class compbio.data.msa.jaxws.CustomAlignResponse
    +
     
    +
    CustomAnalize - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomAnalize() - Constructor for class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    customAnalize(List<FastaSequence>, List<Option<T>>) - Method in interface compbio.data.msa.SequenceAnnotation
    +
    +
    Analyse the sequences according to custom settings defined in options + list.
    +
    +
    customAnalize(List<FastaSequence>, List<Option<AACon>>) - Method in class compbio.ws.server.AAConWS
    +
     
    +
    customAnalize(List<FastaSequence>, List<Option<Disembl>>) - Method in class compbio.ws.server.DisemblWS
    +
     
    +
    customAnalize(List<FastaSequence>, List<Option<GlobPlot>>) - Method in class compbio.ws.server.GlobPlotWS
    +
     
    +
    customAnalize(List<FastaSequence>, List<Option<RNAalifold>>) - Method in class compbio.ws.server.RNAalifoldWS
    +
     
    +
    customAnalize(List<FastaSequence>, List<Option<T>>) - Method in class compbio.ws.server.SequenceAnnotationService
    +
     
    +
    CustomAnalizeResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomAnalizeResponse() - Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse
    +
     
    +
    CustomFold - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomFold() - Constructor for class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    CustomFoldResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    CustomFoldResponse() - Constructor for class compbio.data.msa.jaxws.CustomFoldResponse
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-4.html b/website/docs/full_javadoc/index-files/index-4.html new file mode 100644 index 0000000..9c01fd5 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-4.html @@ -0,0 +1,292 @@ + + + + + +D-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    D

    +
    +
    DATE_TIME - Static variable in class compbio.stat.collector.JobStat
    +
     
    +
    deepClean() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    deepClean() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    deepCleanSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Removes all special characters and digits as well as whitespace chars + from the sequence
    +
    +
    DEFAULT_COLUMN_SCORE - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default column scoring schema
    +
    +
    DEFAULT_GAP_THRESHOLD - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default gap threshold value for SMERFS algorithm
    +
    +
    DEFAULT_WINDOW_SIZE - Static variable in enum compbio.data.sequence.SMERFSConstraints
    +
    +
    Default window size value for SMERFS algorithm
    +
    +
    defaultDelay - Static variable in class compbio.engine.FilePuller
    +
     
    +
    defaultValue - Variable in class compbio.metadata.Option
    +
     
    +
    delay - Variable in class compbio.engine.FilePuller
    +
     
    +
    deleteAllFiles(String) - Static method in class compbio.engine.Cleaner
    +
     
    +
    deleteDirectory(String) - Static method in class compbio.engine.Cleaner
    +
     
    +
    deleteFiles(ConfiguredExecutable<?>) - Static method in class compbio.engine.Cleaner
    +
    +
    This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty)
    +
    +
    DELIM - Variable in class compbio.data.sequence.FastaReader
    +
    +
    Delimiter for the scanner
    +
    +
    DELIM - Static variable in class compbio.engine.conf.DirectoryManager
    +
     
    +
    description - Variable in class compbio.metadata.Option
    +
     
    +
    description - Variable in class compbio.metadata.Preset
    +
     
    +
    details - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    DF - Static variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    DIGIT - Static variable in class compbio.data.sequence.SequenceUtil
    +
    +
    A digit
    +
    +
    dir - Variable in class compbio.engine.conf.RunnerConfigMarshaller.MySchemaOutputResolver
    +
     
    +
    DirCleaner - Class in compbio.stat.collector
    +
    +
    Number of runs of each WS = number of folders with name + + Number of successful runs = all runs with no result file + + Per period of time = limit per file creating time Runtime (avg/max) = + + started time - finished time + + Task & result size = result.size + + Abandoned runs - not collected runs + + Cancelled runs - cancelled + + Cluster vs local runs + + Reasons for failure = look in the err out? + + Metadata required: + + work directory for local and cluster tasks = from Helper or cmd parameter.
    +
    +
    DirCleaner(String, int) - Constructor for class compbio.stat.collector.DirCleaner
    +
     
    +
    directories - Static variable in class compbio.stat.collector.DirCleaner
    +
     
    +
    directories - Static variable in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    DirectoryManager - Class in compbio.engine.conf
    +
     
    +
    DirectoryManager() - Constructor for class compbio.engine.conf.DirectoryManager
    +
     
    +
    disconnect() - Method in class compbio.engine.FilePuller
    +
     
    +
    disconnected() - Method in class compbio.engine.FilePuller
    +
     
    +
    Disembl - Class in compbio.runner.disorder
    +
    +
    DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops + fold_rem465 sequence_file print + + 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' + + This version of DisEMBL is 1.4 (latest available for download in Feb 2011) + capable of outputting raw values + + The values of the parameters are hard coded in DisEMBL.py script.
    +
    +
    Disembl() - Constructor for class compbio.runner.disorder.Disembl
    +
     
    +
    DISEMBL_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    DisemblResult - Enum in compbio.data.sequence
    +
     
    +
    DisemblResult() - Constructor for enum compbio.data.sequence.DisemblResult
    +
     
    +
    DisemblWS - Class in compbio.ws.server
    +
     
    +
    DisemblWS() - Constructor for class compbio.ws.server.DisemblWS
    +
     
    +
    DisorderMethod - Enum in compbio.data.sequence
    +
     
    +
    DisorderMethod() - Constructor for enum compbio.data.sequence.DisorderMethod
    +
     
    +
    DisplayStat - Class in compbio.stat.servlet
    +
     
    +
    DisplayStat() - Constructor for class compbio.stat.servlet.DisplayStat
    +
     
    +
    doCleaning() - Method in class compbio.stat.collector.DirCleaner
    +
     
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.AnnualStat
    +
     
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DisplayStat
    +
     
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DownloadRedirector
    +
     
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.HttpCodeResponseServiceStatus
    +
     
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.Joblist
    +
    +
    Input: + + ws=${ws.key} + + where=everywhere cluster local + + type=cancelled all incomplete + + from=${startDate} + + to=${stopDate}
    +
    +
    doGet(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.ServiceStatus
    +
     
    +
    doHead(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.HttpCodeResponseServiceStatus
    +
     
    +
    doPost(HttpServletRequest, HttpServletResponse) - Method in class compbio.stat.servlet.DownloadRedirector
    +
     
    +
    DownloadRedirector - Class in compbio.stat.servlet
    +
     
    +
    DownloadRedirector() - Constructor for class compbio.stat.servlet.DownloadRedirector
    +
     
    +
    driver - Static variable in class compbio.stat.collector.StatDB
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-5.html b/website/docs/full_javadoc/index-files/index-5.html new file mode 100644 index 0000000..45b12bf --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-5.html @@ -0,0 +1,259 @@ + + + + + +E-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    E

    +
    +
    end_time - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    energyP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    EngineUtil - Class in compbio.engine.client
    +
     
    +
    EngineUtil() - Constructor for class compbio.engine.client.EngineUtil
    +
     
    +
    ensembleFreqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    EnvVariableProcessor - Class in compbio.engine.client
    +
     
    +
    EnvVariableProcessor() - Constructor for class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    equals(Object) - Method in class compbio.data.msa.Category
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Alignment
    +
    +
    Please note that this implementation does not take the order of sequences + into account!
    +
    +
    equals(Object) - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Range
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.Score
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    equals(Object) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    equals(Object) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    equals(Object) - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    equals(Object) - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    equals(Object) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    equals(Object) - Method in class compbio.engine.ClusterJobId
    +
     
    +
    equals(Object) - Method in class compbio.engine.FilePuller
    +
     
    +
    equals(Object) - Method in class compbio.engine.Job
    +
     
    +
    equals(Object) - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Limit
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Option
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Parameter
    +
     
    +
    equals(Object) - Method in class compbio.metadata.Preset
    +
     
    +
    equals(Object) - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    equals(Object) - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    equals(Object) - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    equals(Object) - Method in class compbio.stat.collector.JobStat
    +
     
    +
    equals(Object) - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    equals(Object) - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    error - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Input option
    +
    +
    ERROR - Static variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    errorFile - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    es - Static variable in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    exec - Variable in class compbio.engine.client.ConfExecutable
    +
     
    +
    exec - Variable in class compbio.ws.server.GenericMetadataService
    +
     
    +
    EXEC_STAT_FILE - Static variable in class compbio.runner.msa.ClustalO
    +
     
    +
    EXEC_STAT_FILE - Static variable in class compbio.runner.msa.ClustalW
    +
     
    +
    EXEC_STAT_FILE - Static variable in class compbio.runner.msa.Muscle
    +
     
    +
    ExecProvider() - Constructor for enum compbio.engine.client.Executable.ExecProvider
    +
     
    +
    Executable<T> - Interface in compbio.engine.client
    +
    +
    Interface to a native executable.
    +
    +
    executable - Variable in class compbio.engine.local.LocalRunner
    +
     
    +
    Executable.ExecProvider - Enum in compbio.engine.client
    +
     
    +
    ExecutableWrapper - Class in compbio.engine.local
    +
     
    +
    ExecutableWrapper(ConfiguredExecutable<?>, String) - Constructor for class compbio.engine.local.ExecutableWrapper
    +
     
    +
    executeJob() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    executeJob() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    executeJob() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    executeJob() - Method in interface compbio.engine.SyncExecutor
    +
    +
    Execute the job
    +
    +
    ExecutionStatCollector - Class in compbio.stat.collector
    +
    +
    Class assumptions: + 1.
    +
    +
    ExecutionStatCollector(String, int) - Constructor for class compbio.stat.collector.ExecutionStatCollector
    +
    +
    List subdirectories in the job directory
    +
    +
    executor - Variable in class compbio.engine.local.LocalRunner
    +
     
    +
    executor - Variable in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    executor - Variable in class compbio.ws.server.MainManager
    +
     
    +
    exit_status - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-6.html b/website/docs/full_javadoc/index-files/index-6.html new file mode 100644 index 0000000..5b87e7f --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-6.html @@ -0,0 +1,226 @@ + + + + + +F-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    F

    +
    +
    failed - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    failed - Variable in class compbio.stat.servlet.util.Totals
    +
     
    +
    FAILED - Static variable in class compbio.ws.client.WSTester
    +
    +
    Status strings
    +
    +
    fasta4mafft - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    fastaAlignment - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    fastaInput1record - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    fastaInput2records - Static variable in class compbio.ws.client.WSTester
    +
    +
    Test sequences to be used as input for WS
    +
    +
    FastaReader - Class in compbio.data.sequence
    +
    +
    Reads files with FASTA formatted sequences.
    +
    +
    FastaReader(String) - Constructor for class compbio.data.sequence.FastaReader
    +
    +
    Header data can contain non-ASCII symbols and read in UTF8
    +
    +
    FastaReader(InputStream) - Constructor for class compbio.data.sequence.FastaReader
    +
    +
    This class will not close the incoming stream! So the client should do + so.
    +
    +
    fastaRNAAlignment - Static variable in class compbio.ws.client.WSTester
    +
     
    +
    FastaSequence - Class in compbio.data.sequence
    +
    +
    A FASTA formatted sequence.
    +
    +
    FastaSequence() - Constructor for class compbio.data.sequence.FastaSequence
    +
     
    +
    FastaSequence(String, String) - Constructor for class compbio.data.sequence.FastaSequence
    +
    +
    Upon construction the any whitespace characters are removed from the + sequence
    +
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.Align
    +
     
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.Analize
    +
     
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    fastaSequences - Variable in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    file - Variable in exception compbio.data.sequence.UnknownFileFormatException
    +
     
    +
    file - Variable in class compbio.engine.FilePuller
    +
     
    +
    FilePuller - Class in compbio.engine
    +
     
    +
    FilePuller(String, int) - Constructor for class compbio.engine.FilePuller
    +
     
    +
    FilePuller(String) - Constructor for class compbio.engine.FilePuller
    +
     
    +
    files - Variable in class compbio.stat.collector.JobDirectory
    +
     
    +
    finish - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    FIRST - Static variable in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    floatP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    Fold - Class in compbio.data.msa.jaxws
    +
     
    +
    Fold() - Constructor for class compbio.data.msa.jaxws.Fold
    +
     
    +
    fold(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    FoldResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    FoldResponse() - Constructor for class compbio.data.msa.jaxws.FoldResponse
    +
     
    +
    formatTime(String) - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
    +
    Convert grid engine time format End time: 1250701672.0000 to a readable + time representation as defined in Util.dataf
    +
    +
    freeEnergyP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    freqP - Static variable in class compbio.data.sequence.RNAStructReader
    +
     
    +
    from - Variable in class compbio.data.sequence.Range
    +
     
    +
    furtherDetails - Variable in class compbio.metadata.Option
    +
     
    +
    future - Variable in class compbio.engine.local.LocalRunner
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-7.html b/website/docs/full_javadoc/index-files/index-7.html new file mode 100644 index 0000000..d33ebf3 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-7.html @@ -0,0 +1,1553 @@ + + + + + +G-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    G

    +
    +
    gapchar - Variable in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    gapchar - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Dash char to be used as gap char in the alignments
    +
    +
    GAUtils - Class in compbio.ws.server
    +
     
    +
    GAUtils() - Constructor for class compbio.ws.server.GAUtils
    +
     
    +
    generateSchema(String, String) - Method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    GenericMetadataService<T> - Class in compbio.ws.server
    +
     
    +
    GenericMetadataService(SkeletalExecutable<T>, Logger) - Constructor for class compbio.ws.server.GenericMetadataService
    +
     
    +
    get(String) - Static method in class compbio.engine.PulledFileCache
    +
     
    +
    getAbandoned() - Method in class compbio.stat.servlet.util.Totals
    +
     
    +
    getAbandonedCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getAbandonedJobs() - Method in class compbio.stat.collector.StatProcessor
    +
    +
    Not collected.
    +
    +
    getActualNumberofSequences() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    getActualNumberofSequences() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getAlignment() - Method in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    getAlignment() - Method in class compbio.data.msa.jaxws.Fold
    +
     
    +
    getAlignment() - Method in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    getAllConstrainedParametersWithBorderValues(boolean) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getAllConstrainedParametersWithRandomValues() - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getAllOptions() - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getAllParameters() - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getAllStat() - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getAllStats() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    GetAnnotation - Class in compbio.data.msa.jaxws
    +
     
    +
    GetAnnotation() - Constructor for class compbio.data.msa.jaxws.GetAnnotation
    +
     
    +
    getAnnotation(String) - Method in interface compbio.data.msa.SequenceAnnotation
    +
    +
    Return the result of the job.
    +
    +
    getAnnotation(String) - Method in class compbio.ws.server.SequenceAnnotationService
    +
     
    +
    getAnnotation(String, Logger) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    getAnnotationForSequence(String) - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    GetAnnotationResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetAnnotationResponse() - Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse
    +
     
    +
    getArg0() - Method in class compbio.data.msa.jaxws.GetLastTested
    +
     
    +
    getArg0() - Method in class compbio.data.msa.jaxws.GetLastTestedOn
    +
     
    +
    getArg0() - Method in class compbio.data.msa.jaxws.GetServiceDescription
    +
     
    +
    getArg0() - Method in class compbio.data.msa.jaxws.IsOperating
    +
     
    +
    getArg0() - Method in class compbio.data.msa.jaxws.TestService
    +
     
    +
    getArgument(RunnerConfig<T>, String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    getArgument(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the argument by its name if found, NULL otherwise.
    +
    +
    getArgumentByOptionName(String) - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the argument by option name, NULL if the argument is not found
    +
    +
    getArguments(RunnerConfig<T>) - Method in class compbio.metadata.Preset
    +
    +
    Converts list of options as String to type Option
    +
    +
    getArguments() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns list of Parameter and Option supported by current + runner
    +
    +
    getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
    +
     
    +
    getAsyncEngine(ConfiguredExecutable<?>) - Static method in class compbio.engine.Configurator
    +
     
    +
    getAsyncEngine(String) - Static method in class compbio.engine.Configurator
    +
     
    +
    getAvgSeqLength() - Method in class compbio.metadata.Limit
    +
     
    +
    getAvgSequenceLength(List<FastaSequence>) - Static method in class compbio.metadata.Limit
    +
    +
    Calculates an average sequence length of the dataset
    +
    +
    getBasicURL() - Method in class compbio.metadata.Option
    +
     
    +
    getBooleanProperty(String) - Static method in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    getBooleanProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getByJobId(String, List<Job>) - Static method in class compbio.engine.Job
    +
     
    +
    getByTaskId(String, List<Job>) - Static method in class compbio.engine.Job
    +
     
    +
    getCalculationTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getCancelled() - Method in class compbio.stat.servlet.util.Totals
    +
     
    +
    getCancelledCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getCancelledJobs() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getCategories() - Static method in class compbio.data.msa.Category
    +
     
    +
    getChunk() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    getClass(String) - Static method in class compbio.engine.conf.DirectoryManager
    +
     
    +
    getClusterCpuNum(Class<? extends Executable<?>>) - Static method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getClusterJobDir() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getClusterJobDir() - Static method in class compbio.ws.server.MainManager
    +
     
    +
    getClusterJobId(String) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    getClusterJobID() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getClusterJobId() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getClusterJobs() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getClusterJobSettings() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getClusterJobSettings() - Method in interface compbio.engine.client.Executable
    +
     
    +
    getClusterJobSettings() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getClusterJobTimeOut() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getClusterStat() - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getCommand(Executable.ExecProvider) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getCommand(Executable.ExecProvider) - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getCommand(Executable.ExecProvider, Class<?>) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    getCommand(Executable.ExecProvider, Class<?>) - Static method in class compbio.engine.client.Util
    +
     
    +
    getCommandList() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getCommands() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getCommands(List<Option<T>>, String) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    getCommandString() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getConfExecutable() - Method in class compbio.engine.Job
    +
     
    +
    getCPUTimeStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getCPUUsageTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getCreatedFiles() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getCreatedFiles() - Method in interface compbio.engine.client.Executable
    +
    +
    Deprecated.
    +
    +
    getCreatedFiles() - Method in class compbio.engine.client.SkeletalExecutable
    +
    +
    This method cannot really tell whether the files has actually been + created or not.
    +
    +
    getCreatedFiles() - Method in class compbio.runner.conservation.AACon
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.ClustalW
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.GLprobs
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.MSAprobs
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.Muscle
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.Probcons
    +
     
    +
    getCreatedFiles() - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    getData() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    getDataTransfered() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getDBConnection() - Static method in class compbio.stat.collector.StatDB
    +
     
    +
    getDefaultLimit() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    getDefaultValue() - Method in interface compbio.metadata.Argument
    +
     
    +
    getDefaultValue() - Method in class compbio.metadata.Option
    +
    +
    A default value of the option.
    +
    +
    getDelay(TimeUnit) - Method in class compbio.engine.FilePuller
    +
     
    +
    getDelayValue(TimeUnit) - Method in class compbio.engine.FilePuller
    +
     
    +
    getDescription() - Method in interface compbio.metadata.Argument
    +
     
    +
    getDescription() - Method in class compbio.metadata.Option
    +
    +
    A long description of the Option
    +
    +
    getDescription() - Method in class compbio.metadata.Preset
    +
     
    +
    getDetails() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getEarliestRecord() - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getEndPoints() - Method in class compbio.stat.servlet.ServiceStatus
    +
     
    +
    getEndTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getEngine(Executable<?>) - Static method in class compbio.engine.LoadBalancer
    +
     
    +
    getEngine(Executable<V>, List<FastaSequence>) - Static method in class compbio.engine.LoadBalancer
    +
     
    +
    getEngine(ConfiguredExecutable<?>) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    getEnvironment() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getEnvironment() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getEnvVariableList(String) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    getEnvVariableName(String) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    getEnvVariables(String, Class<?>) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    getEnvVariableValue(String) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    getError() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getError() - Method in interface compbio.engine.client.Executable
    +
     
    +
    getError() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    getError() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getError() - Method in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    getEscJobname() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getExecProperty(String, Executable<?>) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    getExecProperty(String, Class<?>) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    getExecProperty(String, Executable<?>) - Static method in class compbio.engine.client.Util
    +
     
    +
    getExecProperty(String, Class<?>) - Static method in class compbio.engine.client.Util
    +
     
    +
    getExecProvider() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getExecProvider() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getExecProvider(ConfiguredExecutable<?>, List<FastaSequence>) - Static method in class compbio.engine.Configurator
    +
    +
    Depending on the values defined in the properties + (engine.cluster.enable=true and engine.local.enable=true) return either + Cluster job submission engine #JobRunner or local job submission + engine #LocalRunner If both engines enabled than ask + LoadBalancer for an engine.
    +
    +
    getExecutable() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getExecutable() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getExecutionStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getExecutor() - Static method in class compbio.engine.local.LocalExecutorService
    +
    +
    This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally
    +
    +
    getExitStatus() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getFailed() - Method in class compbio.stat.servlet.util.Totals
    +
     
    +
    getFailedJobs() - Method in class compbio.stat.collector.StatProcessor
    +
    +
    Started & finished but did not produce result
    +
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.Align
    +
     
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.Analize
    +
     
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    getFastaSequences() - Method in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    getFile() - Method in class compbio.engine.FilePuller
    +
     
    +
    getFile(String[], String, boolean) - Static method in class compbio.ws.client.IOHelper
    +
    +
    Checks -i options and return the File if one was provided, null otherwise
    +
    +
    getFinish() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getFinishedTime() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getFormatedSequence(int) - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Format sequence per width letter in one string.
    +
    +
    getFormattedFasta() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getFullPath(List<String>) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getFullPath(String, String) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    getFullPath(String, String) - Static method in class compbio.engine.client.Util
    +
     
    +
    getFurtherDetails() - Method in interface compbio.metadata.Argument
    +
     
    +
    getFurtherDetails() - Method in class compbio.metadata.Option
    +
    +
    The URL where further details about the option can be found
    +
    +
    getFuture() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    getGapchar() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    getGroup() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getHost(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Extracts host name from the command line
    +
    +
    getId() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Gets the value of id
    +
    +
    getIncomplete() - Method in class compbio.stat.servlet.util.Totals
    +
     
    +
    getIncompleteCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getIncompleteJobs() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getInput() - Method in class compbio.engine.client.ConfExecutable
    +
    +
    Not all input paths are relative! Input path could be absolute!
    +
    +
    getInput() - Method in interface compbio.engine.client.Executable
    +
     
    +
    getInput() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    getInput() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getInputSize() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getInputSize() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getInstance(ConfiguredExecutable<?>) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    getInstance() - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    getInstance(ConfiguredExecutable<?>) - Static method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    getInterface(Service) - Method in enum compbio.ws.client.Services
    +
     
    +
    getIntProperty(String) - Static method in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    getIntProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getIntResult(Timestamp, Timestamp, String) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getIOWait() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getIsCancelled() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getIsCollected() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getIsFinished() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getJabawsVersion() - Method in enum compbio.ws.client.Services
    +
     
    +
    getJava() - Static method in class compbio.engine.client.EngineUtil
    +
    +
    Returns the absolute path to the Java executable from JAVA_HOME
    +
    +
    getJava() - Static method in class compbio.engine.client.Util
    +
    +
    Returns the absolute path to the Java executable from JAVA_HOME
    +
    +
    getJobCounts(Date, Date) - Static method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getJobId() - Method in class compbio.data.msa.jaxws.CancelJob
    +
     
    +
    getJobId() - Method in class compbio.data.msa.jaxws.GetAnnotation
    +
     
    +
    getJobId() - Method in class compbio.data.msa.jaxws.GetJobStatus
    +
     
    +
    getJobId() - Method in class compbio.data.msa.jaxws.GetResult
    +
     
    +
    getJobId() - Method in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    getJobId() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getJobId() - Method in class compbio.engine.ClusterJobId
    +
     
    +
    getJobId() - Method in class compbio.engine.Job
    +
     
    +
    getJobInfo() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
    +
    This method will block before the calculation has completed and then + return the object containing a job execution statistics
    +
    +
    getJobInfo() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
    +
    This method will block before the calculation has completed and then + return the object containing a job execution statistics
    +
    +
    getJobname() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getJobNumber() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getJobPriority() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getJobReport() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getJobReportTabulated() - Method in class compbio.stat.collector.JobStat
    +
    +
    Header Job Started Finished Runtime Input Result
    +
    +
    getJobs() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getJobStat() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    GetJobStatus - Class in compbio.data.msa.jaxws
    +
     
    +
    GetJobStatus() - Constructor for class compbio.data.msa.jaxws.GetJobStatus
    +
     
    +
    getJobStatus(String) - Method in interface compbio.data.msa.JManagement
    +
    +
    Return the status of the job.
    +
    +
    getJobStatus(String) - Method in interface compbio.engine.AsyncExecutor
    +
    +
    Query the status of the job
    +
    +
    getJobStatus(String) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    getJobStatus(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
    +
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    +
    +
    getJobStatus(String) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
    +
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    +
    +
    getJobStatus() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    getJobStatus(ClusterJobId) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
    +
    Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed.
    +
    +
    getJobStatus(int) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
    +
    Deprecated.
    +
    +
    getJobStatus(String) - Static method in class compbio.engine.cluster.drmaa.JobRunner
    +
    +
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    +
    +
    getJobStatus() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    getJobStatus(String) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    getJobStatus(Future<ConfiguredExecutable<?>>) - Static method in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    getJobStatus() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    getJobStatus() - Method in interface compbio.engine.SyncExecutor
    +
    +
    Query the status of the job by its id.
    +
    +
    getJobStatus(String) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getJobStatus(String) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    getJobStatus(String) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetJobStatusResponse() - Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse
    +
     
    +
    getJobSubset(boolean) - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    GetLastTested - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLastTested() - Constructor for class compbio.data.msa.jaxws.GetLastTested
    +
     
    +
    getLastTested(Services) - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Number of seconds since the last test.
    +
    +
    getLastTested(Services) - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    GetLastTestedOn - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLastTestedOn() - Constructor for class compbio.data.msa.jaxws.GetLastTestedOn
    +
     
    +
    getLastTestedOn(Services) - Method in interface compbio.data.msa.RegistryWS
    +
    +
    The date and time the service has been verified to work last time
    +
    +
    getLastTestedOn(Services) - Method in class compbio.ws.server.RegistryWS
    +
    +
    Can potentially return null if the service has not been tested yet.
    +
    +
    GetLastTestedOnResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLastTestedOnResponse() - Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse
    +
     
    +
    GetLastTestedResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLastTestedResponse() - Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse
    +
     
    +
    getLength() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getLibPath() - Static method in class compbio.runner.conservation.AACon
    +
     
    +
    getLibPath() - Static method in class compbio.runner.disorder.Jronn
    +
     
    +
    GetLimit - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLimit() - Constructor for class compbio.data.msa.jaxws.GetLimit
    +
     
    +
    getLimit(String) - Method in interface compbio.data.msa.Metadata
    +
    +
    Get a Limit for a preset.
    +
    +
    getLimit(String) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getLimit(String) - Method in interface compbio.engine.client.Executable
    +
     
    +
    getLimit(String) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getLimit(String) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    getLimitByName(String) - Method in class compbio.metadata.LimitsManager
    +
     
    +
    GetLimitResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLimitResponse() - Constructor for class compbio.data.msa.jaxws.GetLimitResponse
    +
     
    +
    GetLimits - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLimits() - Constructor for class compbio.data.msa.jaxws.GetLimits
    +
     
    +
    getLimits() - Method in interface compbio.data.msa.Metadata
    +
    +
    List Limits supported by a web service.
    +
    +
    getLimits() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getLimits(Class<T>) - Static method in class compbio.engine.client.EngineUtil
    +
    +
    For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +
    +
    getLimits() - Method in interface compbio.engine.client.Executable
    +
     
    +
    getLimits() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getLimits(Class<T>) - Static method in class compbio.engine.client.Util
    +
    +
    For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +
    +
    getLimits() - Method in class compbio.metadata.LimitsManager
    +
     
    +
    getLimits(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Returns a list of limits supported by web service Each limit correspond + to a particular preset.
    +
    +
    getLimits() - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    getLimits() - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getLimits() - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    GetLimitsResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetLimitsResponse() - Constructor for class compbio.data.msa.jaxws.GetLimitsResponse
    +
     
    +
    getLocalJobDir() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getLocalJobDir() - Static method in class compbio.ws.server.MainManager
    +
     
    +
    getLocalJobs() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getLocalJobTimeOut() - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getLocalPath() - Static method in class compbio.engine.conf.PropertyHelperManager
    +
    +
    Method return the absolute path to the project root directory.
    +
    +
    getLocalStat() - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getLongestUntestedServiceTime() - Method in class compbio.ws.server.RegistryWS
    +
    +
    Return time in seconds for the test for the oldest unchecked service
    +
    +
    getLowBorderValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getMax() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getMaxVMem() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getMemoryStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getMessage() - Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean
    +
     
    +
    getMessage() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    getMessage() - Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
    +
     
    +
    getMessage() - Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
    +
     
    +
    getMessage() - Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean
    +
     
    +
    getMetadata() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getMethod(String) - Static method in enum compbio.data.sequence.ConservationMethod
    +
     
    +
    getMethod() - Method in class compbio.data.sequence.Score
    +
    +
    Returns the ConservationMethod
    +
    +
    getMin() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getName(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getName() - Method in interface compbio.metadata.Argument
    +
     
    +
    getName() - Method in class compbio.metadata.Option
    +
    +
    Human readable name of the option
    +
    +
    getName() - Method in class compbio.metadata.Preset
    +
     
    +
    getName(String) - Method in class compbio.metadata.Preset
    +
     
    +
    getNCore() - Method in class compbio.runner.conservation.AACon
    +
     
    +
    getNCore() - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    getNCore() - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    getNCore() - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    getNextPosition() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    GetNonoperatedServices - Class in compbio.data.msa.jaxws
    +
     
    +
    GetNonoperatedServices() - Constructor for class compbio.data.msa.jaxws.GetNonoperatedServices
    +
     
    +
    GetNonoperatedServicesResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetNonoperatedServicesResponse() - Constructor for class compbio.data.msa.jaxws.GetNonoperatedServicesResponse
    +
     
    +
    getNonRepeatableNumber() - Static method in class compbio.engine.conf.DirectoryManager
    +
     
    +
    getNumberOfScores() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getNumberOfSeq() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    getNumberOfSequencesAllowed() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    getNumberOfSequencesAllowed() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getNumericalFinish() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getNumericalStart() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getOnelineFasta() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    getOptionName() - Method in class compbio.metadata.Parameter
    +
     
    +
    getOptionNames() - Method in class compbio.metadata.Option
    +
     
    +
    getOptions() - Method in class compbio.data.msa.jaxws.CustomAlign
    +
     
    +
    getOptions() - Method in class compbio.data.msa.jaxws.CustomAnalize
    +
     
    +
    getOptions() - Method in class compbio.data.msa.jaxws.CustomFold
    +
     
    +
    getOptions() - Method in class compbio.metadata.Preset
    +
     
    +
    getOptions() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the list of the Options supported by the executable of type T
    +
    +
    getOptionsAtRandom() - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getOutput() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getOutput() - Method in interface compbio.engine.client.Executable
    +
     
    +
    getOutput() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    getOutput() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getOutput() - Method in class compbio.engine.local.ExecutableWrapper
    +
     
    +
    getOutput() - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    getParameters() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getParameters() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in interface compbio.engine.client.Executable
    +
     
    +
    getParameters() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getParameters() - Method in class compbio.metadata.RunnerConfig
    +
    +
    Returns the list of parameters supported executable of type T.
    +
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.runner.conservation.AACon
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    getParameters(Executable.ExecProvider) - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    getParametersList(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Returns a list of options supported by web service
    +
    +
    getParametersList(Metadata<T>, String) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Returns a list of options supported by web service
    +
    +
    getParamName(String) - Static method in class compbio.ws.client.MetadataHelper
    +
     
    +
    getParamValue(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getParamValue(String) - Static method in class compbio.ws.client.MetadataHelper
    +
     
    +
    getPosition() - Method in class compbio.data.msa.jaxws.PullExecStatistics
    +
     
    +
    getPossibleValues() - Method in interface compbio.metadata.Argument
    +
     
    +
    getPossibleValues() - Method in class compbio.metadata.Option
    +
    +
    List of possible optionNames
    +
    +
    getPossibleValues() - Method in class compbio.metadata.Parameter
    +
    +
    List is more convenient to work with
    +
    +
    getPreset() - Method in class compbio.data.msa.jaxws.PresetAlign
    +
     
    +
    getPreset() - Method in class compbio.data.msa.jaxws.PresetAnalize
    +
     
    +
    getPreset() - Method in class compbio.data.msa.jaxws.PresetFold
    +
     
    +
    getPreset() - Method in class compbio.metadata.Limit
    +
     
    +
    getPreset(Metadata<T>, String) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Returns Preset by its name
    +
    +
    getPresetByName(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    getPresetList(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
    +
    +
    Returns an objects from which the list of presets supported by web + service can be obtained
    +
    +
    getPresetName() - Method in class compbio.data.msa.jaxws.GetLimit
    +
     
    +
    getPresetName(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Extracts preset name from the command line is any
    +
    +
    GetPresets - Class in compbio.data.msa.jaxws
    +
     
    +
    GetPresets() - Constructor for class compbio.data.msa.jaxws.GetPresets
    +
     
    +
    getPresets() - Method in interface compbio.data.msa.Metadata
    +
    +
    Get presets supported by a web service
    +
    +
    getPresets() - Method in class compbio.metadata.PresetManager
    +
     
    +
    getPresets(Class<? extends Executable<T>>) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    getPresets(Class<? extends Executable<T>>) - Static method in class compbio.runner.Util
    +
     
    +
    getPresets() - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    getPresets() - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getPresets() - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    GetPresetsResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetPresetsResponse() - Constructor for class compbio.data.msa.jaxws.GetPresetsResponse
    +
     
    +
    getPrmSeparator() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    getProgram() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    getProgress() - Method in class compbio.engine.FilePuller
    +
     
    +
    getProgress(String, long, TimeUnit) - Static method in class compbio.engine.ProgressGetter
    +
     
    +
    getProgress(String) - Static method in class compbio.engine.ProgressGetter
    +
     
    +
    getProgress(String) - Static method in class compbio.ws.server.WSUtil
    +
     
    +
    getPropertyHelper() - Static method in class compbio.engine.conf.PropertyHelperManager
    +
    +
    Ways to fix path problem: + 1) find a path to WEB-INF directory based on the path to a known class.
    +
    +
    getRandomValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getRanges() - Method in class compbio.data.sequence.Score
    +
    +
    Return Ranges if any Collections.EMPTY_SET otherwise
    +
    +
    getRawUsage() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getRecordedJobStatus(String) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    getRecordedJobStatus(String) - Static method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    getRecordedJobStatus(String) - Static method in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    getReference() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getReference() - Method in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    getResourceFromClasspath(String) - Static method in class compbio.engine.conf.PropertyHelperManager
    +
     
    +
    GetResult - Class in compbio.data.msa.jaxws
    +
     
    +
    GetResult() - Constructor for class compbio.data.msa.jaxws.GetResult
    +
     
    +
    getResult(String) - Method in interface compbio.data.msa.MsaWS
    +
    +
    Return the result of the job.
    +
    +
    getResult(String) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getResult(String) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    GetResultResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetResultResponse() - Constructor for class compbio.data.msa.jaxws.GetResultResponse
    +
     
    +
    getResults(String) - Method in interface compbio.engine.AsyncExecutor
    +
    +
    Retrieve the results of the job.
    +
    +
    getResults() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getResults(String) - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getResults() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getResults(String) - Method in interface compbio.engine.client.Executable
    +
     
    +
    getResults(String) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    getResults(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    getResults(String) - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    getResults(String) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    getResults(Future<ConfiguredExecutable<?>>, String) - Static method in class compbio.engine.local.LocalEngineUtil
    +
     
    +
    getResults(String) - Method in class compbio.runner.conservation.AACon
    +
     
    +
    getResults(String) - Method in class compbio.runner.disorder.Disembl
    +
     
    +
    getResults(String) - Method in class compbio.runner.disorder.GlobPlot
    +
     
    +
    getResults(String) - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    getResults(String) - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.ClustalW
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.GLprobs
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.Mafft
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.MSAprobs
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.Muscle
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.Probcons
    +
     
    +
    getResults(String) - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    getResults(String) - Method in class compbio.runner.structure.RNAalifold
    +
     
    +
    getResultSize() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getResultSize() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.AlignResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.AnalizeResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.CustomAlignResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.CustomAnalizeResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.CustomFoldResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.FoldResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetAnnotationResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetJobStatusResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetLastTestedResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetLimitResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetLimitsResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetNonoperatedServicesResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetPresetsResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetResultResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.PresetAlignResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.PresetAnalizeResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.PresetFoldResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.TestAllServicesResponse
    +
     
    +
    getReturn() - Method in class compbio.data.msa.jaxws.TestServiceResponse
    +
     
    +
    getRunConfiguration() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getRunnerByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    getRunnerClassName() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    getRunnerClassName() - Method in class compbio.metadata.PresetManager
    +
     
    +
    getRunnerClassName() - Method in class compbio.metadata.RunnerConfig
    +
     
    +
    getRunnerConfiguration(Class<V>, Class<?>, String) - Static method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getRunnerLimits(Class<V>) - Static method in class compbio.engine.client.ConfExecutable
    +
    +
    This method should be executed once and result of its execution reused.
    +
    +
    getRunnerNameByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    GetRunnerOptions - Class in compbio.data.msa.jaxws
    +
     
    +
    GetRunnerOptions() - Constructor for class compbio.data.msa.jaxws.GetRunnerOptions
    +
     
    +
    getRunnerOptions() - Method in interface compbio.data.msa.Metadata
    +
    +
    Get options supported by a web service
    +
    +
    getRunnerOptions(Class<? extends Executable<V>>) - Static method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.MafftWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    getRunnerOptions() - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetRunnerOptionsResponse() - Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse
    +
     
    +
    getRunnerPresets(Class<? extends Executable<V>>) - Static method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getRuntime() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getSchema(String) - Static method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    getScoreByMethod(Enum<?>) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getScoreByMethod(String) - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    getScores() - Method in class compbio.data.sequence.Score
    +
    +
    The column scores for the alignment
    +
    +
    getSeqNumber() - Method in class compbio.metadata.Limit
    +
     
    +
    getSequence() - Method in class compbio.data.sequence.FastaSequence
    +
    +
    Gets the value of sequence
    +
    +
    getSequenceLenghtActual() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    getSequenceLenghtActual() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getSequenceLenghtAllowed() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
    +
     
    +
    getSequenceLenghtAllowed() - Method in exception compbio.metadata.LimitExceededException
    +
     
    +
    getSequences() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getServerIP() - Static method in class compbio.ws.server.GAUtils
    +
     
    +
    getService() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getService() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getService(String) - Static method in enum compbio.ws.client.Services
    +
     
    +
    getService(URL, String) - Method in enum compbio.ws.client.Services
    +
     
    +
    getServiceByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    getServiceByRunner(Class<? extends Executable>) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    getServiceByRunnerName(String) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    GetServiceCategories - Class in compbio.data.msa.jaxws
    +
     
    +
    GetServiceCategories() - Constructor for class compbio.data.msa.jaxws.GetServiceCategories
    +
     
    +
    getServiceCategories() - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Gets the list of services per category.
    +
    +
    getServiceCategories() - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    GetServiceCategoriesResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetServiceCategoriesResponse() - Constructor for class compbio.data.msa.jaxws.GetServiceCategoriesResponse
    +
     
    +
    GetServiceDescription - Class in compbio.data.msa.jaxws
    +
     
    +
    GetServiceDescription() - Constructor for class compbio.data.msa.jaxws.GetServiceDescription
    +
     
    +
    getServiceDescription(Services) - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Gives the description of the service.
    +
    +
    getServiceDescription(Services) - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    GetServiceDescriptionResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetServiceDescriptionResponse() - Constructor for class compbio.data.msa.jaxws.GetServiceDescriptionResponse
    +
     
    +
    getServiceGroup() - Method in enum compbio.ws.client.Services
    +
     
    +
    getServiceImpl(Services) - Static method in class compbio.ws.client.ServicesUtil
    +
     
    +
    getServiceInfo() - Method in enum compbio.ws.client.Services
    +
     
    +
    getServiceName(String[]) - Static method in class compbio.ws.client.CmdHelper
    +
    +
    Extracts service name from the command line
    +
    +
    getServiceNamespace() - Method in enum compbio.ws.client.Services
    +
     
    +
    getServicePath() - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    getServiceReference() - Method in enum compbio.ws.client.Services
    +
     
    +
    getServices() - Method in class compbio.data.msa.Category
    +
     
    +
    getServiceType() - Method in enum compbio.ws.client.Services
    +
     
    +
    getServiceVersion() - Method in enum compbio.ws.client.Services
    +
     
    +
    getSession() - Method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    getSingleWSStat(Services) - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getSize() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    getSize() - Static method in class compbio.engine.PulledFileCache
    +
     
    +
    getSMERFSColumnScore(String) - Static method in enum compbio.data.sequence.SMERFSConstraints
    +
     
    +
    getStart() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getStartTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getStartTime() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    getStatFile() - Static method in class compbio.runner.conservation.AACon
    +
     
    +
    getStatFile() - Static method in class compbio.runner.disorder.Jronn
    +
     
    +
    getStatFile() - Static method in class compbio.runner.msa.ClustalO
    +
     
    +
    getStatFile() - Static method in class compbio.runner.msa.ClustalW
    +
     
    +
    getStatFile() - Static method in class compbio.runner.msa.Muscle
    +
     
    +
    getStatistics(JobInfo) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    getStats() - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    getStats(int) - Static method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getStats(Date) - Static method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    getStatus() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getStringProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
    +
     
    +
    getStructs() - Method in class compbio.data.sequence.RNAStructScoreManager
    +
     
    +
    getSubmissionTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getSupportedOptions(Class<? extends Executable<T>>) - Static method in class compbio.runner.RunnerUtil
    +
     
    +
    getSupportedOptions(Class<? extends Executable<T>>) - Static method in class compbio.runner.Util
    +
     
    +
    getSupportedRuntimes() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getSupportedRuntimes() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getSupportedRuntimes(Class<?>) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    getSupportedRuntimes(Class<?>) - Static method in class compbio.engine.client.Util
    +
     
    +
    GetSupportedServices - Class in compbio.data.msa.jaxws
    +
     
    +
    GetSupportedServices() - Constructor for class compbio.data.msa.jaxws.GetSupportedServices
    +
     
    +
    getSupportedServices() - Method in interface compbio.data.msa.RegistryWS
    +
    +
    List of services that are functioning on the server.
    +
    +
    getSupportedServices() - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    GetSupportedServicesResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    GetSupportedServicesResponse() - Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse
    +
     
    +
    getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
    +
     
    +
    getSyncEngine(ConfiguredExecutable<?>) - Static method in class compbio.engine.Configurator
    +
     
    +
    getTask(String) - Static method in class compbio.engine.SubmissionManager
    +
     
    +
    getTaskDirectory(Class<?>) - Static method in class compbio.engine.conf.DirectoryManager
    +
     
    +
    getTaskId() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getTaskId() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getTaskId() - Method in class compbio.engine.Job
    +
     
    +
    getTestDBConnection() - Static method in class compbio.stat.collector.StatDB
    +
     
    +
    getTimeStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getTotal() - Method in class compbio.stat.servlet.util.Totals
    +
     
    +
    getTotalJobsCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    getTotalRuntime() - Method in class compbio.stat.collector.StatProcessor
    +
     
    +
    getType(File) - Static method in enum compbio.data.sequence.IUPredResult
    +
     
    +
    getType() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    getType() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    getType() - Method in class compbio.runner.conservation.AACon
    +
     
    +
    getType() - Method in class compbio.runner.disorder.Disembl
    +
     
    +
    getType() - Method in class compbio.runner.disorder.GlobPlot
    +
     
    +
    getType() - Method in class compbio.runner.disorder.IUPred
    +
     
    +
    getType() - Method in class compbio.runner.disorder.Jronn
    +
     
    +
    getType() - Method in class compbio.runner.msa.ClustalO
    +
     
    +
    getType() - Method in class compbio.runner.msa.ClustalW
    +
     
    +
    getType() - Method in class compbio.runner.msa.GLprobs
    +
     
    +
    getType() - Method in class compbio.runner.msa.Mafft
    +
     
    +
    getType() - Method in class compbio.runner.msa.MSAprobs
    +
     
    +
    getType() - Method in class compbio.runner.msa.Muscle
    +
     
    +
    getType() - Method in class compbio.runner.msa.Probcons
    +
     
    +
    getType() - Method in class compbio.runner.msa.Tcoffee
    +
     
    +
    getType() - Method in class compbio.runner.structure.RNAalifold
    +
     
    +
    getUpperBorderValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
    +
     
    +
    getUsedSysTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getUsedUserTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getValidator(String) - Static method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    getValidator(Schema) - Static method in class compbio.engine.conf.RunnerConfigMarshaller
    +
     
    +
    getValidValue() - Method in class compbio.metadata.Parameter
    +
     
    +
    getValue(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    getValue() - Method in class compbio.metadata.Parameter
    +
     
    +
    getValue(String) - Method in class compbio.metadata.Preset
    +
     
    +
    getValue(Parameter<?>) - Static method in class compbio.runner.OptionCombinator
    +
     
    +
    getVersion() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    getVersion() - Method in class compbio.ws.client.Services.ServiceInfo
    +
     
    +
    getVMem() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    getWebService() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    getWorkDirectory(String) - Method in interface compbio.engine.AsyncExecutor
    +
     
    +
    getWorkDirectory() - Method in class compbio.engine.client.ConfExecutable
    +
     
    +
    getWorkDirectory() - Method in interface compbio.engine.client.ConfiguredExecutable
    +
     
    +
    getWorkDirectory(String) - Method in class compbio.engine.cluster.drmaa.AsyncClusterRunner
    +
     
    +
    getWorkDirectory(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
    +
     
    +
    getWorkDirectory() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
    +
     
    +
    getWorkDirectory() - Method in class compbio.engine.cluster.drmaa.JobRunner
    +
     
    +
    getWorkDirectory(String) - Static method in class compbio.engine.Configurator
    +
     
    +
    getWorkDirectory(String) - Method in class compbio.engine.local.AsyncLocalRunner
    +
     
    +
    getWorkDirectory() - Method in class compbio.engine.local.LocalRunner
    +
     
    +
    getWorkDirectory() - Method in interface compbio.engine.SyncExecutor
    +
     
    +
    getWriter(File) - Static method in class compbio.ws.client.IOHelper
    +
     
    +
    GLOB_OUTPUT - Static variable in class compbio.runner.disorder.IUPred
    +
     
    +
    GlobPlot - Class in compbio.runner.disorder
    +
    +
    ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5.
    +
    +
    GlobPlot() - Constructor for class compbio.runner.disorder.GlobPlot
    +
     
    +
    GLOBPLOT_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    GlobPlotWS - Class in compbio.ws.server
    +
     
    +
    GlobPlotWS() - Constructor for class compbio.ws.server.GlobPlotWS
    +
     
    +
    GlobProtResult - Enum in compbio.data.sequence
    +
     
    +
    GlobProtResult() - Constructor for enum compbio.data.sequence.GlobProtResult
    +
     
    +
    GLprobs - Class in compbio.runner.msa
    +
     
    +
    GLprobs() - Constructor for class compbio.runner.msa.GLprobs
    +
     
    +
    GLPROBS_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    GLprobsOptions - Static variable in class compbio.ws.server.GLprobsWS
    +
     
    +
    GLprobsWS - Class in compbio.ws.server
    +
     
    +
    GLprobsWS() - Constructor for class compbio.ws.server.GLprobsWS
    +
     
    +
    group - Variable in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-8.html b/website/docs/full_javadoc/index-files/index-8.html new file mode 100644 index 0000000..a3c1460 --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-8.html @@ -0,0 +1,221 @@ + + + + + +H-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    H

    +
    +
    hasCompleted(JobDirectory) - Method in class compbio.stat.collector.DirCleaner
    +
     
    +
    hasCompleted(JobDirectory) - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    hasDump() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    hasExited() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    hashCode() - Method in class compbio.data.msa.Category
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.Alignment
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.AlignmentMetadata
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.FastaSequence
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.Range
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.Score
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.ScoreManager
    +
     
    +
    hashCode() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    hashCode() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    hashCode() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    hashCode() - Method in class compbio.engine.client.RunConfiguration
    +
     
    +
    hashCode() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    hashCode() - Method in class compbio.engine.ClusterJobId
    +
     
    +
    hashCode() - Method in class compbio.engine.FilePuller
    +
     
    +
    hashCode() - Method in class compbio.engine.Job
    +
     
    +
    hashCode() - Method in class compbio.metadata.ChunkHolder
    +
     
    +
    hashCode() - Method in class compbio.metadata.Limit
    +
     
    +
    hashCode() - Method in class compbio.metadata.Option
    +
     
    +
    hashCode() - Method in class compbio.metadata.Parameter
    +
     
    +
    hashCode() - Method in class compbio.metadata.Preset
    +
     
    +
    hashCode() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hashCode() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    hashCode() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    hashCode() - Method in class compbio.stat.servlet.ServiceTestResult
    +
     
    +
    hashCode() - Method in class compbio.stat.servlet.util.StatCollection
    +
     
    +
    hasMaxValue() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hasMinValue() - Method in class compbio.metadata.ValueConstrain
    +
     
    +
    hasMoreData() - Method in class compbio.engine.FilePuller
    +
     
    +
    hasNext() - Method in class compbio.data.sequence.FastaReader
    +
    hasParam(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    hasResult() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    hasSignaled() - Method in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    hasStarted() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    hasStatus(JobStatus) - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    hasTimedOut(JobDirectory) - Method in class compbio.stat.collector.ExecutionStatCollector
    +
     
    +
    help_text - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    hostkey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    hostname - Static variable in class compbio.ws.client.AAConClient
    +
    +
    Web service host
    +
    +
    hostname - Variable in class compbio.ws.client.WSTester
    +
     
    +
    HttpCodeResponseServiceStatus - Class in compbio.stat.servlet
    +
    +
    This servlet checks the webservice coming as pathinfo and returns http code + as a reply.
    +
    +
    HttpCodeResponseServiceStatus() - Constructor for class compbio.stat.servlet.HttpCodeResponseServiceStatus
    +
     
    +
    +A B C D E F G H I J K L M N O P Q R S T U V W _ 
    + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + + + diff --git a/website/docs/full_javadoc/index-files/index-9.html b/website/docs/full_javadoc/index-files/index-9.html new file mode 100644 index 0000000..3feb41b --- /dev/null +++ b/website/docs/full_javadoc/index-files/index-9.html @@ -0,0 +1,360 @@ + + + + + +I-Index + + + + + + + + +
    + + +
    Skip navigation links
    + + + + +
    +
    + + + +
    + +
    + + +
    + +
    A B C D E F G H I J K L M N O P Q R S T U V W _  + + +

    I

    +
    +
    id - Variable in class compbio.data.sequence.FastaSequence
    +
    +
    Sequence id
    +
    +
    id - Variable in class compbio.data.sequence.ScoreManager.ScoreHolder
    +
     
    +
    identify(String) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    identifyLine(String) - Static method in class compbio.data.sequence.RNAStructReader
    +
     
    +
    incomplete - Variable in class compbio.stat.servlet.util.Totals
    +
     
    +
    init() - Static method in class compbio.data.msa.Category
    +
     
    +
    init() - Method in class compbio.engine.FilePuller
    +
     
    +
    init() - Static method in class compbio.engine.local.LocalExecutorService
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.ClustalOWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.ClustalWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.GenericMetadataService
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.GLprobsWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.MafftWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.MSAprobsWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.MuscleWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.ProbconsWS
    +
     
    +
    init() - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    init(List<FastaSequence>) - Method in class compbio.ws.server.TcoffeeWS
    +
     
    +
    initBooleanValue(String) - Static method in class compbio.engine.Configurator
    +
     
    +
    initClusterWorkDirectory() - Static method in class compbio.engine.Configurator
    +
     
    +
    initLocalDirectory() - Static method in class compbio.engine.Configurator
    +
     
    +
    initPull() - Method in class compbio.engine.FilePuller
    +
     
    +
    input - Variable in class compbio.data.sequence.FastaReader
    +
     
    +
    input - Variable in class compbio.engine.client.RunConfiguration
    +
    +
    Input
    +
    +
    INPUT - Static variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    inputFile - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    InputFilter - Class in compbio.stat.collector
    +
     
    +
    InputFilter() - Constructor for class compbio.stat.collector.InputFilter
    +
     
    +
    inputkey - Static variable in class compbio.ws.client.Constraints
    +
     
    +
    inputSize - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    insertData(Set<JobStat>) - Method in class compbio.stat.collector.StatDB
    +
     
    +
    INSTANCE - Static variable in class compbio.engine.cluster.drmaa.ClusterSession
    +
     
    +
    INSTANCE - Static variable in class compbio.engine.local.LocalExecutorService
    +
     
    +
    io - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    IOHelper - Class in compbio.ws.client
    +
     
    +
    IOHelper() - Constructor for class compbio.ws.client.IOHelper
    +
     
    +
    iow - Variable in class compbio.engine.cluster.drmaa.StatisticManager
    +
     
    +
    is - Variable in class compbio.engine.local.StreamGobbler
    +
     
    +
    IS_CLUSTER_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator
    +
     
    +
    IS_GA_ENABLED - Static variable in class compbio.ws.server.GAUtils
    +
     
    +
    IS_LOCAL_ENGINE_ENABLED - Static variable in class compbio.engine.Configurator
    +
     
    +
    isAbsolutePath(String) - Static method in class compbio.engine.client.PathValidator
    +
    +
    Whether a certain path is absolute or not is operation system dependent!
    +
    +
    isAdmin(HttpServletRequest) - Static method in class compbio.stat.servlet.AnnualStat
    +
     
    +
    isAmbiguosProtein(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Check whether the sequence confirms to amboguous protein sequence
    +
    +
    isCancelled() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    isCancelled - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    isClusterJob() - Method in class compbio.stat.collector.JobStat
    +
     
    +
    isCollected() - Method in class compbio.stat.collector.JobDirectory
    +
     
    +
    isCollected - Variable in class compbio.stat.collector.JobStat
    +
     
    +
    isCombinedValue(String) - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    isComposite(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    isDefault - Variable in class compbio.metadata.Limit
    +
     
    +
    isDefault() - Method in class compbio.metadata.Limit
    +
     
    +
    isErrorSet - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isErrorSet() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isExceeded(List<FastaSequence>) - Method in class compbio.metadata.Limit
    +
    +
    Checks if the number of sequences or their average length in the dataset + exceeds this limit.
    +
    +
    isFileCreated() - Method in class compbio.engine.FilePuller
    +
     
    +
    isFirst() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    isGoogleAnalyticsEnabled() - Static method in class compbio.ws.server.GAUtils
    +
     
    +
    isInputSet - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isInputSet() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isJavaLibrary(Class<?>) - Static method in class compbio.engine.client.EngineUtil
    +
    +
    Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
    +
    +
    isJavaLibrary(Class<?>) - Static method in class compbio.engine.client.Util
    +
    +
    Returns true of executableName.jar.file property has some value in the + Executable.properties file, false otherwise.
    +
    +
    isLast() - Method in class compbio.engine.client.CommandBuilder.Parameter
    +
     
    +
    isLocal(String) - Static method in class compbio.engine.Configurator
    +
     
    +
    isMarked(String, JobStatus) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    isMarked(String, JobStatus) - Static method in class compbio.engine.client.Util
    +
     
    +
    isNonAmbNucleotideSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
    +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
    +
    +
    isNucleotideSequence(FastaSequence) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    isNumeric(String) - Method in class compbio.metadata.PresetManager
    +
     
    +
    IsOperating - Class in compbio.data.msa.jaxws
    +
     
    +
    IsOperating() - Constructor for class compbio.data.msa.jaxws.IsOperating
    +
     
    +
    isOperating(Services) - Method in interface compbio.data.msa.RegistryWS
    +
    +
    Check whether a particular web service is working on this server
    +
    +
    isOperating(Services) - Method in class compbio.ws.server.RegistryWS
    +
     
    +
    IsOperatingResponse - Class in compbio.data.msa.jaxws
    +
     
    +
    IsOperatingResponse() - Constructor for class compbio.data.msa.jaxws.IsOperatingResponse
    +
     
    +
    isOutputSet - Variable in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isOutputSet() - Method in class compbio.engine.client.SkeletalExecutable
    +
     
    +
    isParameter(String) - Static method in class compbio.ws.client.MetadataHelper
    +
     
    +
    isProteinSequence(String) - Static method in class compbio.data.sequence.SequenceUtil
    +
     
    +
    isRequired - Variable in class compbio.metadata.Option
    +
     
    +
    isRequired() - Method in class compbio.metadata.Option
    +
    +
    Flag that indicated that this option must be specified in the command + line for an executable to run
    +
    +
    isReturn() - Method in class compbio.data.msa.jaxws.CancelJobResponse
    +
     
    +
    isReturn() - Method in class compbio.data.msa.jaxws.IsOperatingResponse
    +
     
    +
    isTargetedForLocalExecution(ConfiguredExecutable<?>) - Static method in class compbio.engine.Configurator
    +
     
    +
    isValidClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil
    +
    +
    Please note this method closes the input stream provided as a parameter
    +
    +
    isValidDirectory(String) - Static method in class compbio.engine.client.PathValidator
    +
     
    +
    isValidEnvVariableProperty(String) - Static method in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    isValidExecutable(String) - Static method in class compbio.engine.client.PathValidator
    +
     
    +
    isValidJobId(String) - Static method in class compbio.engine.client.EngineUtil
    +
     
    +
    isValidJobId(String) - Static method in class compbio.engine.client.Util
    +
     
    +
    isValidValue(String) - Method in class compbio.metadata.Parameter
    +
     
    +
    isWhiteSpaceSeparator() - Method in class compbio.engine.client.CommandBuilder
    +
     
    +
    IUPred - Class in compbio.runner.disorder
    +
    +
    iupred sequenceFile + + Maximum sequence length is 40000 chars.
    +
    +
    IUPred() - Constructor for class compbio.runner.disorder.IUPred
    +
     
    +
    IUPRED_INFO - Static variable in enum compbio.ws.client.Services
    +
     
    +
    iupred_path - Static variable in class compbio.engine.client.EnvVariableProcessor
    +
     
    +
    IUPredResult - Enum in compbio.data.sequence
    +
     
    +
    IUPredResult() - Constructor for enum compbio.data.sequence.IUPredResult
    +
     
    +
    IUPredWS - Class in compbio.ws.server
    +
     
    +
    IUPredWS() - Constructor for class compbio.ws.server.IUPredWS
    +
     
    +
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    JABAWS 2.2 JavaDoc

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    PackageDescription
    compbio.data.msa +
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    +
    compbio.data.msa.jaxws 
    compbio.data.sequence +
    A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    +
    compbio.engine 
    compbio.engine.client 
    compbio.engine.cluster.drmaa 
    compbio.engine.conf 
    compbio.engine.local 
    compbio.metadata +
    A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    +
    compbio.runner +
    Utilities commonly used by all runners.
    +
    compbio.runner.conservation 
    compbio.runner.disorder 
    compbio.runner.msa +
    Wrappers for native executables for multiple sequence alignment (msa)
    +
    compbio.runner.structure 
    compbio.stat.collector 
    compbio.stat.servlet 
    compbio.stat.servlet.util 
    compbio.ws.client +
    A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
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    -
    - - - diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html deleted file mode 100644 index 355b0e2..0000000 --- a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JnetAnnotation - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.data._structure -
    -Enum JnetAnnotation

    -
    -java.lang.Object
-  extended by java.lang.Enum<JnetAnnotation>
-      extended by compbio.data._structure.JnetAnnotation
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<JnetAnnotation>
    -
    -
    -
    -
    public enum JnetAnnotation
    extends Enum<JnetAnnotation>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    JNETCONF - -
    -           
    JNETHMM - -
    -           
    jnetpred - -
    -           
    JNETPROPE - -
    -           
    JNETPROPH - -
    -           
    JNETSOL0 - -
    -           
    JNETSOL25 - -
    -           
    JNETSOL5 - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static JnetAnnotationvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JnetAnnotation[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -jnetpred

    -
    -public static final JnetAnnotation jnetpred
    -
    -
    -
    -
    -
    - -

    -JNETCONF

    -
    -public static final JnetAnnotation JNETCONF
    -
    -
    -
    -
    -
    - -

    -JNETSOL25

    -
    -public static final JnetAnnotation JNETSOL25
    -
    -
    -
    -
    -
    - -

    -JNETSOL5

    -
    -public static final JnetAnnotation JNETSOL5
    -
    -
    -
    -
    -
    - -

    -JNETSOL0

    -
    -public static final JnetAnnotation JNETSOL0
    -
    -
    -
    -
    -
    - -

    -JNETHMM

    -
    -public static final JnetAnnotation JNETHMM
    -
    -
    -
    -
    -
    - -

    -JNETPROPH

    -
    -public static final JnetAnnotation JNETPROPH
    -
    -
    -
    -
    -
    - -

    -JNETPROPE

    -
    -public static final JnetAnnotation JNETPROPE
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static JnetAnnotation[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (JnetAnnotation c : JnetAnnotation.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static JnetAnnotation valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html deleted file mode 100644 index b775769..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JpredAnnotation - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.data._structure -
    -Enum JpredAnnotation

    -
    -java.lang.Object
-  extended by java.lang.Enum<JpredAnnotation>
-      extended by compbio.data._structure.JpredAnnotation
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<JpredAnnotation>
    -
    -
    -
    -
    public enum JpredAnnotation
    extends Enum<JpredAnnotation>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    JNETCONF - -
    -           
    JNETHMM - -
    -           
    jnetpred - -
    -           
    JNETPROPE - -
    -           
    JNETPROPH - -
    -           
    JNETSOL0 - -
    -           
    JNETSOL25 - -
    -           
    JNETSOL5 - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static JpredAnnotationvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JpredAnnotation[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -jnetpred

    -
    -public static final JpredAnnotation jnetpred
    -
    -
    -
    -
    -
    - -

    -JNETCONF

    -
    -public static final JpredAnnotation JNETCONF
    -
    -
    -
    -
    -
    - -

    -JNETSOL25

    -
    -public static final JpredAnnotation JNETSOL25
    -
    -
    -
    -
    -
    - -

    -JNETSOL5

    -
    -public static final JpredAnnotation JNETSOL5
    -
    -
    -
    -
    -
    - -

    -JNETSOL0

    -
    -public static final JpredAnnotation JNETSOL0
    -
    -
    -
    -
    -
    - -

    -JNETHMM

    -
    -public static final JpredAnnotation JNETHMM
    -
    -
    -
    -
    -
    - -

    -JNETPROPH

    -
    -public static final JpredAnnotation JNETPROPH
    -
    -
    -
    -
    -
    - -

    -JNETPROPE

    -
    -public static final JpredAnnotation JNETPROPE
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static JpredAnnotation[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (JpredAnnotation c : JpredAnnotation.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static JpredAnnotation valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredResult.html b/website/full_javadoc/compbio/data/_structure/JpredResult.html deleted file mode 100644 index 4b37056..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredResult.html +++ /dev/null @@ -1,260 +0,0 @@ - - - - - - -JpredResult - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data._structure -
    -Class JpredResult

    -
    -java.lang.Object
-  extended by compbio.data._structure.JpredResult
-
    -
    -
    -
    public class JpredResult
    extends Object
    - - -

    -Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784, -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    JpredResult() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JpredResult

    -
    -public JpredResult()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html deleted file mode 100644 index ade6f7c..0000000 --- a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Class compbio.data._structure.JnetAnnotation - - - - - - - - - - - - -
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    compbio.data._structure  
    -  -

    - - - - - -
    -Uses of JnetAnnotation in compbio.data._structure
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data._structure that return JnetAnnotation
    -static JnetAnnotationJnetAnnotation.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JnetAnnotation[]JnetAnnotation.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

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    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data._structure that return JpredAnnotation
    -static JpredAnnotationJpredAnnotation.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JpredAnnotation[]JpredAnnotation.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

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    -Classes  - -
    -JpredResult
    - - - - - - -
    -Enums  - -
    -JnetAnnotation -
    -JpredAnnotation
    - - - - diff --git a/website/full_javadoc/compbio/data/_structure/package-summary.html b/website/full_javadoc/compbio/data/_structure/package-summary.html deleted file mode 100644 index 39e4ddc..0000000 --- a/website/full_javadoc/compbio/data/_structure/package-summary.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - -compbio.data._structure - - - - - - - - - - - - -
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    - - - -
    -

    -Package compbio.data._structure -

    - - - - - - - - - -
    -Class Summary
    JpredResultJnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    -  - -

    - - - - - - - - - - - - - -
    -Enum Summary
    JnetAnnotation 
    JpredAnnotation 
    -  - -

    -

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    -Hierarchy For Package compbio.data._structure -

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    All Packages
    -
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    -Packages that use compbio.data._structure
    compbio.data._structure  
    -  -

    - - - - - - - - - - - -
    -Classes in compbio.data._structure used by compbio.data._structure
    JnetAnnotation - -
    -           
    JpredAnnotation - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/data/msa/Category.html b/website/full_javadoc/compbio/data/msa/Category.html deleted file mode 100644 index 2e8c975..0000000 --- a/website/full_javadoc/compbio/data/msa/Category.html +++ /dev/null @@ -1,390 +0,0 @@ - - - - - - -Category - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa -
    -Class Category

    -
    -java.lang.Object
-  extended by compbio.data.msa.Category
-
    -
    -
    -
    public class Category
    extends Object
    - - -

    -Class that splits Services to categories. Services themselves have no - knowledge which category they belongs to. - - This class is responsible for initialization of all the categories (done - statically) and holds the category names as constrains. - - Two categories considered equals if their names are equals. -

    - -

    -

    -
    Version:
    -
    1.0 September 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringCATEGORY_ALIGNMENT - -
    -          All of the Category names
    -static StringCATEGORY_CONSERVATION - -
    -           
    -static StringCATEGORY_DISORDER - -
    -           
    - Stringname - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    -static Set<Category>getCategories() - -
    -           
    - Set<Services>getServices() - -
    -           
    - inthashCode() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -CATEGORY_ALIGNMENT

    -
    -public static final String CATEGORY_ALIGNMENT
    -
    -
    All of the Category names -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -CATEGORY_DISORDER

    -
    -public static final String CATEGORY_DISORDER
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -CATEGORY_CONSERVATION

    -
    -public static final String CATEGORY_CONSERVATION
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -name

    -
    -public String name
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getServices

    -
    -public Set<Services> getServices()
    -
    -
    -
    -
    -
    -
    - -

    -getCategories

    -
    -public static Set<Category> getCategories()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/JABAService.html b/website/full_javadoc/compbio/data/msa/JABAService.html deleted file mode 100644 index 43c3a13..0000000 --- a/website/full_javadoc/compbio/data/msa/JABAService.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -JABAService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa -
    -Interface JABAService

    -
    -
    All Known Subinterfaces:
    MsaWS<T>, RegistryWS, SequenceAnnotation<T>
    -
    -
    -
    All Known Implementing Classes:
    AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, RegistryWS, TcoffeeWS
    -
    -
    -
    -
    public interface JABAService
    - - -

    -This is a marker interface, contains no methods -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringSERVICE_NAMESPACE - -
    -           
    -static StringV2_SERVICE_NAMESPACE - -
    -           
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -SERVICE_NAMESPACE

    -
    -static final String SERVICE_NAMESPACE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -V2_SERVICE_NAMESPACE

    -
    -static final String V2_SERVICE_NAMESPACE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/JManagement.html b/website/full_javadoc/compbio/data/msa/JManagement.html deleted file mode 100644 index 8a38695..0000000 --- a/website/full_javadoc/compbio/data/msa/JManagement.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -JManagement - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa -
    -Interface JManagement

    -
    -
    All Known Subinterfaces:
    MsaWS<T>, SequenceAnnotation<T>
    -
    -
    -
    All Known Implementing Classes:
    AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
    -
    -
    -
    -
    public interface JManagement
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -cancelJob

    -
    -boolean cancelJob(String jobId)
    -
    -
    Stop running the job jobId but leave its output untouched -

    -

    - -
    Returns:
    true if job was cancelled successfully, false otherwise -
    Throws: -
    InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
    -
    -
    -
    - -

    -getJobStatus

    -
    -JobStatus getJobStatus(String jobId)
    -
    -
    Return the status of the job. -

    -

    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job -
    Throws: -
    InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in - invalid format
    See Also:
    JobStatus
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -ChunkHolder pullExecStatistics(String jobId,
-                               long position)
    -
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read -
    Throws: -
    InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format and also if the position value is negative
    See Also:
    ChunkHolder
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/Metadata.html b/website/full_javadoc/compbio/data/msa/Metadata.html deleted file mode 100644 index 0ab10eb..0000000 --- a/website/full_javadoc/compbio/data/msa/Metadata.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - -Metadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa -
    -Interface Metadata<T>

    -
    -
    All Known Subinterfaces:
    MsaWS<T>, SequenceAnnotation<T>
    -
    -
    -
    All Known Implementing Classes:
    AAConWS, ClustalOWS, ClustalWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
    -
    -
    -
    -
    public interface Metadata<T>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Limit<T>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<T>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<T>getPresets() - -
    -          Get presets supported by a web service
    - RunnerConfig<T>getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getRunnerOptions

    -
    -RunnerConfig<T> getRunnerOptions()
    -
    -
    Get options supported by a web service -

    -

    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getPresets

    -
    -PresetManager<T> getPresets()
    -
    -
    Get presets supported by a web service -

    -

    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getLimit

    -
    -Limit<T> getLimit(String presetName)
    -
    -
    Get a Limit for a preset. -

    -

    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -LimitsManager<T> getLimits()
    -
    -
    List Limits supported by a web service. -

    -

    - -
    Returns:
    LimitManager
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/MsaWS.html b/website/full_javadoc/compbio/data/msa/MsaWS.html deleted file mode 100644 index b4cf3dc..0000000 --- a/website/full_javadoc/compbio/data/msa/MsaWS.html +++ /dev/null @@ -1,436 +0,0 @@ - - - - - - -MsaWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa -
    -Interface MsaWS<T>

    -
    -
    Type Parameters:
    T - executable type / web service type
    -
    -
    All Superinterfaces:
    JABAService, JManagement, Metadata<T>
    -
    -
    -
    All Known Implementing Classes:
    ClustalOWS, ClustalWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
    -
    -
    -
    -
    public interface MsaWS<T>
    extends JABAService, JManagement, Metadata<T>
    - - -

    -Multiple Sequence Alignment (MSA) Web Services Interface -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date November 2010
    -
    -
    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -String align(List<FastaSequence> sequences)
-             throws UnsupportedRuntimeException,
-                    LimitExceededException,
-                    JobSubmissionException
    -
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    InvalidParameterException - thrown if input list of FASTA sequences is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -String customAlign(List<FastaSequence> sequences,
-                   List<Option<T>> options)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException
    -
    -
    Align a list of sequences with options. -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -String presetAlign(List<FastaSequence> sequences,
-                   Preset<T> preset)
-                   throws UnsupportedRuntimeException,
-                          LimitExceededException,
-                          JobSubmissionException,
-                          WrongParameterException
    -
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    InvalidParameterException - thrown if input list of FASTA sequence is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
    InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid - format
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/RegistryWS.html b/website/full_javadoc/compbio/data/msa/RegistryWS.html deleted file mode 100644 index 6576289..0000000 --- a/website/full_javadoc/compbio/data/msa/RegistryWS.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - -RegistryWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa -
    -Interface RegistryWS

    -
    -
    All Superinterfaces:
    JABAService
    -
    -
    -
    All Known Implementing Classes:
    RegistryWS
    -
    -
    -
    -
    public interface RegistryWS
    extends JABAService
    - - -

    -JABAWS services registry -

    - -

    -

    -
    Version:
    -
    1.0 June 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetLastTested(Services service) - -
    -          Number of seconds since the last test.
    - DategetLastTestedOn(Services service) - -
    -          The date and time the service has been verified to work last time
    - Set<Category>getServiceCategories() - -
    -          Gets the list of services per category.
    - StringgetServiceDescription(Services service) - -
    -          Gives the description of the service.
    - Set<Services>getSupportedServices() - -
    -          List of services that are functioning on the server.
    - booleanisOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - StringtestAllServices() - -
    -          Test all JABAWS services on the server
    - StringtestService(Services service) - -
    -          Test a particular service
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getSupportedServices

    -
    -Set<Services> getSupportedServices()
    -
    -
    List of services that are functioning on the server. This function - returns the results of testing performed some time ago by - testAllServices() or testService(Services) methods. The - time of last check can be obtained from - getLastTestedOn(Services) method -

    -

    -
    -
    -
    - -
    Returns:
    the Set of Services which are functioning on the server
    See Also:
    testAllServices()
    -
    -
    -
    - -

    -getLastTested

    -
    -int getLastTested(Services service)
    -
    -
    Number of seconds since the last test. Returns 0 if the service was not - tested or tested less then a one second ago. -

    -

    -
    -
    -
    -
    Parameters:
    service - -
    Returns:
    when last time tested
    -
    -
    -
    - -

    -getLastTestedOn

    -
    -Date getLastTestedOn(Services service)
    -
    -
    The date and time the service has been verified to work last time -

    -

    -
    -
    -
    -
    Parameters:
    service - -
    Returns:
    the Date and time on which the service was last tested
    -
    -
    -
    - -

    -testAllServices

    -
    -String testAllServices()
    -
    -
    Test all JABAWS services on the server -

    -

    -
    -
    -
    - -
    Returns:
    the test log
    -
    -
    -
    - -

    -testService

    -
    -String testService(Services service)
    -
    -
    Test a particular service -

    -

    -
    -
    -
    -
    Parameters:
    service - -
    Returns:
    the testing log
    -
    -
    -
    - -

    -isOperating

    -
    -boolean isOperating(Services service)
    -
    -
    Check whether a particular web service is working on this server -

    -

    -
    -
    -
    -
    Parameters:
    service - -
    Returns:
    true if the service was functioning in time of last testing.
    -
    -
    -
    - -

    -getServiceDescription

    -
    -String getServiceDescription(Services service)
    -
    -
    Gives the description of the service. -

    -

    -
    -
    -
    -
    Parameters:
    service - -
    Returns:
    String, plain text or html formatted piece, but NOT a full html - document
    -
    -
    -
    - -

    -getServiceCategories

    -
    -Set<Category> getServiceCategories()
    -
    -
    Gets the list of services per category. ServiceClassifier has the method - that returns Map> -

    -

    -
    -
    -
    - -
    Returns:
    ServiceClassifier the object to represent relation between - Services and Categories
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html b/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html deleted file mode 100644 index 4c1f35c..0000000 --- a/website/full_javadoc/compbio/data/msa/SequenceAnnotation.html +++ /dev/null @@ -1,448 +0,0 @@ - - - - - - -SequenceAnnotation - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa -
    -Interface SequenceAnnotation<T>

    -
    -
    Type Parameters:
    T - executable type / web service type
    -
    -
    All Superinterfaces:
    JABAService, JManagement, Metadata<T>
    -
    -
    -
    All Known Implementing Classes:
    AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS
    -
    -
    -
    -
    public interface SequenceAnnotation<T>
    extends JABAService, JManagement, Metadata<T>
    - - -

    -Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated -

    - -

    -

    -
    Version:
    -
    1.0 November 2010
    -
    Author:
    -
    Peter Troshin
    -
    -
    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringanalize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - ScoreManagergetAnnotation(String jobId) - -
    -          Return the result of the job.
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -analize

    -
    -String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
    -
    -
    Analyse the sequences. The actual analysis algorithm is defined by the - type T. - - Any dataset containing a greater number of sequences or the average - length of the sequences are greater then defined in the default Limit - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    InvalidParameterException - thrown if input list of fasta sequence is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAnalize

    -
    -String customAnalize(List<FastaSequence> sequences,
-                     List<Option<T>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    InvalidParameterException - thrown if input list of fasta sequence is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
    See Also:
    Option
    -
    -
    -
    - -

    -presetAnalize

    -
    -String presetAnalize(List<FastaSequence> sequences,
-                     Preset<T> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    InvalidParameterException - thrown if input list of fasta sequence is null or empty -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit
    -
    -
    -
    - -

    -getAnnotation

    -
    -ScoreManager getAnnotation(String jobId)
-                           throws ResultNotAvailableException
    -
    -
    Return the result of the job. -

    -

    -
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    the Map with the sequence names, sequence group names or the word - 'Alignment' in case of alignments and values the represented by a - Set of Score objects. The alignment can be represented in as - little as one key->value pair in this map, the list of sequences - will be represented by multiple key->value mappings. If multiple - annotations were calculated, then they are represented as a Set - of Scores. -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
    InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/Category.html b/website/full_javadoc/compbio/data/msa/class-use/Category.html deleted file mode 100644 index 1f15a35..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/Category.html +++ /dev/null @@ -1,262 +0,0 @@ - - - - - - -Uses of Class compbio.data.msa.Category - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -Uses of Class
    compbio.data.msa.Category

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use Category
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Category in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that return types with arguments of type Category
    -static Set<Category>Category.getCategories() - -
    -           
    - Set<Category>RegistryWS.getServiceCategories() - -
    -          Gets the list of services per category.
    -  -

    - - - - - -
    -Uses of Category in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Category
    - Set<Category>GetServiceCategoriesResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Category
    - voidGetServiceCategoriesResponse.setReturn(Set<Category> _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Category in compbio.ws.server
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Category
    - Set<Category>RegistryWS.getServiceCategories() - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/JABAService.html b/website/full_javadoc/compbio/data/msa/class-use/JABAService.html deleted file mode 100644 index 7ad467b..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/JABAService.html +++ /dev/null @@ -1,347 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JABAService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -Uses of Interface
    compbio.data.msa.JABAService

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use JABAService
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JABAService in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - -
    Subinterfaces of JABAService in compbio.data.msa
    - interfaceMsaWS<T> - -
    -          Multiple Sequence Alignment (MSA) Web Services Interface
    - interfaceRegistryWS - -
    -          JABAWS services registry
    - interfaceSequenceAnnotation<T> - -
    -          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  -

    - - - - - -
    -Uses of JABAService in compbio.ws.client
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return JABAService
    -static JABAServiceJws2Client.connect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -  -

    - - - - - -
    -Uses of JABAService in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.ws.server that implement JABAService
    - classAAConWS - -
    -           
    - classClustalOWS - -
    -           
    - classClustalWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    - classMafftWS - -
    -           
    - classMuscleWS - -
    -           
    - classProbconsWS - -
    -           
    - classRegistryWS - -
    -          JABAWS services registry
    - classTcoffeeWS - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/JManagement.html b/website/full_javadoc/compbio/data/msa/class-use/JManagement.html deleted file mode 100644 index 30b015a..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/JManagement.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JManagement - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -Uses of Interface
    compbio.data.msa.JManagement

    -
    - - - - - - - - - - - - - -
    -Packages that use JManagement
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JManagement in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Subinterfaces of JManagement in compbio.data.msa
    - interfaceMsaWS<T> - -
    -          Multiple Sequence Alignment (MSA) Web Services Interface
    - interfaceSequenceAnnotation<T> - -
    -          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  -

    - - - - - -
    -Uses of JManagement in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.ws.server that implement JManagement
    - classAAConWS - -
    -           
    - classClustalOWS - -
    -           
    - classClustalWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    - classMafftWS - -
    -           
    - classMuscleWS - -
    -           
    - classProbconsWS - -
    -           
    - classTcoffeeWS - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/Metadata.html b/website/full_javadoc/compbio/data/msa/class-use/Metadata.html deleted file mode 100644 index bc8ec3c..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/Metadata.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.Metadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -Uses of Interface
    compbio.data.msa.Metadata

    -
    - - - - - - - - - - - - - -
    -Packages that use Metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Metadata in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Subinterfaces of Metadata in compbio.data.msa
    - interfaceMsaWS<T> - -
    -          Multiple Sequence Alignment (MSA) Web Services Interface
    - interfaceSequenceAnnotation<T> - -
    -          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  -

    - - - - - -
    -Uses of Metadata in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.ws.server that implement Metadata
    - classAAConWS - -
    -           
    - classClustalOWS - -
    -           
    - classClustalWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    - classMafftWS - -
    -           
    - classMuscleWS - -
    -           
    - classProbconsWS - -
    -           
    - classTcoffeeWS - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html deleted file mode 100644 index 9aa80ac..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.MsaWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Interface
    compbio.data.msa.MsaWS

    -
    - - - - - - - - - -
    -Packages that use MsaWS
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of MsaWS in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.ws.server that implement MsaWS
    - classClustalOWS - -
    -           
    - classClustalWS - -
    -           
    - classMafftWS - -
    -           
    - classMuscleWS - -
    -           
    - classProbconsWS - -
    -           
    - classTcoffeeWS - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html b/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html deleted file mode 100644 index 32b7b02..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/RegistryWS.html +++ /dev/null @@ -1,210 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.RegistryWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -

    -Uses of Interface
    compbio.data.msa.RegistryWS

    -
    - - - - - - - - - - - - - -
    -Packages that use RegistryWS
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of RegistryWS in compbio.ws.client
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return RegistryWS
    -static RegistryWSJws2Client.connectToRegistry(String host) - -
    -          Get a connection of JABAWS registry
    -  -

    - - - - - -
    -Uses of RegistryWS in compbio.ws.server
    -  -

    - - - - - - - - - -
    Classes in compbio.ws.server that implement RegistryWS
    - classRegistryWS - -
    -          JABAWS services registry
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html b/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html deleted file mode 100644 index 959fbb7..0000000 --- a/website/full_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html +++ /dev/null @@ -1,242 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.SequenceAnnotation - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    -
    -

    -Uses of Interface
    compbio.data.msa.SequenceAnnotation

    -
    - - - - - - - - - - - - - -
    -Packages that use SequenceAnnotation
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of SequenceAnnotation in compbio.ws.client
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return SequenceAnnotation
    -static SequenceAnnotation<AAConWS>AAConClient.connect() - -
    -          Connects to a AACon web service by the host and the service name
    -  -

    - - - - - -
    -Uses of SequenceAnnotation in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.ws.server that implement SequenceAnnotation
    - classAAConWS - -
    -           
    - classDisemblWS - -
    -           
    - classGlobPlotWS - -
    -           
    - classIUPredWS - -
    -           
    - classJronnWS - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html deleted file mode 100644 index cc8c823..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/Align.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Align - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class Align

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.Align
-
    -
    -
    -
    public class Align
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Align() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Align

    -
    -public Align()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html deleted file mode 100644 index 908eb6b..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -AlignResponse - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class AlignResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.AlignResponse
-
    -
    -
    -
    public class AlignResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AlignResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AlignResponse

    -
    -public AlignResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Analize.html b/website/full_javadoc/compbio/data/msa/jaxws/Analize.html deleted file mode 100644 index 629f779..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/Analize.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Analize - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class Analize

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.Analize
-
    -
    -
    -
    public class Analize
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Analize() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
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    -Analize

    -
    -public Analize()
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    -Method Detail
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    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
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    Returns:
    returns List
    -
    -
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    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
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    - -compbio.data.msa.jaxws -
    -Class AnalizeResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.AnalizeResponse
-
    -
    -
    -
    public class AnalizeResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AnalizeResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AnalizeResponse

    -
    -public AnalizeResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html deleted file mode 100644 index 751552b..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJob - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class CancelJob

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJob
-
    -
    -
    -
    public class CancelJob
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CancelJob() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetJobId() - -
    -           
    - voidsetJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CancelJob

    -
    -public CancelJob()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setJobId

    -
    -public void setJobId(String jobId)
    -
    -
    -
    Parameters:
    jobId - the value for the jobId property
    -
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    - -compbio.data.msa.jaxws -
    -Class CancelJobResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CancelJobResponse
-
    -
    -
    -
    public class CancelJobResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CancelJobResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanisReturn() - -
    -           
    - voidsetReturn(boolean _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CancelJobResponse

    -
    -public CancelJobResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -isReturn

    -
    -public boolean isReturn()
    -
    -
    - -
    Returns:
    returns boolean
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(boolean _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html deleted file mode 100644 index 4782df5..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -CustomAlign - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class CustomAlign

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlign
-
    -
    -
    -
    public class CustomAlign
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CustomAlign() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - List<Option>getOptions() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidsetOptions(List<Option> options) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CustomAlign

    -
    -public CustomAlign()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
    -
    -
    -
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    -getOptions

    -
    -public List<Option> getOptions()
    -
    -
    - -
    Returns:
    returns List
    -
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    -setOptions

    -
    -public void setOptions(List<Option> options)
    -
    -
    -
    Parameters:
    options - the value for the options property
    -
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    - -compbio.data.msa.jaxws -
    -Class CustomAlignResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAlignResponse
-
    -
    -
    -
    public class CustomAlignResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CustomAlignResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CustomAlignResponse

    -
    -public CustomAlignResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class CustomAnalize

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalize
-
    -
    -
    -
    public class CustomAnalize
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CustomAnalize() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - List<Option>getOptions() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidsetOptions(List<Option> options) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CustomAnalize

    -
    -public CustomAnalize()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
    -
    -
    -
    - -

    -getOptions

    -
    -public List<Option> getOptions()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setOptions

    -
    -public void setOptions(List<Option> options)
    -
    -
    -
    Parameters:
    options - the value for the options property
    -
    -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - -compbio.data.msa.jaxws -
    -Class CustomAnalizeResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.CustomAnalizeResponse
-
    -
    -
    -
    public class CustomAnalizeResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    CustomAnalizeResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CustomAnalizeResponse

    -
    -public CustomAnalizeResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html b/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html deleted file mode 100644 index 791657c..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetAnnotation.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetAnnotation - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetAnnotation

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotation
-
    -
    -
    -
    public class GetAnnotation
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetAnnotation() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetJobId() - -
    -           
    - voidsetJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetAnnotation

    -
    -public GetAnnotation()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setJobId

    -
    -public void setJobId(String jobId)
    -
    -
    -
    Parameters:
    jobId - the value for the jobId property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetAnnotationResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotationResponse
-
    -
    -
    -
    public class GetAnnotationResponse
    extends Object
    - - -

    -

    - -

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    -Constructor Summary
    GetAnnotationResponse() - -
    -           
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    -Method Summary
    - ScoreManagergetReturn() - -
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    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    -Constructor Detail
    - -

    -GetAnnotationResponse

    -
    -public GetAnnotationResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public ScoreManager getReturn()
    -
    -
    - -
    Returns:
    returns ScoreManager
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(ScoreManager _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html deleted file mode 100644 index 8071a18..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetJobStatus - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetJobStatus

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatus
-
    -
    -
    -
    public class GetJobStatus
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetJobStatus() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetJobId() - -
    -           
    - voidsetJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetJobStatus

    -
    -public GetJobStatus()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setJobId

    -
    -public void setJobId(String jobId)
    -
    -
    -
    Parameters:
    jobId - the value for the jobId property
    -
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    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetJobStatusResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetJobStatusResponse
-
    -
    -
    -
    public class GetJobStatusResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetJobStatusResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - JobStatusgetReturn() - -
    -           
    - voidsetReturn(JobStatus _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetJobStatusResponse

    -
    -public GetJobStatusResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public JobStatus getReturn()
    -
    -
    - -
    Returns:
    returns JobStatus
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(JobStatus _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetLastTested

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTested
-
    -
    -
    -
    public class GetLastTested
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLastTested() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ServicesgetArg0() - -
    -           
    - voidsetArg0(Services arg0) - -
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    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLastTested

    -
    -public GetLastTested()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getArg0

    -
    -public Services getArg0()
    -
    -
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    Returns:
    returns Services
    -
    -
    -
    - -

    -setArg0

    -
    -public void setArg0(Services arg0)
    -
    -
    -
    Parameters:
    arg0 - the value for the arg0 property
    -
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    - -
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    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetLastTestedOn

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOn
-
    -
    -
    -
    public class GetLastTestedOn
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLastTestedOn() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ServicesgetArg0() - -
    -           
    - voidsetArg0(Services arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLastTestedOn

    -
    -public GetLastTestedOn()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getArg0

    -
    -public Services getArg0()
    -
    -
    - -
    Returns:
    returns Services
    -
    -
    -
    - -

    -setArg0

    -
    -public void setArg0(Services arg0)
    -
    -
    -
    Parameters:
    arg0 - the value for the arg0 property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetLastTestedOnResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedOnResponse
-
    -
    -
    -
    public class GetLastTestedOnResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLastTestedOnResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - DategetReturn() - -
    -           
    - voidsetReturn(Date _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLastTestedOnResponse

    -
    -public GetLastTestedOnResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public Date getReturn()
    -
    -
    - -
    Returns:
    returns Date
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(Date _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetLastTestedResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLastTestedResponse
-
    -
    -
    -
    public class GetLastTestedResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLastTestedResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetReturn() - -
    -           
    - voidsetReturn(int _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLastTestedResponse

    -
    -public GetLastTestedResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public int getReturn()
    -
    -
    - -
    Returns:
    returns int
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(int _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html deleted file mode 100644 index dba1464..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimit - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class GetLimit

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimit
-
    -
    -
    -
    public class GetLimit
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLimit() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetPresetName() - -
    -           
    - voidsetPresetName(String presetName) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLimit

    -
    -public GetLimit()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getPresetName

    -
    -public String getPresetName()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setPresetName

    -
    -public void setPresetName(String presetName)
    -
    -
    -
    Parameters:
    presetName - the value for the presetName property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class GetLimitResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitResponse
-
    -
    -
    -
    public class GetLimitResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLimitResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - LimitgetReturn() - -
    -           
    - voidsetReturn(Limit _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLimitResponse

    -
    -public GetLimitResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public Limit getReturn()
    -
    -
    - -
    Returns:
    returns Limit
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(Limit _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetLimits

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimits
-
    -
    -
    -
    public class GetLimits
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLimits() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLimits

    -
    -public GetLimits()
    -
    -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetLimitsResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetLimitsResponse
-
    -
    -
    -
    public class GetLimitsResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetLimitsResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - LimitsManagergetReturn() - -
    -           
    - voidsetReturn(LimitsManager _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetLimitsResponse

    -
    -public GetLimitsResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public LimitsManager getReturn()
    -
    -
    - -
    Returns:
    returns LimitsManager
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(LimitsManager _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html deleted file mode 100644 index 936916a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetPresets - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetPresets

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresets
-
    -
    -
    -
    public class GetPresets
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetPresets() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetPresets

    -
    -public GetPresets()
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html deleted file mode 100644 index 2c3b0df..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetPresetsResponse - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class GetPresetsResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetPresetsResponse
-
    -
    -
    -
    public class GetPresetsResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetPresetsResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - PresetManagergetReturn() - -
    -           
    - voidsetReturn(PresetManager _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetPresetsResponse

    -
    -public GetPresetsResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public PresetManager getReturn()
    -
    -
    - -
    Returns:
    returns PresetManager
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(PresetManager _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html deleted file mode 100644 index c69e670..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResult - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetResult

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResult
-
    -
    -
    -
    public class GetResult
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetResult() - -
    -           
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    -Method Summary
    - StringgetJobId() - -
    -           
    - voidsetJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    - - - - - - - - -
    -Constructor Detail
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    -GetResult

    -
    -public GetResult()
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    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
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    Returns:
    returns String
    -
    -
    -
    - -

    -setJobId

    -
    -public void setJobId(String jobId)
    -
    -
    -
    Parameters:
    jobId - the value for the jobId property
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html deleted file mode 100644 index 4b238ef..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResultResponse - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetResultResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetResultResponse
-
    -
    -
    -
    public class GetResultResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetResultResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - AlignmentgetReturn() - -
    -           
    - voidsetReturn(Alignment _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetResultResponse

    -
    -public GetResultResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public Alignment getReturn()
    -
    -
    - -
    Returns:
    returns Alignment
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(Alignment _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html deleted file mode 100644 index 84aabef..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetRunnerOptions - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetRunnerOptions

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptions
-
    -
    -
    -
    public class GetRunnerOptions
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetRunnerOptions() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetRunnerOptions

    -
    -public GetRunnerOptions()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetRunnerOptionsResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetRunnerOptionsResponse
-
    -
    -
    -
    public class GetRunnerOptionsResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetRunnerOptionsResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - RunnerConfiggetReturn() - -
    -           
    - voidsetReturn(RunnerConfig _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    - - - - - - - - -
    -Constructor Detail
    - -

    -GetRunnerOptionsResponse

    -
    -public GetRunnerOptionsResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public RunnerConfig getReturn()
    -
    -
    - -
    Returns:
    returns RunnerConfig
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(RunnerConfig _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html b/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html deleted file mode 100644 index 34daed9..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategories.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetServiceCategories - - - - - - - - - - - - -
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    - -compbio.data.msa.jaxws -
    -Class GetServiceCategories

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceCategories
-
    -
    -
    -
    public class GetServiceCategories
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetServiceCategories() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetServiceCategories

    -
    -public GetServiceCategories()
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html deleted file mode 100644 index db7ed5a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceCategoriesResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetServiceCategoriesResponse - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class GetServiceCategoriesResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceCategoriesResponse
-
    -
    -
    -
    public class GetServiceCategoriesResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetServiceCategoriesResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - Set<Category>getReturn() - -
    -           
    - voidsetReturn(Set<Category> _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetServiceCategoriesResponse

    -
    -public GetServiceCategoriesResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public Set<Category> getReturn()
    -
    -
    - -
    Returns:
    returns Set
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(Set<Category> _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html b/website/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html deleted file mode 100644 index 3089f2d..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetServiceDescription.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetServiceDescription - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetServiceDescription

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceDescription
-
    -
    -
    -
    public class GetServiceDescription
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetServiceDescription() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ServicesgetArg0() - -
    -           
    - voidsetArg0(Services arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetServiceDescription

    -
    -public GetServiceDescription()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getArg0

    -
    -public Services getArg0()
    -
    -
    - -
    Returns:
    returns Services
    -
    -
    -
    - -

    -setArg0

    -
    -public void setArg0(Services arg0)
    -
    -
    -
    Parameters:
    arg0 - the value for the arg0 property
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    - -compbio.data.msa.jaxws -
    -Class GetServiceDescriptionResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetServiceDescriptionResponse
-
    -
    -
    -
    public class GetServiceDescriptionResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetServiceDescriptionResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetServiceDescriptionResponse

    -
    -public GetServiceDescriptionResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
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    - -
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    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class GetSupportedServices

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServices
-
    -
    -
    -
    public class GetSupportedServices
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetSupportedServices() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetSupportedServices

    -
    -public GetSupportedServices()
    -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class GetSupportedServicesResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.GetSupportedServicesResponse
-
    -
    -
    -
    public class GetSupportedServicesResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GetSupportedServicesResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - Set<Services>getReturn() - -
    -           
    - voidsetReturn(Set<Services> _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GetSupportedServicesResponse

    -
    -public GetSupportedServicesResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public Set<Services> getReturn()
    -
    -
    - -
    Returns:
    returns Set
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(Set<Services> _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html b/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html deleted file mode 100644 index 5d3a48a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/IsOperating.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperating - - - - - - - - - - - - -
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    - -

    - -compbio.data.msa.jaxws -
    -Class IsOperating

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperating
-
    -
    -
    -
    public class IsOperating
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    IsOperating() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ServicesgetArg0() - -
    -           
    - voidsetArg0(Services arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IsOperating

    -
    -public IsOperating()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getArg0

    -
    -public Services getArg0()
    -
    -
    - -
    Returns:
    returns Services
    -
    -
    -
    - -

    -setArg0

    -
    -public void setArg0(Services arg0)
    -
    -
    -
    Parameters:
    arg0 - the value for the arg0 property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html deleted file mode 100644 index 8319cc0..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/IsOperatingResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperatingResponse - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class IsOperatingResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.IsOperatingResponse
-
    -
    -
    -
    public class IsOperatingResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    IsOperatingResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanisReturn() - -
    -           
    - voidsetReturn(boolean _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IsOperatingResponse

    -
    -public IsOperatingResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -isReturn

    -
    -public boolean isReturn()
    -
    -
    - -
    Returns:
    returns boolean
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(boolean _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
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    - - - -
    - -

    - -compbio.data.msa.jaxws -
    -Class JobSubmissionExceptionBean

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.JobSubmissionExceptionBean
-
    -
    -
    -
    public class JobSubmissionExceptionBean
    extends Object
    - - -

    -This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

    - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    JobSubmissionExceptionBean() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetMessage() - -
    -           
    - voidsetMessage(String message) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JobSubmissionExceptionBean

    -
    -public JobSubmissionExceptionBean()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getMessage

    -
    -public String getMessage()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
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    -setMessage

    -
    -public void setMessage(String message)
    -
    -
    -
    Parameters:
    message - the value for the message property
    -
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    - -compbio.data.msa.jaxws -
    -Class LimitExceededExceptionBean

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.LimitExceededExceptionBean
-
    -
    -
    -
    public class LimitExceededExceptionBean
    extends Object
    - - -

    -This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

    - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    LimitExceededExceptionBean() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetActualNumberofSequences() - -
    -           
    - StringgetMessage() - -
    -           
    - intgetNumberOfSequencesAllowed() - -
    -           
    - intgetSequenceLenghtActual() - -
    -           
    - intgetSequenceLenghtAllowed() - -
    -           
    - voidsetActualNumberofSequences(int actualNumberofSequences) - -
    -           
    - voidsetMessage(String message) - -
    -           
    - voidsetNumberOfSequencesAllowed(int numberOfSequencesAllowed) - -
    -           
    - voidsetSequenceLenghtActual(int sequenceLenghtActual) - -
    -           
    - voidsetSequenceLenghtAllowed(int sequenceLenghtAllowed) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -LimitExceededExceptionBean

    -
    -public LimitExceededExceptionBean()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getActualNumberofSequences

    -
    -public int getActualNumberofSequences()
    -
    -
    - -
    Returns:
    returns int
    -
    -
    -
    - -

    -setActualNumberofSequences

    -
    -public void setActualNumberofSequences(int actualNumberofSequences)
    -
    -
    -
    Parameters:
    actualNumberofSequences - the value for the actualNumberofSequences property
    -
    -
    -
    - -

    -getMessage

    -
    -public String getMessage()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setMessage

    -
    -public void setMessage(String message)
    -
    -
    -
    Parameters:
    message - the value for the message property
    -
    -
    -
    - -

    -getNumberOfSequencesAllowed

    -
    -public int getNumberOfSequencesAllowed()
    -
    -
    - -
    Returns:
    returns int
    -
    -
    -
    - -

    -setNumberOfSequencesAllowed

    -
    -public void setNumberOfSequencesAllowed(int numberOfSequencesAllowed)
    -
    -
    -
    Parameters:
    numberOfSequencesAllowed - the value for the numberOfSequencesAllowed property
    -
    -
    -
    - -

    -getSequenceLenghtActual

    -
    -public int getSequenceLenghtActual()
    -
    -
    - -
    Returns:
    returns int
    -
    -
    -
    - -

    -setSequenceLenghtActual

    -
    -public void setSequenceLenghtActual(int sequenceLenghtActual)
    -
    -
    -
    Parameters:
    sequenceLenghtActual - the value for the sequenceLenghtActual property
    -
    -
    -
    - -

    -getSequenceLenghtAllowed

    -
    -public int getSequenceLenghtAllowed()
    -
    -
    - -
    Returns:
    returns int
    -
    -
    -
    - -

    -setSequenceLenghtAllowed

    -
    -public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
    -
    -
    -
    Parameters:
    sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
    -
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    - - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html deleted file mode 100644 index d314566..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAlign - - - - - - - - - - - - -
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    - - - -
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    - -compbio.data.msa.jaxws -
    -Class PresetAlign

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlign
-
    -
    -
    -
    public class PresetAlign
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PresetAlign() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - PresetgetPreset() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
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    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PresetAlign

    -
    -public PresetAlign()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
    -
    -
    -
    - -

    -getPreset

    -
    -public Preset getPreset()
    -
    -
    - -
    Returns:
    returns Preset
    -
    -
    -
    - -

    -setPreset

    -
    -public void setPreset(Preset preset)
    -
    -
    -
    Parameters:
    preset - the value for the preset property
    -
    -
    - -
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    - -compbio.data.msa.jaxws -
    -Class PresetAlignResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAlignResponse
-
    -
    -
    -
    public class PresetAlignResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PresetAlignResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    - - - - - - - - -
    -Constructor Detail
    - -

    -PresetAlignResponse

    -
    -public PresetAlignResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
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    - -compbio.data.msa.jaxws -
    -Class PresetAnalize

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalize
-
    -
    -
    -
    public class PresetAnalize
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PresetAnalize() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<FastaSequence>getFastaSequences() - -
    -           
    - PresetgetPreset() - -
    -           
    - voidsetFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidsetPreset(Preset preset) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PresetAnalize

    -
    -public PresetAnalize()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getFastaSequences

    -
    -public List<FastaSequence> getFastaSequences()
    -
    -
    - -
    Returns:
    returns List
    -
    -
    -
    - -

    -setFastaSequences

    -
    -public void setFastaSequences(List<FastaSequence> fastaSequences)
    -
    -
    -
    Parameters:
    fastaSequences - the value for the fastaSequences property
    -
    -
    -
    - -

    -getPreset

    -
    -public Preset getPreset()
    -
    -
    - -
    Returns:
    returns Preset
    -
    -
    -
    - -

    -setPreset

    -
    -public void setPreset(Preset preset)
    -
    -
    -
    Parameters:
    preset - the value for the preset property
    -
    -
    - -
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    - -compbio.data.msa.jaxws -
    -Class PresetAnalizeResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PresetAnalizeResponse
-
    -
    -
    -
    public class PresetAnalizeResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PresetAnalizeResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetReturn() - -
    -           
    - voidsetReturn(String _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PresetAnalizeResponse

    -
    -public PresetAnalizeResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
    -
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    - -compbio.data.msa.jaxws -
    -Class PullExecStatistics

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatistics
-
    -
    -
    -
    public class PullExecStatistics
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PullExecStatistics() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetJobId() - -
    -           
    - longgetPosition() - -
    -           
    - voidsetJobId(String jobId) - -
    -           
    - voidsetPosition(long position) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PullExecStatistics

    -
    -public PullExecStatistics()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setJobId

    -
    -public void setJobId(String jobId)
    -
    -
    -
    Parameters:
    jobId - the value for the jobId property
    -
    -
    -
    - -

    -getPosition

    -
    -public long getPosition()
    -
    -
    - -
    Returns:
    returns long
    -
    -
    -
    - -

    -setPosition

    -
    -public void setPosition(long position)
    -
    -
    -
    Parameters:
    position - the value for the position property
    -
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    - -compbio.data.msa.jaxws -
    -Class PullExecStatisticsResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.PullExecStatisticsResponse
-
    -
    -
    -
    public class PullExecStatisticsResponse
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PullExecStatisticsResponse() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ChunkHoldergetReturn() - -
    -           
    - voidsetReturn(ChunkHolder _return) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PullExecStatisticsResponse

    -
    -public PullExecStatisticsResponse()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getReturn

    -
    -public ChunkHolder getReturn()
    -
    -
    - -
    Returns:
    returns ChunkHolder
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(ChunkHolder _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
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    - -compbio.data.msa.jaxws -
    -Class ResultNotAvailableExceptionBean

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
-
    -
    -
    -
    public class ResultNotAvailableExceptionBean
    extends Object
    - - -

    -This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

    - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ResultNotAvailableExceptionBean() - -
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    Methods inherited from class java.lang.Object
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    -ResultNotAvailableExceptionBean

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    -public ResultNotAvailableExceptionBean()
    -
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    -Method Detail
    - -

    -getMessage

    -
    -public String getMessage()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setMessage

    -
    -public void setMessage(String message)
    -
    -
    -
    Parameters:
    message - the value for the message property
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    - -compbio.data.msa.jaxws -
    -Class TestAllServices

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServices
-
    -
    -
    -
    public class TestAllServices
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    TestAllServices() - -
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    - -compbio.data.msa.jaxws -
    -Class TestAllServicesResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.TestAllServicesResponse
-
    -
    -
    -
    public class TestAllServicesResponse
    extends Object
    - - -

    -

    - -

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    -public TestAllServicesResponse()
    -
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    -Method Detail
    - -

    -getReturn

    -
    -public String getReturn()
    -
    -
    - -
    Returns:
    returns String
    -
    -
    -
    - -

    -setReturn

    -
    -public void setReturn(String _return)
    -
    -
    -
    Parameters:
    _return - the value for the _return property
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    - -compbio.data.msa.jaxws -
    -Class TestService

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.TestService
-
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    public class TestService
    extends Object
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    - ServicesgetArg0() - -
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    -TestService

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    -Method Detail
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    -getArg0

    -
    -public Services getArg0()
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    Returns:
    returns Services
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    -setArg0

    -
    -public void setArg0(Services arg0)
    -
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    Parameters:
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    - -compbio.data.msa.jaxws -
    -Class TestServiceResponse

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.TestServiceResponse
-
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    -
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    public class TestServiceResponse
    extends Object
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    -Method Summary
    - StringgetReturn() - -
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    -getReturn

    -
    -public String getReturn()
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    returns String
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    -setReturn

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    -public void setReturn(String _return)
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    Parameters:
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    -Class UnsupportedRuntimeExceptionBean

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
-
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    public class UnsupportedRuntimeExceptionBean
    extends Object
    - - -

    -This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

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    -getMessage

    -
    -public String getMessage()
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    returns String
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    - -compbio.data.msa.jaxws -
    -Class WrongParameterExceptionBean

    -
    -java.lang.Object
-  extended by compbio.data.msa.jaxws.WrongParameterExceptionBean
-
    -
    -
    -
    public class WrongParameterExceptionBean
    extends Object
    - - -

    -This class was generated by the JAX-WS RI. - JAX-WS RI 2.2.3-b01- - Generated source version: 2.2.3 -

    - -

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    WrongParameterExceptionBean() - -
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    -WrongParameterExceptionBean

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    -getMessage

    -
    -public String getMessage()
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    Returns:
    returns String
    -
    -
    -
    - -

    -setMessage

    -
    -public void setMessage(String message)
    -
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    Parameters:
    message - the value for the message property
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    -Classes  - -
    -Align -
    -AlignResponse -
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    -IsOperating -
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    -JobSubmissionExceptionBean -
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    -PullExecStatistics -
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    -Class Summary
    Align 
    AlignResponse 
    Analize 
    AnalizeResponse 
    CancelJob 
    CancelJobResponse 
    CustomAlign 
    CustomAlignResponse 
    CustomAnalize 
    CustomAnalizeResponse 
    GetAnnotation 
    GetAnnotationResponse 
    GetJobStatus 
    GetJobStatusResponse 
    GetLastTested 
    GetLastTestedOn 
    GetLastTestedOnResponse 
    GetLastTestedResponse 
    GetLimit 
    GetLimitResponse 
    GetLimits 
    GetLimitsResponse 
    GetPresets 
    GetPresetsResponse 
    GetResult 
    GetResultResponse 
    GetRunnerOptions 
    GetRunnerOptionsResponse 
    GetServiceCategories 
    GetServiceCategoriesResponse 
    GetServiceDescription 
    GetServiceDescriptionResponse 
    GetSupportedServices 
    GetSupportedServicesResponse 
    IsOperating 
    IsOperatingResponse 
    JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
    LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
    PresetAlign 
    PresetAlignResponse 
    PresetAnalize 
    PresetAnalizeResponse 
    PullExecStatistics 
    PullExecStatisticsResponse 
    ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
    TestAllServices 
    TestAllServicesResponse 
    TestService 
    TestServiceResponse 
    UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
    WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
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    -Interfaces  - -
    -JABAService -
    -JManagement -
    -Metadata -
    -MsaWS -
    -RegistryWS -
    -SequenceAnnotation
    - - - - - - -
    -Classes  - -
    -Category
    - - - - diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html deleted file mode 100644 index 64a76c5..0000000 --- a/website/full_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - - -
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    -Package compbio.data.msa -

    -Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Interface Summary
    JABAServiceThis is a marker interface, contains no methods
    JManagement 
    Metadata<T> 
    MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
    RegistryWSJABAWS services registry
    SequenceAnnotation<T>Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  - -

    - - - - - - - - - -
    -Class Summary
    CategoryClass that splits Services to categories.
    -  - -

    -

    -Package compbio.data.msa Description -

    - -

    -Web Service interfaces for JAva Bioinformatics Analysis Web Services. -

    - -

    -

    -
    Version:
    -
    1.0 April 2010
    -
    Author:
    -
    Peter Troshin
    -
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    -Uses of Package
    compbio.data.msa

    -
    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.data.msa
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.data.msa used by compbio.data.msa
    Category - -
    -          Class that splits Services to categories.
    JABAService - -
    -          This is a marker interface, contains no methods
    JManagement - -
    -           
    Metadata - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.data.msa used by compbio.data.msa.jaxws
    Category - -
    -          Class that splits Services to categories.
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.data.msa used by compbio.ws.client
    JABAService - -
    -          This is a marker interface, contains no methods
    RegistryWS - -
    -          JABAWS services registry
    SequenceAnnotation - -
    -          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.data.msa used by compbio.ws.server
    Category - -
    -          Class that splits Services to categories.
    JABAService - -
    -          This is a marker interface, contains no methods
    JManagement - -
    -           
    Metadata - -
    -           
    MsaWS - -
    -          Multiple Sequence Alignment (MSA) Web Services Interface
    RegistryWS - -
    -          JABAWS services registry
    SequenceAnnotation - -
    -          Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class Alignment

    -
    -java.lang.Object
-  extended by compbio.data.sequence.Alignment
-
    -
    -
    -
    @Immutable
-public final class Alignment
    extends Object
    - - -

    -Multiple sequence alignment. - - Does not give any guarantees on the content of individual FastaSequece - records. It does not guarantee neither the uniqueness of the names of - sequences nor it guarantees the uniqueness of the sequences. -

    - -

    -

    -
    Version:
    -
    1.0 September 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    FastaSequence, -AlignmentMetadata
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
    -           
    Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -          Please note that this implementation does not take the order of sequences - into account!
    - AlignmentMetadatagetMetadata() - -
    -           
    - List<FastaSequence>getSequences() - -
    -           
    - intgetSize() - -
    -           
    - inthashCode() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Alignment

    -
    -public Alignment(List<FastaSequence> sequences,
-                 Program program,
-                 char gapchar)
    -
    -
    -
    Parameters:
    sequences -
    program -
    gapchar -
    -
    -
    - -

    -Alignment

    -
    -public Alignment(List<FastaSequence> sequences,
-                 AlignmentMetadata metadata)
    -
    -
    -
    Parameters:
    sequences -
    metadata -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getSequences

    -
    -public List<FastaSequence> getSequences()
    -
    -
    - -
    Returns:
    list of FastaSequence records
    -
    -
    -
    - -

    -getSize

    -
    -public int getSize()
    -
    -
    - -
    Returns:
    a number of sequence in the alignment
    -
    -
    -
    - -

    -getMetadata

    -
    -public AlignmentMetadata getMetadata()
    -
    -
    - -
    Returns:
    AlignmentMetadata object
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    Please note that this implementation does not take the order of sequences - into account! -

    -

    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html deleted file mode 100644 index 982d9f5..0000000 --- a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -AlignmentMetadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.data.sequence -
    -Class AlignmentMetadata

    -
    -java.lang.Object
-  extended by compbio.data.sequence.AlignmentMetadata
-
    -
    -
    -
    @Immutable
-public class AlignmentMetadata
    extends Object
    - - -

    -Alignment metadata e.g. method/program being used to generate the alignment - and its parameters -

    - -

    -

    -
    Version:
    -
    1.0 September 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AlignmentMetadata(Program program, - char gapchar) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - chargetGapchar() - -
    -           
    - ProgramgetProgram() - -
    -           
    - inthashCode() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AlignmentMetadata

    -
    -public AlignmentMetadata(Program program,
-                         char gapchar)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getProgram

    -
    -public Program getProgram()
    -
    -
    -
    -
    -
    -
    - -

    -getGapchar

    -
    -public char getGapchar()
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index 879d767..0000000 --- a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html +++ /dev/null @@ -1,387 +0,0 @@ - - - - - - -ClustalAlignmentUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class ClustalAlignmentUtil

    -
    -java.lang.Object
-  extended by compbio.data.sequence.ClustalAlignmentUtil
-
    -
    -
    -
    public final class ClustalAlignmentUtil
    extends Object
    - - -

    -Tools to read and write clustal formated files -

    - -

    -

    -
    Version:
    -
    1.0 September 2009
    -
    Author:
    -
    Petr Troshin based on jimp class
    -
    -
    - -

    - - - - - - - - - - - -
    -Field Summary
    -static chargapchar - -
    -          Dash char to be used as gap char in the alignments
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalAlignmentUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static booleanisValidClustalFile(InputStream input) - -
    -          Please note this method closes the input stream provided as a parameter
    -static AlignmentreadClustalFile(File file) - -
    -           
    -static AlignmentreadClustalFile(InputStream instream) - -
    -          Read Clustal formatted alignment.
    -static voidwriteClustalAlignment(Writer out, - Alignment alignment) - -
    -          Write Clustal formatted alignment Limitations: does not record the - consensus.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -gapchar

    -
    -public static final char gapchar
    -
    -
    Dash char to be used as gap char in the alignments -

    -

    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalAlignmentUtil

    -
    -public ClustalAlignmentUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -readClustalFile

    -
    -public static Alignment readClustalFile(InputStream instream)
-                                 throws IOException,
-                                        UnknownFileFormatException
    -
    -
    Read Clustal formatted alignment. Limitations: Does not read consensus - - Sequence names as well as the sequences are not guaranteed to be unique! -

    -

    - -
    Throws: -
    {@link - IOException} -
    {@link - UnknownFileFormatException} -
    IOException -
    UnknownFileFormatException
    -
    -
    -
    - -

    -isValidClustalFile

    -
    -public static boolean isValidClustalFile(InputStream input)
    -
    -
    Please note this method closes the input stream provided as a parameter -

    -

    -
    Parameters:
    input - -
    Returns:
    true if the file is recognised as Clustal formatted alignment, - false otherwise
    -
    -
    -
    - -

    -writeClustalAlignment

    -
    -public static void writeClustalAlignment(Writer out,
-                                         Alignment alignment)
-                                  throws IOException
    -
    -
    Write Clustal formatted alignment Limitations: does not record the - consensus. Potential bug - records 60 chars length alignment where - Clustal would have recorded 50 chars. -

    -

    -
    Parameters:
    out -
    alignment - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -readClustalFile

    -
    -public static Alignment readClustalFile(File file)
-                                 throws UnknownFileFormatException,
-                                        IOException
    -
    -
    - -
    Throws: -
    UnknownFileFormatException -
    IOException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/ConservationMethod.html b/website/full_javadoc/compbio/data/sequence/ConservationMethod.html deleted file mode 100644 index 02eb959..0000000 --- a/website/full_javadoc/compbio/data/sequence/ConservationMethod.html +++ /dev/null @@ -1,605 +0,0 @@ - - - - - - -ConservationMethod - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Enum ConservationMethod

    -
    -java.lang.Object
-  extended by java.lang.Enum<ConservationMethod>
-      extended by compbio.data.sequence.ConservationMethod
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<ConservationMethod>
    -
    -
    -
    -
    public enum ConservationMethod
    extends Enum<ConservationMethod>
    - - -

    -Enumeration listing of all the supported methods. -

    - -

    -

    -
    Author:
    -
    Agnieszka Golicz & Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    ARMON - -
    -           
    GERSTEIN - -
    -           
    JORES - -
    -           
    KABAT - -
    -           
    KARLIN - -
    -           
    LANDGRAF - -
    -           
    MIRNY - -
    -           
    NOT_LANCET - -
    -           
    SANDER - -
    -           
    SCHNEIDER - -
    -           
    SHENKIN - -
    -           
    SMERFS - -
    -           
    TAYLOR_GAPS - -
    -           
    TAYLOR_NO_GAPS - -
    -           
    THOMPSON - -
    -           
    VALDAR - -
    -           
    WILLIAMSON - -
    -           
    ZVELIBIL - -
    -           
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ConservationMethodgetMethod(String meth) - -
    -           
    -static ConservationMethodvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ConservationMethod[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -KABAT

    -
    -public static final ConservationMethod KABAT
    -
    -
    -
    -
    -
    - -

    -JORES

    -
    -public static final ConservationMethod JORES
    -
    -
    -
    -
    -
    - -

    -SCHNEIDER

    -
    -public static final ConservationMethod SCHNEIDER
    -
    -
    -
    -
    -
    - -

    -SHENKIN

    -
    -public static final ConservationMethod SHENKIN
    -
    -
    -
    -
    -
    - -

    -GERSTEIN

    -
    -public static final ConservationMethod GERSTEIN
    -
    -
    -
    -
    -
    - -

    -TAYLOR_GAPS

    -
    -public static final ConservationMethod TAYLOR_GAPS
    -
    -
    -
    -
    -
    - -

    -TAYLOR_NO_GAPS

    -
    -public static final ConservationMethod TAYLOR_NO_GAPS
    -
    -
    -
    -
    -
    - -

    -ZVELIBIL

    -
    -public static final ConservationMethod ZVELIBIL
    -
    -
    -
    -
    -
    - -

    -KARLIN

    -
    -public static final ConservationMethod KARLIN
    -
    -
    -
    -
    -
    - -

    -ARMON

    -
    -public static final ConservationMethod ARMON
    -
    -
    -
    -
    -
    - -

    -THOMPSON

    -
    -public static final ConservationMethod THOMPSON
    -
    -
    -
    -
    -
    - -

    -NOT_LANCET

    -
    -public static final ConservationMethod NOT_LANCET
    -
    -
    -
    -
    -
    - -

    -MIRNY

    -
    -public static final ConservationMethod MIRNY
    -
    -
    -
    -
    -
    - -

    -WILLIAMSON

    -
    -public static final ConservationMethod WILLIAMSON
    -
    -
    -
    -
    -
    - -

    -LANDGRAF

    -
    -public static final ConservationMethod LANDGRAF
    -
    -
    -
    -
    -
    - -

    -SANDER

    -
    -public static final ConservationMethod SANDER
    -
    -
    -
    -
    -
    - -

    -VALDAR

    -
    -public static final ConservationMethod VALDAR
    -
    -
    -
    -
    -
    - -

    -SMERFS

    -
    -public static final ConservationMethod SMERFS
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static ConservationMethod[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (ConservationMethod c : ConservationMethod.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static ConservationMethod valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    -
    - -

    -getMethod

    -
    -public static ConservationMethod getMethod(String meth)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/DisorderMethod.html b/website/full_javadoc/compbio/data/sequence/DisorderMethod.html deleted file mode 100644 index 071fed3..0000000 --- a/website/full_javadoc/compbio/data/sequence/DisorderMethod.html +++ /dev/null @@ -1,322 +0,0 @@ - - - - - - -DisorderMethod - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.data.sequence -
    -Enum DisorderMethod

    -
    -java.lang.Object
-  extended by java.lang.Enum<DisorderMethod>
-      extended by compbio.data.sequence.DisorderMethod
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<DisorderMethod>
    -
    -
    -
    -
    public enum DisorderMethod
    extends Enum<DisorderMethod>
    - - -

    -

    - -

    - - - - - - - - - - - - - -
    -Enum Constant Summary
    Disembl - -
    -           
    JRonn - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static DisorderMethodvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static DisorderMethod[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -JRonn

    -
    -public static final DisorderMethod JRonn
    -
    -
    -
    -
    -
    - -

    -Disembl

    -
    -public static final DisorderMethod Disembl
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static DisorderMethod[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (DisorderMethod c : DisorderMethod.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static DisorderMethod valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/FastaReader.html b/website/full_javadoc/compbio/data/sequence/FastaReader.html deleted file mode 100644 index f707652..0000000 --- a/website/full_javadoc/compbio/data/sequence/FastaReader.html +++ /dev/null @@ -1,415 +0,0 @@ - - - - - - -FastaReader - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class FastaReader

    -
    -java.lang.Object
-  extended by compbio.data.sequence.FastaReader
-
    -
    -
    All Implemented Interfaces:
    Iterator<FastaSequence>
    -
    -
    -
    -
    public class FastaReader
    extends Object
    implements Iterator<FastaSequence>
    - - -

    -Reads files with FASTA formatted sequences. All the information in the FASTA - header is preserved including trailing white spaces. All the white spaces are - removed from the sequence. - - Examples of the correct input: - - 

    - 
- >zedpshvyzg
- GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
- 
- >xovkactesa
- CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
- FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
- FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
- DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
- 
- >ntazzewyvv
- CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
- EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      
- EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW 
-   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    
-   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   
-   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
- 
-    > 12 d t y wi               k       jbke    
-   KLSHHDCD
-    N
-     H
-     HSKCTEPHCGNSHQMLHRDP
-     CCDQCQSWEAENWCASMRKAILF
- 
-
    -

    - -

    -

    -
    Version:
    -
    1.0 April 2011
    -
    Author:
    -
    Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    FastaReader(InputStream inputStream) - -
    -          This class will not close the incoming stream! So the client should do - so.
    FastaReader(String inputFile) - -
    -          Header data can contain non-ASCII symbols and read in UTF8
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - voidclose() - -
    -          Call this method to close the connection to the input file if you want to - free up the resources.
    - booleanhasNext() - -
    -          
    - FastaSequencenext() - -
    -          Reads the next FastaSequence from the input
    - voidremove() - -
    -          Not implemented
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -FastaReader

    -
    -public FastaReader(String inputFile)
-            throws FileNotFoundException
    -
    -
    Header data can contain non-ASCII symbols and read in UTF8 -

    -

    -
    Parameters:
    inputFile - the file containing the list of FASTA formatted sequences to - read from -
    Throws: -
    FileNotFoundException - if the input file is not found -
    IllegalStateException - if the close method was called on this instance
    -
    -
    - -

    -FastaReader

    -
    -public FastaReader(InputStream inputStream)
-            throws FileNotFoundException
    -
    -
    This class will not close the incoming stream! So the client should do - so. -

    -

    -
    Parameters:
    inputStream - -
    Throws: -
    FileNotFoundException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -hasNext

    -
    -public boolean hasNext()
    -
    -
    -

    -

    -
    Specified by:
    hasNext in interface Iterator<FastaSequence>
    -
    -
    - -
    Throws: -
    IllegalStateException - if the close method was called on this instance
    -
    -
    -
    - -

    -next

    -
    -public FastaSequence next()
    -
    -
    Reads the next FastaSequence from the input -

    -

    -
    Specified by:
    next in interface Iterator<FastaSequence>
    -
    -
    - -
    Throws: -
    AssertionError - if the header or the sequence is missing -
    IllegalStateException - if the close method was called on this instance
    -
    -
    -
    - -

    -remove

    -
    -public void remove()
    -
    -
    Not implemented -

    -

    -
    Specified by:
    remove in interface Iterator<FastaSequence>
    -
    -
    -
    -
    -
    -
    - -

    -close

    -
    -public void close()
    -
    -
    Call this method to close the connection to the input file if you want to - free up the resources. The connection will be closed on the JVM shutdown - if this method was not called explicitly. No further reading on this - instance of the FastaReader will be possible after calling this method. -

    -

    -
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index fc16c25..0000000 --- a/website/full_javadoc/compbio/data/sequence/FastaSequence.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -FastaSequence - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class FastaSequence

    -
    -java.lang.Object
-  extended by compbio.data.sequence.FastaSequence
-
    -
    -
    -
    @Immutable
-public class FastaSequence
    extends Object
    - - -

    -A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it stores e.g. it could be nucleotide, - protein or even gapped alignment sequence! The only guarantee it makes is - that the sequence does not contain white space characters e.g. spaces, new - lines etc -

    - -

    -

    -
    Version:
    -
    1.0 September 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    FastaSequence(String id, - String sequence) - -
    -          Upon construction the any whitespace characters are removed from the - sequence
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static intcountMatchesInSequence(String theString, - String theRegExp) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - StringgetFormatedSequence(int width) - -
    -          Format sequence per width letter in one string.
    - StringgetFormattedFasta() - -
    -           
    - StringgetId() - -
    -          Gets the value of id
    - intgetLength() - -
    -           
    - StringgetOnelineFasta() - -
    -           
    - StringgetSequence() - -
    -          Gets the value of sequence
    - inthashCode() - -
    -           
    - StringtoString() - -
    -          Same as oneLineFasta
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -FastaSequence

    -
    -public FastaSequence(String id,
-                     String sequence)
    -
    -
    Upon construction the any whitespace characters are removed from the - sequence -

    -

    -
    Parameters:
    id -
    sequence -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getId

    -
    -public String getId()
    -
    -
    Gets the value of id -

    -

    - -
    Returns:
    the value of id
    -
    -
    -
    - -

    -getSequence

    -
    -public String getSequence()
    -
    -
    Gets the value of sequence -

    -

    - -
    Returns:
    the value of sequence
    -
    -
    -
    - -

    -countMatchesInSequence

    -
    -public static int countMatchesInSequence(String theString,
-                                         String theRegExp)
    -
    -
    -
    -
    -
    -
    - -

    -getFormattedFasta

    -
    -public String getFormattedFasta()
    -
    -
    -
    -
    -
    -
    - -

    -getOnelineFasta

    -
    -public String getOnelineFasta()
    -
    -
    - -
    Returns:
    one line name, next line sequence, no matter what the sequence - length is
    -
    -
    -
    - -

    -getFormatedSequence

    -
    -public String getFormatedSequence(int width)
    -
    -
    Format sequence per width letter in one string. Without spaces. -

    -

    - -
    Returns:
    multiple line formated sequence, one line width letters length
    -
    -
    -
    - -

    -getLength

    -
    -public int getLength()
    -
    -
    - -
    Returns:
    sequence length
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    Same as oneLineFasta -

    -

    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/Program.html b/website/full_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index 930fb6b..0000000 --- a/website/full_javadoc/compbio/data/sequence/Program.html +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - -Program - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Enum Program

    -
    -java.lang.Object
-  extended by java.lang.Enum<Program>
-      extended by compbio.data.sequence.Program
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<Program>
    -
    -
    -
    -
    public enum Program
    extends Enum<Program>
    - - -

    -The list of programmes that can produce alignments -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    CLUSTAL - -
    -          ClustalW
    MAFFT - -
    -          Mafft
    MUSCLE - -
    -          Muscle
    Probcons - -
    -          Probcons
    Tcoffee - -
    -          Tcoffee
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static ProgramvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Program[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -CLUSTAL

    -
    -public static final Program CLUSTAL
    -
    -
    ClustalW -

    -

    -
    -
    -
    - -

    -MAFFT

    -
    -public static final Program MAFFT
    -
    -
    Mafft -

    -

    -
    -
    -
    - -

    -MUSCLE

    -
    -public static final Program MUSCLE
    -
    -
    Muscle -

    -

    -
    -
    -
    - -

    -Tcoffee

    -
    -public static final Program Tcoffee
    -
    -
    Tcoffee -

    -

    -
    -
    -
    - -

    -Probcons

    -
    -public static final Program Probcons
    -
    -
    Probcons -

    -

    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Program[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (Program c : Program.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static Program valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/Range.html b/website/full_javadoc/compbio/data/sequence/Range.html deleted file mode 100644 index 9ab4cde..0000000 --- a/website/full_javadoc/compbio/data/sequence/Range.html +++ /dev/null @@ -1,394 +0,0 @@ - - - - - - -Range - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class Range

    -
    -java.lang.Object
-  extended by compbio.data.sequence.Range
-
    -
    -
    All Implemented Interfaces:
    Comparable<Range>
    -
    -
    -
    -
    public class Range
    extends Object
    implements Comparable<Range>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    - intfrom - -
    -           
    - intto - -
    -           
    -  - - - - - - - - - - - - - -
    -Constructor Summary
    Range(int from, - int to) - -
    -           
    Range(String[] twoElementAr) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intcompareTo(Range o) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - inthashCode() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -from

    -
    -public final int from
    -
    -
    -
    -
    -
    - -

    -to

    -
    -public final int to
    -
    -
    -
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Range

    -
    -public Range(int from,
-             int to)
    -
    -
    -
    - -

    -Range

    -
    -public Range(String[] twoElementAr)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -compareTo

    -
    -public int compareTo(Range o)
    -
    -
    -
    Specified by:
    compareTo in interface Comparable<Range>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html deleted file mode 100644 index 4cdc043..0000000 --- a/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html +++ /dev/null @@ -1,429 +0,0 @@ - - - - - - -SMERFSConstraints - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Enum SMERFSConstraints

    -
    -java.lang.Object
-  extended by java.lang.Enum<SMERFSConstraints>
-      extended by compbio.data.sequence.SMERFSConstraints
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<SMERFSConstraints>
    -
    -
    -
    -
    public enum SMERFSConstraints
    extends Enum<SMERFSConstraints>
    - - -

    -Enumeration defining two constraints for SMERFS columns score calculation. - MAX_SCORE gives the highest core of all the windows the column belongs to. - MID_SCORE gives the window score to the column in the middle. -

    - -

    -

    -
    Author:
    -
    Agnieszka Golicz & Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - - - -
    -Enum Constant Summary
    MAX_SCORE - -
    -           
    MID_SCORE - -
    -           
    -  - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static SMERFSConstraintsDEFAULT_COLUMN_SCORE - -
    -          Default column scoring schema
    -static doubleDEFAULT_GAP_THRESHOLD - -
    -          Default gap threshold value for SMERFS algorithm
    -static intDEFAULT_WINDOW_SIZE - -
    -          Default window size value for SMERFS algorithm
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static SMERFSConstraintsgetSMERFSColumnScore(String score) - -
    -           
    -static SMERFSConstraintsvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static SMERFSConstraints[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -MAX_SCORE

    -
    -public static final SMERFSConstraints MAX_SCORE
    -
    -
    -
    -
    -
    - -

    -MID_SCORE

    -
    -public static final SMERFSConstraints MID_SCORE
    -
    -
    -
    -
    - - - - - - - - -
    -Field Detail
    - -

    -DEFAULT_COLUMN_SCORE

    -
    -public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
    -
    -
    Default column scoring schema -

    -

    -
    -
    -
    - -

    -DEFAULT_WINDOW_SIZE

    -
    -public static final int DEFAULT_WINDOW_SIZE
    -
    -
    Default window size value for SMERFS algorithm -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -DEFAULT_GAP_THRESHOLD

    -
    -public static final double DEFAULT_GAP_THRESHOLD
    -
    -
    Default gap threshold value for SMERFS algorithm -

    -

    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static SMERFSConstraints[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (SMERFSConstraints c : SMERFSConstraints.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static SMERFSConstraints valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    -
    - -

    -getSMERFSColumnScore

    -
    -public static SMERFSConstraints getSMERFSColumnScore(String score)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/Score.html b/website/full_javadoc/compbio/data/sequence/Score.html deleted file mode 100644 index 401dafb..0000000 --- a/website/full_javadoc/compbio/data/sequence/Score.html +++ /dev/null @@ -1,537 +0,0 @@ - - - - - - -Score - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class Score

    -
    -java.lang.Object
-  extended by compbio.data.sequence.Score
-
    -
    -
    All Implemented Interfaces:
    Comparable<Score>
    -
    -
    -
    -
    @Immutable
-public class Score
    extends Object
    implements Comparable<Score>
    - - -

    -A value class for AACon annotation results storage. The objects of this type - are immutable -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    Score(Enum<?> method, - ArrayList<Float> scores) - -
    -          Instantiate the Score
    Score(Enum<?> method, - ArrayList<Float> scores, - TreeSet<Range> ranges) - -
    -           
    Score(Enum<?> method, - float[] scores) - -
    -           
    Score(Enum<?> method, - TreeSet<Range> ranges) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intcompareTo(Score o) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - StringgetMethod() - -
    -          Returns the ConservationMethod
    - TreeSet<Range>getRanges() - -
    -          Return Ranges if any Collections.EMPTY_SET otherwise
    - ArrayList<Float>getScores() - -
    -          The column scores for the alignment
    - inthashCode() - -
    -           
    - voidsetRanges(TreeSet<Range> ranges) - -
    -           
    - StringtoString() - -
    -           
    -static voidwrite(TreeSet<Score> scores, - Writer writer) - -
    -          Outputs the List of Score objects into the Output stream.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Score

    -
    -public Score(Enum<?> method,
-             ArrayList<Float> scores)
    -
    -
    Instantiate the Score -

    -

    -
    Parameters:
    method - the ConservationMethod with which scores were - calculated
    scores - the actual conservation values for each column of the - alignment
    -
    -
    - -

    -Score

    -
    -public Score(Enum<?> method,
-             ArrayList<Float> scores,
-             TreeSet<Range> ranges)
    -
    -
    -
    Parameters:
    method - the ConservationMethod with which scores were - calculated
    scores - the actual conservation values for each column of the - alignment
    ranges - The set of ranges i.e. parts of the sequence with specific - function, usually can be calculated based on scores
    -
    -
    - -

    -Score

    -
    -public Score(Enum<?> method,
-             TreeSet<Range> ranges)
    -
    -
    -
    - -

    -Score

    -
    -public Score(Enum<?> method,
-             float[] scores)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getMethod

    -
    -public String getMethod()
    -
    -
    Returns the ConservationMethod -

    -

    -
    -
    -
    - -
    Returns:
    the ConservationMethod
    -
    -
    -
    - -

    -getScores

    -
    -public ArrayList<Float> getScores()
    -
    -
    The column scores for the alignment -

    -

    -
    -
    -
    - -
    Returns:
    the column scores for the alignment
    -
    -
    -
    - -

    -getRanges

    -
    -public TreeSet<Range> getRanges()
    -
    -
    Return Ranges if any Collections.EMPTY_SET otherwise -

    -

    -
    -
    -
    - -
    Returns:
    ordered set of Range
    -
    -
    -
    - -

    -setRanges

    -
    -public void setRanges(TreeSet<Range> ranges)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -write

    -
    -public static void write(TreeSet<Score> scores,
-                         Writer writer)
-                  throws IOException
    -
    -
    Outputs the List of Score objects into the Output stream. The output - format is as follows: - - 
    - #MethodName <space separated list of values>
- 	  
- For example:
- 	 
- #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
- #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
- 
-
    - - The maximum precision for values is 3 digits, but can be less. -

    -

    -
    -
    -
    -
    Parameters:
    scores - the list of scores to output
    writer - -
    Throws: -
    IOException - if the OutputStream cannot be written into -
    NullPointerException - if the output stream is null
    -
    -
    -
    - -

    -compareTo

    -
    -public int compareTo(Score o)
    -
    -
    -
    Specified by:
    compareTo in interface Comparable<Score>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html b/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html deleted file mode 100644 index 343fa02..0000000 --- a/website/full_javadoc/compbio/data/sequence/ScoreManager.ScoreHolder.html +++ /dev/null @@ -1,380 +0,0 @@ - - - - - - -ScoreManager.ScoreHolder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class ScoreManager.ScoreHolder

    -
    -java.lang.Object
-  extended by compbio.data.sequence.ScoreManager.ScoreHolder
-
    -
    -
    Enclosing class:
    ScoreManager
    -
    -
    -
    -
    public static class ScoreManager.ScoreHolder
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    - Stringid - -
    -           
    - TreeSet<Score>scores - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - intgetNumberOfScores() - -
    -           
    - ScoregetScoreByMethod(Enum<?> method) - -
    -           
    - ScoregetScoreByMethod(String method) - -
    -           
    - inthashCode() - -
    -           
    - voidwriteOut(Writer writer) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -id

    -
    -public String id
    -
    -
    -
    -
    -
    - -

    -scores

    -
    -public TreeSet<Score> scores
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -writeOut

    -
    -public void writeOut(Writer writer)
-              throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -getScoreByMethod

    -
    -public Score getScoreByMethod(Enum<?> method)
    -
    -
    -
    -
    -
    -
    - -

    -getScoreByMethod

    -
    -public Score getScoreByMethod(String method)
    -
    -
    -
    -
    -
    -
    - -

    -getNumberOfScores

    -
    -public int getNumberOfScores()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/ScoreManager.html b/website/full_javadoc/compbio/data/sequence/ScoreManager.html deleted file mode 100644 index 82d5c4a..0000000 --- a/website/full_javadoc/compbio/data/sequence/ScoreManager.html +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - -ScoreManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class ScoreManager

    -
    -java.lang.Object
-  extended by compbio.data.sequence.ScoreManager
-
    -
    -
    -
    public class ScoreManager
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classScoreManager.ScoreHolder - -
    -           
    -  - - - - - - - - - - -
    -Field Summary
    -static StringSINGLE_ENTRY_KEY - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Map<String,TreeSet<Score>>asMap() - -
    -           
    - Set<Score>asSet() - -
    -           
    - booleanequals(Object obj) - -
    -           
    - ScoreManager.ScoreHoldergetAnnotationForSequence(String seqId) - -
    -           
    - intgetNumberOfSeq() - -
    -           
    - inthashCode() - -
    -           
    -static ScoreManagernewInstance(Map<String,Set<Score>> data) - -
    -           
    -static ScoreManagernewInstanceSingleScore(Map<String,Score> seqScoresMap) - -
    -           
    -static ScoreManagernewInstanceSingleSequence(Set<Score> data) - -
    -           
    - voidwriteOut(Writer outStream) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -SINGLE_ENTRY_KEY

    -
    -public static final String SINGLE_ENTRY_KEY
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Method Detail
    - -

    -newInstance

    -
    -public static ScoreManager newInstance(Map<String,Set<Score>> data)
    -
    -
    -
    -
    -
    -
    - -

    -newInstanceSingleScore

    -
    -public static ScoreManager newInstanceSingleScore(Map<String,Score> seqScoresMap)
    -
    -
    -
    -
    -
    -
    - -

    -newInstanceSingleSequence

    -
    -public static ScoreManager newInstanceSingleSequence(Set<Score> data)
    -
    -
    -
    -
    -
    -
    - -

    -asMap

    -
    -public Map<String,TreeSet<Score>> asMap()
    -
    -
    -
    -
    -
    -
    - -

    -asSet

    -
    -public Set<Score> asSet()
    -
    -
    -
    -
    -
    -
    - -

    -getNumberOfSeq

    -
    -public int getNumberOfSeq()
    -
    -
    -
    -
    -
    -
    - -

    -getAnnotationForSequence

    -
    -public ScoreManager.ScoreHolder getAnnotationForSequence(String seqId)
    -
    -
    -
    -
    -
    -
    - -

    -writeOut

    -
    -public void writeOut(Writer outStream)
-              throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index 77c2f5a..0000000 --- a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,946 +0,0 @@ - - - - - - -SequenceUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class SequenceUtil

    -
    -java.lang.Object
-  extended by compbio.data.sequence.SequenceUtil
-
    -
    -
    -
    public final class SequenceUtil
    extends Object
    - - -

    -Utility class for operations on sequences -

    - -

    -

    -
    Since:
    -
    1.0
    -
    Version:
    -
    2.0 June 2011
    -
    Author:
    -
    Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static PatternAA - -
    -          Valid Amino acids
    -static PatternAMBIGUOUS_AA - -
    -          Same as AA pattern but with two additional letters - XU
    -static PatternAMBIGUOUS_NUCLEOTIDE - -
    -          Ambiguous nucleotide
    -static PatternDIGIT - -
    -          A digit
    -static PatternNON_AA - -
    -          inversion of AA pattern
    -static PatternNON_NUCLEOTIDE - -
    -          Non nucleotide
    -static PatternNONWORD - -
    -          Non word
    -static PatternNUCLEOTIDE - -
    -          Nucleotides a, t, g, c, u
    -static PatternWHITE_SPACE - -
    -          A whitespace character: [\t\n\x0B\f\r]
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static StringcleanProteinSequence(String sequence) - -
    -          Remove all non AA chars from the sequence
    -static StringcleanSequence(String sequence) - -
    -          Removes all whitespace chars in the sequence string
    -static voidcloseSilently(Logger log, - Closeable stream) - -
    -          Closes the Closable and logs the exception if any
    -static StringdeepCleanSequence(String sequence) - -
    -          Removes all special characters and digits as well as whitespace chars - from the sequence
    -static booleanisAmbiguosProtein(String sequence) - -
    -          Check whether the sequence confirms to amboguous protein sequence
    -static booleanisNonAmbNucleotideSequence(String sequence) - -
    -          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
    -static booleanisNucleotideSequence(FastaSequence s) - -
    -           
    -static booleanisProteinSequence(String sequence) - -
    -           
    -static List<FastaSequence>openInputStream(String inFilePath) - -
    -          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
    -static HashSet<Score>readAAConResults(InputStream results) - -
    -          Read AACon result with no alignment files.
    -static HashMap<String,Set<Score>>readDisembl(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static List<FastaSequence>readFasta(InputStream inStream) - -
    -          Reads fasta sequences from inStream into the list of FastaSequence - objects
    -static HashMap<String,Set<Score>>readGlobPlot(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static Map<String,Score>readIUPred(File result) - -
    -          Read IUPred output
    -static Map<String,Score>readJRonn(File result) - -
    -           
    -static Map<String,Score>readJRonn(InputStream inStream) - -
    -          Reader for JRonn horizontal file format
    -static voidwriteFasta(OutputStream os, - List<FastaSequence> sequences) - -
    -          Writes FastaSequence in the file, each sequence will take one line only
    -static voidwriteFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
    -          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
    -static voidwriteFastaKeepTheStream(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -WHITE_SPACE

    -
    -public static final Pattern WHITE_SPACE
    -
    -
    A whitespace character: [\t\n\x0B\f\r] -

    -

    -
    -
    -
    - -

    -DIGIT

    -
    -public static final Pattern DIGIT
    -
    -
    A digit -

    -

    -
    -
    -
    - -

    -NONWORD

    -
    -public static final Pattern NONWORD
    -
    -
    Non word -

    -

    -
    -
    -
    - -

    -AA

    -
    -public static final Pattern AA
    -
    -
    Valid Amino acids -

    -

    -
    -
    -
    - -

    -NON_AA

    -
    -public static final Pattern NON_AA
    -
    -
    inversion of AA pattern -

    -

    -
    -
    -
    - -

    -AMBIGUOUS_AA

    -
    -public static final Pattern AMBIGUOUS_AA
    -
    -
    Same as AA pattern but with two additional letters - XU -

    -

    -
    -
    -
    - -

    -NUCLEOTIDE

    -
    -public static final Pattern NUCLEOTIDE
    -
    -
    Nucleotides a, t, g, c, u -

    -

    -
    -
    -
    - -

    -AMBIGUOUS_NUCLEOTIDE

    -
    -public static final Pattern AMBIGUOUS_NUCLEOTIDE
    -
    -
    Ambiguous nucleotide -

    -

    -
    -
    -
    - -

    -NON_NUCLEOTIDE

    -
    -public static final Pattern NON_NUCLEOTIDE
    -
    -
    Non nucleotide -

    -

    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -isNucleotideSequence

    -
    -public static boolean isNucleotideSequence(FastaSequence s)
    -
    -
    - -
    Returns:
    true is the sequence contains only letters a,c, t, g, u
    -
    -
    -
    - -

    -isNonAmbNucleotideSequence

    -
    -public static boolean isNonAmbNucleotideSequence(String sequence)
    -
    -
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -

    -

    -
    -
    -
    -
    - -

    -cleanSequence

    -
    -public static String cleanSequence(String sequence)
    -
    -
    Removes all whitespace chars in the sequence string -

    -

    -
    Parameters:
    sequence - -
    Returns:
    cleaned up sequence
    -
    -
    -
    - -

    -deepCleanSequence

    -
    -public static String deepCleanSequence(String sequence)
    -
    -
    Removes all special characters and digits as well as whitespace chars - from the sequence -

    -

    -
    Parameters:
    sequence - -
    Returns:
    cleaned up sequence
    -
    -
    -
    - -

    -cleanProteinSequence

    -
    -public static String cleanProteinSequence(String sequence)
    -
    -
    Remove all non AA chars from the sequence -

    -

    -
    Parameters:
    sequence - the sequence to clean -
    Returns:
    cleaned sequence
    -
    -
    -
    - -

    -isProteinSequence

    -
    -public static boolean isProteinSequence(String sequence)
    -
    -
    -
    Parameters:
    sequence - -
    Returns:
    true is the sequence is a protein sequence, false overwise
    -
    -
    -
    - -

    -isAmbiguosProtein

    -
    -public static boolean isAmbiguosProtein(String sequence)
    -
    -
    Check whether the sequence confirms to amboguous protein sequence -

    -

    -
    Parameters:
    sequence - -
    Returns:
    return true only if the sequence if ambiguous protein sequence - Return false otherwise. e.g. if the sequence is non-ambiguous - protein or DNA
    -
    -
    -
    - -

    -writeFasta

    -
    -public static void writeFasta(OutputStream outstream,
-                              List<FastaSequence> sequences,
-                              int width)
-                       throws IOException
    -
    -
    Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -

    -

    -
    Parameters:
    outstream -
    sequences -
    width - - the maximum number of characters to write in one line -
    Throws: -
    IOException
    -
    -
    -
    - -

    -writeFastaKeepTheStream

    -
    -public static void writeFastaKeepTheStream(OutputStream outstream,
-                                           List<FastaSequence> sequences,
-                                           int width)
-                                    throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -readFasta

    -
    -public static List<FastaSequence> readFasta(InputStream inStream)
-                                     throws IOException
    -
    -
    Reads fasta sequences from inStream into the list of FastaSequence - objects -

    -

    -
    Parameters:
    inStream - from -
    Returns:
    list of FastaSequence objects -
    Throws: -
    IOException
    -
    -
    -
    - -

    -writeFasta

    -
    -public static void writeFasta(OutputStream os,
-                              List<FastaSequence> sequences)
-                       throws IOException
    -
    -
    Writes FastaSequence in the file, each sequence will take one line only -

    -

    -
    Parameters:
    os -
    sequences - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -readIUPred

    -
    -public static Map<String,Score> readIUPred(File result)
-                                    throws IOException,
-                                           UnknownFileFormatException
    -
    -
    Read IUPred output -

    -

    -
    Parameters:
    result - -
    Returns:
    Map key->sequence name, value->Score -
    Throws: -
    IOException -
    UnknownFileFormatException
    -
    -
    -
    - -

    -readJRonn

    -
    -public static Map<String,Score> readJRonn(File result)
-                                   throws IOException,
-                                          UnknownFileFormatException
    -
    -
    - -
    Throws: -
    IOException -
    UnknownFileFormatException
    -
    -
    -
    - -

    -readJRonn

    -
    -public static Map<String,Score> readJRonn(InputStream inStream)
-                                   throws IOException,
-                                          UnknownFileFormatException
    -
    -
    Reader for JRonn horizontal file format - - 
    - >Foobar M G D T T A G 0.48 0.42
- 0.42 0.48 0.52 0.53 0.54
- 
- 
    - Where all values are tab delimited
-
    
-
    
-
    Parameters:
    inStream - the InputStream connected to the JRonn output file
-
    Returns:
    Map key=sequence name value=Score
-
    Throws:
-
    IOException - is thrown if the inStream has problems accessing the data
-
    UnknownFileFormatException - is thrown if the inStream represents an unknown source of
- data, i.e. not a JRonn output
    
-
    
-
    -
    - -

    -closeSilently

    -
    -public static final void closeSilently(Logger log,
-                                       Closeable stream)
    -
    -
    Closes the Closable and logs the exception if any -

    -

    -
    Parameters:
    log -
    stream -
    -
    -
    -
    - -

    -readDisembl

    -
    -public static HashMap<String,Set<Score>> readDisembl(InputStream input)
-                                              throws IOException,
-                                                     UnknownFileFormatException
    -
    -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

    -

    -
    Parameters:
    input - the InputStream -
    Returns:
    Map key=sequence name, value=set of score -
    Throws: -
    IOException -
    UnknownFileFormatException
    -
    -
    -
    - -

    -readGlobPlot

    -
    -public static HashMap<String,Set<Score>> readGlobPlot(InputStream input)
-                                               throws IOException,
-                                                      UnknownFileFormatException
    -
    -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -

    -

    -
    Parameters:
    input - -
    Returns:
    Map key=sequence name, value=set of score -
    Throws: -
    IOException -
    UnknownFileFormatException
    -
    -
    -
    - -

    -readAAConResults

    -
    -public static HashSet<Score> readAAConResults(InputStream results)
    -
    -
    Read AACon result with no alignment files. This method leaves incoming - InputStream open! -

    -

    -
    Parameters:
    results - output file of AAConservation -
    Returns:
    Map with keys ConservationMethod -> float[]
    -
    -
    -
    - -

    -openInputStream

    -
    -public static List<FastaSequence> openInputStream(String inFilePath)
-                                           throws IOException,
-                                                  UnknownFileFormatException
    -
    -
    Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -

    -

    -
    Parameters:
    inFilePath - the path to the input file -
    Returns:
    the List of FastaSequence objects -
    Throws: -
    IOException - if the file denoted by inFilePath cannot be read -
    UnknownFileFormatException - if the inFilePath points to the file which format cannot be - recognised
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html deleted file mode 100644 index d67f4ef..0000000 --- a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - -UnknownFileFormatException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.data.sequence -
    -Class UnknownFileFormatException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.data.sequence.UnknownFileFormatException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class UnknownFileFormatException
    extends Exception
    - - -

    -

    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    UnknownFileFormatException() - -
    -           
    UnknownFileFormatException(File file, - Throwable cause) - -
    -           
    UnknownFileFormatException(String message) - -
    -           
    UnknownFileFormatException(String message, - Throwable cause) - -
    -           
    UnknownFileFormatException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -UnknownFileFormatException

    -
    -public UnknownFileFormatException()
    -
    -
    -
    - -

    -UnknownFileFormatException

    -
    -public UnknownFileFormatException(File file,
-                                  Throwable cause)
    -
    -
    -
    - -

    -UnknownFileFormatException

    -
    -public UnknownFileFormatException(String message,
-                                  Throwable cause)
    -
    -
    -
    - -

    -UnknownFileFormatException

    -
    -public UnknownFileFormatException(String message)
    -
    -
    -
    - -

    -UnknownFileFormatException

    -
    -public UnknownFileFormatException(Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index 9b8e8eb..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,457 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.data.sequence.Alignment

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Alignment
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Alignment in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return Alignment
    - AlignmentMsaWS.getResult(String jobId) - -
    -          Return the result of the job.
    -  -

    - - - - - -
    -Uses of Alignment in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Alignment
    - AlignmentGetResultResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Alignment
    - voidGetResultResponse.setReturn(Alignment _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Alignment in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return Alignment
    -static AlignmentClustalAlignmentUtil.readClustalFile(File file) - -
    -           
    -static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) - -
    -          Read Clustal formatted alignment.
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence with parameters of type Alignment
    -static voidClustalAlignmentUtil.writeClustalAlignment(Writer out, - Alignment alignment) - -
    -          Write Clustal formatted alignment Limitations: does not record the - consensus.
    -  -

    - - - - - -
    -Uses of Alignment in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return Alignment
    -static AlignmentUtil.readClustalFile(String workDirectory, - String clustFile) - -
    -           
    -  -

    - - - - - -
    -Uses of Alignment in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Alignment
    - AlignmentMafft.getResults(String workDirectory) - -
    -           
    - AlignmentClustalW.getResults(String workDirectory) - -
    -           
    - AlignmentTcoffee.getResults(String workDirectory) - -
    -           
    - AlignmentMuscle.getResults(String workDirectory) - -
    -           
    - AlignmentClustalO.getResults(String workDirectory) - -
    -           
    - AlignmentProbcons.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of Alignment in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return Alignment
    - AlignmentClustalWS.getResult(String jobId) - -
    -           
    - Alignment_MsaService.getResult(String jobId) - -
    -           
    - AlignmentMuscleWS.getResult(String jobId) - -
    -           
    - AlignmentMafftWS.getResult(String jobId) - -
    -           
    - AlignmentTcoffeeWS.getResult(String jobId) - -
    -           
    - AlignmentProbconsWS.getResult(String jobId) - -
    -           
    - AlignmentClustalOWS.getResult(String jobId) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html deleted file mode 100644 index fd8cf85..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.AlignmentMetadata - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.data.sequence.AlignmentMetadata

    -
    - - - - - - - - - -
    -Packages that use AlignmentMetadata
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of AlignmentMetadata in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence that return AlignmentMetadata
    - AlignmentMetadataAlignment.getMetadata() - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
    Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html deleted file mode 100644 index 44db775..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ClustalAlignmentUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.data.sequence.ClustalAlignmentUtil

    -
    -No usage of compbio.data.sequence.ClustalAlignmentUtil -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html b/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html deleted file mode 100644 index 8e43edc..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/ConservationMethod.html +++ /dev/null @@ -1,198 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ConservationMethod - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.data.sequence.ConservationMethod

    -
    - - - - - - - - - -
    -Packages that use ConservationMethod
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of ConservationMethod in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return ConservationMethod
    -static ConservationMethodConservationMethod.getMethod(String meth) - -
    -           
    -static ConservationMethodConservationMethod.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ConservationMethod[]ConservationMethod.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/DisorderMethod.html b/website/full_javadoc/compbio/data/sequence/class-use/DisorderMethod.html deleted file mode 100644 index 8ebff65..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/DisorderMethod.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.DisorderMethod - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    -

    -Uses of Class
    compbio.data.sequence.DisorderMethod

    -
    - - - - - - - - - -
    -Packages that use DisorderMethod
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of DisorderMethod in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return DisorderMethod
    -static DisorderMethodDisorderMethod.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static DisorderMethod[]DisorderMethod.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html deleted file mode 100644 index 0c9d36b..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/FastaReader.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaReader - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.data.sequence.FastaReader

    -
    -No usage of compbio.data.sequence.FastaReader -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html deleted file mode 100644 index 2ec79c0..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html +++ /dev/null @@ -1,985 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaSequence - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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    -
    -

    -Uses of Class
    compbio.data.sequence.FastaSequence

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use FastaSequence
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.engine  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.pipeline._jpred  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa with type arguments of type FastaSequence
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
    - List<FastaSequence>PresetAnalize.getFastaSequences() - -
    -           
    - List<FastaSequence>PresetAlign.getFastaSequences() - -
    -           
    - List<FastaSequence>CustomAnalize.getFastaSequences() - -
    -           
    - List<FastaSequence>CustomAlign.getFastaSequences() - -
    -           
    - List<FastaSequence>Analize.getFastaSequences() - -
    -           
    - List<FastaSequence>Align.getFastaSequences() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
    - voidPresetAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidPresetAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidCustomAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidCustomAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidAnalize.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    - voidAlign.setFastaSequences(List<FastaSequence> fastaSequences) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence that return FastaSequence
    - FastaSequenceFastaReader.next() - -
    -          Reads the next FastaSequence from the input
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return types with arguments of type FastaSequence
    - List<FastaSequence>Alignment.getSequences() - -
    -           
    -static List<FastaSequence>SequenceUtil.openInputStream(String inFilePath) - -
    -          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
    -static List<FastaSequence>SequenceUtil.readFasta(InputStream inStream) - -
    -          Reads fasta sequences from inStream into the list of FastaSequence - objects
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence with parameters of type FastaSequence
    -static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.data.sequence with type arguments of type FastaSequence
    -static voidSequenceUtil.writeFasta(OutputStream os, - List<FastaSequence> sequences) - -
    -          Writes FastaSequence in the file, each sequence will take one line only
    -static voidSequenceUtil.writeFasta(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
    -          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
    -static voidSequenceUtil.writeFastaKeepTheStream(OutputStream outstream, - List<FastaSequence> sequences, - int width) - -
    -           
    -  -

    - - - - - - - - - - - -
    Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
    Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
    -           
    Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.engine with type arguments of type FastaSequence
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    -static - - - - -
    -<T,V> Executable.ExecProvider
    -    		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type FastaSequence
    -static intLimit.getAvgSequenceLength(List<FastaSequence> data) - -
    -          Calculates an average sequence length of the dataset
    - booleanLimit.isExceeded(List<FastaSequence> data) - -
    -          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.pipeline._jpred
    -  -

    - - - - - - - - -
    Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence
    Pairwise(List<FastaSequence> sequences) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.runner
    -  -

    - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type FastaSequence
    -static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  -

    - - - - - -
    -Uses of FastaSequence in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type FastaSequence
    - StringClustalWS.align(List<FastaSequence> sequences) - -
    -           
    - String_MsaService.align(List<FastaSequence> sequences) - -
    -           
    - StringMuscleWS.align(List<FastaSequence> sequences) - -
    -           
    - StringMafftWS.align(List<FastaSequence> sequences) - -
    -           
    - StringTcoffeeWS.align(List<FastaSequence> sequences) - -
    -           
    - StringProbconsWS.align(List<FastaSequence> sequences) - -
    -           
    - StringClustalOWS.align(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -static voidWSUtil.validateAAConInput(List<FastaSequence> sequences) - -
    -           
    -static voidWSUtil.validateFastaInput(List<FastaSequence> sequences) - -
    -           
    -  -

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    -Uses of Class
    compbio.data.sequence.Program

    -
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    -Packages that use Program
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of Program in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return Program
    - ProgramAlignmentMetadata.getProgram() - -
    -           
    -static ProgramProgram.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Program[]Program.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - - - -
    Constructors in compbio.data.sequence with parameters of type Program
    Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
    -           
    AlignmentMetadata(Program program, - char gapchar) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Range.html b/website/full_javadoc/compbio/data/sequence/class-use/Range.html deleted file mode 100644 index 98d1179..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Range.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Range - - - - - - - - - - - - -
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    -Uses of Class
    compbio.data.sequence.Range

    -
    - - - - - - - - - -
    -Packages that use Range
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of Range in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence that return types with arguments of type Range
    - TreeSet<Range>Score.getRanges() - -
    -          Return Ranges if any Collections.EMPTY_SET otherwise
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence with parameters of type Range
    - intRange.compareTo(Range o) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.data.sequence with type arguments of type Range
    - voidScore.setRanges(TreeSet<Range> ranges) - -
    -           
    -  -

    - - - - - - - - - - - -
    Constructor parameters in compbio.data.sequence with type arguments of type Range
    Score(Enum<?> method, - ArrayList<Float> scores, - TreeSet<Range> ranges) - -
    -           
    Score(Enum<?> method, - TreeSet<Range> ranges) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.data.sequence.SMERFSConstraints

    -
    - - - - - - - - - -
    -Packages that use SMERFSConstraints
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of SMERFSConstraints in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Fields in compbio.data.sequence declared as SMERFSConstraints
    -static SMERFSConstraintsSMERFSConstraints.DEFAULT_COLUMN_SCORE - -
    -          Default column scoring schema
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return SMERFSConstraints
    -static SMERFSConstraintsSMERFSConstraints.getSMERFSColumnScore(String score) - -
    -           
    -static SMERFSConstraintsSMERFSConstraints.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static SMERFSConstraints[]SMERFSConstraints.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Score.html b/website/full_javadoc/compbio/data/sequence/class-use/Score.html deleted file mode 100644 index f502e84..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Score.html +++ /dev/null @@ -1,392 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Score - - - - - - - - - - - - -
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    -Uses of Class
    compbio.data.sequence.Score

    -
    - - - - - - - - - - - - - -
    -Packages that use Score
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - -
    -Uses of Score in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Fields in compbio.data.sequence with type parameters of type Score
    - TreeSet<Score>ScoreManager.ScoreHolder.scores - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return Score
    - ScoreScoreManager.ScoreHolder.getScoreByMethod(Enum<?> method) - -
    -           
    - ScoreScoreManager.ScoreHolder.getScoreByMethod(String method) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return types with arguments of type Score
    - Map<String,TreeSet<Score>>ScoreManager.asMap() - -
    -           
    - Set<Score>ScoreManager.asSet() - -
    -           
    -static HashSet<Score>SequenceUtil.readAAConResults(InputStream results) - -
    -          Read AACon result with no alignment files.
    -static HashMap<String,Set<Score>>SequenceUtil.readDisembl(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static HashMap<String,Set<Score>>SequenceUtil.readGlobPlot(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static Map<String,Score>SequenceUtil.readIUPred(File result) - -
    -          Read IUPred output
    -static Map<String,Score>SequenceUtil.readJRonn(File result) - -
    -           
    -static Map<String,Score>SequenceUtil.readJRonn(InputStream inStream) - -
    -          Reader for JRonn horizontal file format
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence with parameters of type Score
    - intScore.compareTo(Score o) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.data.sequence with type arguments of type Score
    -static ScoreManagerScoreManager.newInstance(Map<String,Set<Score>> data) - -
    -           
    -static ScoreManagerScoreManager.newInstanceSingleScore(Map<String,Score> seqScoresMap) - -
    -           
    -static ScoreManagerScoreManager.newInstanceSingleSequence(Set<Score> data) - -
    -           
    -static voidScore.write(TreeSet<Score> scores, - Writer writer) - -
    -          Outputs the List of Score objects into the Output stream.
    -  -

    - - - - - -
    -Uses of Score in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Score
    -static Map<String,Score>Util.readJronnFile(String workDirectory, - String clustFile) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.data.sequence.ScoreManager.ScoreHolder

    -
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    -Packages that use ScoreManager.ScoreHolder
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    -  -

    - - - - - -
    -Uses of ScoreManager.ScoreHolder in compbio.data.sequence
    -  -

    - - - - - - - - - -
    Methods in compbio.data.sequence that return ScoreManager.ScoreHolder
    - ScoreManager.ScoreHolderScoreManager.getAnnotationForSequence(String seqId) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.data.sequence.ScoreManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ScoreManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return ScoreManager
    - ScoreManagerSequenceAnnotation.getAnnotation(String jobId) - -
    -          Return the result of the job.
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return ScoreManager
    - ScoreManagerGetAnnotationResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type ScoreManager
    - voidGetAnnotationResponse.setReturn(ScoreManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that return ScoreManager
    -static ScoreManagerScoreManager.newInstance(Map<String,Set<Score>> data) - -
    -           
    -static ScoreManagerScoreManager.newInstanceSingleScore(Map<String,Score> seqScoresMap) - -
    -           
    -static ScoreManagerScoreManager.newInstanceSingleSequence(Set<Score> data) - -
    -           
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.conservation that return ScoreManager
    - ScoreManagerAACon.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return ScoreManager
    - ScoreManagerJronn.getResults(String workDirectory) - -
    -           
    - ScoreManagerIUPred.getResults(String workDirectory) - -
    -           
    - ScoreManagerGlobPlot.getResults(String workDirectory) - -
    -           
    - ScoreManagerDisembl.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ScoreManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return ScoreManager
    - ScoreManagerSequenceAnnotationService.getAnnotation(String jobId) - -
    -           
    -static - - - - -
    -<T> ScoreManager
    -    		WSUtil.getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
    -           
    -  -

    -

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    compbio.data.sequence.UnknownFileFormatException

    -
    - - - - - - - - - - - - - -
    -Packages that use UnknownFileFormatException
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - -
    -Uses of UnknownFileFormatException in compbio.data.sequence
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.sequence that throw UnknownFileFormatException
    -static List<FastaSequence>SequenceUtil.openInputStream(String inFilePath) - -
    -          Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects
    -static AlignmentClustalAlignmentUtil.readClustalFile(File file) - -
    -           
    -static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) - -
    -          Read Clustal formatted alignment.
    -static HashMap<String,Set<Score>>SequenceUtil.readDisembl(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static HashMap<String,Set<Score>>SequenceUtil.readGlobPlot(InputStream input) - -
    -          > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name
    -static Map<String,Score>SequenceUtil.readIUPred(File result) - -
    -          Read IUPred output
    -static Map<String,Score>SequenceUtil.readJRonn(File result) - -
    -           
    -static Map<String,Score>SequenceUtil.readJRonn(InputStream inStream) - -
    -          Reader for JRonn horizontal file format
    -  -

    - - - - - -
    -Uses of UnknownFileFormatException in compbio.runner
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner that throw UnknownFileFormatException
    -static AlignmentUtil.readClustalFile(String workDirectory, - String clustFile) - -
    -           
    -static Map<String,Score>Util.readJronnFile(String workDirectory, - String clustFile) - -
    -           
    -  -

    -

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    -Classes  - -
    -Alignment -
    -AlignmentMetadata -
    -ClustalAlignmentUtil -
    -FastaReader -
    -FastaSequence -
    -Range -
    -Score -
    -ScoreManager -
    -ScoreManager.ScoreHolder -
    -SequenceUtil
    - - - - - - -
    -Enums  - -
    -ConservationMethod -
    -DisorderMethod -
    -Program -
    -SMERFSConstraints
    - - - - - - -
    -Exceptions  - -
    -UnknownFileFormatException
    - - - - diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html deleted file mode 100644 index ec3db70..0000000 --- a/website/full_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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    -

    -Package compbio.data.sequence -

    -A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AlignmentMultiple sequence alignment.
    AlignmentMetadataAlignment metadata e.g.
    ClustalAlignmentUtilTools to read and write clustal formated files
    FastaReaderReads files with FASTA formatted sequences.
    FastaSequenceA FASTA formatted sequence.
    Range 
    ScoreA value class for AACon annotation results storage.
    ScoreManager 
    ScoreManager.ScoreHolder 
    SequenceUtilUtility class for operations on sequences
    -  - -

    - - - - - - - - - - - - - - - - - - - - - -
    -Enum Summary
    ConservationMethodEnumeration listing of all the supported methods.
    DisorderMethod 
    ProgramThe list of programmes that can produce alignments
    SMERFSConstraintsEnumeration defining two constraints for SMERFS columns score calculation.
    -  - -

    - - - - - - - - - -
    -Exception Summary
    UnknownFileFormatException 
    -  - -

    -

    -Package compbio.data.sequence Description -

    - -

    -A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services. -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    Petr Troshin
    -
    -
    - - - - - - - - - - - - - - - -
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    -Hierarchy For Package compbio.data.sequence -

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    Package Hierarchies:
    All Packages
    -
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    -Class Hierarchy -

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    compbio.data.sequence

    -
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    -Packages that use compbio.data.sequence
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. 
    compbio.engine  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.pipeline._jpred  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.data.msa
    Alignment - -
    -          Multiple sequence alignment.
    FastaSequence - -
    -          A FASTA formatted sequence.
    ScoreManager - -
    -           
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.data.msa.jaxws
    Alignment - -
    -          Multiple sequence alignment.
    FastaSequence - -
    -          A FASTA formatted sequence.
    ScoreManager - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.data.sequence
    Alignment - -
    -          Multiple sequence alignment.
    AlignmentMetadata - -
    -          Alignment metadata e.g.
    ConservationMethod - -
    -          Enumeration listing of all the supported methods.
    DisorderMethod - -
    -           
    FastaSequence - -
    -          A FASTA formatted sequence.
    Program - -
    -          The list of programmes that can produce alignments
    Range - -
    -           
    Score - -
    -          A value class for AACon annotation results storage.
    ScoreManager - -
    -           
    ScoreManager.ScoreHolder - -
    -           
    SMERFSConstraints - -
    -          Enumeration defining two constraints for SMERFS columns score calculation.
    UnknownFileFormatException - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.engine
    FastaSequence - -
    -          A FASTA formatted sequence.
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.metadata
    FastaSequence - -
    -          A FASTA formatted sequence.
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.pipeline._jpred
    FastaSequence - -
    -          A FASTA formatted sequence.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.runner
    Alignment - -
    -          Multiple sequence alignment.
    FastaSequence - -
    -          A FASTA formatted sequence.
    Score - -
    -          A value class for AACon annotation results storage.
    UnknownFileFormatException - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.runner.conservation
    ScoreManager - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.runner.disorder
    ScoreManager - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.runner.msa
    Alignment - -
    -          Multiple sequence alignment.
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.data.sequence used by compbio.ws.server
    Alignment - -
    -          Multiple sequence alignment.
    FastaSequence - -
    -          A FASTA formatted sequence.
    ScoreManager - -
    -           
    -  -

    -

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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine -
    -Interface AsyncExecutor

    -
    -
    All Known Implementing Classes:
    AsyncJobRunner, AsyncLocalRunner
    -
    -
    -
    -
    public interface AsyncExecutor
    - - -

    -An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface. - Implementation agnostic. Executables can be run either locally to the JVM or on the cluster. -

    - -

    -

    -
    Author:
    -
    pvtroshin - Date October 2009
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -          Stop running job.
    - booleancleanup(String jobId) - -
    -          Remove all files and a job directory for a jobid.
    - JobStatusgetJobStatus(String jobId) - -
    -          Query the status of the job
    - ConfiguredExecutable<?>getResults(String jobId) - -
    -          Retrieve the results of the job.
    - StringgetWorkDirectory(String jobId) - -
    -           
    - StringsubmitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -submitJob

    -
    -String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
    -
    -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

    -

    - -
    Returns:
    unique job identifier -
    Throws: -
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    -
    -
    -
    - -

    -getResults

    -
    -ConfiguredExecutable<?> getResults(String jobId)
-                                   throws ResultNotAvailableException
    -
    -
    Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

    -

    -
    Parameters:
    jobId - job identifier obtained at the job submission -
    Returns:
    ConfiguredExecutable object from which result can be obtained -
    Throws: -
    ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -String getWorkDirectory(String jobId)
    -
    -
    -
    Parameters:
    jobId - unique job identifier -
    Returns:
    task working directory
    -
    -
    -
    - -

    -cleanup

    -
    -boolean cleanup(String jobId)
    -
    -
    Remove all files and a job directory for a jobid. -

    -

    -
    Parameters:
    jobId - -
    Returns:
    true if job directory was successfully removed, false otherwise.
    -
    -
    -
    - -

    -cancelJob

    -
    -boolean cancelJob(String jobId)
    -
    -
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

    -

    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -JobStatus getJobStatus(String jobId)
    -
    -
    Query the status of the job -

    -

    -
    Parameters:
    String - jobId - unique job identifier -
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    -
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    - -compbio.engine -
    -Class Cleaner

    -
    -java.lang.Object
-  extended by compbio.engine.Cleaner
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class Cleaner
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Cleaner() - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static booleandeleteAllFiles(String directory) - -
    -          Deprecated.  
    -static booleandeleteFiles(ConfiguredExecutable<?> exec) - -
    -          Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Cleaner

    -
    -public Cleaner()
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -deleteFiles

    -
    -public static boolean deleteFiles(ConfiguredExecutable<?> exec)
    -
    -
    Deprecated. 
    This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -

    -

    -
    Parameters:
    workDirectory -
    files - -
    Returns:
    This method returns true if all files specified by List files - were successfully removed, false otherwise
    -
    -
    -
    - -

    -deleteAllFiles

    -
    -public static boolean deleteAllFiles(String directory)
    -
    -
    Deprecated. 
    -
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    - - - diff --git a/website/full_javadoc/compbio/engine/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html deleted file mode 100644 index dd386b7..0000000 --- a/website/full_javadoc/compbio/engine/ClusterJobId.html +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - -ClusterJobId - - - - - - - - - - - - -
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    - -compbio.engine -
    -Class ClusterJobId

    -
    -java.lang.Object
-  extended by compbio.engine.ClusterJobId
-
    -
    -
    -
    @Immutable
-public class ClusterJobId
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ClusterJobId(String jobId) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetJobId() - -
    -           
    - inthashCode() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ClusterJobId

    -
    -public ClusterJobId(String jobId)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
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    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html deleted file mode 100644 index c10f7a1..0000000 --- a/website/full_javadoc/compbio/engine/Configurator.html +++ /dev/null @@ -1,538 +0,0 @@ - - - - - - -Configurator - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine -
    -Class Configurator

    -
    -java.lang.Object
-  extended by compbio.engine.Configurator
-
    -
    -
    -
    public class Configurator
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringCLUSTER_WORK_DIRECTORY - -
    -           
    -static booleanIS_CLUSTER_ENGINE_ENABLED - -
    -           
    -static booleanIS_LOCAL_ENGINE_ENABLED - -
    -           
    -static StringLOCAL_WORK_DIRECTORY - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Configurator() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    -static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static AsyncExecutorgetAsyncEngine(String taskId) - -
    -           
    -static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static StringgetWorkDirectory(String taskId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -IS_LOCAL_ENGINE_ENABLED

    -
    -public static final boolean IS_LOCAL_ENGINE_ENABLED
    -
    -
    -
    -
    -
    - -

    -IS_CLUSTER_ENGINE_ENABLED

    -
    -public static final boolean IS_CLUSTER_ENGINE_ENABLED
    -
    -
    -
    -
    -
    - -

    -LOCAL_WORK_DIRECTORY

    -
    -public static final String LOCAL_WORK_DIRECTORY
    -
    -
    -
    -
    -
    - -

    -CLUSTER_WORK_DIRECTORY

    -
    -public static final String CLUSTER_WORK_DIRECTORY
    -
    -
    -
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Configurator

    -
    -public Configurator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -configureExecutable

    -
    -public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable)
-                                                   throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -configureExecutable

    -
    -public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              List<FastaSequence> dataSet)
-                                                   throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -configureExecutable

    -
    -public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              Executable.ExecProvider provider)
-                                                   throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getAsyncEngine

    -
    -public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable,
-                                           Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getSyncEngine

    -
    -public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable,
-                                         Executable.ExecProvider provider)
-                                  throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getAsyncEngine

    -
    -public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable)
    -
    -
    -
    -
    -
    -
    - -

    -getAsyncEngine

    -
    -public static AsyncExecutor getAsyncEngine(String taskId)
    -
    -
    -
    -
    -
    -
    - -

    -getSyncEngine

    -
    -public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
-                                  throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -public static String getWorkDirectory(String taskId)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/FilePuller.html b/website/full_javadoc/compbio/engine/FilePuller.html deleted file mode 100644 index 8f9d285..0000000 --- a/website/full_javadoc/compbio/engine/FilePuller.html +++ /dev/null @@ -1,551 +0,0 @@ - - - - - - -FilePuller - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine -
    -Class FilePuller

    -
    -java.lang.Object
-  extended by compbio.engine.FilePuller
-
    -
    -
    All Implemented Interfaces:
    Comparable<Delayed>, Delayed
    -
    -
    -
    -
    public class FilePuller
    extends Object
    implements Delayed
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intcompareTo(Delayed o) - -
    -           
    - voiddisconnect() - -
    -           
    - booleanequals(Object obj) - -
    -           
    - longgetDelay(TimeUnit unit) - -
    -           
    - StringgetFile() - -
    -           
    - bytegetProgress() - -
    -           
    - inthashCode() - -
    -           
    - booleanhasMoreData() - -
    -           
    - voidinitPull() - -
    -           
    - booleanisFileCreated() - -
    -           
    -static FilePullernewFilePuller(String file, - int chunkSize) - -
    -           
    -static FilePullernewProgressPuller(String file) - -
    -          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
    - ChunkHolderpull(long position) - -
    -           
    - StringtoString() - -
    -           
    - voidwaitForFile(long maxWaitSeconds) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -newFilePuller

    -
    -public static FilePuller newFilePuller(String file,
-                                       int chunkSize)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -newProgressPuller

    -
    -public static FilePuller newProgressPuller(String file)
    -
    -
    Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. Intended to be used in conjunction with a tool - which output progress as a percent value from 0 to 100. In any cases - progress could not be more than the largest byte value 255. -

    -

    -
    -
    -
    -
    Parameters:
    file - -
    Returns:
    instance
    -
    -
    -
    - -

    -pull

    -
    -public ChunkHolder pull(long position)
-                 throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -initPull

    -
    -public void initPull()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getFile

    -
    -public String getFile()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -isFileCreated

    -
    -public boolean isFileCreated()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -waitForFile

    -
    -public void waitForFile(long maxWaitSeconds)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -hasMoreData

    -
    -public boolean hasMoreData()
-                    throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -compareTo

    -
    -public int compareTo(Delayed o)
    -
    -
    -
    Specified by:
    compareTo in interface Comparable<Delayed>
    -
    -
    -
    -
    -
    -
    - -

    -getDelay

    -
    -public long getDelay(TimeUnit unit)
    -
    -
    -
    Specified by:
    getDelay in interface Delayed
    -
    -
    -
    -
    -
    -
    - -

    -disconnect

    -
    -public void disconnect()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getProgress

    -
    -public byte getProgress()
-                 throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/Job.html b/website/full_javadoc/compbio/engine/Job.html deleted file mode 100644 index 9bd0ee9..0000000 --- a/website/full_javadoc/compbio/engine/Job.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Job - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine -
    -Class Job

    -
    -java.lang.Object
-  extended by compbio.engine.Job
-
    -
    -
    -
    @Immutable
-public final class Job
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Job(String taskId, - String jobId, - ConfiguredExecutable<?> cexecutable) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    -static JobgetByJobId(String jobId, - List<Job> jobs) - -
    -           
    -static JobgetByTaskId(String taskId, - List<Job> jobs) - -
    -           
    - ConfiguredExecutable<?>getConfExecutable() - -
    -           
    - ClusterJobIdgetJobId() - -
    -           
    - StringgetTaskId() - -
    -           
    - inthashCode() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Job

    -
    -public Job(String taskId,
-           String jobId,
-           ConfiguredExecutable<?> cexecutable)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public ClusterJobId getJobId()
    -
    -
    -
    -
    -
    -
    - -

    -getTaskId

    -
    -public String getTaskId()
    -
    -
    -
    -
    -
    -
    - -

    -getConfExecutable

    -
    -public ConfiguredExecutable<?> getConfExecutable()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getByTaskId

    -
    -public static Job getByTaskId(String taskId,
-                              List<Job> jobs)
    -
    -
    -
    -
    -
    -
    - -

    -getByJobId

    -
    -public static Job getByJobId(String jobId,
-                             List<Job> jobs)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/LoadBalancer.html b/website/full_javadoc/compbio/engine/LoadBalancer.html deleted file mode 100644 index 7d7a585..0000000 --- a/website/full_javadoc/compbio/engine/LoadBalancer.html +++ /dev/null @@ -1,259 +0,0 @@ - - - - - - -LoadBalancer - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine -
    -Class LoadBalancer

    -
    -java.lang.Object
-  extended by compbio.engine.LoadBalancer
-
    -
    -
    -
    public class LoadBalancer
    extends Object
    - - -

    -This class decides where to execute the job. If the local engine is enabled - in the configuration file and it has free threads and the size of the tasks - permits the local execution, then the local execution will be favoured. -

    - -

    -

    -
    Version:
    -
    1.0 March 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Method Summary
    -static Executable.ExecProvidergetEngine(Executable<?> executable) - -
    -           
    -static - - - - -
    -<T,V> Executable.ExecProvider
    -    		getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getEngine

    -
    -public static Executable.ExecProvider getEngine(Executable<?> executable)
    -
    -
    -
    -
    -
    -
    - -

    -getEngine

    -
    -public static <T,V> Executable.ExecProvider getEngine(Executable<V> executable,
-                                                      List<FastaSequence> dataSet)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/ProgressGetter.html b/website/full_javadoc/compbio/engine/ProgressGetter.html deleted file mode 100644 index 7a192eb..0000000 --- a/website/full_javadoc/compbio/engine/ProgressGetter.html +++ /dev/null @@ -1,273 +0,0 @@ - - - - - - -ProgressGetter - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine -
    -Class ProgressGetter

    -
    -java.lang.Object
-  extended by compbio.engine.ProgressGetter
-
    -
    -
    -
    public class ProgressGetter
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ProgressGetter() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static bytegetProgress(String progressFile) - -
    -           
    -static ChunkHolderpull(String file, - long position) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ProgressGetter

    -
    -public ProgressGetter()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -pull

    -
    -public static final ChunkHolder pull(String file,
-                                     long position)
    -
    -
    -
    -
    -
    -
    - -

    -getProgress

    -
    -public static final byte getProgress(String progressFile)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/PulledFileCache.html b/website/full_javadoc/compbio/engine/PulledFileCache.html deleted file mode 100644 index 6edab39..0000000 --- a/website/full_javadoc/compbio/engine/PulledFileCache.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -PulledFileCache - - - - - - - - - - - - -
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    - -

    - -compbio.engine -
    -Class PulledFileCache

    -
    -java.lang.Object
-  extended by compbio.engine.PulledFileCache
-
    -
    -
    -
    public final class PulledFileCache
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PulledFileCache() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static FilePullerget(String fileName) - -
    -           
    -static booleanput(FilePuller fpuller) - -
    -          This method allows duplicates to be added.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PulledFileCache

    -
    -public PulledFileCache()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -get

    -
    -public static FilePuller get(String fileName)
    -
    -
    -
    -
    -
    -
    - -

    -put

    -
    -public static boolean put(FilePuller fpuller)
    -
    -
    This method allows duplicates to be added. This is a responsibility of - the called to ensure this will not happen! -

    -

    -
    Parameters:
    fpuller - -
    Returns:
    true if the same filepooler is already in cache
    -
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    - -compbio.engine -
    -Class SubmissionManager

    -
    -java.lang.Object
-  extended by compbio.engine.SubmissionManager
-
    -
    -
    -
    public class SubmissionManager
    extends Object
    - - -

    -Submit jobs for execution -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static voidaddTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
    -           
    -static Future<ConfiguredExecutable<?>>getTask(String taskId) - -
    -           
    -static voidremoveTask(ConfiguredExecutable<?> executable) - -
    -           
    -static voidremoveTask(String key) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -addTask

    -
    -public static void addTask(ConfiguredExecutable<?> executable,
-                           Future<ConfiguredExecutable<?>> future)
    -
    -
    -
    -
    -
    -
    - -

    -getTask

    -
    -public static Future<ConfiguredExecutable<?>> getTask(String taskId)
    -
    -
    -
    -
    -
    -
    - -

    -removeTask

    -
    -public static void removeTask(ConfiguredExecutable<?> executable)
    -
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    -removeTask

    -
    -public static void removeTask(String key)
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    - -compbio.engine -
    -Interface SyncExecutor

    -
    -
    All Known Implementing Classes:
    JobRunner, LocalRunner
    -
    -
    -
    -
    public interface SyncExecutor
    - - -

    -Synchronous executor, is an engine to run the Executable synchronously. -

    - -

    -

    -
    Author:
    -
    pvtroshin - Date October 2009
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob() - -
    -          Stops running job.
    - booleancleanup() - -
    -          Clean up after the job
    - voidexecuteJob() - -
    -          Execute the job
    - JobStatusgetJobStatus() - -
    -          Query the status of the job by its id.
    - StringgetWorkDirectory() - -
    -           
    - ConfiguredExecutable<?>waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -executeJob

    -
    -void executeJob()
-                throws JobSubmissionException
    -
    -
    Execute the job -

    -

    - -
    Throws: -
    JobSubmissionException - if submission fails
    -
    -
    -
    - -

    -cleanup

    -
    -boolean cleanup()
    -
    -
    Clean up after the job -

    -

    - -
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    -
    -
    -
    - -

    -waitForResult

    -
    -ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
    -
    -
    Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

    -

    - -
    Returns:
    object from wich the result can be obtained -
    Throws: -
    JobExecutionException
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -String getWorkDirectory()
    -
    -
    - -
    Returns:
    working directory if the task
    -
    -
    -
    - -

    -cancelJob

    -
    -boolean cancelJob()
    -
    -
    Stops running job. - Clean up is not performed. -

    -

    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -JobStatus getJobStatus()
    -
    -
    Query the status of the job by its id. -

    -

    - -
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    -Packages that use AsyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of AsyncExecutor in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that return AsyncExecutor
    -static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static AsyncExecutorConfigurator.getAsyncEngine(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of AsyncExecutor in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.cluster.drmaa that implement AsyncExecutor
    - classAsyncJobRunner - -
    -          Single cluster job runner class
    -  -

    - - - - - -
    -Uses of AsyncExecutor in compbio.engine.local
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.local that implement AsyncExecutor
    - classAsyncLocalRunner - -
    -           
    -  -

    - - - - - -
    -Uses of AsyncExecutor in compbio.ws.server
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server that return AsyncExecutor
    -static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
    -           
    -  -

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    compbio.engine  
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    -  -

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    -Uses of ClusterJobId in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that return ClusterJobId
    - ClusterJobIdJob.getJobId() - -
    -           
    -  -

    - - - - - -
    -Uses of ClusterJobId in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return ClusterJobId
    -static ClusterJobIdClusterSession.getClusterJobId(String taskId) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa with parameters of type ClusterJobId
    - intClusterSession.getJobStatus(ClusterJobId jobId) - -
    -          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
    -  -

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    compbio.engine  
    -  -

    - - - - - -
    -Uses of FilePuller in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that return FilePuller
    -static FilePullerPulledFileCache.get(String fileName) - -
    -           
    -static FilePullerFilePuller.newFilePuller(String file, - int chunkSize) - -
    -           
    -static FilePullerFilePuller.newProgressPuller(String file) - -
    -          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
    -  -

    - - - - - - - - - -
    Methods in compbio.engine with parameters of type FilePuller
    -static booleanPulledFileCache.put(FilePuller fpuller) - -
    -          This method allows duplicates to be added.
    -  -

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    -Packages that use Job
    compbio.engine  
    -  -

    - - - - - -
    -Uses of Job in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return Job
    -static JobJob.getByJobId(String jobId, - List<Job> jobs) - -
    -           
    -static JobJob.getByTaskId(String taskId, - List<Job> jobs) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.engine with type arguments of type Job
    -static JobJob.getByJobId(String jobId, - List<Job> jobs) - -
    -           
    -static JobJob.getByTaskId(String taskId, - List<Job> jobs) - -
    -           
    -  -

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    -Packages that use SyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    -  -

    - - - - - -
    -Uses of SyncExecutor in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return SyncExecutor
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of SyncExecutor in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.cluster.drmaa that implement SyncExecutor
    - classJobRunner - -
    -          Single cluster job runner class
    -  -

    - - - - - -
    -Uses of SyncExecutor in compbio.engine.local
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.local that implement SyncExecutor
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    - -compbio.engine.client -
    -Class CommandBuilder<T>

    -
    -java.lang.Object
-  extended by compbio.engine.client.CommandBuilder<T>
-
    -
    -
    -
    public class CommandBuilder<T>
    extends Object
    - - -

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    -Constructor Summary
    CommandBuilder(String nameValueSeparator) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - voidaddParams(List<String> params) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - List<String>getCommands() - -
    -           
    - StringgetCommandString() - -
    -           
    - StringgetParamValue(String paramName) - -
    -           
    - inthashCode() - -
    -           
    - booleanhasParam(String paramName) - -
    -           
    -static - - - - -
    -<T> CommandBuilder<T>
    -    		newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
    -          This produces the same result as getCommands method.
    - booleanremoveParam(String paramName) - -
    -           
    - booleansetFirst(String param) - -
    -           
    - booleansetLast(String paramName) - -
    -           
    - booleansetLast(String paramName, - String paramValue) - -
    -           
    - booleansetParam(String param) - -
    -           
    - booleansetParam(String paramName, - String paramValue) - -
    -           
    - voidsetParams(List<String> params) - -
    -           
    - intsize() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -CommandBuilder

    -
    -public CommandBuilder(String nameValueSeparator)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -addParams

    -
    -public void addParams(List<String> params)
    -
    -
    -
    -
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    -
    - -

    -setParams

    -
    -public void setParams(List<String> params)
    -
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    - -

    -hasParam

    -
    -public boolean hasParam(String paramName)
    -
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    -setFirst

    -
    -public boolean setFirst(String param)
    -
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    - -

    -setParam

    -
    -public boolean setParam(String param)
    -
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    -setLast

    -
    -public boolean setLast(String paramName)
    -
    -
    -
    -
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    -
    - -

    -setLast

    -
    -public boolean setLast(String paramName,
-                       String paramValue)
    -
    -
    -
    -
    -
    -
    - -

    -getParamValue

    -
    -public String getParamValue(String paramName)
    -
    -
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    -
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    - -

    -removeParam

    -
    -public boolean removeParam(String paramName)
    -
    -
    -
    -
    -
    -
    - -

    -setParam

    -
    -public boolean setParam(String paramName,
-                        String paramValue)
    -
    -
    -
    -
    -
    -
    - -

    -getCommands

    -
    -public List<String> getCommands()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandString

    -
    -public String getCommandString()
    -
    -
    -
    -
    -
    -
    - -

    -newCommandBuilder

    -
    -public static <T> CommandBuilder<T> newCommandBuilder(List<? extends Option<T>> arguments,
-                                                      String nameValueSeparator)
    -
    -
    This produces the same result as getCommands method. The only difference - is that it accepts a List of Options as an input -

    -

    -
    Parameters:
    arguments - -
    Returns:
    the instance of the CommandBuilder
    -
    -
    -
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    -size

    -
    -public int size()
    -
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    -hashCode

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    -
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    Overrides:
    hashCode in class Object
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    -equals

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    equals in class Object
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    -toString

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    -public String toString()
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    toString in class Object
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    - - - diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html deleted file mode 100644 index 297f341..0000000 --- a/website/full_javadoc/compbio/engine/client/ConfExecutable.html +++ /dev/null @@ -1,1022 +0,0 @@ - - - - - - -ConfExecutable - - - - - - - - - - - - -
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    - -

    - -compbio.engine.client -
    -Class ConfExecutable<T>

    -
    -java.lang.Object
-  extended by compbio.engine.client.ConfExecutable<T>
-
    -
    -
    All Implemented Interfaces:
    ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>
    -
    -
    -
    -
    public class ConfExecutable<T>
    extends Object
    implements ConfiguredExecutable<T>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringCLUSTER_TASK_ID_PREFIX - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ConfExecutable(Executable<T> executable, - String taskDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Executable<T>addParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - StringgetClusterJobSettings() - -
    -           
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - Map<String,String>getEnvironment() - -
    -           
    - StringgetError() - -
    -           
    - Executable.ExecProvidergetExecProvider() - -
    -           
    - Executable<T>getExecutable() - -
    -           
    - StringgetInput() - -
    -          Not all input paths are relative! Input path could be absolute!
    - Limit<T>getLimit(String presetName) - -
    -           
    - LimitsManager<T>getLimits() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<T>getParameters() - -
    -           
    - CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -           
    - RunConfigurationgetRunConfiguration() - -
    -           
    -static - - - - -
    -<V> LimitsManager<V>
    -    		getRunnerLimits(Class<V> clazz) - -
    -          This method should be executed once and result of its execution reused.
    -static - - - - -
    -<V> RunnerConfig<V>
    -    		getRunnerOptions(Class<? extends Executable<V>> clazz) - -
    -           
    -static - - - - -
    -<V> PresetManager<V>
    -    		getRunnerPresets(Class<? extends Executable<V>> clazz) - -
    -           
    - Executable.ExecProvidergetSupportedRuntimes() - -
    -           
    - StringgetTaskId() - -
    -           
    - StringgetWorkDirectory() - -
    -           
    - ConfiguredExecutable<?>loadRunConfiguration(InputStream input) - -
    -           
    - ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) - -
    -           
    -static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) - -
    -           
    - booleansaveRunConfiguration() - -
    -           
    - voidsetExecProvider(Executable.ExecProvider provider) - -
    -           
    - voidsetWorkDirectory(String workDirectory) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -CLUSTER_TASK_ID_PREFIX

    -
    -public static final String CLUSTER_TASK_ID_PREFIX
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ConfExecutable

    -
    -public ConfExecutable(Executable<T> executable,
-                      String taskDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getExecProvider

    -
    -public Executable.ExecProvider getExecProvider()
    -
    -
    -
    Specified by:
    getExecProvider in interface ConfiguredExecutable<T>
    -
    -
    -
    -
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    -setExecProvider

    -
    -public void setExecProvider(Executable.ExecProvider provider)
    -
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    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
-                  throws UnsupportedRuntimeException
    -
    -
    -
    Specified by:
    getCommand in interface ConfiguredExecutable<T>
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException
    -
    -
    -
    - -

    -getSupportedRuntimes

    -
    -public Executable.ExecProvider getSupportedRuntimes()
    -
    -
    -
    Specified by:
    getSupportedRuntimes in interface ConfiguredExecutable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<T> getLimit(String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<T> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getTaskId

    -
    -public String getTaskId()
    -
    -
    -
    Specified by:
    getTaskId in interface ConfiguredExecutable<T>
    -
    -
    -
    -
    -
    -
    - -

    -setWorkDirectory

    -
    -public void setWorkDirectory(String workDirectory)
    -
    -
    -
    Specified by:
    setWorkDirectory in interface ConfiguredExecutable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -public String getWorkDirectory()
    -
    -
    -
    Specified by:
    getWorkDirectory in interface ConfiguredExecutable<T>
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public Executable<T> addParameters(List<String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<T>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    -
    Specified by:
    getError in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    Specified by:
    getCreatedFiles in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    Not all input paths are relative! Input path could be absolute! -

    -

    -
    Specified by:
    getInput in interface Executable<T>
    -
    -
    -
    See Also:
    compbio.engine.client.Executable#getInputFiles()
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<T> getParameters()
    -
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    Specified by:
    getParameters in interface ConfiguredExecutable<T>
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    -getParameters

    -
    -public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    -
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    getParameters in interface Executable<T>
    -
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    -getExecutable

    -
    -public Executable<T> getExecutable()
    -
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    Specified by:
    getExecutable in interface ConfiguredExecutable<T>
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    -getResults

    -
    -public <V> V getResults()
-             throws ResultNotAvailableException
    -
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    Specified by:
    getResults in interface ConfiguredExecutable<T>
    -
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    Throws: -
    ResultNotAvailableException
    -
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    -
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    -getResults

    -
    -public <V> V getResults(String directory)
-             throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<T>
    -
    -
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    Throws: -
    ResultNotAvailableException
    -
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    -getRunnerOptions

    -
    -public static <V> RunnerConfig<V> getRunnerOptions(Class<? extends Executable<V>> clazz)
-                                        throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
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    -getRunnerPresets

    -
    -public static <V> PresetManager<V> getRunnerPresets(Class<? extends Executable<V>> clazz)
-                                         throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
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    -
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    -getRunnerLimits

    -
    -public static <V> LimitsManager<V> getRunnerLimits(Class<V> clazz)
-                                        throws IOException
    -
    -
    This method should be executed once and result of its execution reused. - If not used carefully it could slow down the system! -

    -

    -
    -
    -
    -
    Type Parameters:
    V -
    Parameters:
    clazz - -
    Returns:
    LimitsManager instance -
    Throws: -
    IOException
    -
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    -
    - -

    -getEnvironment

    -
    -public Map<String,String> getEnvironment()
    -
    -
    -
    Specified by:
    getEnvironment in interface ConfiguredExecutable<T>
    -
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    -loadRunConfiguration

    -
    -public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)
    -
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    -
    Specified by:
    loadRunConfiguration in interface Executable<T>
    -
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    -newConfExecutable

    -
    -public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)
    -
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    -saveRunConfiguration

    -
    -public boolean saveRunConfiguration()
-                             throws IOException
    -
    -
    -
    Specified by:
    saveRunConfiguration in interface ConfiguredExecutable<T>
    -
    -
    - -
    Throws: -
    IOException
    -
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    -getRunConfiguration

    -
    -public RunConfiguration getRunConfiguration()
    -
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    -loadRunConfiguration

    -
    -public ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
-                                             throws IOException
    -
    -
    -
    Specified by:
    loadRunConfiguration in interface ConfiguredExecutable<T>
    -
    -
    - -
    Throws: -
    IOException
    -
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    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
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    -getClusterJobSettings

    -
    -public String getClusterJobSettings()
    -
    -
    -
    Specified by:
    getClusterJobSettings in interface Executable<T>
    -
    -
    -
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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.client -
    -Interface ConfiguredExecutable<T>

    -
    -
    All Superinterfaces:
    Executable<T>, PipedExecutable<T>
    -
    -
    -
    All Known Implementing Classes:
    ConfExecutable
    -
    -
    -
    -
    public interface ConfiguredExecutable<T>
    extends Executable<T>, PipedExecutable<T>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - Map<String,String>getEnvironment() - -
    -           
    - Executable.ExecProvidergetExecProvider() - -
    -           
    - Executable<T>getExecutable() - -
    -           
    - CommandBuilder<T>getParameters() - -
    -           
    - - - - - -
    -<V> V
    -    		getResults() - -
    -           
    - Executable.ExecProvidergetSupportedRuntimes() - -
    -           
    - StringgetTaskId() - -
    -           
    - StringgetWorkDirectory() - -
    -           
    - ConfiguredExecutable<?>loadRunConfiguration(InputStream input) - -
    -           
    - booleansaveRunConfiguration() - -
    -           
    - voidsetWorkDirectory(String workDirectory) - -
    -           
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getEnvironment

    -
    -Map<String,String> getEnvironment()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getTaskId

    -
    -String getTaskId()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -String getCommand(Executable.ExecProvider provider)
-                  throws JobSubmissionException
    -
    -
    -
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getSupportedRuntimes

    -
    -Executable.ExecProvider getSupportedRuntimes()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -String getWorkDirectory()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -setWorkDirectory

    -
    -void setWorkDirectory(String workDirectory)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -<V> V getResults()
-             throws ResultNotAvailableException
    -
    -
    -
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getExecutable

    -
    -Executable<T> getExecutable()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -CommandBuilder<T> getParameters()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -saveRunConfiguration

    -
    -boolean saveRunConfiguration()
-                             throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -ConfiguredExecutable<?> loadRunConfiguration(InputStream input)
-                                             throws IOException
    -
    -
    -
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -getExecProvider

    -
    -Executable.ExecProvider getExecProvider()
    -
    -
    -
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html deleted file mode 100644 index 355ab43..0000000 --- a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -EnvVariableProcessor - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.client -
    -Class EnvVariableProcessor

    -
    -java.lang.Object
-  extended by compbio.engine.client.EnvVariableProcessor
-
    -
    -
    -
    public class EnvVariableProcessor
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringPATH - -
    -          Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable
    -  - - - - - - - - - - -
    -Constructor Summary
    EnvVariableProcessor() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static Map<String,String>getEnvVariables(String property, - Class<?> clazz) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -PATH

    -
    -public static final String PATH
    -
    -
    Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -

    -

    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -EnvVariableProcessor

    -
    -public EnvVariableProcessor()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getEnvVariables

    -
    -public static Map<String,String> getEnvVariables(String property,
-                                                 Class<?> clazz)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html deleted file mode 100644 index 529c91c..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -Executable.ExecProvider - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.engine.client -
    -Enum Executable.ExecProvider

    -
    -java.lang.Object
-  extended by java.lang.Enum<Executable.ExecProvider>
-      extended by compbio.engine.client.Executable.ExecProvider
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<Executable.ExecProvider>
    -
    -
    -
    Enclosing interface:
    Executable<T>
    -
    -
    -
    -
    public static enum Executable.ExecProvider
    extends Enum<Executable.ExecProvider>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    Any - -
    -           
    Cluster - -
    -           
    Local - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static Executable.ExecProvidervalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Executable.ExecProvider[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -Local

    -
    -public static final Executable.ExecProvider Local
    -
    -
    -
    -
    -
    - -

    -Cluster

    -
    -public static final Executable.ExecProvider Cluster
    -
    -
    -
    -
    -
    - -

    -Any

    -
    -public static final Executable.ExecProvider Any
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Executable.ExecProvider[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (Executable.ExecProvider c : Executable.ExecProvider.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static Executable.ExecProvider valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.html b/website/full_javadoc/compbio/engine/client/Executable.html deleted file mode 100644 index 20de800..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.html +++ /dev/null @@ -1,445 +0,0 @@ - - - - - - -Executable - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.engine.client -
    -Interface Executable<T>

    -
    -
    Type Parameters:
    T -
    -
    -
    All Known Subinterfaces:
    ConfiguredExecutable<T>, PipedExecutable<T>
    -
    -
    -
    All Known Implementing Classes:
    _SkeletalCommandBuilder, AACon, BlastAll, ClustalO, ClustalW, ConfExecutable, Disembl, GlobPlot, IUPred, Jronn, Mafft, Mcl, Muscle, NetNglyc, OB, Probcons, PSIBlast, Ronn, RPSBlast, SkeletalExecutable, Tcoffee
    -
    -
    -
    -
    public interface Executable<T>
    - - -

    -Interface to a native executable. -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classExecutable.ExecProvider - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Executable<T>addParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - StringgetClusterJobSettings() - -
    -           
    - List<String>getCreatedFiles() - -
    -          Deprecated. 
    - StringgetError() - -
    -           
    - StringgetInput() - -
    -           
    - Limit<T>getLimit(String presetName) - -
    -           
    - LimitsManager<T>getLimits() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -addParameters

    -
    -Executable<T> addParameters(List<String> parameters)
    -
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Parameters:
    parameters - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -@Deprecated
-List<String> getCreatedFiles()
    -
    -
    Deprecated.  -

    -

    -
    -
    -
    -
    - -

    -getInput

    -
    -String getInput()
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -String getOutput()
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -String getError()
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -<V> V getResults(String directory)
-             throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -Limit<T> getLimit(String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -LimitsManager<T> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobSettings

    -
    -String getClusterJobSettings()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/PathValidator.html b/website/full_javadoc/compbio/engine/client/PathValidator.html deleted file mode 100644 index ef6cd60..0000000 --- a/website/full_javadoc/compbio/engine/client/PathValidator.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - -PathValidator - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.client -
    -Class PathValidator

    -
    -java.lang.Object
-  extended by compbio.engine.client.PathValidator
-
    -
    -
    -
    public final class PathValidator
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    PathValidator() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static booleanisAbsolutePath(String path) - -
    -          Whether a certain path is absolute or not is operation system dependent!
    -static booleanisValidDirectory(String directory) - -
    -           
    -static booleanisValidExecutable(String command) - -
    -           
    -static voidvalidateDirectory(String workDirectory) - -
    -           
    -static voidvalidateExecutable(String command) - -
    -           
    -static voidvalidatePathNames(List<String> filenames, - String type) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -PathValidator

    -
    -public PathValidator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -isValidExecutable

    -
    -public static boolean isValidExecutable(String command)
    -
    -
    -
    -
    -
    -
    - -

    -validateExecutable

    -
    -public static void validateExecutable(String command)
-                               throws IllegalArgumentException
    -
    -
    - -
    Throws: -
    IllegalArgumentException
    -
    -
    -
    - -

    -isValidDirectory

    -
    -public static boolean isValidDirectory(String directory)
    -
    -
    -
    -
    -
    -
    - -

    -validatePathNames

    -
    -public static void validatePathNames(List<String> filenames,
-                                     String type)
-                              throws IllegalArgumentException
    -
    -
    -
    Parameters:
    filenames -
    type - - merely a string to be added to error message to explain what - type of files are lacking -
    Throws: -
    IllegalArgumentException
    -
    -
    -
    - -

    -isAbsolutePath

    -
    -public static boolean isAbsolutePath(String path)
    -
    -
    Whether a certain path is absolute or not is operation system dependent! -

    -

    -
    Parameters:
    path - -
    Returns:
    true is the path is absolute, false otherwise
    -
    -
    -
    - -

    -validateDirectory

    -
    -public static void validateDirectory(String workDirectory)
-                              throws IllegalArgumentException
    -
    -
    - -
    Throws: -
    IllegalArgumentException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/PipedExecutable.html deleted file mode 100644 index c1dc1a1..0000000 --- a/website/full_javadoc/compbio/engine/client/PipedExecutable.html +++ /dev/null @@ -1,230 +0,0 @@ - - - - - - -PipedExecutable - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine.client -
    -Interface PipedExecutable<T>

    -
    -
    Type Parameters:
    T -
    -
    -
    All Superinterfaces:
    Executable<T>
    -
    -
    -
    All Known Subinterfaces:
    ConfiguredExecutable<T>
    -
    -
    -
    All Known Implementing Classes:
    ConfExecutable, Disembl, GlobPlot, Mafft, Probcons, Tcoffee
    -
    -
    -
    -
    public interface PipedExecutable<T>
    extends Executable<T>
    - - -

    -This is a marker interface to indicate that the output of the process must be - captured. It is in generally better for the process to manage its own - streams, but some executables are not capable of this thus require different - handling -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    -  -

    - -

    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/RunConfiguration.html deleted file mode 100644 index e64345c..0000000 --- a/website/full_javadoc/compbio/engine/client/RunConfiguration.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -RunConfiguration - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine.client -
    -Class RunConfiguration

    -
    -java.lang.Object
-  extended by compbio.engine.client.RunConfiguration
-
    -
    -
    -
    public class RunConfiguration
    extends Object
    - - -

    -Value class for persisting ConfExecutable instances -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringrconfigFile - -
    -           
    -  - - - - - - - - - - - - - -
    -Constructor Summary
    RunConfiguration() - -
    -           
    RunConfiguration(ConfExecutable<?> cexec) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetError() - -
    -           
    - StringgetInput() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<?>getParameters() - -
    -           
    - StringgetRunnerClassName() - -
    -           
    - inthashCode() - -
    -           
    -static RunConfigurationload(InputStream input) - -
    -           
    - voidsetError(String error) - -
    -           
    - voidsetInput(String input) - -
    -           
    - voidsetOutput(String output) - -
    -           
    - voidsetParameters(CommandBuilder<?> parameters) - -
    -           
    - StringtoString() - -
    -           
    -static booleanwrite(RunConfiguration rconf) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -rconfigFile

    -
    -public static final String rconfigFile
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -RunConfiguration

    -
    -public RunConfiguration()
    -
    -
    -
    - -

    -RunConfiguration

    -
    -public RunConfiguration(ConfExecutable<?> cexec)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -write

    -
    -public static boolean write(RunConfiguration rconf)
-                     throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -load

    -
    -public static RunConfiguration load(InputStream input)
-                             throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -setOutput

    -
    -public void setOutput(String output)
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<?> getParameters()
    -
    -
    -
    -
    -
    -
    - -

    -setParameters

    -
    -public void setParameters(CommandBuilder<?> parameters)
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    -
    -
    -
    - -

    -setError

    -
    -public void setError(String error)
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public void setInput(String input)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerClassName

    -
    -public String getRunnerClassName()
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html deleted file mode 100644 index c8cdb47..0000000 --- a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html +++ /dev/null @@ -1,782 +0,0 @@ - - - - - - -SkeletalExecutable - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine.client -
    -Class SkeletalExecutable<T>

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<T>
-
    -
    -
    All Implemented Interfaces:
    Executable<T>
    -
    -
    -
    Direct Known Subclasses:
    AACon, ClustalO, ClustalW, Disembl, GlobPlot, IUPred, Jronn, Mafft, Muscle, Probcons, Tcoffee
    -
    -
    -
    -
    public abstract class SkeletalExecutable<T>
    extends Object
    implements Executable<T>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringERROR - -
    -           
    -static StringINPUT - -
    -           
    -static StringOUTPUT - -
    -           
    -  - - - - - - - - - - - - - -
    -Constructor Summary
    SkeletalExecutable() - -
    -           
    SkeletalExecutable(String parameterKeyValueDelimiter) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Executable<T>addParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - booleanequals(Object obj) - -
    -           
    -static intgetClusterCpuNum(Class<? extends Executable<?>> type) - -
    -           
    - StringgetClusterJobSettings() - -
    -           
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - StringgetError() - -
    -           
    - StringgetInput() - -
    -           
    - Limit<T>getLimit(String presetName) - -
    -           
    - LimitsManager<T>getLimits() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
    -           
    -abstract  Class<T>getType() - -
    -           
    - inthashCode() - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - SkeletalExecutable<T>setError(String errFile) - -
    -           
    - SkeletalExecutable<T>setInput(String inFile) - -
    -           
    - SkeletalExecutable<T>setOutput(String outFile) - -
    -           
    - Executable<T>setParameter(String parameter) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getResults
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -INPUT

    -
    -public static final String INPUT
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -OUTPUT

    -
    -public static final String OUTPUT
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -ERROR

    -
    -public static final String ERROR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -SkeletalExecutable

    -
    -public SkeletalExecutable()
    -
    -
    -
    - -

    -SkeletalExecutable

    -
    -public SkeletalExecutable(String parameterKeyValueDelimiter)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setInput

    -
    -public SkeletalExecutable<T> setInput(String inFile)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public SkeletalExecutable<T> setOutput(String outFile)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -setError

    -
    -public SkeletalExecutable<T> setError(String errFile)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public Executable<T> addParameters(List<String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<T>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -setParameter

    -
    -public Executable<T> setParameter(String parameter)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<T>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    Specified by:
    getInput in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    -
    Specified by:
    getError in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    -
    Specified by:
    loadRunConfiguration in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobSettings

    -
    -public String getClusterJobSettings()
    -
    -
    -
    Specified by:
    getClusterJobSettings in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getClusterCpuNum

    -
    -public static int getClusterCpuNum(Class<? extends Executable<?>> type)
    -
    -
    -
    -
    -
    - -
    Returns:
    number of cpus to use on the cluster or 0 if the value is - undefined
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<T> getLimit(String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<T> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<T>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public abstract Class<T> getType()
    -
    -
    -
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html deleted file mode 100644 index c765a17..0000000 --- a/website/full_javadoc/compbio/engine/client/Util.html +++ /dev/null @@ -1,588 +0,0 @@ - - - - - - -Util - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.engine.client -
    -Class Util

    -
    -java.lang.Object
-  extended by compbio.engine.client.Util
-
    -
    -
    -
    public final class Util
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Util() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static StringconvertToAbsolute(String relativePath) - -
    -           
    -static StringgetCommand(Executable.ExecProvider provider, - Class<?> clazz) - -
    -           
    -static StringgetExecProperty(String propertySpec, - Class<?> clazz) - -
    -           
    -static StringgetExecProperty(String propertySpec, - Executable<?> exec) - -
    -           
    -static StringgetFullPath(String workDirectory, - String fileName) - -
    -           
    -static StringgetJava() - -
    -          Returns the absolute path to the Java executable from JAVA_HOME
    -static - - - - -
    -<T> LimitsManager<T>
    -    		getLimits(Class<T> clazz) - -
    -          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then
    -static Executable.ExecProvidergetSupportedRuntimes(Class<?> clazz) - -
    -           
    -static booleanisJavaLibrary(Class<?> clazz) - -
    -          Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise.
    -static booleanisMarked(String workDirectory, - JobStatus marker) - -
    -           
    -static booleanisValidJobId(String key) - -
    -           
    -static ConfiguredExecutable<?>loadExecutable(String taskId) - -
    -           
    -static Map<String,String>mergeEnvVariables(Map<String,String> sysEnvTobeModified, - Map<String,String> variables) - -
    -           
    -static voidwriteFile(String workDirectory, - String fileAndEventName, - String content, - boolean override) - -
    -           
    -static booleanwriteMarker(String workDirectory, - JobStatus fileType) - -
    -           
    -static voidwriteStatFile(String workDirectory, - String fileAndEventName) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Util

    -
    -public Util()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -isValidJobId

    -
    -public static boolean isValidJobId(String key)
    -
    -
    -
    -
    -
    -
    - -

    -writeStatFile

    -
    -public static void writeStatFile(String workDirectory,
-                                 String fileAndEventName)
    -
    -
    -
    -
    -
    -
    - -

    -writeFile

    -
    -public static void writeFile(String workDirectory,
-                             String fileAndEventName,
-                             String content,
-                             boolean override)
    -
    -
    -
    -
    -
    -
    - -

    -writeMarker

    -
    -public static final boolean writeMarker(String workDirectory,
-                                        JobStatus fileType)
    -
    -
    -
    -
    -
    -
    - -

    -isMarked

    -
    -public static boolean isMarked(String workDirectory,
-                               JobStatus marker)
    -
    -
    -
    -
    -
    -
    - -

    -mergeEnvVariables

    -
    -public static Map<String,String> mergeEnvVariables(Map<String,String> sysEnvTobeModified,
-                                                   Map<String,String> variables)
    -
    -
    -
    -
    -
    -
    - -

    -convertToAbsolute

    -
    -public static String convertToAbsolute(String relativePath)
    -
    -
    -
    -
    -
    -
    - -

    -getExecProperty

    -
    -public static String getExecProperty(String propertySpec,
-                                     Executable<?> exec)
    -
    -
    -
    -
    -
    -
    - -

    -getExecProperty

    -
    -public static String getExecProperty(String propertySpec,
-                                     Class<?> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -getFullPath

    -
    -public static String getFullPath(String workDirectory,
-                                 String fileName)
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public static String getCommand(Executable.ExecProvider provider,
-                                Class<?> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -isJavaLibrary

    -
    -public static boolean isJavaLibrary(Class<?> clazz)
    -
    -
    Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise. -

    -

    -
    Parameters:
    clazz - -
    Returns:
    -
    -
    -
    - -

    -getJava

    -
    -public static String getJava()
    -
    -
    Returns the absolute path to the Java executable from JAVA_HOME -

    -

    - -
    Returns:
    returns the absolute path to the Java executable from JAVA_HOME
    -
    -
    -
    - -

    -getSupportedRuntimes

    -
    -public static Executable.ExecProvider getSupportedRuntimes(Class<?> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -loadExecutable

    -
    -public static ConfiguredExecutable<?> loadExecutable(String taskId)
-                                              throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getLimits

    -
    -public static <T> LimitsManager<T> getLimits(Class<T> clazz)
    -
    -
    For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -

    -

    -
    Parameters:
    rconfig - -
    Returns:
    public static List toOptionString(RunnerConfig - rconfig) { String option = ""; List options = new - ArrayList(); for (Parameter par : - rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) - { option = par.getOptionName(); } else { option = - par.getOptionName() + "=" + par.getPossibleValues().get(0); } // - separate options options.add(option); } return options; }
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    compbio.engine.client.CommandBuilder

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    -Packages that use CommandBuilder
    compbio.engine.client  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return CommandBuilder
    - CommandBuilder<?>RunConfiguration.getParameters() - -
    -           
    - CommandBuilder<T>ConfiguredExecutable.getParameters() - -
    -           
    - CommandBuilder<T>ConfExecutable.getParameters() - -
    -           
    - CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> CommandBuilder<T>
    -    		CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
    -          This produces the same result as getCommands method.
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type CommandBuilder
    - voidRunConfiguration.setParameters(CommandBuilder<?> parameters) - -
    -           
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return CommandBuilder
    - CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return CommandBuilder
    - CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.conservation that return CommandBuilder
    - CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return CommandBuilder
    - CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of CommandBuilder in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return CommandBuilder
    - CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

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    compbio.engine.client.ConfExecutable

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    -Packages that use ConfExecutable
    compbio.engine.client  
    -  -

    - - - - - -
    -Uses of ConfExecutable in compbio.engine.client
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.client with parameters of type ConfExecutable
    RunConfiguration(ConfExecutable<?> cexec) - -
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    compbio.engine.client.ConfiguredExecutable

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    -Packages that use ConfiguredExecutable
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that return ConfiguredExecutable
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    - ConfiguredExecutable<?>Job.getConfExecutable() - -
    -           
    - ConfiguredExecutable<?>AsyncExecutor.getResults(String jobId) - -
    -          Retrieve the results of the job.
    - ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that return types with arguments of type ConfiguredExecutable
    -static Future<ConfiguredExecutable<?>>SubmissionManager.getTask(String taskId) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine with parameters of type ConfiguredExecutable
    -static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
    -           
    -static booleanCleaner.deleteFiles(ConfiguredExecutable<?> exec) - -
    -          Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
    -static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static voidSubmissionManager.removeTask(ConfiguredExecutable<?> executable) - -
    -           
    - StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  -

    - - - - - - - - - -
    Method parameters in compbio.engine with type arguments of type ConfiguredExecutable
    -static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - Future<ConfiguredExecutable<?>> future) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine with parameters of type ConfiguredExecutable
    Job(String taskId, - String jobId, - ConfiguredExecutable<?> cexecutable) - -
    -           
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.engine.client
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.client that implement ConfiguredExecutable
    - classConfExecutable<T> - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return ConfiguredExecutable
    -static ConfiguredExecutable<?>Util.loadExecutable(String taskId) - -
    -           
    - ConfiguredExecutable<?>ConfiguredExecutable.loadRunConfiguration(InputStream input) - -
    -           
    - ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(InputStream input) - -
    -           
    - ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
    -           
    -static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
    -           
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable
    - ConfiguredExecutable<?>ClusterSession.getResults(String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncJobRunner.getResults(String jobId) - -
    -           
    - ConfiguredExecutable<?>JobRunner.waitForResult() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
    -static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
    -           
    - StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
    JobRunner(ConfiguredExecutable<?> confExec) - -
    -           
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.engine.local
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.local that return ConfiguredExecutable
    - ConfiguredExecutable<?>ExecutableWrapper.call() - -
    -          It is vital that output and error streams are captured immediately for - this call() to succeed.
    -static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncLocalRunner.getResults(String taskId) - -
    -           
    - ConfiguredExecutable<?>LocalRunner.waitForResult() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local with parameters of type ConfiguredExecutable
    -static booleanLocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable) - -
    -           
    - StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable
    -static booleanLocalEngineUtil.cancelJob(Future<ConfiguredExecutable<?>> future, - String workDirectory) - -
    -           
    -static JobStatusLocalEngineUtil.getJobStatus(Future<ConfiguredExecutable<?>> future) - -
    -           
    -static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
    -           
    -  -

    - - - - - - - - - - - -
    Constructors in compbio.engine.local with parameters of type ConfiguredExecutable
    ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
    -           
    LocalRunner(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type ConfiguredExecutable
    -static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  -

    - - - - - -
    -Uses of ConfiguredExecutable in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type ConfiguredExecutable
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    -static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
    -           
    -  -

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    -Packages that use Executable.ExecProvider
    compbio.engine  
    compbio.engine.client  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return Executable.ExecProvider
    -static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
    -           
    -static - - - - -
    -<T,V> Executable.ExecProvider
    -    		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine with parameters of type Executable.ExecProvider
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return Executable.ExecProvider
    - Executable.ExecProviderConfiguredExecutable.getExecProvider() - -
    -           
    - Executable.ExecProviderConfExecutable.getExecProvider() - -
    -           
    - Executable.ExecProviderConfiguredExecutable.getSupportedRuntimes() - -
    -           
    - Executable.ExecProviderConfExecutable.getSupportedRuntimes() - -
    -           
    -static Executable.ExecProviderUtil.getSupportedRuntimes(Class<?> clazz) - -
    -           
    -static Executable.ExecProviderExecutable.ExecProvider.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Executable.ExecProvider[]Executable.ExecProvider.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type Executable.ExecProvider
    - StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    - StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -static StringUtil.getCommand(Executable.ExecProvider provider, - Class<?> clazz) - -
    -           
    - CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
    -           
    - voidConfExecutable.setExecProvider(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type Executable.ExecProvider
    - CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner._impl with parameters of type Executable.ExecProvider
    - StringRPSBlast.getCommand(Executable.ExecProvider provider) - -
    -           
    - StringPSIBlast.getCommand(Executable.ExecProvider provider) - -
    -           
    - StringRonn.getCommand(Executable.ExecProvider provider) - -
    -           
    - StringMcl.getCommand(Executable.ExecProvider provider) - -
    -           
    - StringBlastAll.getCommand(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.conservation with parameters of type Executable.ExecProvider
    - CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder with parameters of type Executable.ExecProvider
    - CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable.ExecProvider in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa with parameters of type Executable.ExecProvider
    - CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
    -           
    - CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    -

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    compbio.engine.client.Executable

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Executable
    compbio.engine  
    compbio.engine.client  
    compbio.engine.conf  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

    - - - - - -
    -Uses of Executable in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine with parameters of type Executable
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    -static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
    -           
    -static - - - - -
    -<T,V> Executable.ExecProvider
    -    		LoadBalancer.getEngine(Executable<V> executable, - List<FastaSequence> dataSet) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Subinterfaces of Executable in compbio.engine.client
    - interfaceConfiguredExecutable<T> - -
    -           
    - interfacePipedExecutable<T> - -
    -          This is a marker interface to indicate that the output of the process must be - captured.
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.engine.client that implement Executable
    - classConfExecutable<T> - -
    -           
    - classSkeletalExecutable<T> - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return Executable
    - Executable<T>Executable.addParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - Executable<T>SkeletalExecutable.addParameters(List<String> parameters) - -
    -           
    - Executable<T>ConfExecutable.addParameters(List<String> parameters) - -
    -           
    - Executable<T>ConfiguredExecutable.getExecutable() - -
    -           
    - Executable<T>ConfExecutable.getExecutable() - -
    -           
    - Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - Executable<T>SkeletalExecutable.setParameter(String parameter) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type Executable
    -static StringUtil.getExecProperty(String propertySpec, - Executable<?> exec) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.engine.client with type arguments of type Executable
    -static intSkeletalExecutable.getClusterCpuNum(Class<? extends Executable<?>> type) - -
    -           
    -static - - - - -
    -<V> RunnerConfig<V>
    -    		ConfExecutable.getRunnerOptions(Class<? extends Executable<V>> clazz) - -
    -           
    -static - - - - -
    -<V> PresetManager<V>
    -    		ConfExecutable.getRunnerPresets(Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.client with parameters of type Executable
    ConfExecutable(Executable<T> executable, - String taskDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.engine.conf
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.conf that return types with arguments of type Executable
    -static Class<Executable<?>>DirectoryManager.getClass(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.runner
    -  -

    - - - - - - - - - -
    Classes in compbio.runner that implement Executable
    - class_SkeletalCommandBuilder - -
    -          Deprecated. 
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return Executable
    - Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
    -          Deprecated.  
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Executable
    -static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -static - - - - -
    -<T> PresetManager<T>
    -    		Util.getPresets(Class<? extends Executable<T>> clazz) - -
    -           
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		Util.getSupportedOptions(Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - - - - -
    Constructor parameters in compbio.runner with type arguments of type Executable
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.runner._impl that implement Executable
    - classBlastAll - -
    -           
    - classMcl - -
    -           
    - classNetNglyc - -
    -           
    - classOB - -
    -          TODO this needs fixing! Executable does not work
    - classPSIBlast - -
    -           
    - classRonn - -
    -           
    - classRPSBlast - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Executable
    - Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Classes in compbio.runner.conservation that implement Executable
    - classAACon - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - -
    -Uses of Executable in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.runner.disorder that implement Executable
    - classDisembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    - classGlobPlot - -
    -          ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    - classIUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    - classJronn - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - -
    -Uses of Executable in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Classes in compbio.runner.msa that implement Executable
    - classClustalO - -
    -           
    - classClustalW - -
    -           
    - classMafft - -
    -           
    - classMuscle - -
    -           
    - classProbcons - -
    -           
    - classTcoffee - -
    -           
    -  -

    - - - - - -
    -Uses of Executable in compbio.ws.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type Executable
    -static Class<? extends Executable<?>>ServicesUtil.getRunnerByJobDirectory(File jobdir) - -
    -           
    -static Class<? extends Executable<?>>ServicesUtil.getServiceImpl(Services service) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.client with type arguments of type Executable
    -static ServicesServicesUtil.getServiceByRunner(Class<? extends Executable> class1) - -
    -           
    -  -

    -

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    compbio.engine.client.PathValidator

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    -Uses of Interface
    compbio.engine.client.PipedExecutable

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use PipedExecutable
    compbio.engine.client  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    -  -

    - - - - - -
    -Uses of PipedExecutable in compbio.engine.client
    -  -

    - - - - - - - - - -
    Subinterfaces of PipedExecutable in compbio.engine.client
    - interfaceConfiguredExecutable<T> - -
    -           
    -  -

    - - - - - - - - - -
    Classes in compbio.engine.client that implement PipedExecutable
    - classConfExecutable<T> - -
    -           
    -  -

    - - - - - -
    -Uses of PipedExecutable in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.runner.disorder that implement PipedExecutable
    - classDisembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    - classGlobPlot - -
    -          ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    -  -

    - - - - - -
    -Uses of PipedExecutable in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - -
    Classes in compbio.runner.msa that implement PipedExecutable
    - classMafft - -
    -           
    - classProbcons - -
    -           
    - classTcoffee - -
    -           
    -  -

    -

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    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.engine.client.RunConfiguration

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use RunConfiguration
    compbio.engine.client  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of RunConfiguration in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return RunConfiguration
    - RunConfigurationConfExecutable.getRunConfiguration() - -
    -           
    -static RunConfigurationRunConfiguration.load(InputStream input) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type RunConfiguration
    - Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
    -           
    -static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
    -           
    -static booleanRunConfiguration.write(RunConfiguration rconf) - -
    -           
    -  -

    - - - - - -
    -Uses of RunConfiguration in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type RunConfiguration
    - Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of RunConfiguration in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl with parameters of type RunConfiguration
    - Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.engine.client.SkeletalExecutable

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    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use SkeletalExecutable
    compbio.engine.client  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    -  -

    - - - - - -
    -Uses of SkeletalExecutable in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return SkeletalExecutable
    - SkeletalExecutable<T>SkeletalExecutable.setError(String errFile) - -
    -           
    - SkeletalExecutable<T>SkeletalExecutable.setInput(String inFile) - -
    -           
    - SkeletalExecutable<T>SkeletalExecutable.setOutput(String outFile) - -
    -           
    -  -

    - - - - - -
    -Uses of SkeletalExecutable in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Subclasses of SkeletalExecutable in compbio.runner.conservation
    - classAACon - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - -
    -Uses of SkeletalExecutable in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of SkeletalExecutable in compbio.runner.disorder
    - classDisembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    - classGlobPlot - -
    -          ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    - classIUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    - classJronn - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - -
    -Uses of SkeletalExecutable in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of SkeletalExecutable in compbio.runner.msa
    - classClustalO - -
    -           
    - classClustalW - -
    -           
    - classMafft - -
    -           
    - classMuscle - -
    -           
    - classProbcons - -
    -           
    - classTcoffee - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Interface Summary
    ConfiguredExecutable<T> 
    Executable<T>Interface to a native executable.
    PipedExecutable<T>This is a marker interface to indicate that the output of the process must be - captured.
    -  - -

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    -Class Summary
    CommandBuilder<T> 
    ConfExecutable<T> 
    EnvVariableProcessor 
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    RunConfigurationValue class for persisting ConfExecutable instances
    SkeletalExecutable<T> 
    Util 
    -  - -

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    -Packages that use compbio.engine.client
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.conf  
    compbio.engine.local  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.engine
    ConfiguredExecutable - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.engine.client
    CommandBuilder - -
    -           
    ConfExecutable - -
    -           
    ConfiguredExecutable - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    PipedExecutable - -
    -          This is a marker interface to indicate that the output of the process must be - captured.
    RunConfiguration - -
    -          Value class for persisting ConfExecutable instances
    SkeletalExecutable - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.engine.cluster.drmaa
    ConfiguredExecutable - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.engine.conf
    Executable - -
    -          Interface to a native executable.
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.engine.local
    ConfiguredExecutable - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.runner
    CommandBuilder - -
    -           
    ConfiguredExecutable - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    RunConfiguration - -
    -          Value class for persisting ConfExecutable instances
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.runner._impl
    CommandBuilder - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    RunConfiguration - -
    -          Value class for persisting ConfExecutable instances
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.runner.conservation
    CommandBuilder - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    SkeletalExecutable - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.runner.disorder
    CommandBuilder - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    PipedExecutable - -
    -          This is a marker interface to indicate that the output of the process must be - captured.
    SkeletalExecutable - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.runner.msa
    CommandBuilder - -
    -           
    Executable - -
    -          Interface to a native executable.
    Executable.ExecProvider - -
    -           
    PipedExecutable - -
    -          This is a marker interface to indicate that the output of the process must be - captured.
    SkeletalExecutable - -
    -           
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.ws.client
    Executable - -
    -          Interface to a native executable.
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.client used by compbio.ws.server
    ConfiguredExecutable - -
    -           
    -  -

    -

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    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.cluster.drmaa -
    -Class AsyncJobRunner

    -
    -java.lang.Object
-  extended by compbio.engine.cluster.drmaa.AsyncJobRunner
-
    -
    -
    All Implemented Interfaces:
    AsyncExecutor
    -
    -
    -
    -
    public class AsyncJobRunner
    extends Object
    implements AsyncExecutor
    - - -

    -Single cluster job runner class -

    - -

    -

    -
    Version:
    -
    1.0 August 2009 - - TODO after call to submitJob() no setters really work as the job - template gets deleted, this needs to be taken into account in this - class design!
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AsyncJobRunner() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -          Stop running job.
    - booleancleanup(String jobId) - -
    -          Remove all files and a job directory for a jobid.
    - JobStatusgetJobStatus(String jobId) - -
    -          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
    - ConfiguredExecutable<?>getResults(String jobId) - -
    -          Retrieve the results of the job.
    - StringgetWorkDirectory(String jobId) - -
    -           
    - StringsubmitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AsyncJobRunner

    -
    -public AsyncJobRunner()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -submitJob

    -
    -public String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

    -

    -
    Specified by:
    submitJob in interface AsyncExecutor
    -
    -
    - -
    Returns:
    unique job identifier -
    Throws: -
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

    -

    -
    Specified by:
    cancelJob in interface AsyncExecutor
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. Cancelled jobs needs to be - tracked manually! -

    -

    -
    Specified by:
    getJobStatus in interface AsyncExecutor
    -
    -
    - -
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -cleanup

    -
    -public boolean cleanup(String jobId)
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Remove all files and a job directory for a jobid. -

    -

    -
    Specified by:
    cleanup in interface AsyncExecutor
    -
    -
    - -
    Returns:
    true if job directory was successfully removed, false otherwise.
    -
    -
    -
    - -

    -getResults

    -
    -public ConfiguredExecutable<?> getResults(String jobId)
-                                   throws ResultNotAvailableException
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

    -

    -
    Specified by:
    getResults in interface AsyncExecutor
    -
    -
    -
    Parameters:
    jobId - job identifier obtained at the job submission -
    Returns:
    ConfiguredExecutable object from which result can be obtained -
    Throws: -
    ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -public String getWorkDirectory(String jobId)
    -
    -
    -
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    -
    -
    -
    Parameters:
    jobId - unique job identifier -
    Returns:
    task working directory
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html deleted file mode 100644 index 1d015a1..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -ClusterSession - - - - - - - - - - - - -
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    - -

    - -compbio.engine.cluster.drmaa -
    -Class ClusterSession

    -
    -java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterSession
-
    -
    -
    -
    public final class ClusterSession
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringJOBID - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - voidclose() - -
    -           
    -static ClusterJobIdgetClusterJobId(String taskId) - -
    -           
    - intgetJobStatus(ClusterJobId jobId) - -
    -          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
    -static StringgetJobStatus(int status) - -
    -          Deprecated. 
    - ConfiguredExecutable<?>getResults(String taskId) - -
    -           
    - org.ggf.drmaa.SessiongetSession() - -
    -           
    -static StatisticManagergetStatistics(org.ggf.drmaa.JobInfo status) - -
    -           
    - voidremoveJob(String taskId) - -
    -           
    - org.ggf.drmaa.JobInfowaitForJob(String taskId) - -
    -           
    - org.ggf.drmaa.JobInfowaitForJob(String jobId, - long waitingTime) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -JOBID

    -
    -public static final String JOBID
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getSession

    -
    -public org.ggf.drmaa.Session getSession()
    -
    -
    -
    -
    -
    -
    - -

    -close

    -
    -public void close()
    -
    -
    -
    -
    -
    -
    - -

    -removeJob

    -
    -public void removeJob(String taskId)
    -
    -
    -
    -
    -
    -
    - -

    -waitForJob

    -
    -public org.ggf.drmaa.JobInfo waitForJob(String taskId)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        IOException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException -
    IOException
    -
    -
    -
    - -

    -getClusterJobId

    -
    -public static ClusterJobId getClusterJobId(String taskId)
-                                    throws IOException
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    -
    - -

    -waitForJob

    -
    -public org.ggf.drmaa.JobInfo waitForJob(String jobId,
-                                        long waitingTime)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        IOException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException -
    IOException
    -
    -
    -
    - -

    -getResults

    -
    -public ConfiguredExecutable<?> getResults(String taskId)
-                                   throws org.ggf.drmaa.DrmaaException,
-                                          ResultNotAvailableException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getStatistics

    -
    -public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
-                                      throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -getJobStatus

    -
    -public int getJobStatus(ClusterJobId jobId)
-                 throws org.ggf.drmaa.DrmaaException,
-                        org.ggf.drmaa.InvalidJobException
    -
    -
    Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -

    -

    - -
    Throws: -
    org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it - will throw this exception for all finished or cancelled jobs -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -getJobStatus

    -
    -@Deprecated
-public static String getJobStatus(int status)
-                           throws org.ggf.drmaa.DrmaaException
    -
    -
    Deprecated.  -

    -

    Method for getting jobs status by quering the cluster, It returns status - in therms of a Sessions, not a JobStatus Should only be used for testing! -

    -

    -
    Parameters:
    status - -
    Returns:
    job status -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.cluster.drmaa -
    -Class ClusterUtil

    -
    -java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterUtil
-
    -
    -
    -
    public class ClusterUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static NumberFormatCLUSTER_STAT_IN_SEC - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ClusterUtil() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static booleancancelJob(String jobId, - ClusterSession csession) - -
    -           
    -static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, - String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -CLUSTER_STAT_IN_SEC

    -
    -public static final NumberFormat CLUSTER_STAT_IN_SEC
    -
    -
    -
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ClusterUtil

    -
    -public ClusterUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -cancelJob

    -
    -public static final boolean cancelJob(String jobId,
-                                      ClusterSession csession)
    -
    -
    -
    -
    -
    -
    - -

    -waitForResult

    -
    -public static final org.ggf.drmaa.JobInfo waitForResult(ClusterSession csession,
-                                                        String jobId)
-                                                 throws JobExecutionException
    -
    -
    - -
    Throws: -
    JobExecutionException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html deleted file mode 100644 index c74bb59..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html +++ /dev/null @@ -1,487 +0,0 @@ - - - - - - -JobRunner - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.cluster.drmaa -
    -Class JobRunner

    -
    -java.lang.Object
-  extended by compbio.engine.cluster.drmaa.JobRunner
-
    -
    -
    All Implemented Interfaces:
    SyncExecutor
    -
    -
    -
    -
    public class JobRunner
    extends Object
    implements SyncExecutor
    - - -

    -Single cluster job runner class -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    JobRunner(ConfiguredExecutable<?> confExec) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob() - -
    -          Stops running job.
    - booleancleanup() - -
    -          Clean up after the job
    - booleandeepClean() - -
    -           
    - voidexecuteJob() - -
    -          Execute the job
    -static JobRunnergetInstance(ConfiguredExecutable<?> executable) - -
    -           
    - org.ggf.drmaa.JobInfogetJobInfo() - -
    -          This method will block before the calculation has completed and then - return the object containing a job execution statistics
    - JobStatusgetJobStatus() - -
    -          Query the status of the job by its id.
    - StringgetWorkDirectory() - -
    -           
    - ConfiguredExecutable<?>waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JobRunner

    -
    -public JobRunner(ConfiguredExecutable<?> confExec)
-          throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -deepClean

    -
    -public boolean deepClean()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -cleanup

    -
    -public boolean cleanup()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Clean up after the job -

    -

    -
    Specified by:
    cleanup in interface SyncExecutor
    -
    -
    - -
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Stops running job. - Clean up is not performed. -

    -

    -
    Specified by:
    cancelJob in interface SyncExecutor
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getWorkDirectory

    -
    -public String getWorkDirectory()
    -
    -
    -
    Specified by:
    getWorkDirectory in interface SyncExecutor
    -
    -
    - -
    Returns:
    working directory if the task
    -
    -
    -
    - -

    -executeJob

    -
    -public void executeJob()
-                throws JobSubmissionException
    -
    -
    Description copied from interface: SyncExecutor
    -
    Execute the job -

    -

    -
    Specified by:
    executeJob in interface SyncExecutor
    -
    -
    - -
    Throws: -
    JobSubmissionException - if submission fails
    -
    -
    -
    - -

    -getJobInfo

    -
    -public org.ggf.drmaa.JobInfo getJobInfo()
-                                 throws JobExecutionException
    -
    -
    This method will block before the calculation has completed and then - return the object containing a job execution statistics -

    -

    -
    -
    -
    - -
    Returns:
    -
    Throws: -
    JobExecutionException
    -
    -
    -
    - -

    -waitForResult

    -
    -public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
    -
    -
    Description copied from interface: SyncExecutor
    -
    Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

    -

    -
    Specified by:
    waitForResult in interface SyncExecutor
    -
    -
    - -
    Returns:
    object from wich the result can be obtained -
    Throws: -
    JobExecutionException
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Query the status of the job by its id. -

    -

    -
    Specified by:
    getJobStatus in interface SyncExecutor
    -
    -
    - -
    Returns:
    - JobStatus
    -
    -
    -
    - -

    -getInstance

    -
    -public static JobRunner getInstance(ConfiguredExecutable<?> executable)
-                             throws JobSubmissionException
    -
    -
    -
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html deleted file mode 100644 index 85a911f..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html +++ /dev/null @@ -1,759 +0,0 @@ - - - - - - -StatisticManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.cluster.drmaa -
    -Class StatisticManager

    -
    -java.lang.Object
-  extended by compbio.engine.cluster.drmaa.StatisticManager
-
    -
    -
    -
    public class StatisticManager
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatisticManager(org.ggf.drmaa.JobInfo status) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetAllStats() - -
    -           
    - StringgetCalculationTime() - -
    -           
    - StringgetCPUTimeStat() - -
    -           
    - StringgetCPUUsageTime() - -
    -           
    - StringgetDataTransfered() - -
    -           
    - StringgetEndTime() - -
    -           
    - StringgetExecutionStat() - -
    -           
    - StringgetExitStatus() - -
    -           
    - StringgetIOWait() - -
    -           
    - StringgetJobId() - -
    -           
    - StringgetJobPriority() - -
    -           
    - StringgetMaxVMem() - -
    -           
    - StringgetMemoryStat() - -
    -           
    - Map<String,String>getRawUsage() - -
    -           
    - StringgetStartTime() - -
    -           
    - StringgetSubmissionTime() - -
    -           
    - StringgetTimeStat() - -
    -           
    - StringgetUsedSysTime() - -
    -           
    - StringgetUsedUserTime() - -
    -           
    - StringgetVMem() - -
    -           
    - booleanhasDump() - -
    -           
    - booleanhasExited() - -
    -           
    - booleanhasSignaled() - -
    -           
    - StringtermSignal() - -
    -           
    - StringtoString() - -
    -           
    - booleanwasAborted() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatisticManager

    -
    -public StatisticManager(org.ggf.drmaa.JobInfo status)
-                 throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getJobId

    -
    -public String getJobId()
-                throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -hasExited

    -
    -public boolean hasExited()
-                  throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -hasSignaled

    -
    -public boolean hasSignaled()
-                    throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -hasDump

    -
    -public boolean hasDump()
-                throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -termSignal

    -
    -public String termSignal()
-                  throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -wasAborted

    -
    -public boolean wasAborted()
-                   throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -getSubmissionTime

    -
    -public String getSubmissionTime()
    -
    -
    -
    -
    -
    -
    - -

    -getVMem

    -
    -public String getVMem()
    -
    -
    -
    -
    -
    -
    - -

    -getMaxVMem

    -
    -public String getMaxVMem()
    -
    -
    -
    -
    -
    -
    - -

    -getUsedSysTime

    -
    -public String getUsedSysTime()
    -
    -
    -
    -
    -
    -
    - -

    -getUsedUserTime

    -
    -public String getUsedUserTime()
    -
    -
    -
    -
    -
    -
    - -

    -getCalculationTime

    -
    -public String getCalculationTime()
    -
    -
    -
    -
    -
    -
    - -

    -getEndTime

    -
    -public String getEndTime()
    -
    -
    -
    -
    -
    -
    - -

    -getStartTime

    -
    -public String getStartTime()
    -
    -
    -
    -
    -
    -
    - -

    -getIOWait

    -
    -public String getIOWait()
    -
    -
    -
    -
    -
    -
    - -

    -getCPUUsageTime

    -
    -public String getCPUUsageTime()
    -
    -
    -
    -
    -
    -
    - -

    -getDataTransfered

    -
    -public String getDataTransfered()
    -
    -
    -
    -
    -
    -
    - -

    -getJobPriority

    -
    -public String getJobPriority()
    -
    -
    -
    -
    -
    -
    - -

    -getExitStatus

    -
    -public String getExitStatus()
    -
    -
    -
    -
    -
    -
    - -

    -getAllStats

    -
    -public String getAllStats()
-                   throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -getExecutionStat

    -
    -public String getExecutionStat()
-                        throws org.ggf.drmaa.DrmaaException
    -
    -
    - -
    Throws: -
    org.ggf.drmaa.DrmaaException
    -
    -
    -
    - -

    -getMemoryStat

    -
    -public String getMemoryStat()
    -
    -
    -
    -
    -
    -
    - -

    -getCPUTimeStat

    -
    -public String getCPUTimeStat()
    -
    -
    -
    -
    -
    -
    - -

    -getTimeStat

    -
    -public String getTimeStat()
    -
    -
    -
    -
    -
    -
    - -

    -getRawUsage

    -
    -public Map<String,String> getRawUsage()
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
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    - - - - - - - - - -
    -Packages that use ClusterSession
    compbio.engine.cluster.drmaa  
    -  -

    - - - - - -
    -Uses of ClusterSession in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa with parameters of type ClusterSession
    -static booleanClusterUtil.cancelJob(String jobId, - ClusterSession csession) - -
    -           
    -static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - String jobId) - -
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    - - - - - - - - - -
    -Packages that use JobRunner
    compbio.engine.cluster.drmaa  
    -  -

    - - - - - -
    -Uses of JobRunner in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return JobRunner
    -static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
    -           
    -  -

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    compbio.engine.cluster.drmaa.StatisticManager

    -
    - - - - - - - - - -
    -Packages that use StatisticManager
    compbio.engine.cluster.drmaa  
    -  -

    - - - - - -
    -Uses of StatisticManager in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return StatisticManager
    -static StatisticManagerClusterSession.getStatistics(org.ggf.drmaa.JobInfo status) - -
    -           
    -  -

    -

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    -Classes  - -
    -AsyncJobRunner -
    -ClusterSession -
    -ClusterUtil -
    -JobRunner -
    -StatisticManager
    - - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html deleted file mode 100644 index 006d168..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - -compbio.engine.cluster.drmaa - - - - - - - - - - - - -
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    -Package compbio.engine.cluster.drmaa -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AsyncJobRunnerSingle cluster job runner class
    ClusterSession 
    ClusterUtil 
    JobRunnerSingle cluster job runner class
    StatisticManager 
    -  - -

    -

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    -Packages that use compbio.engine.cluster.drmaa
    compbio.engine.cluster.drmaa  
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.engine.cluster.drmaa used by compbio.engine.cluster.drmaa
    ClusterSession - -
    -           
    JobRunner - -
    -          Single cluster job runner class
    StatisticManager - -
    -           
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    - - - -
    - -

    - -compbio.engine.cluster.dundee -
    -Enum _Queue

    -
    -java.lang.Object
-  extended by java.lang.Enum<_Queue>
-      extended by compbio.engine.cluster.dundee._Queue
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<_Queue>
    -
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public enum _Queue
    extends Enum<_Queue>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    BIGINT - -
    -          Deprecated.  
    BIGMEM - -
    -          Deprecated.  
    BIT64 - -
    -          Deprecated.  
    DEVEL - -
    -          Deprecated. Order of the constraint reflect the priority of the queue
    PRIBIT64 - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetMemoryLimit() - -
    -          Deprecated. return max memory limit in Mb
    -static _QueuegetQueue(int maxMemory, - int timeLimitInHours) - -
    -          Deprecated.  
    - _QueuegetQueue(String queueName) - -
    -          Deprecated.  
    -static _QueuegetQueueByMemoryRequirements(int maxMemory) - -
    -          Deprecated.  
    - intgetTimeLimit() - -
    -          Deprecated. 0 - unlimited
    - booleanhasTimeLimit() - -
    -          Deprecated.  
    - StringtoString() - -
    -          Deprecated.  
    -static _QueuevalueOf(String name) - -
    -          Deprecated. Returns the enum constant of this type with the specified name.
    -static _Queue[]values() - -
    -          Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -DEVEL

    -
    -public static final _Queue DEVEL
    -
    -
    Deprecated. 
    Order of the constraint reflect the priority of the queue -

    -

    -
    -
    -
    - -

    -PRIBIT64

    -
    -public static final _Queue PRIBIT64
    -
    -
    Deprecated. 
    -
    -
    -
    - -

    -BIT64

    -
    -public static final _Queue BIT64
    -
    -
    Deprecated. 
    -
    -
    -
    - -

    -BIGINT

    -
    -public static final _Queue BIGINT
    -
    -
    Deprecated. 
    -
    -
    -
    - -

    -BIGMEM

    -
    -public static final _Queue BIGMEM
    -
    -
    Deprecated. 
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static _Queue[] values()
    -
    -
    Deprecated. 
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (_Queue c : _Queue.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static _Queue valueOf(String name)
    -
    -
    Deprecated. 
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    Deprecated. 
    -
    Overrides:
    toString in class Enum<_Queue>
    -
    -
    -
    -
    -
    -
    - -

    -getTimeLimit

    -
    -public int getTimeLimit()
    -
    -
    Deprecated. 
    0 - unlimited -

    -

    - -
    Returns:
    max runtime in hours
    -
    -
    -
    - -

    -hasTimeLimit

    -
    -public boolean hasTimeLimit()
    -
    -
    Deprecated. 
    - -
    Returns:
    true if the queue has time limit, false overwise
    -
    -
    -
    - -

    -getMemoryLimit

    -
    -public int getMemoryLimit()
    -
    -
    Deprecated. 
    return max memory limit in Mb -

    -

    - -
    Returns:
    -
    -
    -
    - -

    -getQueueByMemoryRequirements

    -
    -public static _Queue getQueueByMemoryRequirements(int maxMemory)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getQueue

    -
    -public static _Queue getQueue(int maxMemory,
-                              int timeLimitInHours)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getQueue

    -
    -public _Queue getQueue(String queueName)
    -
    -
    Deprecated. 
    -
    -
    -
    - -
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    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html deleted file mode 100644 index 847edac..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - -Uses of Class compbio.engine.cluster.dundee._Queue - - - - - - - - - - - - -
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    -Packages that use _Queue
    compbio.engine.cluster.dundee  
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - -
    -Uses of _Queue in compbio.engine.cluster.dundee
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.dundee that return _Queue
    -static _Queue_Queue.getQueue(int maxMemory, - int timeLimitInHours) - -
    -          Deprecated.  
    - _Queue_Queue.getQueue(String queueName) - -
    -          Deprecated.  
    -static _Queue_Queue.getQueueByMemoryRequirements(int maxMemory) - -
    -          Deprecated.  
    -static _Queue_Queue.valueOf(String name) - -
    -          Deprecated. Returns the enum constant of this type with the specified name.
    -static _Queue[]_Queue.values() - -
    -          Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - -
    -Uses of _Queue in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return _Queue
    - _Queue_NativeSpecHelper.getApproprieteQueue() - -
    -          Deprecated.  
    -  -

    -

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    -Enums  - -
    -_Queue
    - - - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html deleted file mode 100644 index 2f7e728..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.engine.cluster.dundee - - - - - - - - - - - - -
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    -Package compbio.engine.cluster.dundee -

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    -Enum Summary
    _QueueDeprecated.
    -  - -

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    -Packages that use compbio.engine.cluster.dundee
    compbio.engine.cluster.dundee  
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.cluster.dundee used by compbio.engine.cluster.dundee
    _Queue - -
    -          Deprecated. 
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.cluster.dundee used by compbio.runner
    _Queue - -
    -          Deprecated. 
    -  -

    -

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    - - - -
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    - -compbio.engine.conf -
    -Class DirectoryManager

    -
    -java.lang.Object
-  extended by compbio.engine.conf.DirectoryManager
-
    -
    -
    -
    public class DirectoryManager
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringDELIM - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    DirectoryManager() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static Class<Executable<?>>getClass(String taskId) - -
    -           
    -static StringgetTaskDirectory(Class<?> clazz) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
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    - -

    -DELIM

    -
    -public static final String DELIM
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -DirectoryManager

    -
    -public DirectoryManager()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTaskDirectory

    -
    -public static String getTaskDirectory(Class<?> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -getClass

    -
    -public static Class<Executable<?>> getClass(String taskId)
    -
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    - - - -
    - -

    - -compbio.engine.conf -
    -Class PropertyHelperManager

    -
    -java.lang.Object
-  extended by compbio.engine.conf.PropertyHelperManager
-
    -
    -
    -
    public final class PropertyHelperManager
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringconfDir - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    PropertyHelperManager() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static StringgetLocalPath() - -
    -          Method return the absolute path to the project root directory.
    -static compbio.util.PropertyHelpergetPropertyHelper() - -
    -          Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -confDir

    -
    -public static final String confDir
    -
    -
    -
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -PropertyHelperManager

    -
    -public PropertyHelperManager()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getPropertyHelper

    -
    -public static compbio.util.PropertyHelper getPropertyHelper()
    -
    -
    Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. Then prepend this absolute path to the rest of - paths pros: no input from user cons: relocation of the source may cause - problems 2) Require users to add configuration directories to the class - path and then load entries from it. pros: cons: Many paths needs to be - added. Put significant burden on the user. Hard to tell web appl server - to add these entries to its class path. 3) Ask for project source - directory explicitly in the configuration. pros cons: similar to 1, but - this initial configuration file must reside in well known location! Why - ask users what can be found automatically? 4) Have everything in the - location already in class path for tomcat. cons: only classes and - lib/*.jar are added, eclipse will remove non classses from classes dir. - - Try 1 - succeed. -

    -

    - -
    Returns:
    an instance
    -
    -
    -
    - -

    -getLocalPath

    -
    -public static String getLocalPath()
    -
    -
    Method return the absolute path to the project root directory. It assumes - the following structure of the project project root conf settings - binaries WEB-INF classes compbio engine conf If the structure changes it - must be reflected in this method -

    -

    - -
    Returns:
    the local path -
    Throws: -
    RuntimeException - if cannot determine the local path
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html deleted file mode 100644 index fe2287e..0000000 --- a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html +++ /dev/null @@ -1,507 +0,0 @@ - - - - - - -RunnerConfigMarshaller - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.conf -
    -Class RunnerConfigMarshaller<T>

    -
    -java.lang.Object
-  extended by compbio.engine.conf.RunnerConfigMarshaller<T>
-
    -
    -
    -
    public class RunnerConfigMarshaller<T>
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    RunnerConfigMarshaller(Class<?> rootClass) - -
    -           
    RunnerConfigMarshaller(Class<?> rootClass, - Class<?>... classes) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static SchemagetSchema(String schemafile) - -
    -           
    -static ValidatorgetValidator(Schema schema) - -
    -           
    -static ValidatorgetValidator(String schemafile) - -
    -           
    - - - - - -
    -<V> V
    -    		read(InputStream instream, - Class<V> resultElemType) - -
    -           
    - - - - - -
    -<V> V
    -    		read(InputStream instream, - Class<V> resultElemType, - Class<?>... classes) - -
    -           
    - - - - - -
    -<V> V
    -    		readAndValidate(InputStream document, - Class<V> resultElemType) - -
    -           
    -static booleanvalidate(Validator validator, - String document) - -
    -           
    - voidwrite(Object xmlRootElement, - OutputStream out) - -
    -           
    - voidwriteAndValidate(Object xmlRootElement, - String schemafile, - OutputStream out) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -RunnerConfigMarshaller

    -
    -public RunnerConfigMarshaller(Class<?> rootClass)
-                       throws JAXBException
    -
    -
    - -
    Throws: -
    JAXBException
    -
    -
    - -

    -RunnerConfigMarshaller

    -
    -public RunnerConfigMarshaller(Class<?> rootClass,
-                              Class<?>... classes)
-                       throws JAXBException
    -
    -
    - -
    Throws: -
    JAXBException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -write

    -
    -public void write(Object xmlRootElement,
-                  OutputStream out)
-           throws JAXBException,
-                  IOException
    -
    -
    - -
    Throws: -
    JAXBException -
    IOException
    -
    -
    -
    - -

    -writeAndValidate

    -
    -public void writeAndValidate(Object xmlRootElement,
-                             String schemafile,
-                             OutputStream out)
-                      throws JAXBException,
-                             IOException,
-                             SAXException
    -
    -
    - -
    Throws: -
    JAXBException -
    IOException -
    SAXException
    -
    -
    -
    - -

    -getSchema

    -
    -public static Schema getSchema(String schemafile)
-                        throws SAXException
    -
    -
    - -
    Throws: -
    SAXException
    -
    -
    -
    - -

    -getValidator

    -
    -public static Validator getValidator(String schemafile)
-                              throws SAXException
    -
    -
    - -
    Returns:
    validator instance -
    Throws: -
    SAXException
    -
    -
    -
    - -

    -getValidator

    -
    -public static Validator getValidator(Schema schema)
-                              throws SAXException
    -
    -
    - -
    Throws: -
    SAXException
    -
    -
    -
    - -

    -validate

    -
    -public static boolean validate(Validator validator,
-                               String document)
-                        throws IOException,
-                               SAXException
    -
    -
    - -
    Throws: -
    IOException -
    SAXException
    -
    -
    -
    - -

    -readAndValidate

    -
    -public <V> V readAndValidate(InputStream document,
-                             Class<V> resultElemType)
-                  throws JAXBException,
-                         IOException,
-                         SAXException
    -
    -
    - -
    Throws: -
    JAXBException -
    IOException -
    SAXException
    -
    -
    -
    - -

    -read

    -
    -public <V> V read(InputStream instream,
-                  Class<V> resultElemType)
-       throws JAXBException
    -
    -
    - -
    Throws: -
    JAXBException
    -
    -
    -
    - -

    -read

    -
    -public <V> V read(InputStream instream,
-                  Class<V> resultElemType,
-                  Class<?>... classes)
-       throws JAXBException
    -
    -
    - -
    Throws: -
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    - -

    - -compbio.engine.conf -
    -Class _Key

    -
    -java.lang.Object
-  extended by compbio.engine.conf._Key
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public final class _Key
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringDELIM - -
    -          Deprecated.  
    -  - - - - - - - - - - -
    -Constructor Summary
    _Key(Class<?> clazz) - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -          Deprecated.  
    - inthashCode() - -
    -          Deprecated.  
    -static _Keyparse(String key) - -
    -          Deprecated.  
    - StringtoString() - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -DELIM

    -
    -public static final String DELIM
    -
    -
    Deprecated. 
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -_Key

    -
    -public _Key(Class<?> clazz)
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    Deprecated. 
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    Deprecated. 
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    Deprecated. 
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -parse

    -
    -public static _Key parse(String key)
    -
    -
    Deprecated. 
    -
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    -Uses of Class
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    -
    - - - - - - - - - -
    -Packages that use _Key
    compbio.engine.conf  
    -  -

    - - - - - -
    -Uses of _Key in compbio.engine.conf
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.conf that return _Key
    -static _Key_Key.parse(String key) - -
    -          Deprecated.  
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -_Key -
    -DirectoryManager -
    -PropertyHelperManager -
    -RunnerConfigMarshaller
    - - - - diff --git a/website/full_javadoc/compbio/engine/conf/package-summary.html b/website/full_javadoc/compbio/engine/conf/package-summary.html deleted file mode 100644 index cd728a9..0000000 --- a/website/full_javadoc/compbio/engine/conf/package-summary.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - -compbio.engine.conf - - - - - - - - - - - - -
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    -

    -Package compbio.engine.conf -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    _KeyDeprecated.
    DirectoryManager 
    PropertyHelperManager 
    RunnerConfigMarshaller<T> 
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
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    -Hierarchy For Package compbio.engine.conf -

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    -Packages that use compbio.engine.conf
    compbio.engine.conf  
    -  -

    - - - - - - - - -
    -Classes in compbio.engine.conf used by compbio.engine.conf
    _Key - -
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    - - - -
    - -

    - -compbio.engine.local -
    -Class AsyncLocalRunner

    -
    -java.lang.Object
-  extended by compbio.engine.local.AsyncLocalRunner
-
    -
    -
    All Implemented Interfaces:
    AsyncExecutor
    -
    -
    -
    -
    public final class AsyncLocalRunner
    extends Object
    implements AsyncExecutor
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    AsyncLocalRunner() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -          Stop running job.
    - booleancleanup(String jobId) - -
    -          Remove all files and a job directory for a jobid.
    - JobStatusgetJobStatus(String jobId) - -
    -          Query the status of the job
    - ConfiguredExecutable<?>getResults(String taskId) - -
    -          Retrieve the results of the job.
    - StringgetWorkDirectory(String jobId) - -
    -           
    - StringsubmitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AsyncLocalRunner

    -
    -public AsyncLocalRunner()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getWorkDirectory

    -
    -public String getWorkDirectory(String jobId)
    -
    -
    -
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    -
    -
    -
    Parameters:
    jobId - unique job identifier -
    Returns:
    task working directory
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

    -

    -
    Specified by:
    cancelJob in interface AsyncExecutor
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Query the status of the job -

    -

    -
    Specified by:
    getJobStatus in interface AsyncExecutor
    -
    -
    - -
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -submitJob

    -
    -public String submitJob(ConfiguredExecutable<?> executable)
-                 throws JobSubmissionException
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

    -

    -
    Specified by:
    submitJob in interface AsyncExecutor
    -
    -
    - -
    Returns:
    unique job identifier -
    Throws: -
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    -
    -
    -
    - -

    -cleanup

    -
    -public boolean cleanup(String jobId)
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Remove all files and a job directory for a jobid. -

    -

    -
    Specified by:
    cleanup in interface AsyncExecutor
    -
    -
    -
    Parameters:
    jobId - -
    Returns:
    true if all files were removed, false otherwise
    -
    -
    -
    - -

    -getResults

    -
    -public ConfiguredExecutable<?> getResults(String taskId)
-                                   throws ResultNotAvailableException
    -
    -
    Description copied from interface: AsyncExecutor
    -
    Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

    -

    -
    Specified by:
    getResults in interface AsyncExecutor
    -
    -
    -
    Parameters:
    taskId - job identifier obtained at the job submission -
    Returns:
    ConfiguredExecutable object from which result can be obtained -
    Throws: -
    ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.local -
    -Class ExecutableWrapper

    -
    -java.lang.Object
-  extended by compbio.engine.local.ExecutableWrapper
-
    -
    -
    All Implemented Interfaces:
    Callable<ConfiguredExecutable<?>>
    -
    -
    -
    -
    @Immutable
-public final class ExecutableWrapper
    extends Object
    implements Callable<ConfiguredExecutable<?>>
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringPROC_ERR_FILE - -
    -           
    -static StringPROC_OUT_FILE - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - ConfiguredExecutable<?>call() - -
    -          It is vital that output and error streams are captured immediately for - this call() to succeed.
    -static voidshutdownService() - -
    -          Stops internal executor service which captures streams of native - executables.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -PROC_OUT_FILE

    -
    -public static final String PROC_OUT_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -PROC_ERR_FILE

    -
    -public static final String PROC_ERR_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ExecutableWrapper

    -
    -public ExecutableWrapper(ConfiguredExecutable<?> executable,
-                         String workDirectory)
-                  throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -shutdownService

    -
    -public static final void shutdownService()
    -
    -
    Stops internal executor service which captures streams of native - executables. This method is intended for stopping service if deployed in - the web application content. There is NO NEED of using this method - otherwise as the executor service is taken care of internally. -

    -

    -
    -
    -
    -
    -
    -
    -
    - -

    -call

    -
    -public ConfiguredExecutable<?> call()
-                             throws IOException
    -
    -
    It is vital that output and error streams are captured immediately for - this call() to succeed. Thus each instance if ExecutableWrapper has 2 its - own thread ready to capture the output. If executor could not execute - capture immediately this could lead to the call method to stale, as - execution could not proceed without output being captured. Every call to - call() method will use 2 threads -

    -

    -
    Specified by:
    call in interface Callable<ConfiguredExecutable<?>>
    -
    -
    - -
    Throws: -
    IOException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html deleted file mode 100644 index 5718816..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - -LocalEngineUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.local -
    -Class LocalEngineUtil

    -
    -java.lang.Object
-  extended by compbio.engine.local.LocalEngineUtil
-
    -
    -
    -
    public final class LocalEngineUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    LocalEngineUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static booleancancelJob(Future<ConfiguredExecutable<?>> future, - String workDirectory) - -
    -           
    -static booleancleanup(ConfiguredExecutable<?> confExecutable) - -
    -           
    -static JobStatusgetJobStatus(Future<ConfiguredExecutable<?>> future) - -
    -           
    -static JobStatusgetRecordedJobStatus(String jobId) - -
    -           
    -static ConfiguredExecutable<?>getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -LocalEngineUtil

    -
    -public LocalEngineUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -cancelJob

    -
    -public static boolean cancelJob(Future<ConfiguredExecutable<?>> future,
-                                String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getJobStatus

    -
    -public static JobStatus getJobStatus(Future<ConfiguredExecutable<?>> future)
    -
    -
    -
    -
    -
    -
    - -

    -getRecordedJobStatus

    -
    -public static JobStatus getRecordedJobStatus(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -cleanup

    -
    -public static boolean cleanup(ConfiguredExecutable<?> confExecutable)
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public static ConfiguredExecutable<?> getResults(Future<ConfiguredExecutable<?>> future,
-                                                 String taskId)
-                                          throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html deleted file mode 100644 index f30d7e4..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html +++ /dev/null @@ -1,315 +0,0 @@ - - - - - - -LocalExecutorService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.local -
    -Class LocalExecutorService

    -
    -java.lang.Object
-  extended by java.util.concurrent.AbstractExecutorService
-      extended by java.util.concurrent.ThreadPoolExecutor
-          extended by compbio.engine.local.LocalExecutorService
-
    -
    -
    All Implemented Interfaces:
    Executor, ExecutorService
    -
    -
    -
    -
    public final class LocalExecutorService
    extends ThreadPoolExecutor
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor
    ThreadPoolExecutor.AbortPolicy, ThreadPoolExecutor.CallerRunsPolicy, ThreadPoolExecutor.DiscardOldestPolicy, ThreadPoolExecutor.DiscardPolicy
    -  - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancanAcceptMoreWork() - -
    -          If the Executor queue is empty
    -static LocalExecutorServicegetExecutor() - -
    -          This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally
    -static voidshutDown() - -
    -          This stops all executing processes via interruption.
    -  - - - - - - - -
    Methods inherited from class java.util.concurrent.ThreadPoolExecutor
    allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow
    -  - - - - - - - -
    Methods inherited from class java.util.concurrent.AbstractExecutorService
    invokeAll, invokeAll, invokeAny, invokeAny, submit, submit, submit
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getExecutor

    -
    -public static LocalExecutorService getExecutor()
    -
    -
    This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -

    -

    - -
    Returns:
    the instance
    -
    -
    -
    - -

    -shutDown

    -
    -public static void shutDown()
    -
    -
    This stops all executing processes via interruption. Thus it is vital - that all processes that use this service respond to interruption - - Stops internal executor service which captures streams of native - executables. This method is intended for stopping service if deployed in - the web application context. There is NO NEED of using this method - otherwise as the executor service is taken care of internally. -

    -

    -
    -
    -
    -
    - -

    -canAcceptMoreWork

    -
    -public boolean canAcceptMoreWork()
    -
    -
    If the Executor queue is empty -

    -

    - -
    Returns:
    true is not all threads are busy, false otherwise
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/local/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html deleted file mode 100644 index 832aed9..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalRunner.html +++ /dev/null @@ -1,398 +0,0 @@ - - - - - - -LocalRunner - - - - - - - - - - - - -
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    - -

    - -compbio.engine.local -
    -Class LocalRunner

    -
    -java.lang.Object
-  extended by compbio.engine.local.LocalRunner
-
    -
    -
    All Implemented Interfaces:
    SyncExecutor
    -
    -
    -
    -
    public final class LocalRunner
    extends Object
    implements SyncExecutor
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    LocalRunner(ConfiguredExecutable<?> executable) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob() - -
    -          Stops running job.
    - booleancleanup() - -
    -          Clean up after the job
    - voidexecuteJob() - -
    -          Execute the job
    - JobStatusgetJobStatus() - -
    -          Query the status of the job by its id.
    - StringgetWorkDirectory() - -
    -           
    - ConfiguredExecutable<?>waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -LocalRunner

    -
    -public LocalRunner(ConfiguredExecutable<?> executable)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getWorkDirectory

    -
    -public String getWorkDirectory()
    -
    -
    -
    Specified by:
    getWorkDirectory in interface SyncExecutor
    -
    -
    - -
    Returns:
    working directory if the task
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Stops running job. - Clean up is not performed. -

    -

    -
    Specified by:
    cancelJob in interface SyncExecutor
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Query the status of the job by its id. -

    -

    -
    Specified by:
    getJobStatus in interface SyncExecutor
    -
    -
    - -
    Returns:
    - JobStatus
    -
    -
    -
    - -

    -executeJob

    -
    -public void executeJob()
-                throws JobSubmissionException
    -
    -
    Description copied from interface: SyncExecutor
    -
    Execute the job -

    -

    -
    Specified by:
    executeJob in interface SyncExecutor
    -
    -
    - -
    Throws: -
    JobSubmissionException - if submission fails
    -
    -
    -
    - -

    -waitForResult

    -
    -public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
    -
    -
    Description copied from interface: SyncExecutor
    -
    Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

    -

    -
    Specified by:
    waitForResult in interface SyncExecutor
    -
    -
    - -
    Returns:
    object from wich the result can be obtained -
    Throws: -
    CancellationException -
    JobExecutionException
    -
    -
    -
    - -

    -cleanup

    -
    -public boolean cleanup()
    -
    -
    Description copied from interface: SyncExecutor
    -
    Clean up after the job -

    -

    -
    Specified by:
    cleanup in interface SyncExecutor
    -
    -
    - -
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html deleted file mode 100644 index c155b2e..0000000 --- a/website/full_javadoc/compbio/engine/local/StreamGobbler.html +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - -StreamGobbler - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.engine.local -
    -Class StreamGobbler

    -
    -java.lang.Object
-  extended by compbio.engine.local.StreamGobbler
-
    -
    -
    All Implemented Interfaces:
    Runnable
    -
    -
    -
    -
    @ThreadSafe
-public class StreamGobbler
    extends Object
    implements Runnable
    - - -

    -

    - -

    - - - - - - - - - - - - -
    -Method Summary
    - voidrun() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -run

    -
    -public void run()
    -
    -
    -
    Specified by:
    run in interface Runnable
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html deleted file mode 100644 index e11ca46..0000000 --- a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.engine.local.AsyncLocalRunner - - - - - - - - - - - - -
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    -Uses of Class
    compbio.engine.local.AsyncLocalRunner

    -
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    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
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    -

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    -Interface Summary
    AsyncExecutorAn asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    SyncExecutorSynchronous executor, is an engine to run the Executable synchronously.
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    CleanerDeprecated.
    ClusterJobId 
    Configurator 
    FilePuller 
    Job 
    LoadBalancerThis class decides where to execute the job.
    ProgressGetter 
    PulledFileCache 
    SubmissionManagerSubmit jobs for execution
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    compbio.engine  
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    compbio.engine.local  
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.engine used by compbio.engine
    AsyncExecutor - -
    -          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    ClusterJobId - -
    -           
    FilePuller - -
    -           
    Job - -
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    SyncExecutor - -
    -          Synchronous executor, is an engine to run the Executable synchronously.
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.engine used by compbio.engine.cluster.drmaa
    AsyncExecutor - -
    -          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    ClusterJobId - -
    -           
    SyncExecutor - -
    -          Synchronous executor, is an engine to run the Executable synchronously.
    -  -

    - - - - - - - - - - - -
    -Classes in compbio.engine used by compbio.engine.local
    AsyncExecutor - -
    -          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    SyncExecutor - -
    -          Synchronous executor, is an engine to run the Executable synchronously.
    -  -

    - - - - - - - - -
    -Classes in compbio.engine used by compbio.ws.server
    AsyncExecutor - -
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    - -compbio.metadata -
    -Interface Argument<T>

    -
    -
    Type Parameters:
    T - executable type
    -
    -
    All Known Implementing Classes:
    Option, Parameter
    -
    -
    -
    -
    public interface Argument<T>
    - - -

    -An unmodifiable view for the options and parameters, with one exception - it - allows to set a value -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date December 2009
    -
    See Also:
    Parameter, -Option
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetDefaultValue() - -
    -           
    - StringgetDescription() - -
    -           
    - URLgetFurtherDetails() - -
    -           
    - StringgetName() - -
    -           
    - List<String>getPossibleValues() - -
    -           
    - voidsetValue(String defaultValue) - -
    -          Set default values for the parameter or an option
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getFurtherDetails

    -
    -URL getFurtherDetails()
    -
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    -getDefaultValue

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    -String getDefaultValue()
    -
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    -getDescription

    -
    -String getDescription()
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    -getName

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    -String getName()
    -
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    -getPossibleValues

    -
    -List<String> getPossibleValues()
    -
    -
    - -
    Returns:
    List of values allowed for an Argument
    -
    -
    -
    - -

    -setValue

    -
    -void setValue(String defaultValue)
-              throws WrongParameterException
    -
    -
    Set default values for the parameter or an option -

    -

    -
    Parameters:
    defaultValue - the value to be set -
    Throws: -
    WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
    See Also:
    ValueConstrain
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    - -compbio.metadata -
    -Class ChunkHolder

    -
    -java.lang.Object
-  extended by compbio.metadata.ChunkHolder
-
    -
    -
    -
    public class ChunkHolder
    extends Object
    - - -

    -Represents a chunk of a string data together with the position in a file for - the next read operation. -

    - -

    -

    -
    Version:
    -
    1.0 December 2009
    -
    Author:
    -
    pvtroshin
    -
    -
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    - - - - - - - - - - - -
    -Constructor Summary
    ChunkHolder(String chunk, - long position) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetChunk() - -
    -           
    - longgetNextPosition() - -
    -           
    - inthashCode() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ChunkHolder

    -
    -public ChunkHolder(String chunk,
-                   long position)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getChunk

    -
    -public String getChunk()
    -
    -
    -
    -
    -
    -
    - -

    -getNextPosition

    -
    -public long getNextPosition()
    -
    -
    -
    -
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    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
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    Overrides:
    equals in class Object
    -
    -
    -
    -
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    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
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    -
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    -hashCode

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    -public int hashCode()
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    Overrides:
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    - - - diff --git a/website/full_javadoc/compbio/metadata/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index e4a8220..0000000 --- a/website/full_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -
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    - -compbio.metadata -
    -Class JobExecutionException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobExecutionException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class JobExecutionException
    extends Exception
    - - -

    -JobExecutionException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides DrmaaException -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    JobExecutionException(String message) - -
    -           
    JobExecutionException(String message, - Throwable cause) - -
    -           
    JobExecutionException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JobExecutionException

    -
    -public JobExecutionException(String message)
    -
    -
    -
    - -

    -JobExecutionException

    -
    -public JobExecutionException(Throwable cause)
    -
    -
    -
    - -

    -JobExecutionException

    -
    -public JobExecutionException(String message,
-                             Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 2de22a6..0000000 --- a/website/full_javadoc/compbio/metadata/JobStatus.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -JobStatus - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Enum JobStatus

    -
    -java.lang.Object
-  extended by java.lang.Enum<JobStatus>
-      extended by compbio.metadata.JobStatus
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<JobStatus>
    -
    -
    -
    -
    public enum JobStatus
    extends Enum<JobStatus>
    - - -

    -The status of the job. -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    CANCELLED - -
    -          Jobs that has been cancelled
    COLLECTED - -
    -          Results has been collected
    FAILED - -
    -          Failed jobs
    FINISHED - -
    -          Finished jobs
    PENDING - -
    -          Jobs which are in the queue and awaiting execution reported for cluster - jobs only
    RUNNING - -
    -          Jobs that are running
    STARTED - -
    -          Job calculation has been started.
    SUBMITTED - -
    -          Job has been submitted.
    UNDEFINED - -
    -          Represents jobs with unknown status
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static JobStatusvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JobStatus[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -PENDING

    -
    -public static final JobStatus PENDING
    -
    -
    Jobs which are in the queue and awaiting execution reported for cluster - jobs only -

    -

    -
    -
    -
    - -

    -RUNNING

    -
    -public static final JobStatus RUNNING
    -
    -
    Jobs that are running -

    -

    -
    -
    -
    - -

    -CANCELLED

    -
    -public static final JobStatus CANCELLED
    -
    -
    Jobs that has been cancelled -

    -

    -
    -
    -
    - -

    -FINISHED

    -
    -public static final JobStatus FINISHED
    -
    -
    Finished jobs -

    -

    -
    -
    -
    - -

    -FAILED

    -
    -public static final JobStatus FAILED
    -
    -
    Failed jobs -

    -

    -
    -
    -
    - -

    -UNDEFINED

    -
    -public static final JobStatus UNDEFINED
    -
    -
    Represents jobs with unknown status -

    -

    -
    -
    -
    - -

    -STARTED

    -
    -public static final JobStatus STARTED
    -
    -
    Job calculation has been started. First status reported by the local - engine -

    -

    -
    -
    -
    - -

    -SUBMITTED

    -
    -public static final JobStatus SUBMITTED
    -
    -
    Job has been submitted. This status is only set for cluster jobs -

    -

    -
    -
    -
    - -

    -COLLECTED

    -
    -public static final JobStatus COLLECTED
    -
    -
    Results has been collected -

    -

    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static JobStatus[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (JobStatus c : JobStatus.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static JobStatus valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index 3ee4bad..0000000 --- a/website/full_javadoc/compbio/metadata/JobSubmissionException.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -JobSubmissionException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class JobSubmissionException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    Direct Known Subclasses:
    LimitExceededException, UnsupportedRuntimeException
    -
    -
    -
    -
    public class JobSubmissionException
    extends Exception
    - - -

    -Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException. If - this exception is thrown the task has not been calculated -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date December 2009
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    JobSubmissionException(String message) - -
    -           
    JobSubmissionException(String message, - Throwable cause) - -
    -           
    JobSubmissionException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JobSubmissionException

    -
    -public JobSubmissionException(String message)
    -
    -
    -
    - -

    -JobSubmissionException

    -
    -public JobSubmissionException(Throwable cause)
    -
    -
    -
    - -

    -JobSubmissionException

    -
    -public JobSubmissionException(String message,
-                              Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index 8e90c39..0000000 --- a/website/full_javadoc/compbio/metadata/Limit.html +++ /dev/null @@ -1,478 +0,0 @@ - - - - - - -Limit - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class Limit<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.Limit<T>
-
    -
    -
    Type Parameters:
    T - the type of an executable for which this limit is defined.
    -
    -
    -
    public class Limit<T>
    extends Object
    - - -

    -A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. Also contains static method for determining the - number of sequence and their average length in the List -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    LimitsManager
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    Limit(int seqNumber, - int seqLength, - String preset) - -
    -          Instantiate the limit
    Limit(int seqNumber, - int seqLength, - String preset, - boolean isDefault) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - intgetAvgSeqLength() - -
    -           
    -static intgetAvgSequenceLength(List<FastaSequence> data) - -
    -          Calculates an average sequence length of the dataset
    - StringgetPreset() - -
    -           
    - intgetSeqNumber() - -
    -           
    - inthashCode() - -
    -           
    - booleanisDefault() - -
    -           
    - booleanisExceeded(List<FastaSequence> data) - -
    -          Checks if the number of sequences or their average length in the dataset - exceeds this limit.
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Limit

    -
    -public Limit(int seqNumber,
-             int seqLength,
-             String preset)
    -
    -
    Instantiate the limit -

    -

    -
    Parameters:
    seqNumber - the maximum number of sequences allowed for calculation. - Required
    seqLength - the average length of the sequence, optional
    preset - the name of preset if any, optional -
    Throws: -
    IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
    -
    -
    - -

    -Limit

    -
    -public Limit(int seqNumber,
-             int seqLength,
-             String preset,
-             boolean isDefault)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getPreset

    -
    -public String getPreset()
    -
    -
    -
    -
    -
    -
    - -

    -getAvgSeqLength

    -
    -public int getAvgSeqLength()
    -
    -
    - -
    Returns:
    the allowed average sequence length
    -
    -
    -
    - -

    -getSeqNumber

    -
    -public int getSeqNumber()
    -
    -
    - -
    Returns:
    the maximum number of sequences allowed
    -
    -
    -
    - -

    -isDefault

    -
    -public boolean isDefault()
    -
    -
    - -
    Returns:
    true is this is a default limit to be used, false otherwise
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -isExceeded

    -
    -public boolean isExceeded(List<FastaSequence> data)
    -
    -
    Checks if the number of sequences or their average length in the dataset - exceeds this limit. -

    -

    -
    Parameters:
    data - the dataset to measure -
    Returns:
    true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise. First check the number of sequences - in the dataset and if it exceeds the limit return true - irrespective of the average length. If the number of sequences in - the dataset is less than the limit and average length is defined, - then check whether the total number of letters (number of - sequence multiplied by the average sequence length) is greater - then the total number of letters in the dataset. Returns true if - the total number of letters in the dataset is greater than the - limit, false otherwise.
    -
    -
    -
    - -

    -getAvgSequenceLength

    -
    -public static int getAvgSequenceLength(List<FastaSequence> data)
    -
    -
    Calculates an average sequence length of the dataset -

    -

    -
    Parameters:
    data - -
    Returns:
    an average sequence length in the input dataset
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/LimitExceededException.html b/website/full_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index 536f610..0000000 --- a/website/full_javadoc/compbio/metadata/LimitExceededException.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -LimitExceededException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class LimitExceededException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.LimitExceededException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class LimitExceededException
    extends JobSubmissionException
    - - -

    -This exception is thrown if the task larger in size that the limit that - applies to the calculation. -

    - -

    -

    -
    Version:
    -
    1.0 February 2010
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Limit, -Serialized Form
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    LimitExceededException(String message) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetActualNumberofSequences() - -
    -           
    - intgetNumberOfSequencesAllowed() - -
    -           
    - intgetSequenceLenghtActual() - -
    -           
    - intgetSequenceLenghtAllowed() - -
    -           
    -static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -LimitExceededException

    -
    -public LimitExceededException(String message)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -newLimitExceeded

    -
    -public static LimitExceededException newLimitExceeded(Limit<?> limit,
-                                                      List<FastaSequence> seqs)
    -
    -
    -
    -
    -
    -
    - -

    -getNumberOfSequencesAllowed

    -
    -public int getNumberOfSequencesAllowed()
    -
    -
    -
    -
    -
    -
    - -

    -getActualNumberofSequences

    -
    -public int getActualNumberofSequences()
    -
    -
    -
    -
    -
    -
    - -

    -getSequenceLenghtAllowed

    -
    -public int getSequenceLenghtAllowed()
    -
    -
    -
    -
    -
    -
    - -

    -getSequenceLenghtActual

    -
    -public int getSequenceLenghtActual()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/LimitsManager.html b/website/full_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index 8916f78..0000000 --- a/website/full_javadoc/compbio/metadata/LimitsManager.html +++ /dev/null @@ -1,363 +0,0 @@ - - - - - - -LimitsManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class LimitsManager<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.LimitsManager<T>
-
    -
    -
    Type Parameters:
    T - executable type
    -
    -
    -
    public class LimitsManager<T>
    extends Object
    - - -

    -A collection of Limits -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Limit
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    LimitsManager() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Limit<T>getDefaultLimit() - -
    -           
    - Limit<T>getLimitByName(String presetName) - -
    -           
    - List<Limit<T>>getLimits() - -
    -           
    - StringtoString() - -
    -           
    - voidvalidate(PresetManager<T> presets) - -
    -          Validate Limits
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -LimitsManager

    -
    -public LimitsManager()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getLimits

    -
    -public List<Limit<T>> getLimits()
    -
    -
    - -
    Returns:
    all limits defined for an executable T
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getLimitByName

    -
    -public Limit<T> getLimitByName(String presetName)
    -
    -
    -
    Parameters:
    presetName - -
    Returns:
    Limit defined for the executable T and presetName. If no limit is - defined for the presetName then default Limit is returned. If - presetName is empty or null than the default Limit will be - returned. If not limit defined for the type T than NULL will be - returned
    -
    -
    -
    - -

    -getDefaultLimit

    -
    -public Limit<T> getDefaultLimit()
    -
    -
    - -
    Returns:
    the default Limit for an executable type T
    -
    -
    -
    - -

    -validate

    -
    -public void validate(PresetManager<T> presets)
-              throws ValidationException
    -
    -
    Validate Limits -

    -

    -
    Parameters:
    presets - -
    Throws: -
    ValidationException - if any of the Limit defined is found to be invalid. That is - when - - 1) No default limit is defined - - 2) More than 1 default limit is defined - - 3) Limit's preset name does not match any presets for type T
    See Also:
    Limit, -Preset
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/Option.html b/website/full_javadoc/compbio/metadata/Option.html deleted file mode 100644 index c488542..0000000 --- a/website/full_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,714 +0,0 @@ - - - - - - -Option - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class Option<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.Option<T>
-
    -
    -
    Type Parameters:
    T - type of executable
    -
    -
    All Implemented Interfaces:
    Argument<T>
    -
    -
    -
    Direct Known Subclasses:
    Parameter
    -
    -
    -
    -
    public class Option<T>
    extends Object
    implements Argument<T>
    - - -

    -Command line option/flag or multiple exclusive options with no value. Example - -protein, -dna, -auto -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Option(String name, - String description) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Set<String>addOptionNames(String... value) - -
    -          Adds an option to the optionName list
    - booleanequals(Object obj) - -
    -           
    - StringgetDefaultValue() - -
    -          A default value of the option.
    - StringgetDescription() - -
    -          A long description of the Option
    - URLgetFurtherDetails() - -
    -          The URL where further details about the option can be found
    - StringgetName() - -
    -          Human readable name of the option
    - List<String>getOptionNames() - -
    -           
    - List<String>getPossibleValues() - -
    -          List of possible optionNames
    - inthashCode() - -
    -           
    - booleanisRequired() - -
    -          Flag that indicated that this option must be specified in the command - line for an executable to run
    - voidsetDefaultValue(String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidsetDescription(String description) - -
    -           
    - voidsetFurtherDetails(URL furtherDetails) - -
    -           
    - voidsetName(String name) - -
    -           
    - voidsetOptionNames(Set<String> optionNames) - -
    -           
    - voidsetRequired(boolean isRequired) - -
    -           
    - voidsetValue(String dValue) - -
    -          Set default values for the parameter or an option
    - StringtoCommand(String nameValueSeparator) - -
    -          Convert the option to the command string.
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Option

    -
    -public Option(String name,
-              String description)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getName

    -
    -public String getName()
    -
    -
    Human readable name of the option -

    -

    -
    Specified by:
    getName in interface Argument<T>
    -
    -
    -
    -
    -
    -
    - -

    -setName

    -
    -public void setName(String name)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getDescription

    -
    -public String getDescription()
    -
    -
    A long description of the Option -

    -

    -
    Specified by:
    getDescription in interface Argument<T>
    -
    -
    -
    -
    -
    -
    - -

    -setDescription

    -
    -public void setDescription(String description)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getFurtherDetails

    -
    -public URL getFurtherDetails()
    -
    -
    The URL where further details about the option can be found -

    -

    -
    Specified by:
    getFurtherDetails in interface Argument<T>
    -
    -
    -
    -
    -
    -
    - -

    -setFurtherDetails

    -
    -public void setFurtherDetails(URL furtherDetails)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getDefaultValue

    -
    -public String getDefaultValue()
    -
    -
    A default value of the option. Defaults to command line argument name - e.g. -auto -

    -

    -
    Specified by:
    getDefaultValue in interface Argument<T>
    -
    -
    -
    -
    -
    -
    - -

    -setDefaultValue

    -
    -public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException
    -
    -
    Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

    -

    -
    -
    -
    -
    Parameters:
    defaultVal - -
    Throws: -
    WrongParameterException - is thrown if the defaultValue is not found in optionList
    -
    -
    -
    - -

    -isRequired

    -
    -public boolean isRequired()
    -
    -
    Flag that indicated that this option must be specified in the command - line for an executable to run -

    -

    -
    -
    -
    - -
    Returns:
    true is the option is required, false otherwise
    -
    -
    -
    - -

    -setRequired

    -
    -public void setRequired(boolean isRequired)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getOptionNames

    -
    -public List<String> getOptionNames()
    -
    -
    -
    -
    -
    - -
    Returns:
    List of option names
    -
    -
    -
    - -

    -setOptionNames

    -
    -public void setOptionNames(Set<String> optionNames)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -addOptionNames

    -
    -public Set<String> addOptionNames(String... value)
    -
    -
    Adds an option to the optionName list -

    -

    -
    -
    -
    -
    Parameters:
    value - -
    Returns:
    modified optionName list
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toCommand

    -
    -public String toCommand(String nameValueSeparator)
    -
    -
    Convert the option to the command string. -

    -

    -
    -
    -
    - -
    Returns:
    If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getPossibleValues

    -
    -public List<String> getPossibleValues()
    -
    -
    List of possible optionNames -

    -

    -
    Specified by:
    getPossibleValues in interface Argument<T>
    -
    -
    - -
    Returns:
    List of values allowed for an Argument
    -
    -
    -
    - -

    -setValue

    -
    -public void setValue(String dValue)
-              throws WrongParameterException
    -
    -
    Description copied from interface: Argument
    -
    Set default values for the parameter or an option -

    -

    -
    Specified by:
    setValue in interface Argument<T>
    -
    -
    -
    Parameters:
    dValue - the value to be set -
    Throws: -
    WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
    See Also:
    ValueConstrain
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/Parameter.html b/website/full_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index 981fc96..0000000 --- a/website/full_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -Parameter - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class Parameter<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.Option<T>
-      extended by compbio.metadata.Parameter<T>
-
    -
    -
    All Implemented Interfaces:
    Argument<T>
    -
    -
    -
    -
    public class Parameter<T>
    extends Option<T>
    - - -

    -A single value containing an option supported by the web service e.g. - seqType=protein. Where seqType is a optionName and protein is one of - possibleValues -

    - -

    -

    -
    Version:
    -
    1.0 November 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Option, -Argument
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Parameter(String name, - String description) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Set<String>addOptionNames(String... value) - -
    -          Adds an option to the optionName list
    - Set<String>addPossibleValues(String... value) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - StringgetOptionName() - -
    -           
    - List<String>getPossibleValues() - -
    -          List is more convenient to work with
    - ValueConstraingetValidValue() - -
    -           
    - inthashCode() - -
    -           
    - voidsetDefaultValue(String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidsetOptionName(String optionName) - -
    -           
    - voidsetOptionNames(Set<String> optionName) - -
    -           
    - voidsetPossibleValues(Set<String> possibleValues) - -
    -           
    - voidsetValidValue(ValueConstrain validValue) - -
    -           
    - StringtoCommand(String nameValueSeparator) - -
    -          Convert the option to the command string.
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.metadata.Option
    getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Parameter

    -
    -public Parameter(String name,
-                 String description)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getValidValue

    -
    -public ValueConstrain getValidValue()
    -
    -
    -
    -
    -
    -
    - -

    -setValidValue

    -
    -public void setValidValue(ValueConstrain validValue)
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Option<T>
    -
    -
    -
    -
    -
    -
    - -

    -toCommand

    -
    -public String toCommand(String nameValueSeparator)
    -
    -
    Description copied from class: Option
    -
    Convert the option to the command string. -

    -

    -
    Overrides:
    toCommand in class Option<T>
    -
    -
    - -
    Returns:
    If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Option<T>
    -
    -
    -
    -
    -
    -
    - -

    -getPossibleValues

    -
    -public List<String> getPossibleValues()
    -
    -
    List is more convenient to work with -

    -

    -
    Specified by:
    getPossibleValues in interface Argument<T>
    Overrides:
    getPossibleValues in class Option<T>
    -
    -
    - -
    Returns:
    List of String
    -
    -
    -
    - -

    -setPossibleValues

    -
    -public void setPossibleValues(Set<String> possibleValues)
    -
    -
    -
    -
    -
    -
    - -

    -addPossibleValues

    -
    -public Set<String> addPossibleValues(String... value)
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Option<T>
    -
    -
    -
    -
    -
    -
    - -

    -setOptionNames

    -
    -public void setOptionNames(Set<String> optionName)
    -
    -
    -
    Overrides:
    setOptionNames in class Option<T>
    -
    -
    -
    -
    -
    -
    - -

    -addOptionNames

    -
    -public Set<String> addOptionNames(String... value)
    -
    -
    Description copied from class: Option
    -
    Adds an option to the optionName list -

    -

    -
    Overrides:
    addOptionNames in class Option<T>
    -
    -
    - -
    Returns:
    modified optionName list
    -
    -
    -
    - -

    -getOptionName

    -
    -public String getOptionName()
    -
    -
    -
    -
    -
    -
    - -

    -setOptionName

    -
    -public void setOptionName(String optionName)
    -
    -
    -
    -
    -
    -
    - -

    -setDefaultValue

    -
    -public void setDefaultValue(String defaultVal)
-                     throws WrongParameterException
    -
    -
    Description copied from class: Option
    -
    Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

    -

    -
    Overrides:
    setDefaultValue in class Option<T>
    -
    -
    - -
    Throws: -
    WrongParameterException - is thrown if the defaultValue is not found in optionList
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/Preset.html b/website/full_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index 33c388c..0000000 --- a/website/full_javadoc/compbio/metadata/Preset.html +++ /dev/null @@ -1,455 +0,0 @@ - - - - - - -Preset - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class Preset<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.Preset<T>
-
    -
    -
    Type Parameters:
    T - executable type
    -
    -
    -
    public class Preset<T>
    extends Object
    - - -

    -Collection of Options and Parameters with their values -

    - -

    -

    -
    Version:
    -
    1.0 December 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Option, -Parameter
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Preset() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - List<Option<T>>getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - StringgetDescription() - -
    -           
    - StringgetName() - -
    -           
    - List<String>getOptions() - -
    -           
    - inthashCode() - -
    -           
    - voidsetDescription(String description) - -
    -           
    - voidsetName(String name) - -
    -           
    - voidsetOptions(List<String> option) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Preset

    -
    -public Preset()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setOptions

    -
    -public void setOptions(List<String> option)
    -
    -
    -
    -
    -
    -
    - -

    -setName

    -
    -public void setName(String name)
    -
    -
    -
    -
    -
    -
    - -

    -setDescription

    -
    -public void setDescription(String description)
    -
    -
    -
    -
    -
    -
    - -

    -getOptions

    -
    -public List<String> getOptions()
    -
    -
    - -
    Returns:
    a List of Options as a String
    -
    -
    -
    - -

    -getName

    -
    -public String getName()
    -
    -
    - -
    Returns:
    - name of the Preset
    -
    -
    -
    - -

    -getDescription

    -
    -public String getDescription()
    -
    -
    - -
    Returns:
    - a long description of the Preset
    -
    -
    -
    - -

    -getArguments

    -
    -public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
-                             throws WrongParameterException
    -
    -
    Converts list of options as String to type Option -

    -

    -
    Parameters:
    rconfig - -
    Returns:
    List of Options -
    Throws: -
    WrongParameterException - if the value of the parameter is invalid @see - Parameter
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/PresetManager.html b/website/full_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index 678ec50..0000000 --- a/website/full_javadoc/compbio/metadata/PresetManager.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - -PresetManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class PresetManager<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.PresetManager<T>
-
    -
    -
    Type Parameters:
    T - type of executable.
    -
    -
    -
    public class PresetManager<T>
    extends Object
    - - -

    -Collection of presets and methods to manipulate them @see Preset -

    - -

    -

    -
    Version:
    -
    1.0 December 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Field Summary
    -static StringLOCAL_ENGINE_LIMIT_PRESET - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    PresetManager() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Preset<T>getPresetByName(String presetName) - -
    -           
    - List<Preset<T>>getPresets() - -
    -           
    - StringgetRunnerClassName() - -
    -           
    - voidsetPresets(List<Preset<T>> presets) - -
    -           
    - voidsetRunnerClassName(String runnerClassName) - -
    -           
    - StringtoString() - -
    -           
    - voidvalidate(RunnerConfig<T> options) - -
    -          Checks whether preset option and parameter are defined in RunnerConfig - object.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -LOCAL_ENGINE_LIMIT_PRESET

    -
    -public static final String LOCAL_ENGINE_LIMIT_PRESET
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -PresetManager

    -
    -public PresetManager()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getPresets

    -
    -public List<Preset<T>> getPresets()
    -
    -
    -
    -
    -
    -
    - -

    -setPresets

    -
    -public void setPresets(List<Preset<T>> presets)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerClassName

    -
    -public String getRunnerClassName()
    -
    -
    - -
    Returns:
    fully qualified class name of type T
    -
    -
    -
    - -

    -setRunnerClassName

    -
    -public void setRunnerClassName(String runnerClassName)
    -
    -
    -
    -
    -
    -
    - -

    -getPresetByName

    -
    -public Preset<T> getPresetByName(String presetName)
    -
    -
    -
    Parameters:
    presetName - -
    Returns:
    preset by its name, null if no preset found
    -
    -
    -
    - -

    -validate

    -
    -public void validate(RunnerConfig<T> options)
-              throws ValidationException
    -
    -
    Checks whether preset option and parameter are defined in RunnerConfig - object. - - TODO handle parameters with values properly! -

    -

    - -
    Throws: -
    ValidationException - if preset is found to be invalid.
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html deleted file mode 100644 index 66c499d..0000000 --- a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -ResultNotAvailableException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class ResultNotAvailableException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.ResultNotAvailableException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class ResultNotAvailableException
    extends Exception
    - - -

    -ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides lower level exceptions - like DrmaaException -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date October 2009
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    ResultNotAvailableException(String message) - -
    -           
    ResultNotAvailableException(String message, - Throwable cause) - -
    -           
    ResultNotAvailableException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ResultNotAvailableException

    -
    -public ResultNotAvailableException(String message)
    -
    -
    -
    - -

    -ResultNotAvailableException

    -
    -public ResultNotAvailableException(Throwable cause)
    -
    -
    -
    - -

    -ResultNotAvailableException

    -
    -public ResultNotAvailableException(String message,
-                                   Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index 71c68da..0000000 --- a/website/full_javadoc/compbio/metadata/RunnerConfig.html +++ /dev/null @@ -1,706 +0,0 @@ - - - - - - -RunnerConfig - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class RunnerConfig<T>

    -
    -java.lang.Object
-  extended by compbio.metadata.RunnerConfig<T>
-
    -
    -
    Type Parameters:
    T - type of an Executable
    -
    -
    -
    @NotThreadSafe
-public class RunnerConfig<T>
    extends Object
    - - -

    -The list of Parameters and Options supported by executable. - The lists is defined in and loaded from Parameters.xml file. -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    RunnerConfig() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - voidaddOption(Option<T> option) - -
    -          Adds Option to the internal list of options
    - voidaddParameter(Parameter<T> param) - -
    -          Adds parameter to the internal parameter list
    - RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    - booleanequals(Object obj) - -
    -           
    - Option<T>getArgument(String name) - -
    -          Returns the argument by its name if found, NULL otherwise.
    - Option<T>getArgumentByOptionName(String optionName) - -
    -          Returns the argument by option name, NULL if the argument is not found
    - List<Option<T>>getArguments() - -
    -          Returns list of Parameter and Option supported by current - runner
    - List<Option<T>>getOptions() - -
    -          Returns the list of the Options supported by the executable of type T
    - List<Parameter<T>>getParameters() - -
    -          Returns the list of parameters supported executable of type T.
    - StringgetPrmSeparator() - -
    -           
    - StringgetRunnerClassName() - -
    -           
    - booleanremoveArgument(String name) - -
    -          Removes the argument Argument if found.
    - booleanremoveArgumentByOptionName(String optionName) - -
    -          Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor.
    - voidsetOptions(List<Option<T>> parameters) - -
    -          Adds the list of options or parameters to the internal list of options
    - voidsetParameters(List<Parameter<T>> parameters) - -
    -          Sets the list of parameters as internal list
    - voidsetPrmSeparator(String prmSeparator) - -
    -          Sets name value separator character
    - voidsetRunnerClassName(String runnerClassName) - -
    -          Set the name of a runner class
    - StringtoString() - -
    -           
    - voidvalidate() - -
    -          Validate the value of the argument.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -RunnerConfig

    -
    -public RunnerConfig()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -copyAndValidateRConfig

    -
    -public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
    -
    -
    -
    -
    -
    -
    - -

    -getOptions

    -
    -public List<Option<T>> getOptions()
    -
    -
    Returns the list of the Options supported by the executable of type T -

    -

    - -
    Returns:
    list of Option supported by type T
    See Also:
    Option
    -
    -
    -
    - -

    -addParameter

    -
    -public void addParameter(Parameter<T> param)
    -
    -
    Adds parameter to the internal parameter list -

    -

    -
    Parameters:
    param - the Parameter to add
    See Also:
    Parameter
    -
    -
    -
    - -

    -addOption

    -
    -public void addOption(Option<T> option)
    -
    -
    Adds Option to the internal list of options -

    -

    -
    Parameters:
    option - the Option to add
    -
    -
    -
    - -

    -getArguments

    -
    -public List<Option<T>> getArguments()
    -
    -
    Returns list of Parameter and Option supported by current - runner -

    -

    - -
    Returns:
    list of Option and Parameter supported by type T
    -
    -
    -
    - -

    -getPrmSeparator

    -
    -public String getPrmSeparator()
    -
    -
    - -
    Returns:
    name value separator character
    -
    -
    -
    - -

    -setPrmSeparator

    -
    -public void setPrmSeparator(String prmSeparator)
    -
    -
    Sets name value separator character -

    -

    -
    Parameters:
    prmSeparator - the separator char
    -
    -
    -
    - -

    -setOptions

    -
    -public void setOptions(List<Option<T>> parameters)
    -
    -
    Adds the list of options or parameters to the internal list of options -

    -

    -
    Parameters:
    parameters - the list of parameters to add
    -
    -
    -
    - -

    -getRunnerClassName

    -
    -public String getRunnerClassName()
    -
    -
    - -
    Returns:
    fully qualified class name for type T
    -
    -
    -
    - -

    -setRunnerClassName

    -
    -public void setRunnerClassName(String runnerClassName)
    -
    -
    Set the name of a runner class -

    -

    -
    Parameters:
    runnerClassName - the name of the executable wrapping class
    -
    -
    -
    - -

    -setParameters

    -
    -public void setParameters(List<Parameter<T>> parameters)
    -
    -
    Sets the list of parameters as internal list -

    -

    -
    Parameters:
    parameters - the list of parameters
    -
    -
    -
    - -

    -getParameters

    -
    -public List<Parameter<T>> getParameters()
    -
    -
    Returns the list of parameters supported executable of type T. Where - Parameter is an Option with value. -

    -

    - -
    Returns:
    List of Parameter supported by type T.
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getArgument

    -
    -public Option<T> getArgument(String name)
    -
    -
    Returns the argument by its name if found, NULL otherwise. Where the - Argument is a common interface for Option and Parameter - therefore this method can return either. If you need to retrieve the - Option by its optionNames use @link - getArgumentByOptionName(String) method. The - difference between option name and optionName is explained by the - following example: - - 
    - Sequence type
-         
-         --nuc - Assume the sequences are nucleotide.
-         --amino - Assume the sequences are amino acid. 
-         --amino
-         --nuc
-         --auto
-
    - - In the example, the "Sequence type" is a name whereas --amino, --nuc and - --auto are all optionNames. This dichotomy only manifests in - Option never in Parameters as the latter can - only have single element -

    -

    -
    Parameters:
    name - the Parameter of Option name -
    Returns:
    Argument
    -
    -
    -
    - -

    -removeArgument

    -
    -public boolean removeArgument(String name)
    -
    -
    Removes the argument Argument if found. Where Argument is either - Option or Parameter. -

    -

    -
    Parameters:
    name - of the argument -
    Returns:
    true if argument was removed, false otherwise
    -
    -
    -
    - -

    -getArgumentByOptionName

    -
    -public Option<T> getArgumentByOptionName(String optionName)
    -
    -
    Returns the argument by option name, NULL if the argument is not found -

    -

    -
    Parameters:
    optionName - - the optionName. This is not the same as an Option name. - - For example: - - 
    -            Output sequences order
-                          --inputorder - Output order: same as input. 
-                           --reorder - Output order: aligned. Default: same as input
-                          --inputorder
-                          --reorder
-
    - - The name of the option in the example is - "Output sequences order" whereas optionNames are - "--inputorder" and "--reorder". If you need to retrieve the - Option or Parameter by its names use - getArgument(String) method -
    Returns:
    Option
    -
    -
    -
    - -

    -removeArgumentByOptionName

    -
    -public boolean removeArgumentByOptionName(String optionName)
    -
    -
    Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -

    -

    -
    Parameters:
    optionName - the optionName of the option, do not confuse with the name! -
    Returns:
    true if argument with optionName exists and was removed, false - otherwise
    See Also:
    for destinctions - between optionNames and the name of the Option
    -
    -
    -
    - -

    -validate

    -
    -public void validate()
-              throws ValidationException
    -
    -
    Validate the value of the argument. Checks whether the argument value is - in the valid values range. -

    -

    - -
    Throws: -
    ValidationException - if any of the arguments found invalid which is when -
    -
  • Parameter value outside ValueConstrain boundary
    • -
  • Parameter name is not listed in possible values
    • -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index d310cc2..0000000 --- a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class UnsupportedRuntimeException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.UnsupportedRuntimeException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    - - -

    -Indicates that the server could not execute native executables. e.g. If Mafft - (unix executable) is asked to be run on Windows. In context of JABAWS this - exception indicates that the service is deployed but is not able to run. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date February 2010
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    UnsupportedRuntimeException(String message) - -
    -           
    UnsupportedRuntimeException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(String message)
    -
    -
    -
    - -

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html deleted file mode 100644 index 8ade71a..0000000 --- a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - -ValueConstrain.Type - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Enum ValueConstrain.Type

    -
    -java.lang.Object
-  extended by java.lang.Enum<ValueConstrain.Type>
-      extended by compbio.metadata.ValueConstrain.Type
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<ValueConstrain.Type>
    -
    -
    -
    Enclosing class:
    ValueConstrain
    -
    -
    -
    -
    public static enum ValueConstrain.Type
    extends Enum<ValueConstrain.Type>
    - - -

    -

    - -

    - - - - - - - - - - - - - -
    -Enum Constant Summary
    Float - -
    -           
    Integer - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static ValueConstrain.TypevalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -Integer

    -
    -public static final ValueConstrain.Type Integer
    -
    -
    -
    -
    -
    - -

    -Float

    -
    -public static final ValueConstrain.Type Float
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static ValueConstrain.Type[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (ValueConstrain.Type c : ValueConstrain.Type.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static ValueConstrain.Type valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index d2951b7..0000000 --- a/website/full_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class ValueConstrain

    -
    -java.lang.Object
-  extended by compbio.metadata.ValueConstrain
-
    -
    -
    -
    public class ValueConstrain
    extends Object
    - - -

    -The type and the lower and upper boundaries for numerical value. -

    - -

    -

    -
    Version:
    -
    1.0 November 2009
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classValueConstrain.Type - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ValueConstrain() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - NumbergetMax() - -
    -           
    - NumbergetMin() - -
    -           
    - ValueConstrain.TypegetType() - -
    -           
    - inthashCode() - -
    -           
    - voidsetMax(String max) - -
    -           
    - voidsetMin(String min) - -
    -           
    - voidsetType(ValueConstrain.Type type) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ValueConstrain

    -
    -public ValueConstrain()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getType

    -
    -public ValueConstrain.Type getType()
    -
    -
    -
    -
    -
    -
    - -

    -setType

    -
    -public void setType(ValueConstrain.Type type)
    -
    -
    -
    -
    -
    -
    - -

    -getMax

    -
    -public Number getMax()
    -
    -
    -
    -
    -
    -
    - -

    -setMax

    -
    -public void setMax(String max)
    -
    -
    -
    -
    -
    -
    - -

    -getMin

    -
    -public Number getMin()
    -
    -
    -
    -
    -
    -
    - -

    -setMin

    -
    -public void setMin(String min)
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index 5c65ccb..0000000 --- a/website/full_javadoc/compbio/metadata/WrongParameterException.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -WrongParameterException - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class WrongParameterException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.WrongParameterException
-
    -
    -
    All Implemented Interfaces:
    Serializable
    -
    -
    -
    -
    public class WrongParameterException
    extends Exception
    - - -

    -WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value. -

    - -

    -

    -
    Version:
    -
    1.0 October 2009
    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    WrongParameterException(Option<?> option) - -
    -           
    WrongParameterException(String message) - -
    -           
    WrongParameterException(String message, - Throwable cause) - -
    -           
    WrongParameterException(Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WrongParameterException

    -
    -public WrongParameterException(Option<?> option)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(String message)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(Throwable cause)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(String message,
-                               Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/Argument.html b/website/full_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index a50fc20..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/Argument.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.metadata.Argument - - - - - - - - - - - - -
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    -Uses of Interface
    compbio.metadata.Argument

    -
    - - - - - - - - - -
    -Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Argument in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.metadata that implement Argument
    - classOption<T> - -
    -          Command line option/flag or multiple exclusive options with no value.
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html deleted file mode 100644 index 455a58f..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,385 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ChunkHolder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.metadata.ChunkHolder

    -
    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ChunkHolder
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return ChunkHolder
    - ChunkHolderJManagement.pullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return ChunkHolder
    - ChunkHolderPullExecStatisticsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    - voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return ChunkHolder
    - ChunkHolderFilePuller.pull(long position) - -
    -           
    -static ChunkHolderProgressGetter.pull(String file, - long position) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return ChunkHolder
    - ChunkHolderGenericMetadataService.pullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    - ChunkHolderClustalWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolder_MsaService.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderAAConWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderMuscleWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderJronnWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderMafftWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderTcoffeeWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderProbconsWS.pullExecStatistics(String jobId, - long position) - -
    -           
    - ChunkHolderClustalOWS.pullExecStatistics(String jobId, - long position) - -
    -           
    -static ChunkHolderWSUtil.pullFile(String file, - long position) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.metadata.JobExecutionException

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use JobExecutionException
    compbio.engine  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw JobExecutionException
    - ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobExecutionException
    - org.ggf.drmaa.JobInfoJobRunner.getJobInfo() - -
    -          This method will block before the calculation has completed and then - return the object containing a job execution statistics
    - ConfiguredExecutable<?>JobRunner.waitForResult() - -
    -           
    -static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.local
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.local that throw JobExecutionException
    - ConfiguredExecutable<?>LocalRunner.waitForResult() - -
    -           
    -  -

    -

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    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.JobStatus

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use JobStatus
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return JobStatus
    - JobStatusJManagement.getJobStatus(String jobId) - -
    -          Return the status of the job.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return JobStatus
    - JobStatusGetJobStatusResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type JobStatus
    - voidGetJobStatusResponse.setReturn(JobStatus _return) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return JobStatus
    - JobStatusSyncExecutor.getJobStatus() - -
    -          Query the status of the job by its id.
    - JobStatusAsyncExecutor.getJobStatus(String jobId) - -
    -          Query the status of the job
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type JobStatus
    -static booleanUtil.isMarked(String workDirectory, - JobStatus marker) - -
    -           
    -static booleanUtil.writeMarker(String workDirectory, - JobStatus fileType) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return JobStatus
    - JobStatusJobRunner.getJobStatus() - -
    -           
    - JobStatusAsyncJobRunner.getJobStatus(String jobId) - -
    -          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.local
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.local that return JobStatus
    - JobStatusLocalRunner.getJobStatus() - -
    -           
    -static JobStatusLocalEngineUtil.getJobStatus(Future<ConfiguredExecutable<?>> future) - -
    -           
    - JobStatusAsyncLocalRunner.getJobStatus(String jobId) - -
    -           
    -static JobStatusLocalEngineUtil.getRecordedJobStatus(String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return JobStatus
    -static JobStatusJobStatus.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static JobStatus[]JobStatus.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return JobStatus
    - JobStatusGenericMetadataService.getJobStatus(String jobId) - -
    -           
    - JobStatusClustalWS.getJobStatus(String jobId) - -
    -           
    - JobStatusMuscleWS.getJobStatus(String jobId) - -
    -           
    - JobStatusMafftWS.getJobStatus(String jobId) - -
    -           
    - JobStatusTcoffeeWS.getJobStatus(String jobId) - -
    -           
    - JobStatusProbconsWS.getJobStatus(String jobId) - -
    -           
    - JobStatusClustalOWS.getJobStatus(String jobId) - -
    -           
    -static JobStatusWSUtil.getJobStatus(String jobId) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.JobSubmissionException

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use JobSubmissionException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw JobSubmissionException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that throw JobSubmissionException
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - List<FastaSequence> dataSet) - -
    -           
    - voidSyncExecutor.executeJob() - -
    -          Execute the job
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    - StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw JobSubmissionException
    - StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException
    - voidJobRunner.executeJob() - -
    -           
    -static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
    -           
    - StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
    JobRunner(ConfiguredExecutable<?> confExec) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw JobSubmissionException
    - voidLocalRunner.executeJob() - -
    -           
    - StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.local that throw JobSubmissionException
    ExecutableWrapper(ConfiguredExecutable<?> executable, - String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Subclasses of JobSubmissionException in compbio.metadata
    - classLimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    - classUnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that throw JobSubmissionException
    -static voidUtil.writeInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw JobSubmissionException
    - StringClustalWS.align(List<FastaSequence> sequences) - -
    -           
    - String_MsaService.align(List<FastaSequence> sequences) - -
    -           
    - StringMuscleWS.align(List<FastaSequence> sequences) - -
    -           
    - StringMafftWS.align(List<FastaSequence> sequences) - -
    -           
    - StringTcoffeeWS.align(List<FastaSequence> sequences) - -
    -           
    - StringProbconsWS.align(List<FastaSequence> sequences) - -
    -           
    - StringClustalOWS.align(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -static voidWSUtil.validateAAConInput(List<FastaSequence> sequences) - -
    -           
    -static voidWSUtil.validateFastaInput(List<FastaSequence> sequences) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/Limit.html b/website/full_javadoc/compbio/metadata/class-use/Limit.html deleted file mode 100644 index f7d7559..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/Limit.html +++ /dev/null @@ -1,522 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Limit - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.metadata.Limit

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Limit
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return Limit
    - Limit<T>Metadata.getLimit(String presetName) - -
    -          Get a Limit for a preset.
    -  -

    - - - - - -
    -Uses of Limit in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Limit
    - LimitGetLimitResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Limit
    - voidGetLimitResponse.setReturn(Limit _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return Limit
    - Limit<T>Executable.getLimit(String presetName) - -
    -           
    - Limit<T>SkeletalExecutable.getLimit(String presetName) - -
    -           
    - Limit<T>ConfExecutable.getLimit(String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Limit
    - Limit<T>LimitsManager.getDefaultLimit() - -
    -           
    - Limit<T>LimitsManager.getLimitByName(String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Limit
    - List<Limit<T>>LimitsManager.getLimits() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Limit
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return Limit
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(String presetName) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Limit
    - Limit<NetNglyc>NetNglyc.getLimit(String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return Limit
    - Limit<T>GenericMetadataService.getLimit(String presetName) - -
    -           
    - Limit<ClustalW>ClustalWS.getLimit(String presetName) - -
    -           
    - Limit<Muscle>MuscleWS.getLimit(String presetName) - -
    -           
    - Limit<Mafft>MafftWS.getLimit(String presetName) - -
    -           
    - Limit<Tcoffee>TcoffeeWS.getLimit(String presetName) - -
    -           
    - Limit<Probcons>ProbconsWS.getLimit(String presetName) - -
    -           
    - Limit<ClustalO>ClustalOWS.getLimit(String presetName) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Limit
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    -static - - - - -
    -<T> String
    -    		WSUtil.analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html deleted file mode 100644 index c7dce66..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html +++ /dev/null @@ -1,375 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.LimitExceededException - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.LimitExceededException

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use LimitExceededException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw LimitExceededException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return LimitExceededException
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw LimitExceededException
    -static - - - - -
    -<T> String
    -    		WSUtil.align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html deleted file mode 100644 index f587b09..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html +++ /dev/null @@ -1,436 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.LimitsManager - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.LimitsManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return LimitsManager
    - LimitsManager<T>Metadata.getLimits() - -
    -          List Limits supported by a web service.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return LimitsManager
    - LimitsManagerGetLimitsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type LimitsManager
    - voidGetLimitsResponse.setReturn(LimitsManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return LimitsManager
    - LimitsManager<T>Executable.getLimits() - -
    -           
    - LimitsManager<T>SkeletalExecutable.getLimits() - -
    -           
    - LimitsManager<T>ConfExecutable.getLimits() - -
    -           
    -static - - - - -
    -<T> LimitsManager<T>
    -    		Util.getLimits(Class<T> clazz) - -
    -          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then
    -static - - - - -
    -<V> LimitsManager<V>
    -    		ConfExecutable.getRunnerLimits(Class<V> clazz) - -
    -          This method should be executed once and result of its execution reused.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return LimitsManager
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return LimitsManager
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return LimitsManager
    - LimitsManager<T>GenericMetadataService.getLimits() - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - LimitsManager<ClustalO>ClustalOWS.getLimits() - -
    -           
    -  -

    -

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    -
    -

    -Uses of Class
    compbio.metadata.Option

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Option
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa with type arguments of type Option
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    -  -

    - - - - - -
    -Uses of Option in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    - List<Option>CustomAnalize.getOptions() - -
    -           
    - List<Option>CustomAlign.getOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    - voidCustomAnalize.setOptions(List<Option> options) - -
    -           
    - voidCustomAlign.setOptions(List<Option> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.engine.client
    -  -

    - - - - - - - - - -
    Method parameters in compbio.engine.client with type arguments of type Option
    -static - - - - -
    -<T> CommandBuilder<T>
    -    		CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, - String nameValueSeparator) - -
    -          This produces the same result as getCommands method.
    -  -

    - - - - - -
    -Uses of Option in compbio.metadata
    -  -

    - - - - - - - - - -
    Subclasses of Option in compbio.metadata
    - classParameter<T> - -
    -          A single value containing an option supported by the web service e.g.
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Option
    - Option<T>RunnerConfig.getArgument(String name) - -
    -          Returns the argument by its name if found, NULL otherwise.
    - Option<T>RunnerConfig.getArgumentByOptionName(String optionName) - -
    -          Returns the argument by option name, NULL if the argument is not found
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Option
    - List<Option<T>>RunnerConfig.getArguments() - -
    -          Returns list of Parameter and Option supported by current - runner
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - List<Option<T>>RunnerConfig.getOptions() - -
    -          Returns the list of the Options supported by the executable of type T
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Option
    - voidRunnerConfig.addOption(Option<T> option) - -
    -          Adds Option to the internal list of options
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Option
    - voidRunnerConfig.setOptions(List<Option<T>> parameters) - -
    -          Adds the list of options or parameters to the internal list of options
    -  -

    - - - - - - - - -
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Option
    - List<Option<?>>OptionCombinator.getAllOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Option
    - List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments) - -
    -           
    -static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - List<String>OptionCombinator.optionsToCommandString(List<Option<?>> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Option
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    -static - - - - -
    -<T> List<String>
    -    		WSUtil.getCommands(List<Option<T>> options, - String keyValueSeparator) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.Parameter

    -
    - - - - - - - - - - - - - -
    -Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    -  -

    - - - - - -
    -Uses of Parameter in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Parameter
    - List<Parameter<T>>RunnerConfig.getParameters() - -
    -          Returns the list of parameters supported executable of type T.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Parameter
    - voidRunnerConfig.addParameter(Parameter<T> param) - -
    -          Adds parameter to the internal parameter list
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Parameter
    - voidRunnerConfig.setParameters(List<Parameter<T>> parameters) - -
    -          Sets the list of parameters as internal list
    -  -

    - - - - - -
    -Uses of Parameter in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Parameter
    - Map<Parameter<?>,String>OptionCombinator.getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - Map<Parameter<?>,String>OptionCombinator.getAllConstrainedParametersWithRandomValues() - -
    -           
    - List<Parameter<?>>OptionCombinator.getAllParameters() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Parameter
    - List<String>OptionCombinator.parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    - List<String>OptionCombinator.parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/Preset.html b/website/full_javadoc/compbio/metadata/class-use/Preset.html deleted file mode 100644 index 809e593..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/Preset.html +++ /dev/null @@ -1,433 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Preset - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.Preset

    -
    - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Preset
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Preset
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of Preset in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Preset
    - PresetPresetAnalize.getPreset() - -
    -           
    - PresetPresetAlign.getPreset() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    - voidPresetAnalize.setPreset(Preset preset) - -
    -           
    - voidPresetAlign.setPreset(Preset preset) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return Preset
    - Preset<T>PresetManager.getPresetByName(String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Preset
    - List<Preset<T>>PresetManager.getPresets() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Preset
    - voidPresetManager.setPresets(List<Preset<T>> presets) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Preset
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.PresetManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use PresetManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return PresetManager
    - PresetManager<T>Metadata.getPresets() - -
    -          Get presets supported by a web service
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return PresetManager
    - PresetManagerGetPresetsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type PresetManager
    - voidGetPresetsResponse.setReturn(PresetManager _return) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return PresetManager
    -static - - - - -
    -<V> PresetManager<V>
    -    		ConfExecutable.getRunnerPresets(Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type PresetManager
    - voidLimitsManager.validate(PresetManager<T> presets) - -
    -          Validate Limits
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return PresetManager
    -static - - - - -
    -<T> PresetManager<T>
    -    		Util.getPresets(Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return PresetManager
    - PresetManager<T>GenericMetadataService.getPresets() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - PresetManager<ClustalO>ClustalOWS.getPresets() - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.ResultNotAvailableException

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw ResultNotAvailableException
    - ScoreManagerSequenceAnnotation.getAnnotation(String jobId) - -
    -          Return the result of the job.
    - AlignmentMsaWS.getResult(String jobId) - -
    -          Return the result of the job.
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw ResultNotAvailableException
    - ConfiguredExecutable<?>AsyncExecutor.getResults(String jobId) - -
    -          Retrieve the results of the job.
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that throw ResultNotAvailableException
    - - - - - -
    -<V> V
    -    		ConfiguredExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		Executable.getResults(String directory) - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults(String directory) - -
    -           
    -static ConfiguredExecutable<?>Util.loadExecutable(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw ResultNotAvailableException
    - ConfiguredExecutable<?>ClusterSession.getResults(String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncJobRunner.getResults(String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw ResultNotAvailableException
    -static ConfiguredExecutable<?>LocalEngineUtil.getResults(Future<ConfiguredExecutable<?>> future, - String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncLocalRunner.getResults(String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.conservation
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.conservation that throw ResultNotAvailableException
    - ScoreManagerAACon.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that throw ResultNotAvailableException
    - ScoreManagerJronn.getResults(String workDirectory) - -
    -           
    - ScoreManagerIUPred.getResults(String workDirectory) - -
    -           
    - ScoreManagerGlobPlot.getResults(String workDirectory) - -
    -           
    - ScoreManagerDisembl.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that throw ResultNotAvailableException
    - AlignmentMafft.getResults(String workDirectory) - -
    -           
    - AlignmentClustalW.getResults(String workDirectory) - -
    -           
    - AlignmentTcoffee.getResults(String workDirectory) - -
    -           
    - AlignmentMuscle.getResults(String workDirectory) - -
    -           
    - AlignmentClustalO.getResults(String workDirectory) - -
    -           
    - AlignmentProbcons.getResults(String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw ResultNotAvailableException
    - ScoreManagerSequenceAnnotationService.getAnnotation(String jobId) - -
    -           
    -static - - - - -
    -<T> ScoreManager
    -    		WSUtil.getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
    -           
    - AlignmentClustalWS.getResult(String jobId) - -
    -           
    - Alignment_MsaService.getResult(String jobId) - -
    -           
    - AlignmentMuscleWS.getResult(String jobId) - -
    -           
    - AlignmentMafftWS.getResult(String jobId) - -
    -           
    - AlignmentTcoffeeWS.getResult(String jobId) - -
    -           
    - AlignmentProbconsWS.getResult(String jobId) - -
    -           
    - AlignmentClustalOWS.getResult(String jobId) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.RunnerConfig

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use RunnerConfig
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine.client  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return RunnerConfig
    - RunnerConfig<T>Metadata.getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return RunnerConfig
    - RunnerConfigGetRunnerOptionsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type RunnerConfig
    - voidGetRunnerOptionsResponse.setReturn(RunnerConfig _return) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return RunnerConfig
    -static - - - - -
    -<V> RunnerConfig<V>
    -    		ConfExecutable.getRunnerOptions(Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata with parameters of type RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidPresetManager.validate(RunnerConfig<T> options) - -
    -          Checks whether preset option and parameter are defined in RunnerConfig - object.
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return RunnerConfig
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		Util.getSupportedOptions(Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type RunnerConfig
    -static List<String>OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.runner with parameters of type RunnerConfig
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return RunnerConfig
    - RunnerConfig<T>GenericMetadataService.getRunnerOptions() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    - RunnerConfig<ClustalO>ClustalOWS.getRunnerOptions() - -
    -           
    -  -

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    -Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.engine.client  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    - StringMsaWS.align(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - StringSequenceAnnotation.analize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw UnsupportedRuntimeException
    - StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw UnsupportedRuntimeException
    - StringAAConWS.analize(List<FastaSequence> sequences) - -
    -           
    - StringSequenceAnnotationService.analize(List<FastaSequence> sequences) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  -

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    compbio.metadata.ValueConstrain.Type

    -
    - - - - - - - - - -
    -Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain.Type in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain.Type
    - ValueConstrain.TypeValueConstrain.getType() - -
    -           
    -static ValueConstrain.TypeValueConstrain.Type.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]ValueConstrain.Type.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    - voidValueConstrain.setType(ValueConstrain.Type type) - -
    -           
    -  -

    -

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    -Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of ValueConstrain in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain
    - ValueConstrainParameter.getValidValue() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain
    - voidParameter.setValidValue(ValueConstrain validValue) - -
    -           
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    -Packages that use WrongParameterException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.data.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw WrongParameterException
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringSequenceAnnotation.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    - StringSequenceAnnotation.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that throw WrongParameterException
    - List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidParameter.setDefaultValue(String defaultVal) - -
    -           
    - voidOption.setDefaultValue(String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidArgument.setValue(String defaultValue) - -
    -          Set default values for the parameter or an option
    - voidOption.setValue(String dValue) - -
    -           
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw WrongParameterException
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - String_MsaService.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringSequenceAnnotationService.customAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - String_MsaService.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    - StringSequenceAnnotationService.presetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
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    -ValueConstrain
    - - - - - - -
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    -ValueConstrain.Type
    - - - - - - -
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    -LimitExceededException -
    -ResultNotAvailableException -
    -UnsupportedRuntimeException -
    -WrongParameterException
    - - - - diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html deleted file mode 100644 index 6f878d7..0000000 --- a/website/full_javadoc/compbio/metadata/package-summary.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -compbio.metadata - - - - - - - - - - - - -
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    -Package compbio.metadata -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. -

    -See: -
    -          Description -

    - - - - - - - - - -
    -Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ChunkHolderRepresents a chunk of a string data together with the position in a file for - the next read operation.
    Limit<T>A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing an option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    -  - -

    - - - - - - - - - - - - - -
    -Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThis exception is thrown if the task larger in size that the limit that - applies to the calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  - -

    -

    -Package compbio.metadata Description -

    - -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. - They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) -

    - -

    -

    -
    Version:
    -
    1.0 January 2010
    -
    Author:
    -
    Peter Troshin
    -
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    -Hierarchy For Package compbio.metadata -

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    -Uses of Package
    compbio.metadata

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.client  
    compbio.engine.cluster.drmaa  
    compbio.engine.local  
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.conservation  
    compbio.runner.disorder  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa.jaxws
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.client
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.cluster.drmaa
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.local
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.metadata
    Argument - -
    -          An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing an option supported by the web service e.g.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    ValueConstrain - -
    -          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type - -
    -           
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing an option supported by the web service e.g.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner._impl
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.conservation
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.disorder
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.msa
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.ws.server
    ChunkHolder - -
    -          Represents a chunk of a string data together with the position in a file for - the next read operation.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    -

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    - -compbio.pipeline._jpred -
    -Class BlastBlastComparator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastBlastComparator
-
    -
    -
    -
    public class BlastBlastComparator
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    BlastBlastComparator() - -
    -           
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    -Method Summary
    -static voidmain(String[] args) - -
    -          args[0] is assumed to be the name of a Blast output file
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
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    -  -

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    -Constructor Detail
    - -

    -BlastBlastComparator

    -
    -public BlastBlastComparator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws FileNotFoundException,
-                        XMLStreamException
    -
    -
    args[0] is assumed to be the name of a Blast output file -

    -

    - -
    Throws: -
    XMLStreamException -
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    -
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    - -compbio.pipeline._jpred -
    -Class BlastHmmerComparator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastHmmerComparator
-
    -
    -
    -
    public class BlastHmmerComparator
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    BlastHmmerComparator() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          args[0] is assumed to be the name of a Blast output file
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -BlastHmmerComparator

    -
    -public BlastHmmerComparator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws XMLStreamException,
-                        IOException
    -
    -
    args[0] is assumed to be the name of a Blast output file -

    -

    - -
    Throws: -
    XMLStreamException -
    IOException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.pipeline._jpred -
    -Class BlastParser

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastParser
-
    -
    -
    -
    public class BlastParser
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    BlastParser(String file) - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          args[0] is assumed to be the name of a Blast output file
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -BlastParser

    -
    -public BlastParser(String file)
-            throws FileNotFoundException,
-                   XMLStreamException
    -
    -
    - -
    Throws: -
    FileNotFoundException -
    XMLStreamException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws FileNotFoundException,
-                        XMLStreamException
    -
    -
    args[0] is assumed to be the name of a Blast output file -

    -

    - -
    Throws: -
    XMLStreamException -
    FileNotFoundException
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Hit.EvalueComporator.html b/website/full_javadoc/compbio/pipeline/_jpred/Hit.EvalueComporator.html deleted file mode 100644 index 024fc0d..0000000 --- a/website/full_javadoc/compbio/pipeline/_jpred/Hit.EvalueComporator.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Hit.EvalueComporator - - - - - - - - - - - - -
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    - -compbio.pipeline._jpred -
    -Class Hit.EvalueComporator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit.EvalueComporator
-
    -
    -
    All Implemented Interfaces:
    Comparator<Hit>
    -
    -
    -
    Enclosing class:
    Hit
    -
    -
    -
    -
    public static final class Hit.EvalueComporator
    extends Object
    implements Comparator<Hit>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Hit.EvalueComporator() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - intcompare(Hit o1, - Hit o2) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface java.util.Comparator
    equals
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Hit.EvalueComporator

    -
    -public Hit.EvalueComporator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -compare

    -
    -public int compare(Hit o1,
-                   Hit o2)
    -
    -
    -
    Specified by:
    compare in interface Comparator<Hit>
    -
    -
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Hit.NumberComporator.html b/website/full_javadoc/compbio/pipeline/_jpred/Hit.NumberComporator.html deleted file mode 100644 index bf756e3..0000000 --- a/website/full_javadoc/compbio/pipeline/_jpred/Hit.NumberComporator.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Hit.NumberComporator - - - - - - - - - - - - -
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    - -compbio.pipeline._jpred -
    -Class Hit.NumberComporator

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit.NumberComporator
-
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    -
    All Implemented Interfaces:
    Comparator<Hit>
    -
    -
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    Enclosing class:
    Hit
    -
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    -
    -
    public static final class Hit.NumberComporator
    extends Object
    implements Comparator<Hit>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Hit.NumberComporator() - -
    -           
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    -Method Summary
    - intcompare(Hit o1, - Hit o2) - -
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    Methods inherited from class java.lang.Object
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    Methods inherited from interface java.util.Comparator
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    -  -

    - - - - - - - - -
    -Constructor Detail
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    -Hit.NumberComporator

    -
    -public Hit.NumberComporator()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -compare

    -
    -public int compare(Hit o1,
-                   Hit o2)
    -
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    Specified by:
    compare in interface Comparator<Hit>
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    - -compbio.pipeline._jpred -
    -Class Hit

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Hit
-
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    -
    public class Hit
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Nested Class Summary
    -static classHit.EvalueComporator - -
    -           
    -static classHit.NumberComporator - -
    -           
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    -Constructor Summary
    Hit() - -
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    - booleanequals(Object obj) - -
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    -Hit

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    -public Hit()
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    Overrides:
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    - -compbio.pipeline._jpred -
    -Class JackHmmerHitParser

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.JackHmmerHitParser
-
    -
    -
    -
    public class JackHmmerHitParser
    extends Object
    - - -

    -Parser for the following files: -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    JackHmmerHitParser(String file) - -
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    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
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    -Constructor Detail
    - -

    -JackHmmerHitParser

    -
    -public JackHmmerHitParser(String file)
-                   throws IOException
    -
    -
    - -
    Throws: -
    IOException
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    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws IOException
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    - -compbio.pipeline._jpred -
    -Class Jpred4

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Jpred4
-
    -
    -
    -
    public class Jpred4
    extends Object
    - - -

    -jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying. Default: uniref90 ( - /homes/www-jpred/databases/uniref90.filt) Please note that database must be - psi-blast indexed - - [--pred-nohits] Toggle allowing Jpred to make predictions even when there are - no PSI-BLAST hits. - - [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help] -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
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    - - - - - - - - - - - -
    -Constructor Summary
    Jpred4() - -
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    -  - - - - - - - - - - - -
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    - voidrunPsiBlast() - -
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    -Jpred4

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    - -compbio.pipeline._jpred -
    -Class PScore

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.PScore
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    -
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    -
    public class PScore
    extends Object
    - - -

    -

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    PScore() - -
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    - -compbio.pipeline._jpred -
    -Class Pairwise

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Pairwise
-
    -
    -
    -
    public class Pairwise
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Pairwise(List<FastaSequence> sequences) - -
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    -Pairwise

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    -public Pairwise(List<FastaSequence> sequences)
    -
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    -Method Detail
    - -

    -main

    -
    -public static final void main(String[] args)
-                       throws FileNotFoundException,
-                              IOException
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    Throws: -
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    -Uses of Hit in compbio.pipeline._jpred
    -  -

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    Methods in compbio.pipeline._jpred with parameters of type Hit
    - intHit.NumberComporator.compare(Hit o1, - Hit o2) - -
    -           
    - intHit.EvalueComporator.compare(Hit o1, - Hit o2) - -
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    -

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    -Classes  - -
    -BlastBlastComparator -
    -BlastHmmerComparator -
    -BlastParser -
    -Hit -
    -Hit.EvalueComporator -
    -Hit.NumberComporator -
    -JackHmmerHitParser -
    -Jpred4 -
    -Pairwise -
    -PScore
    - - - - diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html deleted file mode 100644 index 6995eb5..0000000 --- a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - -compbio.pipeline._jpred - - - - - - - - - - - - -
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    -Class Summary
    BlastBlastComparator 
    BlastHmmerComparator 
    BlastParser 
    Hit 
    Hit.EvalueComporator 
    Hit.NumberComporator 
    JackHmmerHitParserParser for the following files:
    Jpred4jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Pairwise 
    PScore 
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    -Uses of Package
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    -Packages that use compbio.pipeline._jpred
    compbio.pipeline._jpred  
    -  -

    - - - - - - - - -
    -Classes in compbio.pipeline._jpred used by compbio.pipeline._jpred
    Hit - -
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    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/OptionCombinator.html b/website/full_javadoc/compbio/runner/OptionCombinator.html deleted file mode 100644 index cb2fd80..0000000 --- a/website/full_javadoc/compbio/runner/OptionCombinator.html +++ /dev/null @@ -1,421 +0,0 @@ - - - - - - -OptionCombinator - - - - - - - - - - - - -
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    - -compbio.runner -
    -Class OptionCombinator

    -
    -java.lang.Object
-  extended by compbio.runner.OptionCombinator
-
    -
    -
    -
    @Immutable
-public final class OptionCombinator
    extends Object
    - - -

    -This class solve the following problems. Given the RunnerConfig - - 1) generate a valid option string with all options and parameters in it - - 2) Permute all possible combinations of options order and parameters values -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>argumentsToCommandString(List<? extends Option<?>> arguments) - -
    -           
    -static List<String>argumentsToCommandString(List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - Map<Parameter<?>,String>getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - Map<Parameter<?>,String>getAllConstrainedParametersWithRandomValues() - -
    -           
    - List<Option<?>>getAllOptions() - -
    -           
    - List<Parameter<?>>getAllParameters() - -
    -           
    - List<String>getOptionsAtRandom() - -
    -           
    - List<String>optionsToCommandString(List<Option<?>> options) - -
    -           
    - List<String>parametersToCommandString(List<Parameter<?>> orderedList, - Map<Parameter<?>,String> prmValue) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -OptionCombinator

    -
    -public OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -optionsToCommandString

    -
    -public List<String> optionsToCommandString(List<Option<?>> options)
    -
    -
    -
    -
    -
    -
    - -

    -getOptionsAtRandom

    -
    -public List<String> getOptionsAtRandom()
    -
    -
    -
    -
    -
    -
    - -

    -getAllOptions

    -
    -public List<Option<?>> getAllOptions()
    -
    -
    -
    -
    -
    -
    - -

    -getAllParameters

    -
    -public List<Parameter<?>> getAllParameters()
    -
    -
    -
    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public List<String> argumentsToCommandString(List<? extends Option<?>> arguments)
    -
    -
    -
    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public static List<String> argumentsToCommandString(List<? extends Option<?>> arguments,
-                                                    RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    -
    -
    -
    -
    - -

    -parametersToCommandString

    -
    -public List<String> parametersToCommandString(List<Parameter<?>> orderedList,
-                                              Map<Parameter<?>,String> prmValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithBorderValues

    -
    -public Map<Parameter<?>,String> getAllConstrainedParametersWithBorderValues(boolean minValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithRandomValues

    -
    -public Map<Parameter<?>,String> getAllConstrainedParametersWithRandomValues()
    -
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    - -compbio.runner -
    -Class Util

    -
    -java.lang.Object
-  extended by compbio.runner.Util
-
    -
    -
    -
    public final class Util
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    -static org.apache.log4j.Loggerlog - -
    -           
    -static StringSPACE - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Util() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> PresetManager<T>
    -    		getPresets(Class<? extends Executable<T>> clazz) - -
    -           
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		getSupportedOptions(Class<? extends Executable<T>> clazz) - -
    -           
    -static AlignmentreadClustalFile(String workDirectory, - String clustFile) - -
    -           
    -static Map<String,Score>readJronnFile(String workDirectory, - String clustFile) - -
    -           
    -static voidwriteInput(List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -log

    -
    -public static org.apache.log4j.Logger log
    -
    -
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    -
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    -SPACE

    -
    -public static final String SPACE
    -
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    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Util

    -
    -public Util()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getSupportedOptions

    -
    -public static <T> RunnerConfig<T> getSupportedOptions(Class<? extends Executable<T>> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -getPresets

    -
    -public static <T> PresetManager<T> getPresets(Class<? extends Executable<T>> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -readClustalFile

    -
    -public static final Alignment readClustalFile(String workDirectory,
-                                              String clustFile)
-                                       throws UnknownFileFormatException,
-                                              IOException,
-                                              FileNotFoundException,
-                                              NullPointerException
    -
    -
    - -
    Throws: -
    UnknownFileFormatException -
    IOException -
    FileNotFoundException -
    NullPointerException
    -
    -
    -
    - -

    -readJronnFile

    -
    -public static final Map<String,Score> readJronnFile(String workDirectory,
-                                                    String clustFile)
-                                             throws UnknownFileFormatException,
-                                                    IOException,
-                                                    FileNotFoundException,
-                                                    NullPointerException
    -
    -
    - -
    Throws: -
    UnknownFileFormatException -
    IOException -
    FileNotFoundException -
    NullPointerException
    -
    -
    -
    - -

    -writeInput

    -
    -public static void writeInput(List<FastaSequence> sequences,
-                              ConfiguredExecutable<?> exec)
-                       throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
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    - - - diff --git a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html deleted file mode 100644 index 04c478a..0000000 --- a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -_NativeSpecHelper - - - - - - - - - - - - -
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    - -compbio.runner -
    -Class _NativeSpecHelper

    -
    -java.lang.Object
-  extended by compbio.runner._NativeSpecHelper
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class _NativeSpecHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    _NativeSpecHelper(int requiredMemory) - -
    -          Deprecated.  
    _NativeSpecHelper(int requiredMemory, - int maxCalculationTime) - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _QueuegetApproprieteQueue() - -
    -          Deprecated.  
    - StringgetNativeSpec() - -
    -          Deprecated.  
    - StringgetQueue() - -
    -          Deprecated.  
    - voidsetQueue(String queue) - -
    -          Deprecated.  
    - voidsetRequiredMemory(int memory) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory)
    -
    -
    Deprecated. 
    -
    - -

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory,
-                         int maxCalculationTime)
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -setRequiredMemory

    -
    -public void setRequiredMemory(int memory)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -setQueue

    -
    -public void setQueue(String queue)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getQueue

    -
    -public String getQueue()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getNativeSpec

    -
    -public String getNativeSpec()
-                     throws UnknownServiceException
    -
    -
    Deprecated. 
    - -
    Throws: -
    UnknownServiceException
    -
    -
    -
    - -

    -getApproprieteQueue

    -
    -public _Queue getApproprieteQueue()
    -
    -
    Deprecated. 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html deleted file mode 100644 index e1f1135..0000000 --- a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html +++ /dev/null @@ -1,611 +0,0 @@ - - - - - - -_SkeletalCommandBuilder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner -
    -Class _SkeletalCommandBuilder

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    Direct Known Subclasses:
    BlastAll, Mcl, OB, PSIBlast, Ronn, RPSBlast
    -
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public abstract class _SkeletalCommandBuilder
    extends Object
    implements Executable<_SkeletalCommandBuilder>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    _SkeletalCommandBuilder() - -
    -          Deprecated.  
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _SkeletalCommandBuilderaddParameter(String parameter) - -
    -          Deprecated.  
    - _SkeletalCommandBuilderaddParameters(List<String> parameters) - -
    -          Deprecated. Adds parameter to the list of parameters for a native executable
    - _SkeletalCommandBuilderaddParameters(String[] parameters) - -
    -          Deprecated.  
    - StringgetClusterJobSettings() - -
    -          Deprecated.  
    - StringgetEmail() - -
    -          Deprecated.  
    - StringgetError() - -
    -          Deprecated.  
    - Limit<_SkeletalCommandBuilder>getLimit(String presetName) - -
    -          Deprecated.  
    - LimitsManager<_SkeletalCommandBuilder>getLimits() - -
    -          Deprecated.  
    - StringgetName() - -
    -          Deprecated.  
    - StringgetOutput() - -
    -          Deprecated.  
    - CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -          Deprecated.  
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -          Deprecated.  
    - _SkeletalCommandBuildersetEmail(String email) - -
    -          Deprecated.  
    - _SkeletalCommandBuildersetName(String name) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getInput
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -_SkeletalCommandBuilder

    -
    -public _SkeletalCommandBuilder()
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -setEmail

    -
    -public _SkeletalCommandBuilder setEmail(String email)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -setName

    -
    -public _SkeletalCommandBuilder setName(String name)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getName

    -
    -public String getName()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getEmail

    -
    -public String getEmail()
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public _SkeletalCommandBuilder addParameters(String[] parameters)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public _SkeletalCommandBuilder addParameters(List<String> parameters)
    -
    -
    Deprecated. 
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
    -
    -
    Deprecated. 
    -
    Specified by:
    getParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -addParameter

    -
    -public _SkeletalCommandBuilder addParameter(String parameter)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public <V> V getResults(String directory)
    -
    -
    Deprecated. 
    -
    Specified by:
    getResults in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    Deprecated. 
    -
    Specified by:
    loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    Deprecated. 
    -
    Specified by:
    getOutput in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public String getError()
    -
    -
    Deprecated. 
    -
    Specified by:
    getError in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<_SkeletalCommandBuilder> getLimit(String presetName)
    -
    -
    Deprecated. 
    -
    Specified by:
    getLimit in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<_SkeletalCommandBuilder> getLimits()
    -
    -
    Deprecated. 
    -
    Specified by:
    getLimits in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobSettings

    -
    -public String getClusterJobSettings()
    -
    -
    Deprecated. 
    -
    Specified by:
    getClusterJobSettings in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/BlastAll.html deleted file mode 100644 index 9412da9..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastAll.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -BlastAll - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class BlastAll

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.BlastAll
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class BlastAll
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    BlastAll(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - booleanremoveOutput(String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -BlastAll

    -
    -public BlastAll(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -removeOutput

    -
    -public boolean removeOutput(String outfile)
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html deleted file mode 100644 index e3b1e38..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html +++ /dev/null @@ -1,199 +0,0 @@ - - - - - - -BlastParameters - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class BlastParameters

    -
    -java.lang.Object
-  extended by compbio.runner._impl.BlastParameters
-
    -
    -
    -
    public class BlastParameters
    extends Object
    - - -

    -Utility class for common Blast parameters -

    - -

    -

    -
    Author:
    -
    pvtroshin TODO
    -
    -
    - -

    - - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - -

    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html deleted file mode 100644 index 7310668..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Environment.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -Environment - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class Environment

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Environment
-
    -
    -
    -
    public final class Environment
    extends Object
    - - -

    -This is utility class to encapsulate environmental variables like directory paths -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static StringgetBlastBinDir() - -
    -           
    -static StringgetBlastDatabasesDir() - -
    -           
    -static StringgetRPSBlastDatabasesDir() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getBlastBinDir

    -
    -public static String getBlastBinDir()
    -
    -
    -
    -
    -
    -
    - -

    -getBlastDatabasesDir

    -
    -public static final String getBlastDatabasesDir()
    -
    -
    -
    -
    -
    -
    - -

    -getRPSBlastDatabasesDir

    -
    -public static final String getRPSBlastDatabasesDir()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html deleted file mode 100644 index 9ed2448..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Mcl.html +++ /dev/null @@ -1,379 +0,0 @@ - - - - - - -Mcl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class Mcl

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Mcl
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Mcl
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Mcl(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -static List<String>getTestParams() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Mcl

    -
    -public Mcl(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTestParams

    -
    -public static List<String> getTestParams()
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

    -
    -public String getCommandName()
    -
    -
    -
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html deleted file mode 100644 index b6f4bca..0000000 --- a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html +++ /dev/null @@ -1,574 +0,0 @@ - - - - - - -NetNglyc - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class NetNglyc

    -
    -java.lang.Object
-  extended by compbio.runner._impl.NetNglyc
-
    -
    -
    All Implemented Interfaces:
    Executable<NetNglyc>
    -
    -
    -
    -
    public class NetNglyc
    extends Object
    implements Executable<NetNglyc>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    NetNglyc() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - NetNglycaddParameters(List<String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - StringgetClusterJobSettings() - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetError() - -
    -           
    - StringgetInput() - -
    -           
    - Limit<NetNglyc>getLimit(String presetName) - -
    -           
    - LimitsManager<NetNglyc>getLimits() - -
    -           
    - StringgetOutput() - -
    -           
    - CommandBuilder<NetNglyc>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(String directory) - -
    -           
    -static List<String>getTestArgs() - -
    -           
    -static StringgetTestCommand() - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -NetNglyc

    -
    -public NetNglyc()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getParameters

    -
    -public CommandBuilder<NetNglyc> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getTestArgs

    -
    -public static List<String> getTestArgs()
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public NetNglyc addParameters(List<String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<NetNglyc>
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    this Executable
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    -getTestCommand

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    -getCommandName

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    -getCreatedFiles

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    -public List<String> getCreatedFiles()
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    getCreatedFiles in interface Executable<NetNglyc>
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    -getInput

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    -public String getInput()
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    getInput in interface Executable<NetNglyc>
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    -getResults

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    -public <V> V getResults(String directory)
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    getResults in interface Executable<NetNglyc>
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    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
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    Specified by:
    loadRunConfiguration in interface Executable<NetNglyc>
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    -getOutput

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    -public String getOutput()
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    Specified by:
    getOutput in interface Executable<NetNglyc>
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    -getError

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    -public String getError()
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    Specified by:
    getError in interface Executable<NetNglyc>
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    -getLimit

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    -public Limit<NetNglyc> getLimit(String presetName)
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    Specified by:
    getLimit in interface Executable<NetNglyc>
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    -getLimits

    -
    -public LimitsManager<NetNglyc> getLimits()
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    Specified by:
    getLimits in interface Executable<NetNglyc>
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    -getClusterJobSettings

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    -public String getClusterJobSettings()
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    Specified by:
    getClusterJobSettings in interface Executable<NetNglyc>
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html deleted file mode 100644 index 31bd3db..0000000 --- a/website/full_javadoc/compbio/runner/_impl/OB.html +++ /dev/null @@ -1,382 +0,0 @@ - - - - - - -OB - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class OB

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.OB
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class OB
    extends _SkeletalCommandBuilder
    - - -

    -TODO this needs fixing! Executable does not work -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - -
    -Constructor Summary
    OB() - -
    -           
    OB(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - List<String>getTestArgs() - -
    -           
    -static StringgetTestCommand() - -
    -           
    -static voidmain(String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -OB

    -
    -public OB()
    -
    -
    -
    - -

    -OB

    -
    -public OB(String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
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    -getTestCommand

    -
    -public static String getTestCommand()
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    -getTestArgs

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    -public List<String> getTestArgs()
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    -main

    -
    -public static void main(String[] args)
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    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
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    -getInput

    -
    -public String getInput()
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    -
    -
    -
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    - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html deleted file mode 100644 index 1f8d9b2..0000000 --- a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -PSIBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class PSIBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.PSIBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class PSIBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    PSIBlast(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    - booleanremoveOutput(String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    - - - - - - - - -
    -Constructor Detail
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    -PSIBlast

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    -public PSIBlast(String workDirectory)
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    -Method Detail
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    -removeOutput

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    -public boolean removeOutput(String outfile)
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    -getCommand

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    -public String getCommand(Executable.ExecProvider provider)
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    -getCommandName

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    -public String getCommandName()
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    -getCreatedFiles

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    -getInput

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    -public String getInput()
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    -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html deleted file mode 100644 index 35a934e..0000000 --- a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -RPSBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class RPSBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.RPSBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
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    -
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    -
    public class RPSBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    RPSBlast(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    -static StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
    -           
    -static StringgetTestCommand() - -
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    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
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    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    -RPSBlast

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    -public RPSBlast(String workDirectory)
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    -getCommand

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    -public String getCommand(Executable.ExecProvider provider)
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    -getTestCommand

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    -public static String getTestCommand()
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    -getInput

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    -public String getInput()
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html deleted file mode 100644 index 8a331fb..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Ronn.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -Ronn - - - - - - - - - - - - -
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    - - - -
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    - -compbio.runner._impl -
    -Class Ronn

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Ronn
-
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    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
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    public class Ronn
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
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    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Ronn(String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - StringgetCommandName() - -
    -           
    - List<String>getCreatedFiles() - -
    -           
    - StringgetInput() - -
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    -static StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getClusterJobSettings, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Ronn

    -
    -public Ronn(String workDirectory)
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    - - - - - - - - -
    -Method Detail
    - -

    -getCommand

    -
    -public String getCommand(Executable.ExecProvider provider)
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    -getTestCommand

    -
    -public static String getTestCommand()
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    -getCommandName

    -
    -public String getCommandName()
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    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
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    -getInput

    -
    -public String getInput()
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    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html deleted file mode 100644 index d10efdf..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Runners.html +++ /dev/null @@ -1,352 +0,0 @@ - - - - - - -Runners - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Runners

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Runners
-
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    -
    -
    public final class Runners
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static BlastAllgetBlastAllRunnable(String workDirectory) - -
    -           
    -static MclgetMclRunnable(String workDirectory) - -
    -           
    -static NetNglycgetNetNglycRunnable(String workDirectory) - -
    -           
    -static OBgetOBRunnable(String workDirectory) - -
    -           
    -static PSIBlastgetPSIBlastRunnable(String workDirectory) - -
    -           
    -static RonngetRonnRunnable(String workDirectory) - -
    -           
    -static RPSBlastgetRPSBlastRunnable(String workDirectory) - -
    -           
    -static compbio.runner._impl.Tmhmm2getTmhmm2Runnable(String workDirectory) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getMclRunnable

    -
    -public static Mcl getMclRunnable(String workDirectory)
    -
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    -getOBRunnable

    -
    -public static OB getOBRunnable(String workDirectory)
    -
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    -getNetNglycRunnable

    -
    -public static NetNglyc getNetNglycRunnable(String workDirectory)
    -
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    -
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    -getRonnRunnable

    -
    -public static Ronn getRonnRunnable(String workDirectory)
    -
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    -
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    -getTmhmm2Runnable

    -
    -public static compbio.runner._impl.Tmhmm2 getTmhmm2Runnable(String workDirectory)
    -
    -
    -
    -
    -
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    - -

    -getRPSBlastRunnable

    -
    -public static RPSBlast getRPSBlastRunnable(String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getBlastAllRunnable

    -
    -public static BlastAll getBlastAllRunnable(String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getPSIBlastRunnable

    -
    -public static PSIBlast getPSIBlastRunnable(String workDirectory)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html deleted file mode 100644 index dc243e4..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.BlastAll - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.runner._impl.BlastAll

    -
    - - - - - - - - - -
    -Packages that use BlastAll
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of BlastAll in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return BlastAll
    -static BlastAllRunners.getBlastAllRunnable(String workDirectory) - -
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    -

    - - - - - - - - - - - - - - - -
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    -Packages that use Mcl
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Mcl in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Mcl
    -static MclRunners.getMclRunnable(String workDirectory) - -
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    -Packages that use NetNglyc
    compbio.runner._impl  
    -  -

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    -Uses of NetNglyc in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return NetNglyc
    - NetNglycNetNglyc.addParameters(List<String> parameters) - -
    -           
    -static NetNglycRunners.getNetNglycRunnable(String workDirectory) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return types with arguments of type NetNglyc
    - Limit<NetNglyc>NetNglyc.getLimit(String presetName) - -
    -           
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    - CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
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    compbio.runner._impl  
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    -Uses of OB in compbio.runner._impl
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    Methods in compbio.runner._impl that return OB
    -static OBRunners.getOBRunnable(String workDirectory) - -
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    compbio.runner._impl  
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    Methods in compbio.runner._impl that return PSIBlast
    -static PSIBlastRunners.getPSIBlastRunnable(String workDirectory) - -
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    compbio.runner._impl  
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    Methods in compbio.runner._impl that return RPSBlast
    -static RPSBlastRunners.getRPSBlastRunnable(String workDirectory) - -
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    compbio.runner._impl  
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    Methods in compbio.runner._impl that return Ronn
    -static RonnRunners.getRonnRunnable(String workDirectory) - -
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    -Classes  - -
    -BlastAll -
    -BlastParameters -
    -Environment -
    -Mcl -
    -NetNglyc -
    -OB -
    -PSIBlast -
    -Ronn -
    -RPSBlast -
    -Runners
    - - - - diff --git a/website/full_javadoc/compbio/runner/_impl/package-summary.html b/website/full_javadoc/compbio/runner/_impl/package-summary.html deleted file mode 100644 index ff96621..0000000 --- a/website/full_javadoc/compbio/runner/_impl/package-summary.html +++ /dev/null @@ -1,193 +0,0 @@ - - - - - - -compbio.runner._impl - - - - - - - - - - - - -
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    -Class Summary
    BlastAll 
    BlastParametersUtility class for common Blast parameters
    EnvironmentThis is utility class to encapsulate environmental variables like directory paths
    Mcl 
    NetNglyc 
    OBTODO this needs fixing! Executable does not work
    PSIBlast 
    Ronn 
    RPSBlast 
    Runners 
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    compbio.runner._impl  
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    -Classes in compbio.runner._impl used by compbio.runner._impl
    BlastAll - -
    -           
    Mcl - -
    -           
    NetNglyc - -
    -           
    OB - -
    -          TODO this needs fixing! Executable does not work
    PSIBlast - -
    -           
    Ronn - -
    -           
    RPSBlast - -
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    -

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    - -compbio.runner._jpred -
    -Class _Jpred

    -
    -java.lang.Object
-  extended by compbio.runner._jpred._Jpred
-
    -
    -
    -
    public class _Jpred
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    _Jpred() - -
    -           
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    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -_Jpred

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    -Classes  - -
    -_Jpred
    - - - - diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html deleted file mode 100644 index eeba4ea..0000000 --- a/website/full_javadoc/compbio/runner/_jpred/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.runner._jpred - - - - - - - - - - - - -
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    _Jpred 
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    compbio.runner.Util

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    compbio.runner._NativeSpecHelper

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    compbio.runner._SkeletalCommandBuilder

    -
    - - - - - - - - - - - - - -
    -Packages that use _SkeletalCommandBuilder
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return _SkeletalCommandBuilder
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameter(String parameter) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(List<String> parameters) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(String[] parameters) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setEmail(String email) - -
    -          Deprecated.  
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setName(String name) - -
    -          Deprecated.  
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type _SkeletalCommandBuilder
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(String presetName) - -
    -          Deprecated.  
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -          Deprecated.  
    - CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
    -          Deprecated.  
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Subclasses of _SkeletalCommandBuilder in compbio.runner._impl
    - classBlastAll - -
    -           
    - classMcl - -
    -           
    - classOB - -
    -          TODO this needs fixing! Executable does not work
    - classPSIBlast - -
    -           
    - classRonn - -
    -           
    - classRPSBlast - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/AACon.html b/website/full_javadoc/compbio/runner/conservation/AACon.html deleted file mode 100644 index 8bf0ab2..0000000 --- a/website/full_javadoc/compbio/runner/conservation/AACon.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - -AACon - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.conservation -
    -Class AACon

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<AACon>
-      extended by compbio.runner.conservation.AACon
-
    -
    -
    All Implemented Interfaces:
    Executable<AACon>
    -
    -
    -
    -
    public class AACon
    extends SkeletalExecutable<AACon>
    - - -

    -Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -static StringSTAT_FILE - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    AACon() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<AACon>getParameters(Executable.ExecProvider provider) - -
    -           
    - ScoreManagergetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<AACon>getType() - -
    -           
    - AAConsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - AAConsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -STAT_FILE

    -
    -public static final String STAT_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -AACon

    -
    -public AACon()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<AACon>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<AACon>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public AACon setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<AACon>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public AACon setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<AACon>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<AACon> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<AACon>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<AACon> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<AACon>
    Overrides:
    getParameters in class SkeletalExecutable<AACon>
    -
    -
    -
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html b/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html deleted file mode 100644 index 07b288d..0000000 --- a/website/full_javadoc/compbio/runner/conservation/class-use/AACon.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -Uses of Class compbio.runner.conservation.AACon - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.conservation.AACon

    -
    - - - - - - - - - -
    -Packages that use AACon
    compbio.runner.conservation  
    -  -

    - - - - - -
    -Uses of AACon in compbio.runner.conservation
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.conservation that return AACon
    - AAConAACon.setInput(String inFile) - -
    -           
    - AAConAACon.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.conservation that return types with arguments of type AACon
    - CommandBuilder<AACon>AACon.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<AACon>AACon.getType() - -
    -           
    -  -

    -

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    -Classes  - -
    -AACon
    - - - - diff --git a/website/full_javadoc/compbio/runner/conservation/package-summary.html b/website/full_javadoc/compbio/runner/conservation/package-summary.html deleted file mode 100644 index 84a5d49..0000000 --- a/website/full_javadoc/compbio/runner/conservation/package-summary.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - -compbio.runner.conservation - - - - - - - - - - - - -
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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    -

    -Package compbio.runner.conservation -

    - - - - - - - - - -
    -Class Summary
    AAConCommand line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
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    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/conservation/package-tree.html b/website/full_javadoc/compbio/runner/conservation/package-tree.html deleted file mode 100644 index 6b6aef6..0000000 --- a/website/full_javadoc/compbio/runner/conservation/package-tree.html +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - -compbio.runner.conservation Class Hierarchy - - - - - - - - - - - - -
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    -Hierarchy For Package compbio.runner.conservation -

    -
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    Package Hierarchies:
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    -
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    -Class Hierarchy -

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    -Uses of Package
    compbio.runner.conservation

    -
    - - - - - - - - - -
    -Packages that use compbio.runner.conservation
    compbio.runner.conservation  
    -  -

    - - - - - - - - -
    -Classes in compbio.runner.conservation used by compbio.runner.conservation
    AACon - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    -

    - - - - - - - - - - - - - - - -
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    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/Disembl.html b/website/full_javadoc/compbio/runner/disorder/Disembl.html deleted file mode 100644 index 3f9f15a..0000000 --- a/website/full_javadoc/compbio/runner/disorder/Disembl.html +++ /dev/null @@ -1,468 +0,0 @@ - - - - - - -Disembl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.disorder -
    -Class Disembl

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Disembl>
-      extended by compbio.runner.disorder.Disembl
-
    -
    -
    All Implemented Interfaces:
    Executable<Disembl>, PipedExecutable<Disembl>
    -
    -
    -
    -
    public class Disembl
    extends SkeletalExecutable<Disembl>
    implements PipedExecutable<Disembl>
    - - -

    -DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script. - smooth_frame=8 peak_frame=8 join_frame=4 fold_coils=1.2 fold_hotloops=1.4 - fold_rem465=1.2 - - Changing these values are not recommended by developers, apart from smoothing - window. However, 5 orders of magnitude changes in this parameter does not - change the output so allowing this change also seems pointless. Finally, the - binary, DisEMBL depends on - Tisean is not happy with arbitruary changes to - these values, so changing them can lead to problems. - - - This is not a standard DisEMBL! The script has been modified! -

    - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    - doubleCOILS_EXPECTATION_THRESHOLD - -
    -          For the region to be considered disordered the values must exceed these
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    - doubleLOOPS_EXPECTATION_THRESHOLD - -
    -           
    - doubleREM_EXPECTATION_THRESHOLD - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Disembl() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - ScoreManagergetResults(String workDirectory) - -
    -           
    - Class<Disembl>getType() - -
    -           
    - DisemblsetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -COILS_EXPECTATION_THRESHOLD

    -
    -public final double COILS_EXPECTATION_THRESHOLD
    -
    -
    For the region to be considered disordered the values must exceed these -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -REM_EXPECTATION_THRESHOLD

    -
    -public final double REM_EXPECTATION_THRESHOLD
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -LOOPS_EXPECTATION_THRESHOLD

    -
    -public final double LOOPS_EXPECTATION_THRESHOLD
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Disembl

    -
    -public Disembl()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Disembl>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public Disembl setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Disembl>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Disembl> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Disembl>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/GlobPlot.html b/website/full_javadoc/compbio/runner/disorder/GlobPlot.html deleted file mode 100644 index 6243d24..0000000 --- a/website/full_javadoc/compbio/runner/disorder/GlobPlot.html +++ /dev/null @@ -1,405 +0,0 @@ - - - - - - -GlobPlot - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.disorder -
    -Class GlobPlot

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<GlobPlot>
-      extended by compbio.runner.disorder.GlobPlot
-
    -
    -
    All Implemented Interfaces:
    Executable<GlobPlot>, PipedExecutable<GlobPlot>
    -
    -
    -
    -
    public class GlobPlot
    extends SkeletalExecutable<GlobPlot>
    implements PipedExecutable<GlobPlot>
    - - -

    -./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5. - - Changing these values are not recommended by developers, apart from smoothing - window. However, the binary, GlobPlot depends on - Tisean which is not happy - with arbitrary changes to these values, so changing them can lead to - problems. May be we can offer preset? - - This is not a standard GlobPlot! The script has been modified! -

    - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    GlobPlot() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - ScoreManagergetResults(String workDirectory) - -
    -           
    - Class<GlobPlot>getType() - -
    -           
    - GlobPlotsetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -GlobPlot

    -
    -public GlobPlot()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<GlobPlot>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public GlobPlot setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<GlobPlot>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<GlobPlot> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<GlobPlot>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/IUPred.html b/website/full_javadoc/compbio/runner/disorder/IUPred.html deleted file mode 100644 index 0f16d75..0000000 --- a/website/full_javadoc/compbio/runner/disorder/IUPred.html +++ /dev/null @@ -1,401 +0,0 @@ - - - - - - -IUPred - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.disorder -
    -Class IUPred

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<IUPred>
-      extended by compbio.runner.disorder.IUPred
-
    -
    -
    All Implemented Interfaces:
    Executable<IUPred>
    -
    -
    -
    -
    public class IUPred
    extends SkeletalExecutable<IUPred>
    - - -

    -iupred sequenceFile - - Maximum sequence length is 40000 chars. Single string length max is a 1000 - chars! -

    - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    IUPred() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetOutput() - -
    -           
    - ScoreManagergetResults(String workDirectory) - -
    -           
    - Class<IUPred>getType() - -
    -           
    - IUPredsetInput(String inFile) - -
    -           
    - IUPredsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IUPred

    -
    -public IUPred()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public IUPred setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public IUPred setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<IUPred>
    Overrides:
    getOutput in class SkeletalExecutable<IUPred>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<IUPred> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<IUPred>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/Jronn.html b/website/full_javadoc/compbio/runner/disorder/Jronn.html deleted file mode 100644 index 91f21e3..0000000 --- a/website/full_javadoc/compbio/runner/disorder/Jronn.html +++ /dev/null @@ -1,514 +0,0 @@ - - - - - - -Jronn - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.disorder -
    -Class Jronn

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Jronn>
-      extended by compbio.runner.disorder.Jronn
-
    -
    -
    All Implemented Interfaces:
    Executable<Jronn>
    -
    -
    -
    -
    public class Jronn
    extends SkeletalExecutable<Jronn>
    - - -

    -Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -static StringSTAT_FILE - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Jronn() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<Jronn>getParameters(Executable.ExecProvider provider) - -
    -           
    - ScoreManagergetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<Jronn>getType() - -
    -           
    - JronnsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - JronnsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -STAT_FILE

    -
    -public static final String STAT_FILE
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Jronn

    -
    -public Jronn()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public ScoreManager getResults(String workDirectory)
-                        throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Jronn>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Jronn>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public Jronn setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
    -
    -
    - -

    -setOutput

    -
    -public Jronn setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Jronn> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Jronn>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<Jronn> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<Jronn>
    Overrides:
    getParameters in class SkeletalExecutable<Jronn>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html b/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html deleted file mode 100644 index d28abbe..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/Disembl.html +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.Disembl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.runner.disorder.Disembl

    -
    - - - - - - - - - - - - - -
    -Packages that use Disembl
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Disembl in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return Disembl
    - DisemblDisembl.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type Disembl
    - Class<Disembl>Disembl.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Disembl in compbio.ws.server
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Disembl
    - StringDisemblWS.customAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -           
    - StringDisemblWS.presetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html b/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html deleted file mode 100644 index f70dbc9..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/GlobPlot.html +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.GlobPlot - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.runner.disorder.GlobPlot

    -
    - - - - - - - - - - - - - -
    -Packages that use GlobPlot
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of GlobPlot in compbio.runner.disorder
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return GlobPlot
    - GlobPlotGlobPlot.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type GlobPlot
    - Class<GlobPlot>GlobPlot.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of GlobPlot in compbio.ws.server
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type GlobPlot
    - StringGlobPlotWS.customAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -           
    - StringGlobPlotWS.presetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html b/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html deleted file mode 100644 index 5512cb1..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/IUPred.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.IUPred - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.disorder.IUPred

    -
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    -Packages that use IUPred
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of IUPred in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return IUPred
    - IUPredIUPred.setInput(String inFile) - -
    -           
    - IUPredIUPred.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type IUPred
    - Class<IUPred>IUPred.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of IUPred in compbio.ws.server
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type IUPred
    - StringIUPredWS.presetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -           
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html b/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html deleted file mode 100644 index 300a671..0000000 --- a/website/full_javadoc/compbio/runner/disorder/class-use/Jronn.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -Uses of Class compbio.runner.disorder.Jronn - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.disorder.Jronn

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    -Packages that use Jronn
    compbio.runner.disorder  
    -  -

    - - - - - -
    -Uses of Jronn in compbio.runner.disorder
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return Jronn
    - JronnJronn.setInput(String inFile) - -
    -           
    - JronnJronn.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.disorder that return types with arguments of type Jronn
    - CommandBuilder<Jronn>Jronn.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<Jronn>Jronn.getType() - -
    -           
    -  -

    -

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    -Classes  - -
    -Disembl -
    -GlobPlot -
    -IUPred -
    -Jronn
    - - - - diff --git a/website/full_javadoc/compbio/runner/disorder/package-summary.html b/website/full_javadoc/compbio/runner/disorder/package-summary.html deleted file mode 100644 index de5cf64..0000000 --- a/website/full_javadoc/compbio/runner/disorder/package-summary.html +++ /dev/null @@ -1,186 +0,0 @@ - - - - - - -compbio.runner.disorder - - - - - - - - - - - - -
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    -Package compbio.runner.disorder -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    DisemblDisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    GlobPlot./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    IUPrediupred sequenceFile - - Maximum sequence length is 40000 chars.
    JronnCommand line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  - -

    -

    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/runner/disorder/package-tree.html b/website/full_javadoc/compbio/runner/disorder/package-tree.html deleted file mode 100644 index c2ccd39..0000000 --- a/website/full_javadoc/compbio/runner/disorder/package-tree.html +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - -compbio.runner.disorder Class Hierarchy - - - - - - - - - - - - -
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    -Hierarchy For Package compbio.runner.disorder -

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    Package Hierarchies:
    All Packages
    -
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    -Class Hierarchy -

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    -Uses of Package
    compbio.runner.disorder

    -
    - - - - - - - - - - - - - -
    -Packages that use compbio.runner.disorder
    compbio.runner.disorder  
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.disorder used by compbio.runner.disorder
    Disembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    GlobPlot - -
    -          ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    IUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    Jronn - -
    -          Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.runner.disorder used by compbio.ws.server
    Disembl - -
    -          DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    GlobPlot - -
    -          ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    IUPred - -
    -          iupred sequenceFile - - Maximum sequence length is 40000 chars.
    -  -

    -

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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/ClustalO.html b/website/full_javadoc/compbio/runner/msa/ClustalO.html deleted file mode 100644 index 69a07e0..0000000 --- a/website/full_javadoc/compbio/runner/msa/ClustalO.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -ClustalO - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.msa -
    -Class ClustalO

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<ClustalO>
-      extended by compbio.runner.msa.ClustalO
-
    -
    -
    All Implemented Interfaces:
    Executable<ClustalO>
    -
    -
    -
    -
    public class ClustalO
    extends SkeletalExecutable<ClustalO>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalO() - -
    -          --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - CommandBuilder<ClustalO>getParameters(Executable.ExecProvider provider) - -
    -           
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<ClustalO>getType() - -
    -           
    - ClustalOsetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    - ClustalOsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalO

    -
    -public ClustalO()
    -
    -
    --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file -

    -

    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public ClustalO setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public ClustalO setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<ClustalO> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<ClustalO>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<ClustalO> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<ClustalO>
    Overrides:
    getParameters in class SkeletalExecutable<ClustalO>
    -
    -
    -
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html deleted file mode 100644 index 69d8c79..0000000 --- a/website/full_javadoc/compbio/runner/msa/ClustalW.html +++ /dev/null @@ -1,445 +0,0 @@ - - - - - - -ClustalW - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.msa -
    -Class ClustalW

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<ClustalW>
-      extended by compbio.runner.msa.ClustalW
-
    -
    -
    All Implemented Interfaces:
    Executable<ClustalW>
    -
    -
    -
    -
    public class ClustalW
    extends SkeletalExecutable<ClustalW>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalW() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<ClustalW>getType() - -
    -           
    - ClustalWsetInput(String inFile) - -
    -           
    - ClustalWsetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalW

    -
    -public ClustalW()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public ClustalW setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public ClustalW setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<ClustalW>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<ClustalW>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<ClustalW> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<ClustalW>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html deleted file mode 100644 index c0aaf06..0000000 --- a/website/full_javadoc/compbio/runner/msa/Mafft.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -Mafft - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.msa -
    -Class Mafft

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Mafft>
-      extended by compbio.runner.msa.Mafft
-
    -
    -
    All Implemented Interfaces:
    Executable<Mafft>, PipedExecutable<Mafft>
    -
    -
    -
    -
    public class Mafft
    extends SkeletalExecutable<Mafft>
    implements PipedExecutable<Mafft>
    - - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Mafft() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - MafftaddParameters(List<String> parameters) - -
    -          Mafft input must always be the last parameter!
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Mafft>getType() - -
    -           
    - MafftsetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    equals, getClusterCpuNum, getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getClusterJobSettings, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Mafft

    -
    -public Mafft()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Mafft>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public Mafft setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Mafft>
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public Mafft addParameters(List<String> parameters)
    -
    -
    Mafft input must always be the last parameter! -

    -

    -
    Specified by:
    addParameters in interface Executable<Mafft>
    Overrides:
    addParameters in class SkeletalExecutable<Mafft>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getType

    -
    -public Class<Mafft> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Mafft>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html deleted file mode 100644 index 2f9af85..0000000 --- a/website/full_javadoc/compbio/runner/msa/Muscle.html +++ /dev/null @@ -1,451 +0,0 @@ - - - - - - -Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Muscle

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Muscle>
-      extended by compbio.runner.msa.Muscle
-
    -
    -
    All Implemented Interfaces:
    Executable<Muscle>
    -
    -
    -
    -
    public class Muscle
    extends SkeletalExecutable<Muscle>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Muscle() - -
    -          Default options are - - -clwstrict - write output in clustal format
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    -static StringgetStatFile() - -
    -           
    - Class<Muscle>getType() - -
    -           
    - MusclesetInput(String inFile) - -
    -           
    - MusclesetOutput(String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Muscle

    -
    -public Muscle()
    -
    -
    Default options are - - -clwstrict - write output in clustal format -

    -

    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public Muscle setOutput(String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public Muscle setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Muscle>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Muscle>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Muscle> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Muscle>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html deleted file mode 100644 index 2b1fb99..0000000 --- a/website/full_javadoc/compbio/runner/msa/Probcons.html +++ /dev/null @@ -1,416 +0,0 @@ - - - - - - -Probcons - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Probcons

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Probcons>
-      extended by compbio.runner.msa.Probcons
-
    -
    -
    All Implemented Interfaces:
    Executable<Probcons>, PipedExecutable<Probcons>
    -
    -
    -
    -
    public class Probcons
    extends SkeletalExecutable<Probcons>
    implements PipedExecutable<Probcons>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Probcons() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Probcons>getType() - -
    -           
    - ProbconssetInput(String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, getParameters, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Probcons

    -
    -public Probcons()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Probcons>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Probcons>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Probcons>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public Probcons setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Probcons>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Probcons> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Probcons>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/Tcoffee.html deleted file mode 100644 index e04b663..0000000 --- a/website/full_javadoc/compbio/runner/msa/Tcoffee.html +++ /dev/null @@ -1,460 +0,0 @@ - - - - - - -Tcoffee - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner.msa -
    -Class Tcoffee

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Tcoffee>
-      extended by compbio.runner.msa.Tcoffee
-
    -
    -
    All Implemented Interfaces:
    Executable<Tcoffee>, PipedExecutable<Tcoffee>
    -
    -
    -
    -
    public class Tcoffee
    extends SkeletalExecutable<Tcoffee>
    implements PipedExecutable<Tcoffee>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - -
    Fields inherited from class compbio.engine.client.SkeletalExecutable
    ERROR, INPUT, OUTPUT
    -  - - - - - - - - - - -
    -Constructor Summary
    Tcoffee() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - CommandBuilder<Tcoffee>getParameters(Executable.ExecProvider provider) - -
    -           
    - AlignmentgetResults(String workDirectory) - -
    -           
    - Class<Tcoffee>getType() - -
    -           
    - TcoffeesetInput(String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterCpuNum, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getClusterJobSettings, getError, getInput, getLimit, getLimits, getOutput, loadRunConfiguration
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -KEY_VALUE_SEPARATOR

    -
    -public static final String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Tcoffee

    -
    -public Tcoffee()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setInput

    -
    -public Tcoffee setInput(String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Tcoffee>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public List<String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Tcoffee>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<Tcoffee> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<Tcoffee>
    Overrides:
    getParameters in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public Class<Tcoffee> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Tcoffee>
    -
    -
    - -
    Returns:
    subclasses must return their type
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html deleted file mode 100644 index 3a0c277..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalO.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.ClustalO - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -Uses of Class
    compbio.runner.msa.ClustalO

    -
    - - - - - - - - - - - - - -
    -Packages that use ClustalO
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ClustalO in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return ClustalO
    - ClustalOClustalO.setInput(String inFile) - -
    -           
    - ClustalOClustalO.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type ClustalO
    - CommandBuilder<ClustalO>ClustalO.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<ClustalO>ClustalO.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of ClustalO in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type ClustalO
    - Limit<ClustalO>ClustalOWS.getLimit(String presetName) - -
    -           
    - LimitsManager<ClustalO>ClustalOWS.getLimits() - -
    -           
    - PresetManager<ClustalO>ClustalOWS.getPresets() - -
    -           
    - RunnerConfig<ClustalO>ClustalOWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type ClustalO
    - StringClustalOWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -           
    - StringClustalOWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html deleted file mode 100644 index 2912d89..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.ClustalW - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.runner.msa.ClustalW

    -
    - - - - - - - - - - - - - -
    -Packages that use ClustalW
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return ClustalW
    - ClustalWClustalW.setInput(String inFile) - -
    -           
    - ClustalWClustalW.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type ClustalW
    - Class<ClustalW>ClustalW.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type ClustalW
    - Limit<ClustalW>ClustalWS.getLimit(String presetName) - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type ClustalW
    - StringClustalWS.customAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -           
    - StringClustalWS.presetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html deleted file mode 100644 index fa5ab59..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Mafft - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.runner.msa.Mafft

    -
    - - - - - - - - - - - - - -
    -Packages that use Mafft
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Mafft in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Mafft
    - MafftMafft.addParameters(List<String> parameters) - -
    -          Mafft input must always be the last parameter!
    - MafftMafft.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Mafft
    - Class<Mafft>Mafft.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Mafft in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Mafft
    - Limit<Mafft>MafftWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Mafft
    - StringMafftWS.customAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -           
    - StringMafftWS.presetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html deleted file mode 100644 index b169e80..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Muscle

    -
    - - - - - - - - - - - - - -
    -Packages that use Muscle
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Muscle in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Muscle
    - MuscleMuscle.setInput(String inFile) - -
    -           
    - MuscleMuscle.setOutput(String outFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Muscle
    - Class<Muscle>Muscle.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Muscle in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Muscle
    - Limit<Muscle>MuscleWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Muscle
    - StringMuscleWS.customAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -           
    - StringMuscleWS.presetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html deleted file mode 100644 index 1831e67..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Probcons - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Probcons

    -
    - - - - - - - - - - - - - -
    -Packages that use Probcons
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Probcons in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Probcons
    - ProbconsProbcons.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Probcons
    - Class<Probcons>Probcons.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Probcons in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Probcons
    - Limit<Probcons>ProbconsWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Probcons
    - StringProbconsWS.customAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -           
    - StringProbconsWS.presetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html deleted file mode 100644 index d54f3b8..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Tcoffee - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner.msa.Tcoffee

    -
    - - - - - - - - - - - - - -
    -Packages that use Tcoffee
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Tcoffee
    - TcoffeeTcoffee.setInput(String inFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Tcoffee
    - CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
    -           
    - Class<Tcoffee>Tcoffee.getType() - -
    -           
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Tcoffee
    - Limit<Tcoffee>TcoffeeWS.getLimit(String presetName) - -
    -           
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Tcoffee
    - StringTcoffeeWS.customAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -           
    - StringTcoffeeWS.presetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -ClustalO -
    -ClustalW -
    -Mafft -
    -Muscle -
    -Probcons -
    -Tcoffee
    - - - - diff --git a/website/full_javadoc/compbio/runner/msa/package-summary.html b/website/full_javadoc/compbio/runner/msa/package-summary.html deleted file mode 100644 index 58ffba2..0000000 --- a/website/full_javadoc/compbio/runner/msa/package-summary.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -compbio.runner.msa - - - - - - - - - - - - -
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    -Package compbio.runner.msa -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ClustalO 
    ClustalW 
    Mafft 
    Muscle 
    Probcons 
    Tcoffee 
    -  - -

    -

    -Package compbio.runner.msa Description -

    - -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
    -
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    -Uses of Package
    compbio.runner.msa

    -
    - - - - - - - - - - - - - -
    -Packages that use compbio.runner.msa
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.runner.msa
    ClustalO - -
    -           
    ClustalW - -
    -           
    Mafft - -
    -           
    Muscle - -
    -           
    Probcons - -
    -           
    Tcoffee - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.ws.server
    ClustalO - -
    -           
    ClustalW - -
    -           
    Mafft - -
    -           
    Muscle - -
    -           
    Probcons - -
    -           
    Tcoffee - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -_NativeSpecHelper -
    -_SkeletalCommandBuilder -
    -OptionCombinator -
    -Util
    - - - - diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html deleted file mode 100644 index 3601344..0000000 --- a/website/full_javadoc/compbio/runner/package-summary.html +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - -compbio.runner - - - - - - - - - - - - -
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    -Package compbio.runner -

    -Utilities commonly used by all runners. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    _NativeSpecHelperDeprecated.
    _SkeletalCommandBuilderDeprecated.
    OptionCombinatorThis class solve the following problems.
    Util 
    -  - -

    -

    -Package compbio.runner Description -

    - -

    -Utilities commonly used by all runners. -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
    -
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    compbio.runner

    -
    - - - - - - - - - - - - - -
    -Packages that use compbio.runner
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - - - - -
    -Classes in compbio.runner used by compbio.runner
    _SkeletalCommandBuilder - -
    -          Deprecated. 
    -  -

    - - - - - - - - -
    -Classes in compbio.runner used by compbio.runner._impl
    _SkeletalCommandBuilder - -
    -          Deprecated. 
    -  -

    -

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    - - - -
    - -

    - -compbio.stat.collector -
    -Class ExecutionStatCollector

    -
    -java.lang.Object
-  extended by compbio.stat.collector.ExecutionStatCollector
-
    -
    -
    All Implemented Interfaces:
    Runnable
    -
    -
    -
    -
    public class ExecutionStatCollector
    extends Object
    implements Runnable
    - - -

    -Number of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter. WS - names - enumeration. Status file names and content. -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ExecutionStatCollector(String workDirectory, - int timeOutInHours) - -
    -          List subdirectories in the job directory
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          Not in use
    - voidrun() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ExecutionStatCollector

    -
    -public ExecutionStatCollector(String workDirectory,
-                              int timeOutInHours)
    -
    -
    List subdirectories in the job directory -

    -

    -
    Parameters:
    workDirectory -
    timeOutInHours -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
-                 throws IOException,
-                        SQLException
    -
    -
    Not in use -

    -

    -
    -
    -
    - -
    Throws: -
    IOException -
    SQLException
    -
    -
    -
    - -

    -run

    -
    -public void run()
    -
    -
    -
    Specified by:
    run in interface Runnable
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/collector/InputFilter.html b/website/full_javadoc/compbio/stat/collector/InputFilter.html deleted file mode 100644 index 988bfa3..0000000 --- a/website/full_javadoc/compbio/stat/collector/InputFilter.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -InputFilter - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class InputFilter

    -
    -java.lang.Object
-  extended by compbio.stat.collector.InputFilter
-
    -
    -
    -
    public class InputFilter
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    InputFilter() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -InputFilter

    -
    -public InputFilter()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/stat/collector/JobStat.html b/website/full_javadoc/compbio/stat/collector/JobStat.html deleted file mode 100644 index 11cce6c..0000000 --- a/website/full_javadoc/compbio/stat/collector/JobStat.html +++ /dev/null @@ -1,551 +0,0 @@ - - - - - - -JobStat - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class JobStat

    -
    -java.lang.Object
-  extended by compbio.stat.collector.JobStat
-
    -
    -
    -
    public class JobStat
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetClusterJobId() - -
    -           
    - StringgetEscJobname() - -
    -           
    - StringgetFinish() - -
    -           
    - longgetInputSize() - -
    -           
    - booleangetIsCancelled() - -
    -           
    - booleangetIsCollected() - -
    -           
    - booleangetIsFinished() - -
    -           
    - StringgetJobname() - -
    -           
    - longgetResultSize() - -
    -           
    - intgetRuntime() - -
    -           
    - StringgetStart() - -
    -           
    - ServicesgetWebService() - -
    -           
    - inthashCode() - -
    -           
    - booleanhasResult() - -
    -           
    - booleanhasStarted() - -
    -           
    - booleanisClusterJob() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -isClusterJob

    -
    -public boolean isClusterJob()
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getRuntime

    -
    -public int getRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getWebService

    -
    -public Services getWebService()
    -
    -
    -
    -
    -
    -
    - -

    -getClusterJobId

    -
    -public String getClusterJobId()
    -
    -
    -
    -
    -
    -
    - -

    -getJobname

    -
    -public String getJobname()
    -
    -
    -
    -
    -
    -
    - -

    -getEscJobname

    -
    -public String getEscJobname()
    -
    -
    -
    -
    -
    -
    - -

    -getStart

    -
    -public String getStart()
    -
    -
    -
    -
    -
    -
    - -

    -getFinish

    -
    -public String getFinish()
    -
    -
    -
    -
    -
    -
    - -

    -getInputSize

    -
    -public long getInputSize()
    -
    -
    -
    -
    -
    -
    - -

    -getResultSize

    -
    -public long getResultSize()
    -
    -
    -
    -
    -
    -
    - -

    -hasResult

    -
    -public boolean hasResult()
    -
    -
    -
    -
    -
    -
    - -

    -hasStarted

    -
    -public boolean hasStarted()
    -
    -
    -
    -
    -
    -
    - -

    -getIsCollected

    -
    -public boolean getIsCollected()
    -
    -
    -
    -
    -
    -
    - -

    -getIsCancelled

    -
    -public boolean getIsCancelled()
    -
    -
    -
    -
    -
    -
    - -

    -getIsFinished

    -
    -public boolean getIsFinished()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/collector/StatDB.html b/website/full_javadoc/compbio/stat/collector/StatDB.html deleted file mode 100644 index c250ccd..0000000 --- a/website/full_javadoc/compbio/stat/collector/StatDB.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -StatDB - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class StatDB

    -
    -java.lang.Object
-  extended by compbio.stat.collector.StatDB
-
    -
    -
    -
    public class StatDB
    extends Object
    - - -

    -The database must be stored in the application root directory and called - "ExecutionStatistic" -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatDB() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetAbandonedCount(Timestamp from, - Timestamp to) - -
    -           
    - intgetCancelledCount(Timestamp from, - Timestamp to) - -
    -           
    - DategetEarliestRecord() - -
    -           
    - intgetIncompleteCount(Timestamp from, - Timestamp to) - -
    -           
    - intgetTotalJobsCount(Timestamp from, - Timestamp to) - -
    -           
    -static voidmain(String[] args) - -
    -           
    - List<JobStat>readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    - voidremoveRecordedJobs(Set<JobStat> fsJobs) - -
    -          Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs.
    -static voidshutdownDBServer() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatDB

    -
    -public StatDB()
-       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getEarliestRecord

    -
    -public Date getEarliestRecord()
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getTotalJobsCount

    -
    -public int getTotalJobsCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getCancelledCount

    -
    -public int getCancelledCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getAbandonedCount

    -
    -public int getAbandonedCount(Timestamp from,
-                             Timestamp to)
-                      throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getIncompleteCount

    -
    -public int getIncompleteCount(Timestamp from,
-                              Timestamp to)
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -readData

    -
    -public List<JobStat> readData(Timestamp from,
-                              Timestamp to,
-                              Services wservice,
-                              Boolean clusterOnly)
-                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -removeRecordedJobs

    -
    -public void removeRecordedJobs(Set<JobStat> fsJobs)
-                        throws SQLException
    -
    -
    Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs. -

    -

    -
    Parameters:
    fsJobs - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -shutdownDBServer

    -
    -public static final void shutdownDBServer()
    -
    -
    -
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/collector/StatProcessor.html b/website/full_javadoc/compbio/stat/collector/StatProcessor.html deleted file mode 100644 index 473c2f4..0000000 --- a/website/full_javadoc/compbio/stat/collector/StatProcessor.html +++ /dev/null @@ -1,527 +0,0 @@ - - - - - - -StatProcessor - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.collector -
    -Class StatProcessor

    -
    -java.lang.Object
-  extended by compbio.stat.collector.StatProcessor
-
    -
    -
    -
    public class StatProcessor
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatProcessor(List<JobStat> stats) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - List<JobStat>getAbandonedJobs() - -
    -          Not collected.
    - List<JobStat>getCancelledJobs() - -
    -           
    - List<JobStat>getClusterJobs() - -
    -           
    - List<JobStat>getFailedJobs() - -
    -          Started & finished but did not produce result
    - List<JobStat>getIncompleteJobs() - -
    -           
    - intgetJobNumber() - -
    -           
    - List<JobStat>getJobs() - -
    -           
    - List<JobStat>getLocalJobs() - -
    -           
    - StatProcessorgetSingleWSStat(Services webService) - -
    -           
    - longgetTotalRuntime() - -
    -           
    - StringreportStat() - -
    -           
    - List<JobStat>sortByResultSize() - -
    -           
    - List<JobStat>sortByRuntime() - -
    -           
    - List<JobStat>sortByStartTime() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatProcessor

    -
    -public StatProcessor(List<JobStat> stats)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getClusterJobs

    -
    -public List<JobStat> getClusterJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getLocalJobs

    -
    -public List<JobStat> getLocalJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getAbandonedJobs

    -
    -public List<JobStat> getAbandonedJobs()
    -
    -
    Not collected. Excludes all cancelled jobs, and jobs with no results as - these are reported separately. -

    -

    -
    -
    -
    -
    - -

    -getFailedJobs

    -
    -public List<JobStat> getFailedJobs()
    -
    -
    Started & finished but did not produce result -

    -

    - -
    Returns:
    -
    -
    -
    - -

    -getCancelledJobs

    -
    -public List<JobStat> getCancelledJobs()
    -
    -
    -
    -
    -
    -
    - -

    -sortByRuntime

    -
    -public List<JobStat> sortByRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -sortByStartTime

    -
    -public List<JobStat> sortByStartTime()
    -
    -
    -
    -
    -
    -
    - -

    -sortByResultSize

    -
    -public List<JobStat> sortByResultSize()
    -
    -
    -
    -
    -
    -
    - -

    -getJobNumber

    -
    -public int getJobNumber()
    -
    -
    -
    -
    -
    -
    - -

    -getJobs

    -
    -public List<JobStat> getJobs()
    -
    -
    -
    -
    -
    -
    - -

    -getSingleWSStat

    -
    -public StatProcessor getSingleWSStat(Services webService)
    -
    -
    -
    -
    -
    -
    - -

    -getTotalRuntime

    -
    -public long getTotalRuntime()
    -
    -
    -
    -
    -
    -
    - -

    -getIncompleteJobs

    -
    -public List<JobStat> getIncompleteJobs()
    -
    -
    -
    -
    -
    -
    - -

    -reportStat

    -
    -public String reportStat()
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -Uses of Class
    compbio.stat.collector.ExecutionStatCollector

    -
    -No usage of compbio.stat.collector.ExecutionStatCollector -

    -

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    - - - - - - - - - - - - -
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    Methods in compbio.stat.collector that return types with arguments of type JobStat
    - List<JobStat>StatProcessor.getAbandonedJobs() - -
    -          Not collected.
    - List<JobStat>StatProcessor.getCancelledJobs() - -
    -           
    - List<JobStat>StatProcessor.getClusterJobs() - -
    -           
    - List<JobStat>StatProcessor.getFailedJobs() - -
    -          Started & finished but did not produce result
    - List<JobStat>StatProcessor.getIncompleteJobs() - -
    -           
    - List<JobStat>StatProcessor.getJobs() - -
    -           
    - List<JobStat>StatProcessor.getLocalJobs() - -
    -           
    - List<JobStat>StatDB.readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    - List<JobStat>StatProcessor.sortByResultSize() - -
    -           
    - List<JobStat>StatProcessor.sortByRuntime() - -
    -           
    - List<JobStat>StatProcessor.sortByStartTime() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.collector with type arguments of type JobStat
    - voidStatDB.removeRecordedJobs(Set<JobStat> fsJobs) - -
    -          Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs.
    -  -

    - - - - - - - - -
    Constructor parameters in compbio.stat.collector with type arguments of type JobStat
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    Methods in compbio.stat.collector that return StatProcessor
    - StatProcessorStatProcessor.getSingleWSStat(Services webService) - -
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    Methods in compbio.stat.servlet.util that return types with arguments of type StatProcessor
    - Map<Services,StatProcessor>StatCollection.getAllStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getClusterStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getLocalStat() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type StatProcessor
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
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    ExecutionStatCollectorNumber of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter.
    InputFilter 
    JobStat 
    StatDBThe database must be stored in the application root directory and called - "ExecutionStatistic"
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    -java.lang.Object
-  extended by javax.servlet.GenericServlet
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    -java.lang.Object
-  extended by javax.servlet.GenericServlet
-      extended by javax.servlet.http.HttpServlet
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    -
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    public class DisplayStat
    extends javax.servlet.http.HttpServlet
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    -java.lang.Object
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    public class HttpCodeResponseServiceStatus
    extends javax.servlet.http.HttpServlet
    - - -

    -This servlet checks the webservice coming as pathinfo and returns http code - as a reply. If the web service functions correctly then OK (200) is returned. - otherwise Service unavailable (503). When the webservice is not recognised - unknown service error (400) is sent as a response. - - If no pathinfo is specified all web services are checked and OK is returned - only if all webservices are functioning. -

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    Joblist() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class javax.servlet.http.HttpServlet
    service
    -  - - - - - - - -
    Methods inherited from class javax.servlet.GenericServlet
    destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Joblist

    -
    -public Joblist()
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/ServiceStatus.html b/website/full_javadoc/compbio/stat/servlet/ServiceStatus.html deleted file mode 100644 index ee85091..0000000 --- a/website/full_javadoc/compbio/stat/servlet/ServiceStatus.html +++ /dev/null @@ -1,258 +0,0 @@ - - - - - - -ServiceStatus - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet -
    -Class ServiceStatus

    -
    -java.lang.Object
-  extended by javax.servlet.GenericServlet
-      extended by javax.servlet.http.HttpServlet
-          extended by compbio.stat.servlet.ServiceStatus
-
    -
    -
    All Implemented Interfaces:
    Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig
    -
    -
    -
    -
    public class ServiceStatus
    extends javax.servlet.http.HttpServlet
    - - -

    -Use cases: -

    -
  • Test web services and display results on the web page
    • -
    -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ServiceStatus() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class javax.servlet.http.HttpServlet
    service
    -  - - - - - - - -
    Methods inherited from class javax.servlet.GenericServlet
    destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ServiceStatus

    -
    -public ServiceStatus()
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/ServiceTestResult.html b/website/full_javadoc/compbio/stat/servlet/ServiceTestResult.html deleted file mode 100644 index 9ed3f70..0000000 --- a/website/full_javadoc/compbio/stat/servlet/ServiceTestResult.html +++ /dev/null @@ -1,365 +0,0 @@ - - - - - - -ServiceTestResult - - - - - - - - - - - - -
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    - -

    - -compbio.stat.servlet -
    -Class ServiceTestResult

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.ServiceTestResult
-
    -
    -
    -
    public class ServiceTestResult
    extends Object
    - - -

    -Value class for test results. Two ServiceTestResult are considered equals if - their services are equals. -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ServiceTestResult(Services service) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - StringgetDetails() - -
    -           
    - ServicesgetService() - -
    -           
    - booleangetStatus() - -
    -           
    - inthashCode() - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ServiceTestResult

    -
    -public ServiceTestResult(Services service)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
    -
    -
    -
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -getService

    -
    -public Services getService()
    -
    -
    -
    -
    -
    -
    - -

    -getStatus

    -
    -public boolean getStatus()
    -
    -
    -
    -
    -
    -
    - -

    -getDetails

    -
    -public String getDetails()
    -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html b/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html deleted file mode 100644 index 72984fe..0000000 --- a/website/full_javadoc/compbio/stat/servlet/StatisticCollector.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -StatisticCollector - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.stat.servlet -
    -Class StatisticCollector

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.StatisticCollector
-
    -
    -
    All Implemented Interfaces:
    EventListener, javax.servlet.ServletContextListener
    -
    -
    -
    -
    public class StatisticCollector
    extends Object
    implements javax.servlet.ServletContextListener
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    StatisticCollector() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - voidcontextDestroyed(javax.servlet.ServletContextEvent arg0) - -
    -           
    - voidcontextInitialized(javax.servlet.ServletContextEvent arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatisticCollector

    -
    -public StatisticCollector()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -contextDestroyed

    -
    -public void contextDestroyed(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextDestroyed in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    -
    - -

    -contextInitialized

    -
    -public void contextInitialized(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextInitialized in interface javax.servlet.ServletContextListener
    -
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    - - - diff --git a/website/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html b/website/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html deleted file mode 100644 index 2c628c7..0000000 --- a/website/full_javadoc/compbio/stat/servlet/class-use/AnnualStat.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.stat.servlet.AnnualStat - - - - - - - - - - - - -
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    -

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    -
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    -

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    compbio.stat.servlet.DownloadRedirector

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    -

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    compbio.stat.servlet.HttpCodeResponseServiceStatus

    -
    -No usage of compbio.stat.servlet.HttpCodeResponseServiceStatus -

    -

    - - - - - - - - - - - - - - - -
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    compbio.stat.servlet.Joblist

    -
    -No usage of compbio.stat.servlet.Joblist -

    -

    - - - - - - - - - - - - - - - -
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    compbio.stat.servlet.ServiceStatus

    -
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    -

    - - - - - - - - - - - - - - - -
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    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -AnnualStat -
    -DisplayStat -
    -DownloadRedirector -
    -HttpCodeResponseServiceStatus -
    -Joblist -
    -ServiceStatus -
    -ServiceTestResult -
    -StatisticCollector
    - - - - diff --git a/website/full_javadoc/compbio/stat/servlet/package-summary.html b/website/full_javadoc/compbio/stat/servlet/package-summary.html deleted file mode 100644 index 37b758e..0000000 --- a/website/full_javadoc/compbio/stat/servlet/package-summary.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -compbio.stat.servlet - - - - - - - - - - - - -
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    -Package compbio.stat.servlet -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AnnualStat 
    DisplayStat 
    DownloadRedirector 
    HttpCodeResponseServiceStatusThis servlet checks the webservice coming as pathinfo and returns http code - as a reply.
    Joblist 
    ServiceStatusUse cases: - - Test web services and display results on the web page -
    ServiceTestResultValue class for test results.
    StatisticCollector 
    -  - -

    -

    -
    -
    - - - - - - - - - - - - - - - -
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    Package Hierarchies:
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    - - - -
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    - -compbio.stat.servlet.util -
    -Enum StatCollection.Stattype

    -
    -java.lang.Object
-  extended by java.lang.Enum<StatCollection.Stattype>
-      extended by compbio.stat.servlet.util.StatCollection.Stattype
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<StatCollection.Stattype>
    -
    -
    -
    Enclosing class:
    StatCollection
    -
    -
    -
    -
    public static enum StatCollection.Stattype
    extends Enum<StatCollection.Stattype>
    - - -

    -Total number of requests - - incomplete abandoned cancelled -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    ALL - -
    -           
    CLUSTER - -
    -           
    LOCAL - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static StatCollection.StattypevalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static StatCollection.Stattype[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -CLUSTER

    -
    -public static final StatCollection.Stattype CLUSTER
    -
    -
    -
    -
    -
    - -

    -LOCAL

    -
    -public static final StatCollection.Stattype LOCAL
    -
    -
    -
    -
    -
    - -

    -ALL

    -
    -public static final StatCollection.Stattype ALL
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static StatCollection.Stattype[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (StatCollection.Stattype c : StatCollection.Stattype.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static StatCollection.Stattype valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
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    - -compbio.stat.servlet.util -
    -Class StatCollection

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.util.StatCollection
-
    -
    -
    -
    public class StatCollection
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classStatCollection.Stattype - -
    -          Total number of requests - - incomplete abandoned cancelled
    -  - - - - - - - - - - -
    -Constructor Summary
    StatCollection() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(Object obj) - -
    -           
    - Map<Services,StatProcessor>getAllStat() - -
    -           
    - Map<Services,StatProcessor>getClusterStat() - -
    -           
    - Map<Services,StatProcessor>getLocalStat() - -
    -           
    -static Map<Date,Totals>getStats(Date fromDate) - -
    -           
    -static Map<Date,Totals>getStats(int monthsToReport) - -
    -           
    - inthashCode() - -
    -           
    -static StatCollectionnewStatCollecton(Date startDate, - Date endDate) - -
    -           
    - StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -StatCollection

    -
    -public StatCollection()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getAllStat

    -
    -public Map<Services,StatProcessor> getAllStat()
    -
    -
    -
    -
    -
    -
    - -

    -getClusterStat

    -
    -public Map<Services,StatProcessor> getClusterStat()
    -
    -
    -
    -
    -
    -
    - -

    -getLocalStat

    -
    -public Map<Services,StatProcessor> getLocalStat()
    -
    -
    -
    -
    -
    -
    - -

    -getStats

    -
    -public static Map<Date,Totals> getStats(int monthsToReport)
-                                 throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -getStats

    -
    -public static Map<Date,Totals> getStats(Date fromDate)
-                                 throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -newStatCollecton

    -
    -public static StatCollection newStatCollecton(Date startDate,
-                                              Date endDate)
-                                       throws SQLException
    -
    -
    - -
    Throws: -
    SQLException
    -
    -
    -
    - -

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class Object
    -
    -
    -
    -
    -
    -
    - -

    -equals

    -
    -public boolean equals(Object obj)
    -
    -
    -
    Overrides:
    equals in class Object
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public String toString()
    -
    -
    -
    Overrides:
    toString in class Object
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    - -compbio.stat.servlet.util -
    -Class Totals

    -
    -java.lang.Object
-  extended by compbio.stat.servlet.util.Totals
-
    -
    -
    -
    public class Totals
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Totals() - -
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    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetAbandoned() - -
    -           
    - intgetCancelled() - -
    -           
    - intgetFailed() - -
    -           
    - intgetIncomplete() - -
    -           
    - intgetTotal() - -
    -           
    -static TotalssumOfTotals(Map<Date,Totals> stat) - -
    -           
    -static TotalssumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -Totals

    -
    -public Totals()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTotal

    -
    -public int getTotal()
    -
    -
    -
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    -
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    -getIncomplete

    -
    -public int getIncomplete()
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    -getAbandoned

    -
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    -
    -public int getCancelled()
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    -
    -
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    -
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    -getFailed

    -
    -public int getFailed()
    -
    -
    -
    -
    -
    -
    - -

    -sumOfTotals

    -
    -public static Totals sumOfTotals(Map<Date,Totals> stat)
    -
    -
    -
    -
    -
    -
    - -

    -sumStats

    -
    -public static Totals sumStats(Map<Services,StatProcessor> stat)
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    -
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    -Packages that use StatCollection.Stattype
    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of StatCollection.Stattype in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return StatCollection.Stattype
    -static StatCollection.StattypeStatCollection.Stattype.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static StatCollection.Stattype[]StatCollection.Stattype.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

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    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of StatCollection in compbio.stat.servlet.util
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return StatCollection
    -static StatCollectionStatCollection.newStatCollecton(Date startDate, - Date endDate) - -
    -           
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    -

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    compbio.stat.servlet.util  
    -  -

    - - - - - -
    -Uses of Totals in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return Totals
    -static TotalsTotals.sumOfTotals(Map<Date,Totals> stat) - -
    -           
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return types with arguments of type Totals
    -static Map<Date,Totals>StatCollection.getStats(Date fromDate) - -
    -           
    -static Map<Date,Totals>StatCollection.getStats(int monthsToReport) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type Totals
    -static TotalsTotals.sumOfTotals(Map<Date,Totals> stat) - -
    -           
    -  -

    -

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    -  - -

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    - -

    - -compbio.ws.client -
    -Class AAConClient

    -
    -java.lang.Object
-  extended by compbio.ws.client.AAConClient
-
    -
    -
    -
    public class AAConClient
    extends Object
    - - -

    -A command line client for AACon web service -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - -
    -Method Summary
    -static SequenceAnnotation<AAConWS>connect() - -
    -          Connects to a AACon web service by the host and the service name
    -static voidmain(String[] args) - -
    -          Starts command line client, if no parameters are supplied prints help.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -connect

    -
    -public static SequenceAnnotation<AAConWS> connect()
-                                           throws WebServiceException
    -
    -
    Connects to a AACon web service by the host and the service name -

    -

    - -
    Returns:
    AlignmentAnnotation -
    Throws: -
    WebServiceException - if cannot connect to a web service
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Starts command line client, if no parameters are supplied prints help. -

    -

    -
    Parameters:
    args - Usage: ACTION [OPTIONS] - - -i= - full path to fasta or Clustal formatted - alignment file - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits. Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write results - -f= - the name of the file with the list - of parameters to use. Please note that -r and -f options - cannot be used together. Conservation is calculated with - either a preset or parameters from the file, but not both!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/IOHelper.html b/website/full_javadoc/compbio/ws/client/IOHelper.html deleted file mode 100644 index 75dae2c..0000000 --- a/website/full_javadoc/compbio/ws/client/IOHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -IOHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class IOHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.IOHelper
-
    -
    -
    -
    public class IOHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    IOHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IOHelper

    -
    -public IOHelper()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html deleted file mode 100644 index 952511b..0000000 --- a/website/full_javadoc/compbio/ws/client/Jws2Client.html +++ /dev/null @@ -1,399 +0,0 @@ - - - - - - -Jws2Client - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class Jws2Client

    -
    -java.lang.Object
-  extended by compbio.ws.client.Jws2Client
-
    -
    -
    -
    public class Jws2Client
    extends Object
    - - -

    -A command line client for JAva Bioinformatics Analysis Web Services -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static JABAServiceconnect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static RegistryWSconnectToRegistry(String host) - -
    -          Get a connection of JABAWS registry
    -static Set<Services>getServices(String hostname) - -
    -           
    -static voidmain(String[] args) - -
    -          Starts command line client, if no parameter are supported print help.
    -static voidtestService(String hostname, - Services service, - PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -static booleanvalidURL(String urlstr) - -
    -          Attempt to construct the URL object from the string
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -validURL

    -
    -public static boolean validURL(String urlstr)
    -
    -
    Attempt to construct the URL object from the string -

    -

    -
    Parameters:
    urlstr - -
    Returns:
    true if it succeed false otherwise
    -
    -
    -
    - -

    -testService

    -
    -public static void testService(String hostname,
-                               Services service,
-                               PrintWriter writer)
-                        throws ConnectException,
-                               WebServiceException
    -
    -
    Asks registry to test the service on the host hostname -

    -

    -
    Parameters:
    hostname -
    service -
    writer - -
    Throws: -
    ConnectException -
    WebServiceException
    -
    -
    -
    - -

    -getServices

    -
    -public static Set<Services> getServices(String hostname)
-                                 throws WebServiceException,
-                                        ConnectException
    -
    -
    - -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    -
    - -

    -connect

    -
    -public static JABAService connect(String host,
-                                  Services service)
-                           throws WebServiceException,
-                                  ConnectException
    -
    -
    Connects to a web service by the host and the service name web service - type -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    service - the name of the JABAWS service to connect to -
    Returns:
    JABAService -
    Throws: -
    WebServiceException -
    ConnectException - if fails to connect to the service on the host
    -
    -
    -
    - -

    -connectToRegistry

    -
    -public static RegistryWS connectToRegistry(String host)
-                                    throws WebServiceException,
-                                           ConnectException
    -
    -
    Get a connection of JABAWS registry -

    -

    -
    Parameters:
    host - the fully qualified name of JABAWS server including JABAWS - context name e.g - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba -
    Returns:
    compbio.data.msa.RegistryWS - instance of a RegistryWS web - service -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Starts command line client, if no parameter are supported print help. Two - parameters are required for successful call the JWS2 host name and a - service name. -

    -

    -
    Parameters:
    args - Usage: -h=host_and_context - -s=serviceName ACTION [OPTIONS] - - -h= - a full URL to the JWS2 web server - including context path e.g. http://10.31.1.159:8080/ws - - -s= - one of [MafftWS, MuscleWS, ClustalWS, - TcoffeeWS, ProbconsWS] ACTIONS: - - -i= - full path to fasta formatted sequence file, - from which to align sequences - - -parameters - lists parameters supported by web service - - -presets - lists presets supported by web service - - -limits - lists web services limits Please note that if input - file is specified other actions are ignored - - OPTIONS: (only for use with -i action): - - -r= - name of the preset to use - - -o= - full path to the file where to write an - alignment -f= - the name of the file with - the list of parameters to use. Please note that -r and -f - options cannot be used together. Alignment is done with either - preset or a parameters from the file, but not both!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/MetadataHelper.html b/website/full_javadoc/compbio/ws/client/MetadataHelper.html deleted file mode 100644 index 10c43c4..0000000 --- a/website/full_javadoc/compbio/ws/client/MetadataHelper.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -MetadataHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class MetadataHelper

    -
    -java.lang.Object
-  extended by compbio.ws.client.MetadataHelper
-
    -
    -
    -
    public class MetadataHelper
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    MetadataHelper() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MetadataHelper

    -
    -public MetadataHelper()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/Services.html b/website/full_javadoc/compbio/ws/client/Services.html deleted file mode 100644 index 6923a97..0000000 --- a/website/full_javadoc/compbio/ws/client/Services.html +++ /dev/null @@ -1,762 +0,0 @@ - - - - - - -Services - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Enum Services

    -
    -java.lang.Object
-  extended by java.lang.Enum<Services>
-      extended by compbio.ws.client.Services
-
    -
    -
    All Implemented Interfaces:
    Serializable, Comparable<Services>
    -
    -
    -
    -
    public enum Services
    extends Enum<Services>
    - - -

    -List of web services currently supported by JABAWS version 2 -

    - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    AAConWS - -
    -           
    ClustalOWS - -
    -           
    ClustalWS - -
    -           
    DisemblWS - -
    -           
    GlobPlotWS - -
    -           
    IUPredWS - -
    -           
    JronnWS - -
    -           
    MafftWS - -
    -           
    MuscleWS - -
    -           
    ProbconsWS - -
    -           
    TcoffeeWS - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringAACON_INFO - -
    -           
    -static StringCLUSTAL_INFO - -
    -           
    -static StringCLUSTAL_OMEGA_INFO - -
    -           
    -static StringDISEMBL_INFO - -
    -           
    -static StringGLOBPLOT_INFO - -
    -           
    -static StringIUPRED_INFO - -
    -           
    -static StringJRONN_INFO - -
    -           
    -static StringMAFFT_INFO - -
    -           
    -static StringMUSCLE_INFO - -
    -           
    -static StringPROBCONS_INFO - -
    -           
    -static StringTCOFFEE_INFO - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ServicesgetService(String servName) - -
    -           
    - StringgetServiceInfo() - -
    -           
    -static voidmain(String[] args) - -
    -           
    -static StringtoString(Set<Services> services) - -
    -           
    -static ServicesvalueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

    - - - - - - - - -
    -Enum Constant Detail
    - -

    -MafftWS

    -
    -public static final Services MafftWS
    -
    -
    -
    -
    -
    - -

    -MuscleWS

    -
    -public static final Services MuscleWS
    -
    -
    -
    -
    -
    - -

    -ClustalWS

    -
    -public static final Services ClustalWS
    -
    -
    -
    -
    -
    - -

    -ClustalOWS

    -
    -public static final Services ClustalOWS
    -
    -
    -
    -
    -
    - -

    -TcoffeeWS

    -
    -public static final Services TcoffeeWS
    -
    -
    -
    -
    -
    - -

    -ProbconsWS

    -
    -public static final Services ProbconsWS
    -
    -
    -
    -
    -
    - -

    -AAConWS

    -
    -public static final Services AAConWS
    -
    -
    -
    -
    -
    - -

    -JronnWS

    -
    -public static final Services JronnWS
    -
    -
    -
    -
    -
    - -

    -DisemblWS

    -
    -public static final Services DisemblWS
    -
    -
    -
    -
    -
    - -

    -GlobPlotWS

    -
    -public static final Services GlobPlotWS
    -
    -
    -
    -
    -
    - -

    -IUPredWS

    -
    -public static final Services IUPredWS
    -
    -
    -
    -
    - - - - - - - - -
    -Field Detail
    - -

    -AACON_INFO

    -
    -public static final String AACON_INFO
    -
    -
    -
    -
    -
    - -

    -CLUSTAL_INFO

    -
    -public static final String CLUSTAL_INFO
    -
    -
    -
    -
    -
    - -

    -CLUSTAL_OMEGA_INFO

    -
    -public static final String CLUSTAL_OMEGA_INFO
    -
    -
    -
    -
    -
    - -

    -DISEMBL_INFO

    -
    -public static final String DISEMBL_INFO
    -
    -
    -
    -
    -
    - -

    -GLOBPLOT_INFO

    -
    -public static final String GLOBPLOT_INFO
    -
    -
    -
    -
    -
    - -

    -IUPRED_INFO

    -
    -public static final String IUPRED_INFO
    -
    -
    -
    -
    -
    - -

    -TCOFFEE_INFO

    -
    -public static final String TCOFFEE_INFO
    -
    -
    -
    -
    -
    - -

    -MUSCLE_INFO

    -
    -public static final String MUSCLE_INFO
    -
    -
    -
    -
    -
    - -

    -PROBCONS_INFO

    -
    -public static final String PROBCONS_INFO
    -
    -
    -
    -
    -
    - -

    -JRONN_INFO

    -
    -public static final String JRONN_INFO
    -
    -
    -
    -
    -
    - -

    -MAFFT_INFO

    -
    -public static final String MAFFT_INFO
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Services[] values()
    -
    -
    Returns an array containing the constants of this enum type, in -the order they are declared. This method may be used to iterate -over the constants as follows: -
    -for (Services c : Services.values())
-    System.out.println(c);
-
    -

    -

    - -
    Returns:
    an array containing the constants of this enum type, in -the order they are declared
    -
    -
    -
    - -

    -valueOf

    -
    -public static Services valueOf(String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    -
    - -

    -getService

    -
    -public static Services getService(String servName)
    -
    -
    -
    -
    -
    -
    - -

    -toString

    -
    -public static String toString(Set<Services> services)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceInfo

    -
    -public String getServiceInfo()
    -
    -
    -
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/ServicesUtil.html b/website/full_javadoc/compbio/ws/client/ServicesUtil.html deleted file mode 100644 index 8de1679..0000000 --- a/website/full_javadoc/compbio/ws/client/ServicesUtil.html +++ /dev/null @@ -1,309 +0,0 @@ - - - - - - -ServicesUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class ServicesUtil

    -
    -java.lang.Object
-  extended by compbio.ws.client.ServicesUtil
-
    -
    -
    -
    public class ServicesUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ServicesUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static Class<? extends Executable<?>>getRunnerByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByRunner(Class<? extends Executable> class1) - -
    -           
    -static Class<? extends Executable<?>>getServiceImpl(Services service) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ServicesUtil

    -
    -public ServicesUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getServiceByRunner

    -
    -public static Services getServiceByRunner(Class<? extends Executable> class1)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceImpl

    -
    -public static Class<? extends Executable<?>> getServiceImpl(Services service)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerByJobDirectory

    -
    -public static Class<? extends Executable<?>> getRunnerByJobDirectory(File jobdir)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceByJobDirectory

    -
    -public static Services getServiceByJobDirectory(File jobdir)
    -
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    - - - -
    - -

    - -compbio.ws.client -
    -Class WSTester

    -
    -java.lang.Object
-  extended by compbio.ws.client.WSTester
-
    -
    -
    -
    public class WSTester
    extends Object
    - - -

    -Class for testing web services -

    - -

    -

    -
    Version:
    -
    1.0 February 2010
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - -
    -Field Summary
    -static StringfastaAlignment - -
    -           
    -static StringfastaInput - -
    -          Sequences to be used as input for all WS
    -  - - - - - - - - - - -
    -Constructor Summary
    WSTester(String hostname, - PrintWriter writer) - -
    -          Construct an instance of JABAWS tester
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancheckService(Services service) - -
    -          Test JABA web service
    -static - - - - -
    -<T> void
    -    		main(String[] args) - -
    -          Test JWS2 web services
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Field Detail
    - -

    -fastaInput

    -
    -public static final String fastaInput
    -
    -
    Sequences to be used as input for all WS -

    -

    -
    See Also:
    Constant Field Values
    -
    -
    - -

    -fastaAlignment

    -
    -public static final String fastaAlignment
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -WSTester

    -
    -public WSTester(String hostname,
-                PrintWriter writer)
    -
    -
    Construct an instance of JABAWS tester -

    -

    -
    Parameters:
    hostname - - fully qualified host and context name of JABAWS e.g. - http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba
    writer - a PrintWriter instance to writer test log to.
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static <T> void main(String[] args)
-                 throws IOException
    -
    -
    Test JWS2 web services -

    -

    -
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested -
    Throws: -
    IOException
    -
    -
    -
    - -

    -checkService

    -
    -public boolean checkService(Services service)
-                     throws ConnectException,
-                            WebServiceException
    -
    -
    Test JABA web service -

    -

    -
    Parameters:
    service - the service to test -
    Returns:
    true if the service works as expected, false otherwise -
    Throws: -
    WebServiceException -
    ConnectException
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/class-use/AAConClient.html b/website/full_javadoc/compbio/ws/client/class-use/AAConClient.html deleted file mode 100644 index 99af7e9..0000000 --- a/website/full_javadoc/compbio/ws/client/class-use/AAConClient.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.ws.client.AAConClient - - - - - - - - - - - - -
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    compbio.ws.client.AAConClient

    -
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    -Uses of Class
    compbio.ws.client.Services

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Services
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.stat.collector  
    compbio.stat.servlet  
    compbio.stat.servlet.util  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Services in compbio.data.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that return types with arguments of type Services
    - Set<Services>Category.getServices() - -
    -           
    - Set<Services>RegistryWS.getSupportedServices() - -
    -          List of services that are functioning on the server.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Services
    - intRegistryWS.getLastTested(Services service) - -
    -          Number of seconds since the last test.
    - DateRegistryWS.getLastTestedOn(Services service) - -
    -          The date and time the service has been verified to work last time
    - StringRegistryWS.getServiceDescription(Services service) - -
    -          Gives the description of the service.
    - booleanRegistryWS.isOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - StringRegistryWS.testService(Services service) - -
    -          Test a particular service
    -  -

    - - - - - -
    -Uses of Services in compbio.data.msa.jaxws
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Services
    - ServicesTestService.getArg0() - -
    -           
    - ServicesIsOperating.getArg0() - -
    -           
    - ServicesGetServiceDescription.getArg0() - -
    -           
    - ServicesGetLastTestedOn.getArg0() - -
    -           
    - ServicesGetLastTested.getArg0() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Services
    - Set<Services>GetSupportedServicesResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Services
    - voidTestService.setArg0(Services arg0) - -
    -           
    - voidIsOperating.setArg0(Services arg0) - -
    -           
    - voidGetServiceDescription.setArg0(Services arg0) - -
    -           
    - voidGetLastTestedOn.setArg0(Services arg0) - -
    -           
    - voidGetLastTested.setArg0(Services arg0) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Services
    - voidGetSupportedServicesResponse.setReturn(Set<Services> _return) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.stat.collector
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.collector that return Services
    - ServicesJobStat.getWebService() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.stat.collector with parameters of type Services
    - StatProcessorStatProcessor.getSingleWSStat(Services webService) - -
    -           
    - List<JobStat>StatDB.readData(Timestamp from, - Timestamp to, - Services wservice, - Boolean clusterOnly) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.stat.servlet
    -  -

    - - - - - - - - - -
    Methods in compbio.stat.servlet that return Services
    - ServicesServiceTestResult.getService() - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.stat.servlet with parameters of type Services
    ServiceTestResult(Services service) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.stat.servlet.util
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.stat.servlet.util that return types with arguments of type Services
    - Map<Services,StatProcessor>StatCollection.getAllStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getClusterStat() - -
    -           
    - Map<Services,StatProcessor>StatCollection.getLocalStat() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.stat.servlet.util with type arguments of type Services
    -static TotalsTotals.sumStats(Map<Services,StatProcessor> stat) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.ws.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Services
    -static ServicesServices.getService(String servName) - -
    -           
    -static ServicesServicesUtil.getServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesServicesUtil.getServiceByRunner(Class<? extends Executable> class1) - -
    -           
    -static ServicesServices.valueOf(String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Services[]Services.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type Services
    -static Set<Services>Jws2Client.getServices(String hostname) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client with parameters of type Services
    - booleanWSTester.checkService(Services service) - -
    -          Test JABA web service
    -static JABAServiceJws2Client.connect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name web service - type
    -static Class<? extends Executable<?>>ServicesUtil.getServiceImpl(Services service) - -
    -           
    -static voidJws2Client.testService(String hostname, - Services service, - PrintWriter writer) - -
    -          Asks registry to test the service on the host hostname
    -  -

    - - - - - - - - - -
    Method parameters in compbio.ws.client with type arguments of type Services
    -static StringServices.toString(Set<Services> services) - -
    -           
    -  -

    - - - - - -
    -Uses of Services in compbio.ws.server
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Services
    - Set<Services>RegistryWS.getSupportedServices() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Services
    - intRegistryWS.getLastTested(Services service) - -
    -           
    - DateRegistryWS.getLastTestedOn(Services service) - -
    -          Can potentially return null if the service has not been tested yet.
    - StringRegistryWS.getServiceDescription(Services service) - -
    -           
    -static _WSLogger_WSLogger.getStatLogger(Services service, - WebServiceContext wsContext) - -
    -          Deprecated.  
    - booleanRegistryWS.isOperating(Services service) - -
    -           
    - StringRegistryWS.testService(Services service) - -
    -           
    -  -

    -

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    -Classes  - -
    -AAConClient -
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    -MetadataHelper -
    -ServicesUtil -
    -WSTester
    - - - - - - -
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    - - - - diff --git a/website/full_javadoc/compbio/ws/client/package-summary.html b/website/full_javadoc/compbio/ws/client/package-summary.html deleted file mode 100644 index 7ca15e4..0000000 --- a/website/full_javadoc/compbio/ws/client/package-summary.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - -compbio.ws.client - - - - - - - - - - - - -
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    - PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -

    -Package compbio.ws.client -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    AAConClientA command line client for AACon web service
    IOHelper 
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    MetadataHelper 
    ServicesUtil 
    WSTesterClass for testing web services
    -  - -

    - - - - - - - - - -
    -Enum Summary
    ServicesList of web services currently supported by JABAWS version 2
    -  - -

    -

    -Package compbio.ws.client Description -

    - -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    - -

    -

    -
    Version:
    -
    1.0 April 2010
    -
    Author:
    -
    Peter Troshin
    -
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    compbio.ws.client

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    -Packages that use compbio.ws.client
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.data.msa.jaxws  
    compbio.stat.collector  
    compbio.stat.servlet  
    compbio.stat.servlet.util  
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.data.msa
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.data.msa.jaxws
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.stat.collector
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.stat.servlet
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.stat.servlet.util
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.client
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.server
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

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    - - - diff --git a/website/full_javadoc/compbio/ws/server/AAConWS.html b/website/full_javadoc/compbio/ws/server/AAConWS.html deleted file mode 100644 index 649a092..0000000 --- a/website/full_javadoc/compbio/ws/server/AAConWS.html +++ /dev/null @@ -1,380 +0,0 @@ - - - - - - -AAConWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class AAConWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<AACon>
-          extended by compbio.ws.server.AAConWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<AACon>, SequenceAnnotation<AACon>
    -
    -
    -
    -
    public class AAConWS
    extends SequenceAnnotationService<AACon>
    implements SequenceAnnotation<AACon>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    AAConWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringanalize(List<FastaSequence> sequences) - -
    -          Analyse the sequences.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -AAConWS

    -
    -public AAConWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -analize

    -
    -public String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences. The actual analysis algorithm is defined by the - type T. - - Any dataset containing a greater number of sequences or the average - length of the sequences are greater then defined in the default Limit - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    analize in interface SequenceAnnotation<AACon>
    Overrides:
    analize in class SequenceAnnotationService<AACon>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception.
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/server/ClustalOWS.html b/website/full_javadoc/compbio/ws/server/ClustalOWS.html deleted file mode 100644 index f7f78a5..0000000 --- a/website/full_javadoc/compbio/ws/server/ClustalOWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ClustalOWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -

    - -compbio.ws.server -
    -Class ClustalOWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ClustalOWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<ClustalO>, MsaWS<ClustalO>
    -
    -
    -
    -
    public class ClustalOWS
    extends Object
    implements MsaWS<ClustalO>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalOWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<ClustalO>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<ClustalO>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<ClustalO>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<ClustalO>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<ClustalO>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<ClustalO> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalOWS

    -
    -public ClustalOWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<ClustalO> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<ClustalO>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<ClustalO> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<ClustalO>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalO> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<ClustalO>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalO> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<ClustalO> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<ClustalO>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ClustalWS.html b/website/full_javadoc/compbio/ws/server/ClustalWS.html deleted file mode 100644 index 8b2a07a..0000000 --- a/website/full_javadoc/compbio/ws/server/ClustalWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ClustalWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class ClustalWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ClustalWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<ClustalW>, MsaWS<ClustalW>
    -
    -
    -
    -
    public class ClustalWS
    extends Object
    implements MsaWS<ClustalW>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<ClustalW>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<ClustalW>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<ClustalW>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<ClustalW>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<ClustalW>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalWS

    -
    -public ClustalWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<ClustalW> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<ClustalW>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<ClustalW> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalW> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<ClustalW>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalW> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<ClustalW> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<ClustalW>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/DisemblWS.html b/website/full_javadoc/compbio/ws/server/DisemblWS.html deleted file mode 100644 index e4ca353..0000000 --- a/website/full_javadoc/compbio/ws/server/DisemblWS.html +++ /dev/null @@ -1,414 +0,0 @@ - - - - - - -DisemblWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class DisemblWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<Disembl>
-          extended by compbio.ws.server.DisemblWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Disembl>, SequenceAnnotation<Disembl>
    -
    -
    -
    -
    public class DisemblWS
    extends SequenceAnnotationService<Disembl>
    implements SequenceAnnotation<Disembl>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    DisemblWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<Disembl>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<Disembl> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -DisemblWS

    -
    -public DisemblWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<Disembl>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

    -

    -
    Specified by:
    customAnalize in interface SequenceAnnotation<Disembl>
    Overrides:
    customAnalize in class SequenceAnnotationService<Disembl>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Option
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<Disembl> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<Disembl>
    Overrides:
    presetAnalize in class SequenceAnnotationService<Disembl>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/GAUtils.html b/website/full_javadoc/compbio/ws/server/GAUtils.html deleted file mode 100644 index 49fd2ae..0000000 --- a/website/full_javadoc/compbio/ws/server/GAUtils.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GAUtils - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class GAUtils

    -
    -java.lang.Object
-  extended by compbio.ws.server.GAUtils
-
    -
    -
    -
    public class GAUtils
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    GAUtils() - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GAUtils

    -
    -public GAUtils()
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/GenericMetadataService.html b/website/full_javadoc/compbio/ws/server/GenericMetadataService.html deleted file mode 100644 index 682d570..0000000 --- a/website/full_javadoc/compbio/ws/server/GenericMetadataService.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -GenericMetadataService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class GenericMetadataService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService<T>
-
    -
    -
    Direct Known Subclasses:
    _MsaService, SequenceAnnotationService
    -
    -
    -
    -
    public abstract class GenericMetadataService<T>
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleancancelJob(String jobId) - -
    -           
    - JobStatusgetJobStatus(String jobId) - -
    -           
    - Limit<T>getLimit(String presetName) - -
    -           
    - LimitsManager<T>getLimits() - -
    -           
    - PresetManager<T>getPresets() - -
    -           
    - RunnerConfig<T>getRunnerOptions() - -
    -           
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<T> getLimit(String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<T> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<T> getPresets()
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<T> getRunnerOptions()
    -
    -
    -
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Assume statistics is not supported -

    -

    -
    Parameters:
    jobId -
    position - -
    Returns:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/GlobPlotWS.html b/website/full_javadoc/compbio/ws/server/GlobPlotWS.html deleted file mode 100644 index 39cca3a..0000000 --- a/website/full_javadoc/compbio/ws/server/GlobPlotWS.html +++ /dev/null @@ -1,414 +0,0 @@ - - - - - - -GlobPlotWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class GlobPlotWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<GlobPlot>
-          extended by compbio.ws.server.GlobPlotWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<GlobPlot>, SequenceAnnotation<GlobPlot>
    -
    -
    -
    -
    public class GlobPlotWS
    extends SequenceAnnotationService<GlobPlot>
    implements SequenceAnnotation<GlobPlot>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    GlobPlotWS() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<GlobPlot>> options) - -
    -          Analyse the sequences according to custom settings defined in options - list.
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<GlobPlot> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -GlobPlotWS

    -
    -public GlobPlotWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<GlobPlot>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to custom settings defined in options - list. The actual analysis algorithm is defined by the type T. Default - Limit is used to decide whether the calculation will be permitted or - denied -

    -

    -
    Specified by:
    customAnalize in interface SequenceAnnotation<GlobPlot>
    Overrides:
    customAnalize in class SequenceAnnotationService<GlobPlot>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Option
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<GlobPlot> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<GlobPlot>
    Overrides:
    presetAnalize in class SequenceAnnotationService<GlobPlot>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/IUPredWS.html b/website/full_javadoc/compbio/ws/server/IUPredWS.html deleted file mode 100644 index 7b5edfc..0000000 --- a/website/full_javadoc/compbio/ws/server/IUPredWS.html +++ /dev/null @@ -1,358 +0,0 @@ - - - - - - -IUPredWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class IUPredWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<IUPred>
-          extended by compbio.ws.server.IUPredWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<IUPred>, SequenceAnnotation<IUPred>
    -
    -
    -
    -
    public class IUPredWS
    extends SequenceAnnotationService<IUPred>
    implements SequenceAnnotation<IUPred>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    IUPredWS() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<IUPred> preset) - -
    -          Analyse the sequences according to the preset settings.
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, customAnalize, getAnnotation
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, customAnalize, getAnnotation
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -IUPredWS

    -
    -public IUPredWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<IUPred> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    Description copied from interface: SequenceAnnotation
    -
    Analyse the sequences according to the preset settings. The actual - analysis algorithm is defined by the type T. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAnalize in interface SequenceAnnotation<IUPred>
    Overrides:
    presetAnalize in class SequenceAnnotationService<IUPred>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/JronnWS.html b/website/full_javadoc/compbio/ws/server/JronnWS.html deleted file mode 100644 index 65ae463..0000000 --- a/website/full_javadoc/compbio/ws/server/JronnWS.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -JronnWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class JronnWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<Jronn>
-          extended by compbio.ws.server.JronnWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Jronn>, SequenceAnnotation<Jronn>
    -
    -
    -
    -
    public class JronnWS
    extends SequenceAnnotationService<Jronn>
    implements SequenceAnnotation<Jronn>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    JronnWS() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.SequenceAnnotationService
    analize, customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.SequenceAnnotation
    analize, customAnalize, getAnnotation, presetAnalize
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.JManagement
    cancelJob, getJobStatus
    -  - - - - - - - -
    Methods inherited from interface compbio.data.msa.Metadata
    getLimit, getLimits, getPresets, getRunnerOptions
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -JronnWS

    -
    -public JronnWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder
    See Also:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html deleted file mode 100644 index 8947e60..0000000 --- a/website/full_javadoc/compbio/ws/server/MafftWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -MafftWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class MafftWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MafftWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Mafft>, MsaWS<Mafft>
    -
    -
    -
    -
    public class MafftWS
    extends Object
    implements MsaWS<Mafft>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    MafftWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Mafft>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Mafft>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Mafft>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Mafft>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Mafft>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MafftWS

    -
    -public MafftWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Mafft>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Mafft> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Mafft> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Mafft>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Mafft> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Mafft> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Mafft> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Mafft>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MuscleWS.html b/website/full_javadoc/compbio/ws/server/MuscleWS.html deleted file mode 100644 index bb8273d..0000000 --- a/website/full_javadoc/compbio/ws/server/MuscleWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -MuscleWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class MuscleWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MuscleWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Muscle>, MsaWS<Muscle>
    -
    -
    -
    -
    public class MuscleWS
    extends Object
    implements MsaWS<Muscle>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    MuscleWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Muscle>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Muscle>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Muscle>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Muscle>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Muscle>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -MuscleWS

    -
    -public MuscleWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Muscle>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Muscle> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Muscle> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Muscle>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Muscle> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Muscle> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Muscle> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Muscle>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/ProbconsWS.html deleted file mode 100644 index de825f0..0000000 --- a/website/full_javadoc/compbio/ws/server/ProbconsWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -ProbconsWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class ProbconsWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ProbconsWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Probcons>, MsaWS<Probcons>
    -
    -
    -
    -
    public class ProbconsWS
    extends Object
    implements MsaWS<Probcons>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    ProbconsWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Probcons>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Probcons>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Probcons>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Probcons>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Probcons>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ProbconsWS

    -
    -public ProbconsWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Probcons>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Probcons> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Probcons> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Probcons>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Probcons> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Probcons> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Probcons> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Probcons>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/RegistryWS.html b/website/full_javadoc/compbio/ws/server/RegistryWS.html deleted file mode 100644 index 7eacf29..0000000 --- a/website/full_javadoc/compbio/ws/server/RegistryWS.html +++ /dev/null @@ -1,477 +0,0 @@ - - - - - - -RegistryWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class RegistryWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.RegistryWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, RegistryWS
    -
    -
    -
    -
    public class RegistryWS
    extends Object
    implements RegistryWS, JABAService
    - - -

    -JABAWS services registry -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    RegistryWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - intgetLastTested(Services service) - -
    -          Number of seconds since the last test.
    - DategetLastTestedOn(Services service) - -
    -          Can potentially return null if the service has not been tested yet.
    - Set<Category>getServiceCategories() - -
    -          Gets the list of services per category.
    - StringgetServiceDescription(Services service) - -
    -          Gives the description of the service.
    - Set<Services>getSupportedServices() - -
    -          List of services that are functioning on the server.
    - booleanisOperating(Services service) - -
    -          Check whether a particular web service is working on this server
    - StringtestAllServices() - -
    -          TODO improve reporting.
    - StringtestService(Services service) - -
    -          Test a particular service
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -RegistryWS

    -
    -public RegistryWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getSupportedServices

    -
    -public Set<Services> getSupportedServices()
    -
    -
    Description copied from interface: RegistryWS
    -
    List of services that are functioning on the server. This function - returns the results of testing performed some time ago by - RegistryWS.testAllServices() or RegistryWS.testService(Services) methods. The - time of last check can be obtained from - RegistryWS.getLastTestedOn(Services) method -

    -

    -
    Specified by:
    getSupportedServices in interface RegistryWS
    -
    -
    - -
    Returns:
    the Set of Services which are functioning on the server
    See Also:
    RegistryWS.testAllServices()
    -
    -
    -
    - -

    -getLastTested

    -
    -public int getLastTested(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Number of seconds since the last test. Returns 0 if the service was not - tested or tested less then a one second ago. -

    -

    -
    Specified by:
    getLastTested in interface RegistryWS
    -
    -
    - -
    Returns:
    when last time tested
    -
    -
    -
    - -

    -getLastTestedOn

    -
    -public Date getLastTestedOn(Services service)
    -
    -
    Can potentially return null if the service has not been tested yet. -

    -

    -
    Specified by:
    getLastTestedOn in interface RegistryWS
    -
    -
    - -
    Returns:
    the Date and time on which the service was last tested
    -
    -
    -
    - -

    -testAllServices

    -
    -public String testAllServices()
    -
    -
    TODO improve reporting. stop testing service on unsupported runtime env - exception -

    -

    -
    Specified by:
    testAllServices in interface RegistryWS
    -
    -
    - -
    Returns:
    the test log
    -
    -
    -
    - -

    -testService

    -
    -public String testService(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Test a particular service -

    -

    -
    Specified by:
    testService in interface RegistryWS
    -
    -
    - -
    Returns:
    the testing log
    -
    -
    -
    - -

    -isOperating

    -
    -public boolean isOperating(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Check whether a particular web service is working on this server -

    -

    -
    Specified by:
    isOperating in interface RegistryWS
    -
    -
    - -
    Returns:
    true if the service was functioning in time of last testing.
    -
    -
    -
    - -

    -getServiceDescription

    -
    -public String getServiceDescription(Services service)
    -
    -
    Description copied from interface: RegistryWS
    -
    Gives the description of the service. -

    -

    -
    Specified by:
    getServiceDescription in interface RegistryWS
    -
    -
    - -
    Returns:
    String, plain text or html formatted piece, but NOT a full html - document
    -
    -
    -
    - -

    -getServiceCategories

    -
    -public Set<Category> getServiceCategories()
    -
    -
    Description copied from interface: RegistryWS
    -
    Gets the list of services per category. ServiceClassifier has the method - that returns Map> -

    -

    -
    Specified by:
    getServiceCategories in interface RegistryWS
    -
    -
    - -
    Returns:
    ServiceClassifier the object to represent relation between - Services and Categories
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html b/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html deleted file mode 100644 index d4d9126..0000000 --- a/website/full_javadoc/compbio/ws/server/SequenceAnnotationService.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - -SequenceAnnotationService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class SequenceAnnotationService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server.SequenceAnnotationService<T>
-
    -
    -
    Type Parameters:
    T -
    -
    -
    Direct Known Subclasses:
    AAConWS, DisemblWS, GlobPlotWS, IUPredWS, JronnWS
    -
    -
    -
    -
    public abstract class SequenceAnnotationService<T>
    extends GenericMetadataService
    - - -

    -Common methods for all SequenceAnnotation web services -

    - -

    -

    -
    Since:
    -
    2.0
    -
    Version:
    -
    1.0 June 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringanalize(List<FastaSequence> sequences) - -
    -           
    - StringcustomAnalize(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - ScoreManagergetAnnotation(String jobId) - -
    -           
    - StringpresetAnalize(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions, pullExecStatistics
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getAnnotation

    -
    -public ScoreManager getAnnotation(String jobId)
-                           throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -analize

    -
    -public String analize(List<FastaSequence> sequences)
-               throws UnsupportedRuntimeException,
-                      LimitExceededException,
-                      JobSubmissionException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException
    -
    -
    -
    - -

    -customAnalize

    -
    -public String customAnalize(List<FastaSequence> sequences,
-                            List<Option<T>> options)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -presetAnalize

    -
    -public String presetAnalize(List<FastaSequence> sequences,
-                            Preset<T> preset)
-                     throws UnsupportedRuntimeException,
-                            LimitExceededException,
-                            JobSubmissionException,
-                            WrongParameterException
    -
    -
    - -
    Throws: -
    UnsupportedRuntimeException -
    LimitExceededException -
    JobSubmissionException -
    WrongParameterException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/SetExecutableFlag.html b/website/full_javadoc/compbio/ws/server/SetExecutableFlag.html deleted file mode 100644 index 9f74aa7..0000000 --- a/website/full_javadoc/compbio/ws/server/SetExecutableFlag.html +++ /dev/null @@ -1,292 +0,0 @@ - - - - - - -SetExecutableFlag - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class SetExecutableFlag

    -
    -java.lang.Object
-  extended by compbio.ws.server.SetExecutableFlag
-
    -
    -
    All Implemented Interfaces:
    EventListener, javax.servlet.ServletContextListener
    -
    -
    -
    -
    public class SetExecutableFlag
    extends Object
    implements javax.servlet.ServletContextListener
    - - -

    -Run setexecflag.sh script if executable flag is not set -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    SetExecutableFlag() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - voidcontextDestroyed(javax.servlet.ServletContextEvent arg0) - -
    -           
    - voidcontextInitialized(javax.servlet.ServletContextEvent arg0) - -
    -          This listener is designed to run only once when the web application is - deployed to set executable flag for binaries.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -SetExecutableFlag

    -
    -public SetExecutableFlag()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -contextDestroyed

    -
    -public void contextDestroyed(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextDestroyed in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    -
    - -

    -contextInitialized

    -
    -public void contextInitialized(javax.servlet.ServletContextEvent arg0)
    -
    -
    This listener is designed to run only once when the web application is - deployed to set executable flag for binaries. -

    -

    -
    Specified by:
    contextInitialized in interface javax.servlet.ServletContextListener
    -
    -
    -
    Parameters:
    arg0 - - ignored
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ShutdownEngines.html b/website/full_javadoc/compbio/ws/server/ShutdownEngines.html deleted file mode 100644 index 0e932b7..0000000 --- a/website/full_javadoc/compbio/ws/server/ShutdownEngines.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -ShutdownEngines - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class ShutdownEngines

    -
    -java.lang.Object
-  extended by compbio.ws.server.ShutdownEngines
-
    -
    -
    All Implemented Interfaces:
    EventListener, javax.servlet.ServletContextListener
    -
    -
    -
    -
    public class ShutdownEngines
    extends Object
    implements javax.servlet.ServletContextListener
    - - -

    -Switch off engines if JABAWS web application is undeployed, or web server is - shutdown -

    - -

    -

    -
    Version:
    -
    1.0
    -
    Author:
    -
    Peter Troshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ShutdownEngines() - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    - voidcontextDestroyed(javax.servlet.ServletContextEvent ignored) - -
    -           
    - voidcontextInitialized(javax.servlet.ServletContextEvent arg0) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -ShutdownEngines

    -
    -public ShutdownEngines()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -contextDestroyed

    -
    -public void contextDestroyed(javax.servlet.ServletContextEvent ignored)
    -
    -
    -
    Specified by:
    contextDestroyed in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    -
    - -

    -contextInitialized

    -
    -public void contextInitialized(javax.servlet.ServletContextEvent arg0)
    -
    -
    -
    Specified by:
    contextInitialized in interface javax.servlet.ServletContextListener
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html deleted file mode 100644 index f83b5fc..0000000 --- a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html +++ /dev/null @@ -1,266 +0,0 @@ - - - - - - -SimpleWSPublisher - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class SimpleWSPublisher

    -
    -java.lang.Object
-  extended by compbio.ws.server.SimpleWSPublisher
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class SimpleWSPublisher
    extends Object
    - - -

    -This class publish a web service. This is not a production implementation. - Should be used only for during development and testing -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    SimpleWSPublisher(Object exec, - String context) - -
    -          Deprecated.  
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(String[] args) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -SimpleWSPublisher

    -
    -public SimpleWSPublisher(Object exec,
-                         String context)
    -
    -
    Deprecated. 
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Deprecated. 
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html deleted file mode 100644 index 59c5a7c..0000000 --- a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html +++ /dev/null @@ -1,635 +0,0 @@ - - - - - - -TcoffeeWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class TcoffeeWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.TcoffeeWS
-
    -
    -
    All Implemented Interfaces:
    JABAService, JManagement, Metadata<Tcoffee>, MsaWS<Tcoffee>
    -
    -
    -
    -
    public class TcoffeeWS
    extends Object
    implements MsaWS<Tcoffee>
    - - -

    -

    - -

    - - - - - - - -
    -Field Summary
    -  - - - - - - - -
    Fields inherited from interface compbio.data.msa.JABAService
    SERVICE_NAMESPACE, V2_SERVICE_NAMESPACE
    -  - - - - - - - - - - -
    -Constructor Summary
    TcoffeeWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(String jobId) - -
    -          Stop running the job jobId but leave its output untouched
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<Tcoffee>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(String jobId) - -
    -          Return the status of the job.
    - Limit<Tcoffee>getLimit(String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Tcoffee>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Tcoffee>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Tcoffee>getRunnerOptions() - -
    -          Get options supported by a web service
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -TcoffeeWS

    -
    -public TcoffeeWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with default settings. - - Any dataset containing a greater number of sequences or when the average - length of the sequences are greater then defined in the default Limit, - will not be accepted for an alignment operation and - JobSubmissionException will be thrown. -

    -

    -
    Specified by:
    align in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to make sure of this -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<Tcoffee>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or their average - length exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<Tcoffee> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    JobSubmissionException - is thrown when the job could not be submitted due to the - following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and - Mafft service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option.
    See Also:
    Preset
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. This method waits for the job - jobId to complete before return. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown due to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Tcoffee> getLimit(String presetName)
    -
    -
    Description copied from interface: Metadata
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface Metadata<Tcoffee>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Tcoffee> getLimits()
    -
    -
    Description copied from interface: Metadata
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from interface: JManagement
    -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. If in time of a request less then - 1kb data is available from the position to the end of the file, then it - returns all the data available from the position to the end of the file. -

    -

    -
    Specified by:
    pullExecStatistics in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - which contains a chunk of data and a next position - within the file from which no data has been read
    See Also:
    ChunkHolder
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Stop running the job jobId but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface JManagement
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(String jobId)
    -
    -
    Description copied from interface: JManagement
    -
    Return the status of the job. -

    -

    -
    Specified by:
    getJobStatus in interface JManagement
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    See Also:
    JobStatus
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Tcoffee> getPresets()
    -
    -
    Description copied from interface: Metadata
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Tcoffee> getRunnerOptions()
    -
    -
    Description copied from interface: Metadata
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface Metadata<Tcoffee>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/WSUtil.html b/website/full_javadoc/compbio/ws/server/WSUtil.html deleted file mode 100644 index 06aea11..0000000 --- a/website/full_javadoc/compbio/ws/server/WSUtil.html +++ /dev/null @@ -1,531 +0,0 @@ - - - - - - -WSUtil - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class WSUtil

    -
    -java.lang.Object
-  extended by compbio.ws.server.WSUtil
-
    -
    -
    -
    public final class WSUtil
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    WSUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> String
    -    		align(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger logger, - String callingMethod, - Limit<T> limit) - -
    -           
    -static - - - - -
    -<T> String
    -    		analize(List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger log, - String method, - Limit<T> limit) - -
    -           
    -static booleancancelJob(String jobId) - -
    -           
    -static - - - - -
    -<T> ScoreManager
    -    		getAnnotation(String jobId, - org.apache.log4j.Logger log) - -
    -           
    -static - - - - -
    -<T> List<String>
    -    		getCommands(List<Option<T>> options, - String keyValueSeparator) - -
    -           
    -static AsyncExecutorgetEngine(ConfiguredExecutable<?> confClustal) - -
    -           
    -static JobStatusgetJobStatus(String jobId) - -
    -           
    -static bytegetProgress(String jobId) - -
    -           
    -static ChunkHolderpullFile(String file, - long position) - -
    -           
    -static voidvalidateAAConInput(List<FastaSequence> sequences) - -
    -           
    -static voidvalidateFastaInput(List<FastaSequence> sequences) - -
    -           
    -static voidvalidateJobId(String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Constructor Detail
    - -

    -WSUtil

    -
    -public WSUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -validateJobId

    -
    -public static final void validateJobId(String jobId)
-                                throws InvalidParameterException
    -
    -
    - -
    Throws: -
    InvalidParameterException
    -
    -
    -
    - -

    -validateFastaInput

    -
    -public static final void validateFastaInput(List<FastaSequence> sequences)
-                                     throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getJobStatus

    -
    -public static JobStatus getJobStatus(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -pullFile

    -
    -public static ChunkHolder pullFile(String file,
-                                   long position)
    -
    -
    -
    -
    -
    -
    - -

    -getProgress

    -
    -public static byte getProgress(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getEngine

    -
    -public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)
    -
    -
    -
    -
    -
    -
    - -

    -cancelJob

    -
    -public static boolean cancelJob(String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -align

    -
    -public static <T> String align(List<FastaSequence> sequences,
-                               ConfiguredExecutable<T> confExec,
-                               org.apache.log4j.Logger logger,
-                               String callingMethod,
-                               Limit<T> limit)
-                    throws LimitExceededException,
-                           JobSubmissionException
    -
    -
    - -
    Throws: -
    LimitExceededException -
    JobSubmissionException
    -
    -
    -
    - -

    -analize

    -
    -public static <T> String analize(List<FastaSequence> sequences,
-                                 ConfiguredExecutable<T> confExec,
-                                 org.apache.log4j.Logger log,
-                                 String method,
-                                 Limit<T> limit)
-                      throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getCommands

    -
    -public static final <T> List<String> getCommands(List<Option<T>> options,
-                                                 String keyValueSeparator)
    -
    -
    -
    -
    -
    -
    - -

    -validateAAConInput

    -
    -public static void validateAAConInput(List<FastaSequence> sequences)
-                               throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -getAnnotation

    -
    -public static <T> ScoreManager getAnnotation(String jobId,
-                                             org.apache.log4j.Logger log)
-                                  throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/_MsaService.html b/website/full_javadoc/compbio/ws/server/_MsaService.html deleted file mode 100644 index 8b2e588..0000000 --- a/website/full_javadoc/compbio/ws/server/_MsaService.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -_MsaService - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class _MsaService<T>

    -
    -java.lang.Object
-  extended by compbio.ws.server.GenericMetadataService
-      extended by compbio.ws.server._MsaService<T>
-
    -
    -
    Type Parameters:
    T -
    -
    -
    -
    public abstract class _MsaService<T>
    extends GenericMetadataService
    - - -

    -TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services -

    - -

    -

    -
    Since:
    -
    2.0
    -
    Version:
    -
    1.0 June 2011
    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Stringalign(List<FastaSequence> sequences) - -
    -           
    - StringcustomAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -           
    - AlignmentgetResult(String jobId) - -
    -           
    - StringpresetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -           
    - ChunkHolderpullExecStatistics(String jobId, - long position) - -
    -          Assume statistics is not supported
    -  - - - - - - - -
    Methods inherited from class compbio.ws.server.GenericMetadataService
    cancelJob, getJobStatus, getLimit, getLimits, getPresets, getRunnerOptions
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -align

    -
    -public String align(List<FastaSequence> sequences)
-             throws JobSubmissionException
    -
    -
    - -
    Throws: -
    JobSubmissionException
    -
    -
    -
    - -

    -presetAlign

    -
    -public String presetAlign(List<FastaSequence> sequences,
-                          Preset<T> preset)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    - -
    Throws: -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -customAlign

    -
    -public String customAlign(List<FastaSequence> sequences,
-                          List<Option<T>> options)
-                   throws JobSubmissionException,
-                          WrongParameterException
    -
    -
    - -
    Throws: -
    JobSubmissionException -
    WrongParameterException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(String jobId)
-                    throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -pullExecStatistics

    -
    -public ChunkHolder pullExecStatistics(String jobId,
-                                      long position)
    -
    -
    Description copied from class: GenericMetadataService
    -
    Assume statistics is not supported -

    -

    -
    Overrides:
    pullExecStatistics in class GenericMetadataService
    -
    -
    - -
    Returns:
    ChunkHolder
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/_WSLogger.html b/website/full_javadoc/compbio/ws/server/_WSLogger.html deleted file mode 100644 index 113e952..0000000 --- a/website/full_javadoc/compbio/ws/server/_WSLogger.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -_WSLogger - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class _WSLogger

    -
    -java.lang.Object
-  extended by compbio.ws.server._WSLogger
-
    -
    -Deprecated. -

    -

    -
    @Deprecated
-public class _WSLogger
    extends Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - StringgetRemoteAddress() - -
    -          Deprecated.  
    -static _WSLoggergetStatLogger(Services service, - WebServiceContext wsContext) - -
    -          Deprecated.  
    - voidlog(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    - voidlog(compbio.util.Timer timer, - String activity, - String jobId) - -
    -          Deprecated.  
    - voidlogAll(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    - voidlogFine(compbio.util.Timer timer, - String activity) - -
    -          Deprecated.  
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

    - - - - - - - - -
    -Method Detail
    - -

    -getStatLogger

    -
    -public static final _WSLogger getStatLogger(Services service,
-                                            WebServiceContext wsContext)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -logAll

    -
    -public void logAll(compbio.util.Timer timer,
-                   String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -logFine

    -
    -public void logFine(compbio.util.Timer timer,
-                    String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -log

    -
    -public void log(compbio.util.Timer timer,
-                String activity)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -log

    -
    -public void log(compbio.util.Timer timer,
-                String activity,
-                String jobId)
    -
    -
    Deprecated. 
    -
    -
    -
    -
    - -

    -getRemoteAddress

    -
    -public String getRemoteAddress()
    -
    -
    Deprecated. 
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html b/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html deleted file mode 100644 index c93ab4f..0000000 --- a/website/full_javadoc/compbio/ws/server/class-use/AAConWS.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - -Uses of Class compbio.ws.server.AAConWS - - - - - - - - - - - - -
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    compbio.ws.server.AAConWS

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    -Packages that use AAConWS
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

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    -Uses of AAConWS in compbio.ws.client
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.client that return types with arguments of type AAConWS
    -static SequenceAnnotation<AAConWS>AAConClient.connect() - -
    -          Connects to a AACon web service by the host and the service name
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    compbio.ws.server  
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    Subclasses of GenericMetadataService in compbio.ws.server
    - class_MsaService<T> - -
    -          TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    - classAAConWS - -
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    - classAAConWS - -
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    _MsaService<T>TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    _WSLoggerDeprecated.
    AAConWS 
    ClustalOWS 
    ClustalWS 
    DisemblWS 
    GAUtils 
    GenericMetadataService<T> 
    GlobPlotWS 
    IUPredWS 
    JronnWS 
    MafftWS 
    MuscleWS 
    ProbconsWS 
    RegistryWSJABAWS services registry
    SequenceAnnotationService<T>Common methods for all SequenceAnnotation web services
    SetExecutableFlagRun setexecflag.sh script if executable flag is not set
    ShutdownEnginesSwitch off engines if JABAWS web application is undeployed, or web server is - shutdown
    SimpleWSPublisherDeprecated.
    TcoffeeWS 
    WSUtil 
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    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    compbio.ws.server  
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    AAConWS - -
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    compbio.data.msa.Category
    -public static final StringCATEGORY_ALIGNMENT"Alignment"
    -public static final StringCATEGORY_CONSERVATION"Conservation"
    -public static final StringCATEGORY_DISORDER"Protein Disorder"
    - -

    - -

    - - - - - - - - - - - - - - - - - -
    compbio.data.msa.JABAService
    -public static final StringSERVICE_NAMESPACE"http://msa.data.compbio/01/01/2010/"
    -public static final StringV2_SERVICE_NAMESPACE"http://msa.data.compbio/01/12/2010/"
    - -

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    compbio.data.sequence.ClustalAlignmentUtil
    -public static final chargapchar45
    - -

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    compbio.data.sequence.ScoreManager
    -public static final StringSINGLE_ENTRY_KEY"Alignment"
    - -

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    compbio.data.sequence.SMERFSConstraints
    -public static final doubleDEFAULT_GAP_THRESHOLD0.1
    -public static final intDEFAULT_WINDOW_SIZE7
    - -

    - -

    - - - - - -
    -compbio.engine.*
    - -

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    compbio.engine.client.ConfExecutable<T>
    -public static final StringCLUSTER_TASK_ID_PREFIX"@"
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    compbio.engine.client.EnvVariableProcessor
    -public static final StringPATH"PATH"
    - -

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    compbio.engine.client.RunConfiguration
    -public static final StringrconfigFile"RunnerConfig.xml"
    - -

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    compbio.engine.client.SkeletalExecutable<T>
    -public static final StringERROR"error.txt"
    -public static final StringINPUT"input.txt"
    -public static final StringOUTPUT"result.txt"
    - -

    - -

    - - - - - - - - - - - - -
    compbio.engine.cluster.drmaa.ClusterSession
    -public static final StringJOBID"JOBID"
    - -

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    compbio.engine.conf._Key
    -public static final StringDELIM"#"
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    compbio.engine.conf.DirectoryManager
    -public static final StringDELIM"#"
    - -

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    compbio.engine.local.ExecutableWrapper
    -public static final StringPROC_ERR_FILE"procError.txt"
    -public static final StringPROC_OUT_FILE"procOutput.txt"
    - -

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    - - - - - -
    -compbio.metadata.*
    - -

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    compbio.metadata.PresetManager<T>
    -public static final StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    - -

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    -compbio.runner.*
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    compbio.runner.Util
    -public static final StringSPACE" "
    - -

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    compbio.runner.conservation.AACon
    -public static final StringKEY_VALUE_SEPARATOR"="
    -public static final StringSTAT_FILE"stat.txt"
    - -

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    compbio.runner.disorder.Disembl
    -public final doubleCOILS_EXPECTATION_THRESHOLD0.43
    -public static final StringKEY_VALUE_SEPARATOR" "
    -public final doubleLOOPS_EXPECTATION_THRESHOLD0.086
    -public final doubleREM_EXPECTATION_THRESHOLD0.5
    - -

    - -

    - - - - - - - - - - - - -
    compbio.runner.disorder.GlobPlot
    -public static final StringKEY_VALUE_SEPARATOR" "
    - -

    - -

    - - - - - - - - - - - - - - - - - -
    compbio.runner.disorder.Jronn
    -public static final StringKEY_VALUE_SEPARATOR" "
    -public static final StringSTAT_FILE"stat.txt"
    - -

    - -

    - - - - - - - - - - - - -
    compbio.runner.msa.ClustalO
    -public static final StringKEY_VALUE_SEPARATOR"="
    - -

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    -public static final StringKEY_VALUE_SEPARATOR"="
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    -public static final StringKEY_VALUE_SEPARATOR" "
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    -public static final StringKEY_VALUE_SEPARATOR" "
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    -public static final StringKEY_VALUE_SEPARATOR" "
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    compbio.ws.client.WSTester
    -public static final StringfastaAlignment">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
    -public static final StringfastaInput">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"
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    -A

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    -
    AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Valid Amino acids -
    AACon - Class in compbio.runner.conservation
    Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    AACon() - -Constructor for class compbio.runner.conservation.AACon -
      -
    AACON_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    AAConClient - Class in compbio.ws.client
    A command line client for AACon web service
    AAConWS - Class in compbio.ws.server
     
    AAConWS() - -Constructor for class compbio.ws.server.AAConWS -
      -
    addOption(Option<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds Option to the internal list of options -
    addOptionNames(String...) - -Method in class compbio.metadata.Option -
    Adds an option to the optionName list -
    addOptionNames(String...) - -Method in class compbio.metadata.Parameter -
      -
    addParameter(Parameter<T>) - -Method in class compbio.metadata.RunnerConfig -
    Adds parameter to the internal parameter list -
    addParameter(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.engine.client.ConfExecutable -
      -
    addParameters(List<String>) - -Method in interface compbio.engine.client.Executable -
    Adds parameter to the list of parameters for a native executable -
    addParameters(List<String>) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    addParameters(List<String>) - -Method in class compbio.runner._impl.NetNglyc -
      -
    addParameters(String[]) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    addParameters(List<String>) - -Method in class compbio.runner.msa.Mafft -
    Mafft input must always be the last parameter! -
    addParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    addPossibleValues(String...) - -Method in class compbio.metadata.Parameter -
      -
    addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.SubmissionManager -
      -
    Align - Class in compbio.data.msa.jaxws
     
    Align() - -Constructor for class compbio.data.msa.jaxws.Align -
      -
    align(List<FastaSequence>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with default settings. -
    align(List<FastaSequence>) - -Method in class compbio.ws.server._MsaService -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MafftWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MuscleWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -
      -
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - -Constructor for class compbio.data.sequence.Alignment -
      -
    Alignment(List<FastaSequence>, AlignmentMetadata) - -Constructor for class compbio.data.sequence.Alignment -
      -
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - -Constructor for class compbio.data.sequence.AlignmentMetadata -
      -
    AlignResponse - Class in compbio.data.msa.jaxws
     
    AlignResponse() - -Constructor for class compbio.data.msa.jaxws.AlignResponse -
      -
    AMBIGUOUS_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Same as AA pattern but with two additional letters - XU -
    AMBIGUOUS_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Ambiguous nucleotide -
    Analize - Class in compbio.data.msa.jaxws
     
    Analize() - -Constructor for class compbio.data.msa.jaxws.Analize -
      -
    analize(List<FastaSequence>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences. -
    analize(List<FastaSequence>) - -Method in class compbio.ws.server.AAConWS -
      -
    analize(List<FastaSequence>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -
      -
    AnalizeResponse - Class in compbio.data.msa.jaxws
     
    AnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.AnalizeResponse -
      -
    AnnualStat - Class in compbio.stat.servlet
     
    AnnualStat() - -Constructor for class compbio.stat.servlet.AnnualStat -
      -
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    argumentsToCommandString(List<? extends Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - -Static method in class compbio.runner.OptionCombinator -
      -
    asMap() - -Method in class compbio.data.sequence.ScoreManager -
      -
    asSet() - -Method in class compbio.data.sequence.ScoreManager -
      -
    AsyncExecutor - Interface in compbio.engine
    An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    AsyncJobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    AsyncJobRunner() - -Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    AsyncLocalRunner - Class in compbio.engine.local
     
    AsyncLocalRunner() - -Constructor for class compbio.engine.local.AsyncLocalRunner -
      -
    -
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    JABAService - Interface in compbio.data.msa
    This is a marker interface, contains no methods
    JackHmmerHitParser - Class in compbio.pipeline._jpred
    Parser for the following files:
    JackHmmerHitParser(String) - -Constructor for class compbio.pipeline._jpred.JackHmmerHitParser -
      -
    JManagement - Interface in compbio.data.msa
     
    JnetAnnotation - Enum in compbio.data._structure
     
    Job - Class in compbio.engine
     
    Job(String, String, ConfiguredExecutable<?>) - -Constructor for class compbio.engine.Job -
      -
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobExecutionException(String) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(String, Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JOBID - -Static variable in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    Joblist - Class in compbio.stat.servlet
     
    Joblist() - -Constructor for class compbio.stat.servlet.Joblist -
      -
    JobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    JobRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.cluster.drmaa.JobRunner -
      -
    JobStat - Class in compbio.stat.collector
     
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(String, Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobSubmissionExceptionBean() - -Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    Jpred4 - Class in compbio.pipeline._jpred
    jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Jpred4() - -Constructor for class compbio.pipeline._jpred.Jpred4 -
      -
    JpredAnnotation - Enum in compbio.data._structure
     
    JpredResult - Class in compbio.data._structure
    Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    JpredResult() - -Constructor for class compbio.data._structure.JpredResult -
      -
    Jronn - Class in compbio.runner.disorder
    Command line - - java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
    Jronn() - -Constructor for class compbio.runner.disorder.Jronn -
      -
    JRONN_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    JronnWS - Class in compbio.ws.server
     
    JronnWS() - -Constructor for class compbio.ws.server.JronnWS -
      -
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
    -
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    -
    -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.conservation.AACon -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.Disembl -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.GlobPlot -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.disorder.Jronn -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.ClustalO -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.ClustalW -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Mafft -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Muscle -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Probcons -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Tcoffee -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    Limit(int, int, String) - -Constructor for class compbio.metadata.Limit -
    Instantiate the limit -
    Limit(int, int, String, boolean) - -Constructor for class compbio.metadata.Limit -
      -
    LimitExceededException - Exception in compbio.metadata
    This exception is thrown if the task larger in size that the limit that - applies to the calculation.
    LimitExceededException(String) - -Constructor for exception compbio.metadata.LimitExceededException -
      -
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    LimitExceededExceptionBean() - -Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - -Constructor for class compbio.metadata.LimitsManager -
      -
    load(InputStream) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    LoadBalancer - Class in compbio.engine
    This class decides where to execute the job.
    loadExecutable(String) - -Static method in class compbio.engine.client.Util -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in interface compbio.engine.client.Executable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._impl.NetNglyc -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    LOCAL_ENGINE_LIMIT_PRESET - -Static variable in class compbio.metadata.PresetManager -
      -
    LOCAL_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    LocalEngineUtil - Class in compbio.engine.local
     
    LocalEngineUtil() - -Constructor for class compbio.engine.local.LocalEngineUtil -
      -
    LocalExecutorService - Class in compbio.engine.local
     
    LocalRunner - Class in compbio.engine.local
     
    LocalRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.local.LocalRunner -
      -
    log - -Static variable in class compbio.runner.Util -
      -
    log(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    log(Timer, String, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    logAll(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    logFine(Timer, String) - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    LOOPS_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
      -
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    -
    -
    Mafft - Class in compbio.runner.msa
     
    Mafft() - -Constructor for class compbio.runner.msa.Mafft -
      -
    MAFFT_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    MafftWS - Class in compbio.ws.server
     
    MafftWS() - -Constructor for class compbio.ws.server.MafftWS -
      -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastBlastComparator -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastHmmerComparator -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastParser -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.JackHmmerHitParser -
      -
    main(String[]) - -Static method in class compbio.pipeline._jpred.Pairwise -
      -
    main(String[]) - -Static method in class compbio.runner._impl.OB -
      -
    main(String[]) - -Static method in class compbio.stat.collector.ExecutionStatCollector -
    Not in use -
    main(String[]) - -Static method in class compbio.stat.collector.StatDB -
      -
    main(String[]) - -Static method in class compbio.ws.client.AAConClient -
    Starts command line client, if no parameters are supplied prints help. -
    main(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Starts command line client, if no parameter are supported print help. -
    main(String[]) - -Static method in enum compbio.ws.client.Services -
      -
    main(String[]) - -Static method in class compbio.ws.client.WSTester -
    Test JWS2 web services -
    main(String[]) - -Static method in class compbio.ws.server.SimpleWSPublisher -
    Deprecated.   -
    Mcl - Class in compbio.runner._impl
     
    Mcl(String) - -Constructor for class compbio.runner._impl.Mcl -
      -
    mergeEnvVariables(Map<String, String>, Map<String, String>) - -Static method in class compbio.engine.client.Util -
      -
    Metadata<T> - Interface in compbio.data.msa
     
    MetadataHelper - Class in compbio.ws.client
     
    MetadataHelper() - -Constructor for class compbio.ws.client.MetadataHelper -
      -
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    Muscle - Class in compbio.runner.msa
     
    Muscle() - -Constructor for class compbio.runner.msa.Muscle -
    Default options are - - -clwstrict - write output in clustal format -
    MUSCLE_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    MuscleWS - Class in compbio.ws.server
     
    MuscleWS() - -Constructor for class compbio.ws.server.MuscleWS -
      -
    -
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    name - -Variable in class compbio.data.msa.Category -
      -
    NetNglyc - Class in compbio.runner._impl
     
    NetNglyc() - -Constructor for class compbio.runner._impl.NetNglyc -
      -
    newCommandBuilder(List<? extends Option<T>>, String) - -Static method in class compbio.engine.client.CommandBuilder -
    This produces the same result as getCommands method. -
    newConfExecutable(RunConfiguration) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    newFilePuller(String, int) - -Static method in class compbio.engine.FilePuller -
      -
    newInstance(Map<String, Set<Score>>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleScore(Map<String, Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newInstanceSingleSequence(Set<Score>) - -Static method in class compbio.data.sequence.ScoreManager -
      -
    newLimitExceeded(Limit<?>, List<FastaSequence>) - -Static method in exception compbio.metadata.LimitExceededException -
      -
    newProgressPuller(String) - -Static method in class compbio.engine.FilePuller -
    Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. -
    newStatCollecton(Date, Date) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    next() - -Method in class compbio.data.sequence.FastaReader -
    Reads the next FastaSequence from the input -
    NON_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    inversion of AA pattern -
    NON_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non nucleotide -
    NONWORD - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non word -
    NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Nucleotides a, t, g, c, u -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    OB - Class in compbio.runner._impl
    TODO this needs fixing! Executable does not work
    OB() - -Constructor for class compbio.runner._impl.OB -
      -
    OB(String) - -Constructor for class compbio.runner._impl.OB -
      -
    openInputStream(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads and parses Fasta or Clustal formatted file into a list of - FastaSequence objects -
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - -Constructor for class compbio.metadata.Option -
      -
    OptionCombinator - Class in compbio.runner
    This class solve the following problems.
    OptionCombinator(RunnerConfig<? extends Executable<?>>) - -Constructor for class compbio.runner.OptionCombinator -
      -
    optionsToCommandString(List<Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    OUTPUT - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    Pairwise - Class in compbio.pipeline._jpred
     
    Pairwise(List<FastaSequence>) - -Constructor for class compbio.pipeline._jpred.Pairwise -
      -
    Parameter<T> - Class in compbio.metadata
    A single value containing an option supported by the web service e.g.
    Parameter(String, String) - -Constructor for class compbio.metadata.Parameter -
      -
    parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - -Method in class compbio.runner.OptionCombinator -
      -
    parse(String) - -Static method in class compbio.engine.conf._Key -
    Deprecated.   -
    PATH - -Static variable in class compbio.engine.client.EnvVariableProcessor -
    Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -
    PathValidator - Class in compbio.engine.client
     
    PathValidator() - -Constructor for class compbio.engine.client.PathValidator -
      -
    PipedExecutable<T> - Interface in compbio.engine.client
    This is a marker interface to indicate that the output of the process must be - captured.
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - -Constructor for class compbio.metadata.Preset -
      -
    PresetAlign - Class in compbio.data.msa.jaxws
     
    PresetAlign() - -Constructor for class compbio.data.msa.jaxws.PresetAlign -
      -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with preset. -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in class compbio.ws.server._MsaService -
      -
    presetAlign(List<FastaSequence>, Preset<ClustalO>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    presetAlign(List<FastaSequence>, Preset<ClustalW>) - -Method in class compbio.ws.server.ClustalWS -
      -
    presetAlign(List<FastaSequence>, Preset<Mafft>) - -Method in class compbio.ws.server.MafftWS -
      -
    presetAlign(List<FastaSequence>, Preset<Muscle>) - -Method in class compbio.ws.server.MuscleWS -
      -
    presetAlign(List<FastaSequence>, Preset<Probcons>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    presetAlign(List<FastaSequence>, Preset<Tcoffee>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PresetAlignResponse - Class in compbio.data.msa.jaxws
     
    PresetAlignResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    PresetAnalize - Class in compbio.data.msa.jaxws
     
    PresetAnalize() - -Constructor for class compbio.data.msa.jaxws.PresetAnalize -
      -
    presetAnalize(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to the preset settings. -
    presetAnalize(List<FastaSequence>, Preset<Disembl>) - -Method in class compbio.ws.server.DisemblWS -
      -
    presetAnalize(List<FastaSequence>, Preset<GlobPlot>) - -Method in class compbio.ws.server.GlobPlotWS -
      -
    presetAnalize(List<FastaSequence>, Preset<IUPred>) - -Method in class compbio.ws.server.IUPredWS -
      -
    presetAnalize(List<FastaSequence>, Preset<T>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    PresetAnalizeResponse - Class in compbio.data.msa.jaxws
     
    PresetAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - -Constructor for class compbio.metadata.PresetManager -
      -
    Probcons - Class in compbio.runner.msa
     
    Probcons() - -Constructor for class compbio.runner.msa.Probcons -
      -
    PROBCONS_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    ProbconsWS - Class in compbio.ws.server
     
    ProbconsWS() - -Constructor for class compbio.ws.server.ProbconsWS -
      -
    PROC_ERR_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    PROC_OUT_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    ProgressGetter - Class in compbio.engine
     
    ProgressGetter() - -Constructor for class compbio.engine.ProgressGetter -
      -
    PropertyHelperManager - Class in compbio.engine.conf
     
    PropertyHelperManager() - -Constructor for class compbio.engine.conf.PropertyHelperManager -
      -
    PScore - Class in compbio.pipeline._jpred
     
    PScore() - -Constructor for class compbio.pipeline._jpred.PScore -
      -
    PSIBlast - Class in compbio.runner._impl
     
    PSIBlast(String) - -Constructor for class compbio.runner._impl.PSIBlast -
      -
    pull(long) - -Method in class compbio.engine.FilePuller -
      -
    pull(String, long) - -Static method in class compbio.engine.ProgressGetter -
      -
    PulledFileCache - Class in compbio.engine
     
    PulledFileCache() - -Constructor for class compbio.engine.PulledFileCache -
      -
    PullExecStatistics - Class in compbio.data.msa.jaxws
     
    PullExecStatistics() - -Constructor for class compbio.data.msa.jaxws.PullExecStatistics -
      -
    pullExecStatistics(String, long) - -Method in interface compbio.data.msa.JManagement -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server._MsaService -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.AAConWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ClustalOWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ClustalWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.GenericMetadataService -
    Assume statistics is not supported -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.JronnWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MafftWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MuscleWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ProbconsWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
     
    PullExecStatisticsResponse() - -Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    pullFile(String, long) - -Static method in class compbio.ws.server.WSUtil -
      -
    put(FilePuller) - -Static method in class compbio.engine.PulledFileCache -
    This method allows duplicates to be added. -
    -
    - - - - - - - - - - - - - - - -
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    Range - Class in compbio.data.sequence
     
    Range(int, int) - -Constructor for class compbio.data.sequence.Range -
      -
    Range(String[]) - -Constructor for class compbio.data.sequence.Range -
      -
    rconfigFile - -Static variable in class compbio.engine.client.RunConfiguration -
      -
    read(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    read(InputStream, Class<V>, Class<?>...) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readAAConResults(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read AACon result with no alignment files. -
    readAndValidate(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Read Clustal formatted alignment. -
    readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    readClustalFile(String, String) - -Static method in class compbio.runner.Util -
      -
    readData(Timestamp, Timestamp, Services, Boolean) - -Method in class compbio.stat.collector.StatDB -
      -
    readDisembl(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readFasta(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads fasta sequences from inStream into the list of FastaSequence - objects -
    readGlobPlot(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
    readIUPred(File) - -Static method in class compbio.data.sequence.SequenceUtil -
    Read IUPred output -
    readJRonn(File) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    readJRonn(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reader for JRonn horizontal file format -
    readJronnFile(String, String) - -Static method in class compbio.runner.Util -
      -
    RegistryWS - Interface in compbio.data.msa
    JABAWS services registry
    RegistryWS - Class in compbio.ws.server
    JABAWS services registry
    RegistryWS() - -Constructor for class compbio.ws.server.RegistryWS -
      -
    REM_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
      -
    remove() - -Method in class compbio.data.sequence.FastaReader -
    Not implemented -
    removeArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument Argument if found. -
    removeArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -
    removeJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.BlastAll -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.PSIBlast -
      -
    removeParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    removeRecordedJobs(Set<JobStat>) - -Method in class compbio.stat.collector.StatDB -
    Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs. -
    removeTask(ConfiguredExecutable<?>) - -Static method in class compbio.engine.SubmissionManager -
      -
    removeTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    reportStat() - -Method in class compbio.stat.collector.StatProcessor -
      -
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    ResultNotAvailableException(String) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(String, Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    ResultNotAvailableExceptionBean() - -Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    Ronn - Class in compbio.runner._impl
     
    Ronn(String) - -Constructor for class compbio.runner._impl.Ronn -
      -
    RPSBlast - Class in compbio.runner._impl
     
    RPSBlast(String) - -Constructor for class compbio.runner._impl.RPSBlast -
      -
    run() - -Method in class compbio.engine.local.StreamGobbler -
      -
    run() - -Method in class compbio.stat.collector.ExecutionStatCollector -
      -
    RunConfiguration - Class in compbio.engine.client
    Value class for persisting ConfExecutable instances
    RunConfiguration() - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunConfiguration(ConfExecutable<?>) - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - -Constructor for class compbio.metadata.RunnerConfig -
      -
    RunnerConfigMarshaller<T> - Class in compbio.engine.conf
     
    RunnerConfigMarshaller(Class<?>) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    RunnerConfigMarshaller(Class<?>, Class<?>...) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    Runners - Class in compbio.runner._impl
     
    runPsiBlast() - -Method in class compbio.pipeline._jpred.Jpred4 -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    saveRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    saveRunConfiguration() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    Score - Class in compbio.data.sequence
    A value class for AACon annotation results storage.
    Score(Enum<?>, ArrayList<Float>) - -Constructor for class compbio.data.sequence.Score -
    Instantiate the Score -
    Score(Enum<?>, ArrayList<Float>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, TreeSet<Range>) - -Constructor for class compbio.data.sequence.Score -
      -
    Score(Enum<?>, float[]) - -Constructor for class compbio.data.sequence.Score -
      -
    ScoreManager - Class in compbio.data.sequence
     
    ScoreManager.ScoreHolder - Class in compbio.data.sequence
     
    scores - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    SequenceAnnotation<T> - Interface in compbio.data.msa
    Interface for tools that results to one or more annotation to sequence(s) - - Single, multiple sequences their groups or alignments can be annotated
    SequenceAnnotationService<T> - Class in compbio.ws.server
    Common methods for all SequenceAnnotation web services
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 2
    ServiceStatus - Class in compbio.stat.servlet
    Use cases: - - Test web services and display results on the web page -
    ServiceStatus() - -Constructor for class compbio.stat.servlet.ServiceStatus -
      -
    ServicesUtil - Class in compbio.ws.client
     
    ServicesUtil() - -Constructor for class compbio.ws.client.ServicesUtil -
      -
    ServiceTestResult - Class in compbio.stat.servlet
    Value class for test results.
    ServiceTestResult(Services) - -Constructor for class compbio.stat.servlet.ServiceTestResult -
      -
    setActualNumberofSequences(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.GetServiceDescription -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    setArg0(Services) - -Method in class compbio.data.msa.jaxws.TestService -
      -
    setDefaultValue(String) - -Method in class compbio.metadata.Option -
    Sets one of the values defined in optionList as default. -
    setDefaultValue(String) - -Method in class compbio.metadata.Parameter -
      -
    setDescription(String) - -Method in class compbio.metadata.Option -
      -
    setDescription(String) - -Method in class compbio.metadata.Preset -
      -
    setEmail(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    setError(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setError(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setExecProvider(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    SetExecutableFlag - Class in compbio.ws.server
    Run setexecflag.sh script if executable flag is not set
    SetExecutableFlag() - -Constructor for class compbio.ws.server.SetExecutableFlag -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Align -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Analize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setFirst(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setFurtherDetails(URL) - -Method in class compbio.metadata.Option -
      -
    setInput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setInput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setInput(String) - -Method in class compbio.runner.conservation.AACon -
      -
    setInput(String) - -Method in class compbio.runner.disorder.Disembl -
      -
    setInput(String) - -Method in class compbio.runner.disorder.GlobPlot -
      -
    setInput(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    setInput(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    setInput(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    setInput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setInput(String) - -Method in class compbio.runner.msa.Mafft -
      -
    setInput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setInput(String) - -Method in class compbio.runner.msa.Probcons -
      -
    setInput(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setLast(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setLast(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setMax(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    setMin(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setName(String) - -Method in class compbio.metadata.Option -
      -
    setName(String) - -Method in class compbio.metadata.Preset -
      -
    setName(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    setNCore(int) - -Method in class compbio.runner.conservation.AACon -
      -
    setNCore(int) - -Method in class compbio.runner.disorder.Jronn -
      -
    setNCore(int) - -Method in class compbio.runner.msa.ClustalO -
      -
    setNCore(int) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setNumberOfSequencesAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setOptionName(String) - -Method in class compbio.metadata.Parameter -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Option -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    setOptions(List<String>) - -Method in class compbio.metadata.Preset -
      -
    setOptions(List<Option<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Adds the list of options or parameters to the internal list of options -
    setOutput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setOutput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setOutput(String) - -Method in class compbio.runner.conservation.AACon -
      -
    setOutput(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    setOutput(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    setOutput(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    setOutput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setOutput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParam(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParameter(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setParameters(CommandBuilder<?>) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Sets the list of parameters as internal list -
    setParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setPosition(long) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setPossibleValues(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    setPresetName(String) - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    setPresets(List<Preset<T>>) - -Method in class compbio.metadata.PresetManager -
      -
    setPrmSeparator(String) - -Method in class compbio.metadata.RunnerConfig -
    Sets name value separator character -
    setQueue(String) - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    setRanges(TreeSet<Range>) - -Method in class compbio.data.sequence.Score -
      -
    setRequired(boolean) - -Method in class compbio.metadata.Option -
      -
    setRequiredMemory(int) - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    setReturn(ScoreManager) - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    setReturn(JobStatus) - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    setReturn(Date) - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    setReturn(int) - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    setReturn(Limit) - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    setReturn(LimitsManager) - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    setReturn(PresetManager) - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    setReturn(Alignment) - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    setReturn(RunnerConfig) - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    setReturn(Set<Category>) - -Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    setReturn(Set<Services>) - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    setReturn(ChunkHolder) - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.PresetManager -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.RunnerConfig -
    Set the name of a runner class -
    setSequenceLenghtActual(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setSequenceLenghtAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setType(ValueConstrain.Type) - -Method in class compbio.metadata.ValueConstrain -
      -
    setValidValue(ValueConstrain) - -Method in class compbio.metadata.Parameter -
      -
    setValue(String) - -Method in interface compbio.metadata.Argument -
    Set default values for the parameter or an option -
    setValue(String) - -Method in class compbio.metadata.Option -
      -
    setWorkDirectory(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    setWorkDirectory(String) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    shutDown() - -Static method in class compbio.engine.local.LocalExecutorService -
    This stops all executing processes via interruption. -
    shutdownDBServer() - -Static method in class compbio.stat.collector.StatDB -
      -
    ShutdownEngines - Class in compbio.ws.server
    Switch off engines if JABAWS web application is undeployed, or web server is - shutdown
    ShutdownEngines() - -Constructor for class compbio.ws.server.ShutdownEngines -
      -
    shutdownService() - -Static method in class compbio.engine.local.ExecutableWrapper -
    Stops internal executor service which captures streams of native - executables. -
    SimpleWSPublisher - Class in compbio.ws.server
    Deprecated. 
    SimpleWSPublisher(Object, String) - -Constructor for class compbio.ws.server.SimpleWSPublisher -
    Deprecated.   -
    SINGLE_ENTRY_KEY - -Static variable in class compbio.data.sequence.ScoreManager -
      -
    size() - -Method in class compbio.engine.client.CommandBuilder -
      -
    SkeletalExecutable<T> - Class in compbio.engine.client
     
    SkeletalExecutable() - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SkeletalExecutable(String) - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SMERFSConstraints - Enum in compbio.data.sequence
    Enumeration defining two constraints for SMERFS columns score calculation.
    sortByResultSize() - -Method in class compbio.stat.collector.StatProcessor -
      -
    sortByRuntime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    sortByStartTime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    SPACE - -Static variable in class compbio.runner.Util -
      -
    STAT_FILE - -Static variable in class compbio.runner.conservation.AACon -
      -
    STAT_FILE - -Static variable in class compbio.runner.disorder.Jronn -
      -
    StatCollection - Class in compbio.stat.servlet.util
     
    StatCollection() - -Constructor for class compbio.stat.servlet.util.StatCollection -
      -
    StatCollection.Stattype - Enum in compbio.stat.servlet.util
    Total number of requests - - incomplete abandoned cancelled
    StatDB - Class in compbio.stat.collector
    The database must be stored in the application root directory and called - "ExecutionStatistic"
    StatDB() - -Constructor for class compbio.stat.collector.StatDB -
      -
    StatisticCollector - Class in compbio.stat.servlet
     
    StatisticCollector() - -Constructor for class compbio.stat.servlet.StatisticCollector -
      -
    StatisticManager - Class in compbio.engine.cluster.drmaa
     
    StatisticManager(JobInfo) - -Constructor for class compbio.engine.cluster.drmaa.StatisticManager -
      -
    StatProcessor - Class in compbio.stat.collector
     
    StatProcessor(List<JobStat>) - -Constructor for class compbio.stat.collector.StatProcessor -
      -
    StreamGobbler - Class in compbio.engine.local
     
    SubmissionManager - Class in compbio.engine
    Submit jobs for execution
    submitJob(ConfiguredExecutable<?>) - -Method in interface compbio.engine.AsyncExecutor -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    sumOfTotals(Map<Date, Totals>) - -Static method in class compbio.stat.servlet.util.Totals -
      -
    sumStats(Map<Services, StatProcessor>) - -Static method in class compbio.stat.servlet.util.Totals -
      -
    SyncExecutor - Interface in compbio.engine
    Synchronous executor, is an engine to run the Executable synchronously.
    -
    - - - - - - - - - - - - - - - -
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    Tcoffee - Class in compbio.runner.msa
     
    Tcoffee() - -Constructor for class compbio.runner.msa.Tcoffee -
      -
    TCOFFEE_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    TcoffeeWS - Class in compbio.ws.server
     
    TcoffeeWS() - -Constructor for class compbio.ws.server.TcoffeeWS -
      -
    termSignal() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    TestAllServices - Class in compbio.data.msa.jaxws
     
    TestAllServices() - -Constructor for class compbio.data.msa.jaxws.TestAllServices -
      -
    testAllServices() - -Method in interface compbio.data.msa.RegistryWS -
    Test all JABAWS services on the server -
    testAllServices() - -Method in class compbio.ws.server.RegistryWS -
    TODO improve reporting. -
    TestAllServicesResponse - Class in compbio.data.msa.jaxws
     
    TestAllServicesResponse() - -Constructor for class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    TestService - Class in compbio.data.msa.jaxws
     
    TestService() - -Constructor for class compbio.data.msa.jaxws.TestService -
      -
    testService(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Test a particular service -
    testService(String, Services, PrintWriter) - -Static method in class compbio.ws.client.Jws2Client -
    Asks registry to test the service on the host hostname -
    testService(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    TestServiceResponse - Class in compbio.data.msa.jaxws
     
    TestServiceResponse() - -Constructor for class compbio.data.msa.jaxws.TestServiceResponse -
      -
    to - -Variable in class compbio.data.sequence.Range -
      -
    toCommand(String) - -Method in class compbio.metadata.Option -
    Convert the option to the command string. -
    toCommand(String) - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.data.sequence.Alignment -
      -
    toString() - -Method in class compbio.data.sequence.FastaSequence -
    Same as oneLineFasta -
    toString() - -Method in class compbio.data.sequence.Range -
      -
    toString() - -Method in class compbio.data.sequence.Score -
      -
    toString() - -Method in class compbio.engine.client.CommandBuilder -
      -
    toString() - -Method in class compbio.engine.client.ConfExecutable -
      -
    toString() - -Method in class compbio.engine.client.RunConfiguration -
      -
    toString() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    toString() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    toString() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    toString() - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    toString() - -Method in class compbio.engine.FilePuller -
      -
    toString() - -Method in class compbio.engine.Job -
      -
    toString() - -Method in class compbio.metadata.ChunkHolder -
      -
    toString() - -Method in class compbio.metadata.Limit -
      -
    toString() - -Method in class compbio.metadata.LimitsManager -
      -
    toString() - -Method in class compbio.metadata.Option -
      -
    toString() - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.metadata.Preset -
      -
    toString() - -Method in class compbio.metadata.PresetManager -
      -
    toString() - -Method in class compbio.metadata.RunnerConfig -
      -
    toString() - -Method in class compbio.metadata.ValueConstrain -
      -
    toString() - -Method in class compbio.pipeline._jpred.Hit -
      -
    toString() - -Method in class compbio.pipeline._jpred.PScore -
      -
    toString() - -Method in class compbio.stat.collector.JobStat -
      -
    toString() - -Method in class compbio.stat.collector.StatProcessor -
      -
    toString() - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    toString() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    toString(Set<Services>) - -Static method in enum compbio.ws.client.Services -
      -
    Totals - Class in compbio.stat.servlet.util
     
    Totals() - -Constructor for class compbio.stat.servlet.util.Totals -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
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    BlastAll - Class in compbio.runner._impl
     
    BlastAll(String) - -Constructor for class compbio.runner._impl.BlastAll -
      -
    BlastBlastComparator - Class in compbio.pipeline._jpred
     
    BlastBlastComparator() - -Constructor for class compbio.pipeline._jpred.BlastBlastComparator -
      -
    BlastHmmerComparator - Class in compbio.pipeline._jpred
     
    BlastHmmerComparator() - -Constructor for class compbio.pipeline._jpred.BlastHmmerComparator -
      -
    BlastParameters - Class in compbio.runner._impl
    Utility class for common Blast parameters
    BlastParser - Class in compbio.pipeline._jpred
     
    BlastParser(String) - -Constructor for class compbio.pipeline._jpred.BlastParser -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(File, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeException(Throwable) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBean() - -Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    Util - Class in compbio.engine.client
     
    Util() - -Constructor for class compbio.engine.client.Util -
      -
    Util - Class in compbio.runner
     
    Util() - -Constructor for class compbio.runner.Util -
      -
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    -
    -
    V2_SERVICE_NAMESPACE - -Static variable in interface compbio.data.msa.JABAService -
      -
    validate(Validator, String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    validate(PresetManager<T>) - -Method in class compbio.metadata.LimitsManager -
    Validate Limits -
    validate(RunnerConfig<T>) - -Method in class compbio.metadata.PresetManager -
    Checks whether preset option and parameter are defined in RunnerConfig - object. -
    validate() - -Method in class compbio.metadata.RunnerConfig -
    Validate the value of the argument. -
    validateAAConInput(List<FastaSequence>) - -Static method in class compbio.ws.server.WSUtil -
      -
    validateDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateFastaInput(List<FastaSequence>) - -Static method in class compbio.ws.server.WSUtil -
      -
    validateJobId(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    validatePathNames(List<String>, String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validURL(String) - -Static method in class compbio.ws.client.Jws2Client -
    Attempt to construct the URL object from the string -
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - -Constructor for class compbio.metadata.ValueConstrain -
      -
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.Program -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.JobStatus -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.stat.servlet.util.StatCollection.Stattype -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.ws.client.Services -
    Returns the enum constant of this type with the specified name. -
    values() - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.ConservationMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.DisorderMethod -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.Program -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.SMERFSConstraints -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.JobStatus -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.metadata.ValueConstrain.Type -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.stat.servlet.util.StatCollection.Stattype -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.ws.client.Services -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
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    -
    -
    waitForFile(long) - -Method in class compbio.engine.FilePuller -
      -
    waitForJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForJob(String, long) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForResult(ClusterSession, String) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    waitForResult() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    waitForResult() - -Method in class compbio.engine.local.LocalRunner -
      -
    waitForResult() - -Method in interface compbio.engine.SyncExecutor -
    Call to this method block for as long as it is required for an executable to finish its job. -
    wasAborted() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    WHITE_SPACE - -Static variable in class compbio.data.sequence.SequenceUtil -
    A whitespace character: [\t\n\x0B\f\r] -
    write(TreeSet<Score>, Writer) - -Static method in class compbio.data.sequence.Score -
    Outputs the List of Score objects into the Output stream. -
    write(RunConfiguration) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    write(Object, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeAndValidate(Object, String, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeClustalAlignment(Writer, Alignment) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Write Clustal formatted alignment Limitations: does not record the - consensus. -
    writeFasta(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line -
    writeFasta(OutputStream, List<FastaSequence>) - -Static method in class compbio.data.sequence.SequenceUtil -
    Writes FastaSequence in the file, each sequence will take one line only -
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    writeFile(String, String, String, boolean) - -Static method in class compbio.engine.client.Util -
      -
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - -Static method in class compbio.runner.Util -
      -
    writeMarker(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    writeOut(Writer) - -Method in class compbio.data.sequence.ScoreManager -
      -
    writeStatFile(String, String) - -Static method in class compbio.engine.client.Util -
      -
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    WrongParameterException(Option<?>) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String, Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    WrongParameterExceptionBean() - -Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester(String, PrintWriter) - -Constructor for class compbio.ws.client.WSTester -
    Construct an instance of JABAWS tester -
    WSUtil - Class in compbio.ws.server
     
    WSUtil() - -Constructor for class compbio.ws.server.WSUtil -
      -
    -
    - - - - - - - - - - - - - - - -
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    _Jpred - Class in compbio.runner._jpred
     
    _Jpred() - -Constructor for class compbio.runner._jpred._Jpred -
      -
    _Key - Class in compbio.engine.conf
    Deprecated. 
    _Key(Class<?>) - -Constructor for class compbio.engine.conf._Key -
    Deprecated.   -
    _MsaService<T> - Class in compbio.ws.server
    TODO to complete after the approach is tested with SequenceAnnotation! - - Common methods for all SequenceAnnotation web services
    _NativeSpecHelper - Class in compbio.runner
    Deprecated. 
    _NativeSpecHelper(int) - -Constructor for class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    _NativeSpecHelper(int, int) - -Constructor for class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    _Queue - Enum in compbio.engine.cluster.dundee
    Deprecated. 
    _SkeletalCommandBuilder - Class in compbio.runner
    Deprecated. 
    _SkeletalCommandBuilder() - -Constructor for class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    _WSLogger - Class in compbio.ws.server
    Deprecated. 
    -
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    -
    -
    call() - -Method in class compbio.engine.local.ExecutableWrapper -
    It is vital that output and error streams are captured immediately for - this call() to succeed. -
    canAcceptMoreWork() - -Method in class compbio.engine.local.LocalExecutorService -
    If the Executor queue is empty -
    CancelJob - Class in compbio.data.msa.jaxws
     
    CancelJob() - -Constructor for class compbio.data.msa.jaxws.CancelJob -
      -
    cancelJob(String) - -Method in interface compbio.data.msa.JManagement -
    Stop running the job jobId but leave its output untouched -
    cancelJob(String) - -Method in interface compbio.engine.AsyncExecutor -
    Stop running job. -
    cancelJob(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cancelJob(String, ClusterSession) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    cancelJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cancelJob(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cancelJob(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cancelJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    cancelJob() - -Method in interface compbio.engine.SyncExecutor -
    Stops running job. -
    cancelJob(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MafftWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    cancelJob(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    CancelJobResponse - Class in compbio.data.msa.jaxws
     
    CancelJobResponse() - -Constructor for class compbio.data.msa.jaxws.CancelJobResponse -
      -
    Category - Class in compbio.data.msa
    Class that splits Services to categories.
    CATEGORY_ALIGNMENT - -Static variable in class compbio.data.msa.Category -
    All of the Category names -
    CATEGORY_CONSERVATION - -Static variable in class compbio.data.msa.Category -
      -
    CATEGORY_DISORDER - -Static variable in class compbio.data.msa.Category -
      -
    checkService(Services) - -Method in class compbio.ws.client.WSTester -
    Test JABA web service -
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of a string data together with the position in a file for - the next read operation.
    ChunkHolder(String, long) - -Constructor for class compbio.metadata.ChunkHolder -
      -
    Cleaner - Class in compbio.engine
    Deprecated. 
    Cleaner() - -Constructor for class compbio.engine.Cleaner -
    Deprecated.   -
    cleanProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Remove all non AA chars from the sequence -
    cleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all whitespace chars in the sequence string -
    cleanup(String) - -Method in interface compbio.engine.AsyncExecutor -
    Remove all files and a job directory for a jobid. -
    cleanup(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cleanup() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cleanup(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cleanup(ConfiguredExecutable<?>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cleanup() - -Method in class compbio.engine.local.LocalRunner -
      -
    cleanup() - -Method in interface compbio.engine.SyncExecutor -
    Clean up after the job -
    close() - -Method in class compbio.data.sequence.FastaReader -
    Call this method to close the connection to the input file if you want to - free up the resources. -
    close() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    closeSilently(Logger, Closeable) - -Static method in class compbio.data.sequence.SequenceUtil -
    Closes the Closable and logs the exception if any -
    CLUSTAL_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    CLUSTAL_OMEGA_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - -Constructor for class compbio.data.sequence.ClustalAlignmentUtil -
      -
    ClustalO - Class in compbio.runner.msa
     
    ClustalO() - -Constructor for class compbio.runner.msa.ClustalO -
    --threads= Number of processors to use - - -l, --log= Log all non-essential output to this file -
    ClustalOWS - Class in compbio.ws.server
     
    ClustalOWS() - -Constructor for class compbio.ws.server.ClustalOWS -
      -
    ClustalW - Class in compbio.runner.msa
     
    ClustalW() - -Constructor for class compbio.runner.msa.ClustalW -
      -
    ClustalWS - Class in compbio.ws.server
     
    ClustalWS() - -Constructor for class compbio.ws.server.ClustalWS -
      -
    CLUSTER_STAT_IN_SEC - -Static variable in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    CLUSTER_TASK_ID_PREFIX - -Static variable in class compbio.engine.client.ConfExecutable -
      -
    CLUSTER_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    ClusterJobId - Class in compbio.engine
     
    ClusterJobId(String) - -Constructor for class compbio.engine.ClusterJobId -
      -
    ClusterSession - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil() - -Constructor for class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    COILS_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -
    For the region to be considered disordered the values must exceed these -
    CommandBuilder<T> - Class in compbio.engine.client
     
    CommandBuilder(String) - -Constructor for class compbio.engine.client.CommandBuilder -
      -
    compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.EvalueComporator -
      -
    compare(Hit, Hit) - -Method in class compbio.pipeline._jpred.Hit.NumberComporator -
      -
    compareTo(Range) - -Method in class compbio.data.sequence.Range -
      -
    compareTo(Score) - -Method in class compbio.data.sequence.Score -
      -
    compareTo(Delayed) - -Method in class compbio.engine.FilePuller -
      -
    compbio.data._structure - package compbio.data._structure
     
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    compbio.pipeline._jpred - package compbio.pipeline._jpred
     
    compbio.runner._jpred - package compbio.runner._jpred
     
    confDir - -Static variable in class compbio.engine.conf.PropertyHelperManager -
      -
    ConfExecutable<T> - Class in compbio.engine.client
     
    ConfExecutable(Executable<T>, String) - -Constructor for class compbio.engine.client.ConfExecutable -
      -
    Configurator - Class in compbio.engine
     
    Configurator() - -Constructor for class compbio.engine.Configurator -
      -
    ConfiguredExecutable<T> - Interface in compbio.engine.client
     
    configureExecutable(Executable<T>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, List<FastaSequence>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    connect() - -Static method in class compbio.ws.client.AAConClient -
    Connects to a AACon web service by the host and the service name -
    connect(String, Services) - -Static method in class compbio.ws.client.Jws2Client -
    Connects to a web service by the host and the service name web service - type -
    connectToRegistry(String) - -Static method in class compbio.ws.client.Jws2Client -
    Get a connection of JABAWS registry -
    ConservationMethod - Enum in compbio.data.sequence
    Enumeration listing of all the supported methods.
    contextDestroyed(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -
      -
    contextDestroyed(ServletContextEvent) - -Method in class compbio.ws.server.SetExecutableFlag -
      -
    contextDestroyed(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -
      -
    contextInitialized(ServletContextEvent) - -Method in class compbio.stat.servlet.StatisticCollector -
      -
    contextInitialized(ServletContextEvent) - -Method in class compbio.ws.server.SetExecutableFlag -
    This listener is designed to run only once when the web application is - deployed to set executable flag for binaries. -
    contextInitialized(ServletContextEvent) - -Method in class compbio.ws.server.ShutdownEngines -
      -
    convertToAbsolute(String) - -Static method in class compbio.engine.client.Util -
      -
    copyAndValidateRConfig(RunnerConfig<?>) - -Method in class compbio.metadata.RunnerConfig -
      -
    countMatchesInSequence(String, String) - -Static method in class compbio.data.sequence.FastaSequence -
      -
    CustomAlign - Class in compbio.data.msa.jaxws
     
    CustomAlign() - -Constructor for class compbio.data.msa.jaxws.CustomAlign -
      -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with options. -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in class compbio.ws.server._MsaService -
      -
    customAlign(List<FastaSequence>, List<Option<ClustalO>>) - -Method in class compbio.ws.server.ClustalOWS -
      -
    customAlign(List<FastaSequence>, List<Option<ClustalW>>) - -Method in class compbio.ws.server.ClustalWS -
      -
    customAlign(List<FastaSequence>, List<Option<Mafft>>) - -Method in class compbio.ws.server.MafftWS -
      -
    customAlign(List<FastaSequence>, List<Option<Muscle>>) - -Method in class compbio.ws.server.MuscleWS -
      -
    customAlign(List<FastaSequence>, List<Option<Probcons>>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    CustomAlignResponse - Class in compbio.data.msa.jaxws
     
    CustomAlignResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    CustomAnalize - Class in compbio.data.msa.jaxws
     
    CustomAnalize() - -Constructor for class compbio.data.msa.jaxws.CustomAnalize -
      -
    customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Analyse the sequences according to custom settings defined in options - list. -
    customAnalize(List<FastaSequence>, List<Option<Disembl>>) - -Method in class compbio.ws.server.DisemblWS -
      -
    customAnalize(List<FastaSequence>, List<Option<GlobPlot>>) - -Method in class compbio.ws.server.GlobPlotWS -
      -
    customAnalize(List<FastaSequence>, List<Option<T>>) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    CustomAnalizeResponse - Class in compbio.data.msa.jaxws
     
    CustomAnalizeResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    -
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    -
    -
    deepClean() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    deepCleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all special characters and digits as well as whitespace chars - from the sequence -
    DEFAULT_COLUMN_SCORE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default column scoring schema -
    DEFAULT_GAP_THRESHOLD - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default gap threshold value for SMERFS algorithm -
    DEFAULT_WINDOW_SIZE - -Static variable in enum compbio.data.sequence.SMERFSConstraints -
    Default window size value for SMERFS algorithm -
    deleteAllFiles(String) - -Static method in class compbio.engine.Cleaner -
    Deprecated.   -
    deleteFiles(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Cleaner -
    Deprecated. This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -
    DELIM - -Static variable in class compbio.engine.conf._Key -
    Deprecated.   -
    DELIM - -Static variable in class compbio.engine.conf.DirectoryManager -
      -
    DIGIT - -Static variable in class compbio.data.sequence.SequenceUtil -
    A digit -
    DirectoryManager - Class in compbio.engine.conf
     
    DirectoryManager() - -Constructor for class compbio.engine.conf.DirectoryManager -
      -
    disconnect() - -Method in class compbio.engine.FilePuller -
      -
    Disembl - Class in compbio.runner.disorder
    DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops - fold_rem465 sequence_file print - - 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out' - - This version of DisEMBL is 1.4 (latest available for download in Feb 2011) - capable of outputting raw values - - The values of the parameters are hard coded in DisEMBL.py script.
    Disembl() - -Constructor for class compbio.runner.disorder.Disembl -
      -
    DISEMBL_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    DisemblWS - Class in compbio.ws.server
     
    DisemblWS() - -Constructor for class compbio.ws.server.DisemblWS -
      -
    DisorderMethod - Enum in compbio.data.sequence
     
    DisplayStat - Class in compbio.stat.servlet
     
    DisplayStat() - -Constructor for class compbio.stat.servlet.DisplayStat -
      -
    DownloadRedirector - Class in compbio.stat.servlet
     
    DownloadRedirector() - -Constructor for class compbio.stat.servlet.DownloadRedirector -
      -
    -
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    Environment - Class in compbio.runner._impl
    This is utility class to encapsulate environmental variables like directory paths
    EnvVariableProcessor - Class in compbio.engine.client
     
    EnvVariableProcessor() - -Constructor for class compbio.engine.client.EnvVariableProcessor -
      -
    equals(Object) - -Method in class compbio.data.msa.Category -
      -
    equals(Object) - -Method in class compbio.data.sequence.Alignment -
    Please note that this implementation does not take the order of sequences - into account! -
    equals(Object) - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    equals(Object) - -Method in class compbio.data.sequence.FastaSequence -
      -
    equals(Object) - -Method in class compbio.data.sequence.Range -
      -
    equals(Object) - -Method in class compbio.data.sequence.Score -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager -
      -
    equals(Object) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    equals(Object) - -Method in class compbio.engine.client.CommandBuilder -
      -
    equals(Object) - -Method in class compbio.engine.client.RunConfiguration -
      -
    equals(Object) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    equals(Object) - -Method in class compbio.engine.ClusterJobId -
      -
    equals(Object) - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    equals(Object) - -Method in class compbio.engine.FilePuller -
      -
    equals(Object) - -Method in class compbio.engine.Job -
      -
    equals(Object) - -Method in class compbio.metadata.ChunkHolder -
      -
    equals(Object) - -Method in class compbio.metadata.Limit -
      -
    equals(Object) - -Method in class compbio.metadata.Option -
      -
    equals(Object) - -Method in class compbio.metadata.Parameter -
      -
    equals(Object) - -Method in class compbio.metadata.Preset -
      -
    equals(Object) - -Method in class compbio.metadata.RunnerConfig -
      -
    equals(Object) - -Method in class compbio.metadata.ValueConstrain -
      -
    equals(Object) - -Method in class compbio.pipeline._jpred.Hit -
      -
    equals(Object) - -Method in class compbio.pipeline._jpred.PScore -
      -
    equals(Object) - -Method in class compbio.stat.collector.JobStat -
      -
    equals(Object) - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    equals(Object) - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    ERROR - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    Executable<T> - Interface in compbio.engine.client
    Interface to a native executable.
    Executable.ExecProvider - Enum in compbio.engine.client
     
    ExecutableWrapper - Class in compbio.engine.local
     
    ExecutableWrapper(ConfiguredExecutable<?>, String) - -Constructor for class compbio.engine.local.ExecutableWrapper -
      -
    executeJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    executeJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    executeJob() - -Method in interface compbio.engine.SyncExecutor -
    Execute the job -
    ExecutionStatCollector - Class in compbio.stat.collector
    Number of runs of each WS = number of folders with name - - Number of successful runs = all runs with no result file - - Per period of time = limit per file creating time Runtime (avg/max) = - - started time - finished time - - Task & result size = result.size - - Abandoned runs - not collected runs - - Cancelled runs - cancelled - - Cluster vs local runs - - Reasons for failure = look in the err out? - - - Metadata required: - - work directory for local and cluster tasks = from Helper or cmd parameter.
    ExecutionStatCollector(String, int) - -Constructor for class compbio.stat.collector.ExecutionStatCollector -
    List subdirectories in the job directory -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -
    -
    fastaAlignment - -Static variable in class compbio.ws.client.WSTester -
      -
    fastaInput - -Static variable in class compbio.ws.client.WSTester -
    Sequences to be used as input for all WS -
    FastaReader - Class in compbio.data.sequence
    Reads files with FASTA formatted sequences.
    FastaReader(String) - -Constructor for class compbio.data.sequence.FastaReader -
    Header data can contain non-ASCII symbols and read in UTF8 -
    FastaReader(InputStream) - -Constructor for class compbio.data.sequence.FastaReader -
    This class will not close the incoming stream! So the client should do - so. -
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - -Constructor for class compbio.data.sequence.FastaSequence -
    Upon construction the any whitespace characters are removed from the - sequence -
    FilePuller - Class in compbio.engine
     
    from - -Variable in class compbio.data.sequence.Range -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -
    -
    gapchar - -Static variable in class compbio.data.sequence.ClustalAlignmentUtil -
    Dash char to be used as gap char in the alignments -
    GAUtils - Class in compbio.ws.server
     
    GAUtils() - -Constructor for class compbio.ws.server.GAUtils -
      -
    GenericMetadataService<T> - Class in compbio.ws.server
     
    get(String) - -Static method in class compbio.engine.PulledFileCache -
      -
    getAbandoned() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getAbandonedCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getAbandonedJobs() - -Method in class compbio.stat.collector.StatProcessor -
    Not collected. -
    getActualNumberofSequences() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getActualNumberofSequences() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getAllConstrainedParametersWithBorderValues(boolean) - -Method in class compbio.runner.OptionCombinator -
      -
    getAllConstrainedParametersWithRandomValues() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllOptions() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllParameters() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getAllStats() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    GetAnnotation - Class in compbio.data.msa.jaxws
     
    GetAnnotation() - -Constructor for class compbio.data.msa.jaxws.GetAnnotation -
      -
    getAnnotation(String) - -Method in interface compbio.data.msa.SequenceAnnotation -
    Return the result of the job. -
    getAnnotation(String) - -Method in class compbio.ws.server.SequenceAnnotationService -
      -
    getAnnotation(String, Logger) - -Static method in class compbio.ws.server.WSUtil -
      -
    getAnnotationForSequence(String) - -Method in class compbio.data.sequence.ScoreManager -
      -
    GetAnnotationResponse - Class in compbio.data.msa.jaxws
     
    GetAnnotationResponse() - -Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getApproprieteQueue() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTested -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.GetServiceDescription -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.IsOperating -
      -
    getArg0() - -Method in class compbio.data.msa.jaxws.TestService -
      -
    getArgument(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by its name if found, NULL otherwise. -
    getArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -
    Returns the argument by option name, NULL if the argument is not found -
    getArguments(RunnerConfig<T>) - -Method in class compbio.metadata.Preset -
    Converts list of options as String to type Option -
    getArguments() - -Method in class compbio.metadata.RunnerConfig -
    Returns list of Parameter and Option supported by current - runner -
    getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(String) - -Static method in class compbio.engine.Configurator -
      -
    getAvgSeqLength() - -Method in class compbio.metadata.Limit -
      -
    getAvgSequenceLength(List<FastaSequence>) - -Static method in class compbio.metadata.Limit -
    Calculates an average sequence length of the dataset -
    getBlastAllRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getBlastBinDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getByJobId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getByTaskId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getCalculationTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCancelled() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getCancelledCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getCancelledJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getCategories() - -Static method in class compbio.data.msa.Category -
      -
    getChunk() - -Method in class compbio.metadata.ChunkHolder -
      -
    getClass(String) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getClusterCpuNum(Class<? extends Executable<?>>) - -Static method in class compbio.engine.client.SkeletalExecutable -
      -
    getClusterJobId(String) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getClusterJobId() - -Method in class compbio.stat.collector.JobStat -
      -
    getClusterJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getClusterJobSettings() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getClusterJobSettings() - -Method in interface compbio.engine.client.Executable -
      -
    getClusterJobSettings() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getClusterJobSettings() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getClusterJobSettings() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getClusterStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCommand(Executable.ExecProvider) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getCommand(Executable.ExecProvider, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Mcl -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Ronn -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommandName() - -Method in class compbio.runner._impl.Mcl -
      -
    getCommandName() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCommandName() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.Ronn -
      -
    getCommandName() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getCommands() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getCommands(List<Option<T>>, String) - -Static method in class compbio.ws.server.WSUtil -
      -
    getCommandString() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getConfExecutable() - -Method in class compbio.engine.Job -
      -
    getCPUTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCPUUsageTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCreatedFiles() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCreatedFiles() - -Method in interface compbio.engine.client.Executable -
    Deprecated.  -
    getCreatedFiles() - -Method in class compbio.engine.client.SkeletalExecutable -
    This method cannot really tell whether the files has actually been - created or not. -
    getCreatedFiles() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Mcl -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.OB -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Ronn -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner.conservation.AACon -
      -
    getCreatedFiles() - -Method in class compbio.runner.disorder.Jronn -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.ClustalW -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Muscle -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Probcons -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getDataTransfered() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getDefaultLimit() - -Method in class compbio.metadata.LimitsManager -
      -
    getDefaultValue() - -Method in interface compbio.metadata.Argument -
      -
    getDefaultValue() - -Method in class compbio.metadata.Option -
    A default value of the option. -
    getDelay(TimeUnit) - -Method in class compbio.engine.FilePuller -
      -
    getDescription() - -Method in interface compbio.metadata.Argument -
      -
    getDescription() - -Method in class compbio.metadata.Option -
    A long description of the Option -
    getDescription() - -Method in class compbio.metadata.Preset -
      -
    getDetails() - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    getEarliestRecord() - -Method in class compbio.stat.collector.StatDB -
      -
    getEmail() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getEndTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getEngine(Executable<?>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(Executable<V>, List<FastaSequence>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(ConfiguredExecutable<?>) - -Static method in class compbio.ws.server.WSUtil -
      -
    getEnvironment() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getEnvironment() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getEnvVariables(String, Class<?>) - -Static method in class compbio.engine.client.EnvVariableProcessor -
      -
    getError() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getError() - -Method in interface compbio.engine.client.Executable -
      -
    getError() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getError() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getError() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getError() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getEscJobname() - -Method in class compbio.stat.collector.JobStat -
      -
    getExecProperty(String, Executable<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProperty(String, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProvider() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecProvider() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutable() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecutable() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutionStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getExecutor() - -Static method in class compbio.engine.local.LocalExecutorService -
    This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -
    getExitStatus() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getFailed() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getFailedJobs() - -Method in class compbio.stat.collector.StatProcessor -
    Started & finished but did not produce result -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Align -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Analize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getFile() - -Method in class compbio.engine.FilePuller -
      -
    getFinish() - -Method in class compbio.stat.collector.JobStat -
      -
    getFormatedSequence(int) - -Method in class compbio.data.sequence.FastaSequence -
    Format sequence per width letter in one string. -
    getFormattedFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getFullPath(String, String) - -Static method in class compbio.engine.client.Util -
      -
    getFurtherDetails() - -Method in interface compbio.metadata.Argument -
      -
    getFurtherDetails() - -Method in class compbio.metadata.Option -
    The URL where further details about the option can be found -
    getGapchar() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getId() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of id -
    getIncomplete() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getIncompleteCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getIncompleteJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getInput() - -Method in class compbio.engine.client.ConfExecutable -
    Not all input paths are relative! Input path could be absolute! -
    getInput() - -Method in interface compbio.engine.client.Executable -
      -
    getInput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getInput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getInput() - -Method in class compbio.runner._impl.BlastAll -
      -
    getInput() - -Method in class compbio.runner._impl.Mcl -
      -
    getInput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getInput() - -Method in class compbio.runner._impl.OB -
      -
    getInput() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getInput() - -Method in class compbio.runner._impl.Ronn -
      -
    getInput() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getInputSize() - -Method in class compbio.stat.collector.JobStat -
      -
    getInstance(ConfiguredExecutable<?>) - -Static method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getIOWait() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getIsCancelled() - -Method in class compbio.stat.collector.JobStat -
      -
    getIsCollected() - -Method in class compbio.stat.collector.JobStat -
      -
    getIsFinished() - -Method in class compbio.stat.collector.JobStat -
      -
    getJava() - -Static method in class compbio.engine.client.Util -
    Returns the absolute path to the Java executable from JAVA_HOME -
    getJobId() - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetAnnotation -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getJobId() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobId() - -Method in class compbio.engine.ClusterJobId -
      -
    getJobId() - -Method in class compbio.engine.Job -
      -
    getJobInfo() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
    This method will block before the calculation has completed and then - return the object containing a job execution statistics -
    getJobname() - -Method in class compbio.stat.collector.JobStat -
      -
    getJobNumber() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getJobPriority() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - -Constructor for class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobStatus(String) - -Method in interface compbio.data.msa.JManagement -
    Return the status of the job. -
    getJobStatus(String) - -Method in interface compbio.engine.AsyncExecutor -
    Query the status of the job -
    getJobStatus(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. -
    getJobStatus(ClusterJobId) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
    Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -
    getJobStatus(int) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
    Deprecated.  -
    getJobStatus() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getJobStatus(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getJobStatus(Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getJobStatus() - -Method in class compbio.engine.local.LocalRunner -
      -
    getJobStatus() - -Method in interface compbio.engine.SyncExecutor -
    Query the status of the job by its id. -
    getJobStatus(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getJobStatus(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
     
    GetJobStatusResponse() - -Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    GetLastTested - Class in compbio.data.msa.jaxws
     
    GetLastTested() - -Constructor for class compbio.data.msa.jaxws.GetLastTested -
      -
    getLastTested(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Number of seconds since the last test. -
    getLastTested(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    GetLastTestedOn - Class in compbio.data.msa.jaxws
     
    GetLastTestedOn() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOn -
      -
    getLastTestedOn(Services) - -Method in interface compbio.data.msa.RegistryWS -
    The date and time the service has been verified to work last time -
    getLastTestedOn(Services) - -Method in class compbio.ws.server.RegistryWS -
    Can potentially return null if the service has not been tested yet. -
    GetLastTestedOnResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedOnResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    GetLastTestedResponse - Class in compbio.data.msa.jaxws
     
    GetLastTestedResponse() - -Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getLength() - -Method in class compbio.data.sequence.FastaSequence -
      -
    GetLimit - Class in compbio.data.msa.jaxws
     
    GetLimit() - -Constructor for class compbio.data.msa.jaxws.GetLimit -
      -
    getLimit(String) - -Method in interface compbio.data.msa.Metadata -
    Get a Limit for a preset. -
    getLimit(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimit(String) - -Method in interface compbio.engine.client.Executable -
      -
    getLimit(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getLimit(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimit(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getLimit(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getLimit(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getLimitByName(String) - -Method in class compbio.metadata.LimitsManager -
      -
    GetLimitResponse - Class in compbio.data.msa.jaxws
     
    GetLimitResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitResponse -
      -
    GetLimits - Class in compbio.data.msa.jaxws
     
    GetLimits() - -Constructor for class compbio.data.msa.jaxws.GetLimits -
      -
    getLimits() - -Method in interface compbio.data.msa.Metadata -
    List Limits supported by a web service. -
    getLimits() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimits() - -Method in interface compbio.engine.client.Executable -
      -
    getLimits() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getLimits(Class<T>) - -Static method in class compbio.engine.client.Util -
    For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -
    getLimits() - -Method in class compbio.metadata.LimitsManager -
      -
    getLimits() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimits() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getLimits() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getLimits() - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimits() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getLimits() - -Method in class compbio.ws.server.MafftWS -
      -
    getLimits() - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimits() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimits() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetLimitsResponse - Class in compbio.data.msa.jaxws
     
    GetLimitsResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getLocalJobs() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getLocalPath() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Method return the absolute path to the project root directory. -
    getLocalStat() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    getMax() - -Method in class compbio.metadata.ValueConstrain -
      -
    getMaxVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMclRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getMemoryLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. return max memory limit in Mb -
    getMemoryStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    getMetadata() - -Method in class compbio.data.sequence.Alignment -
      -
    getMethod(String) - -Static method in enum compbio.data.sequence.ConservationMethod -
      -
    getMethod() - -Method in class compbio.data.sequence.Score -
    Returns the ConservationMethod -
    getMin() - -Method in class compbio.metadata.ValueConstrain -
      -
    getName() - -Method in interface compbio.metadata.Argument -
      -
    getName() - -Method in class compbio.metadata.Option -
    Human readable name of the option -
    getName() - -Method in class compbio.metadata.Preset -
      -
    getName() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getNativeSpec() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getNetNglycRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getNextPosition() - -Method in class compbio.metadata.ChunkHolder -
      -
    getNumberOfScores() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getNumberOfSeq() - -Method in class compbio.data.sequence.ScoreManager -
      -
    getNumberOfSequencesAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getNumberOfSequencesAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getOBRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getOnelineFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getOptionName() - -Method in class compbio.metadata.Parameter -
      -
    getOptionNames() - -Method in class compbio.metadata.Option -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAnalize -
      -
    getOptions() - -Method in class compbio.metadata.Preset -
      -
    getOptions() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of the Options supported by the executable of type T -
    getOptionsAtRandom() - -Method in class compbio.runner.OptionCombinator -
      -
    getOutput() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getOutput() - -Method in interface compbio.engine.client.Executable -
      -
    getOutput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getOutput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getOutput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getOutput() - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getOutput() - -Method in class compbio.runner.disorder.IUPred -
      -
    getParameters() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in interface compbio.engine.client.Executable -
      -
    getParameters() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getParameters() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of parameters supported executable of type T. -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.conservation.AACon -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.disorder.Jronn -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.msa.ClustalO -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getParamValue(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    getPosition() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getPossibleValues() - -Method in interface compbio.metadata.Argument -
      -
    getPossibleValues() - -Method in class compbio.metadata.Option -
    List of possible optionNames -
    getPossibleValues() - -Method in class compbio.metadata.Parameter -
    List is more convenient to work with -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAnalize -
      -
    getPreset() - -Method in class compbio.metadata.Limit -
      -
    getPresetByName(String) - -Method in class compbio.metadata.PresetManager -
      -
    getPresetName() - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    GetPresets - Class in compbio.data.msa.jaxws
     
    GetPresets() - -Constructor for class compbio.data.msa.jaxws.GetPresets -
      -
    getPresets() - -Method in interface compbio.data.msa.Metadata -
    Get presets supported by a web service -
    getPresets() - -Method in class compbio.metadata.PresetManager -
      -
    getPresets(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getPresets() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getPresets() - -Method in class compbio.ws.server.ClustalWS -
      -
    getPresets() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getPresets() - -Method in class compbio.ws.server.MafftWS -
      -
    getPresets() - -Method in class compbio.ws.server.MuscleWS -
      -
    getPresets() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getPresets() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetPresetsResponse - Class in compbio.data.msa.jaxws
     
    GetPresetsResponse() - -Constructor for class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getPrmSeparator() - -Method in class compbio.metadata.RunnerConfig -
      -
    getProgram() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getProgress() - -Method in class compbio.engine.FilePuller -
      -
    getProgress(String) - -Static method in class compbio.engine.ProgressGetter -
      -
    getProgress(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    getPropertyHelper() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. -
    getPSIBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getQueue(int, int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getQueue(String) - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getQueue() - -Method in class compbio.runner._NativeSpecHelper -
    Deprecated.   -
    getQueueByMemoryRequirements(int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    getRanges() - -Method in class compbio.data.sequence.Score -
    Return Ranges if any Collections.EMPTY_SET otherwise -
    getRawUsage() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getRecordedJobStatus(String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getRemoteAddress() - -Method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    GetResult - Class in compbio.data.msa.jaxws
     
    GetResult() - -Constructor for class compbio.data.msa.jaxws.GetResult -
      -
    getResult(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the result of the job. -
    getResult(String) - -Method in class compbio.ws.server._MsaService -
      -
    getResult(String) - -Method in class compbio.ws.server.ClustalOWS -
      -
    getResult(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getResult(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getResult(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetResultResponse - Class in compbio.data.msa.jaxws
     
    GetResultResponse() - -Constructor for class compbio.data.msa.jaxws.GetResultResponse -
      -
    getResults(String) - -Method in interface compbio.engine.AsyncExecutor -
    Retrieve the results of the job. -
    getResults() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getResults(String) - -Method in interface compbio.engine.client.Executable -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getResults(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getResults(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getResults(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getResults(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
    Deprecated.   -
    getResults(String) - -Method in class compbio.runner.conservation.AACon -
      -
    getResults(String) - -Method in class compbio.runner.disorder.Disembl -
      -
    getResults(String) - -Method in class compbio.runner.disorder.GlobPlot -
      -
    getResults(String) - -Method in class compbio.runner.disorder.IUPred -
      -
    getResults(String) - -Method in class compbio.runner.disorder.Jronn -
      -
    getResults(String) - -Method in class compbio.runner.msa.ClustalO -
      -
    getResults(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    getResults(String) - -Method in class compbio.runner.msa.Mafft -
      -
    getResults(String) - -Method in class compbio.runner.msa.Muscle -
      -
    getResults(String) - -Method in class compbio.runner.msa.Probcons -
      -
    getResults(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getResultSize() - -Method in class compbio.stat.collector.JobStat -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetAnnotationResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLastTestedResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAnalizeResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestAllServicesResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.TestServiceResponse -
      -
    getRonnRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRPSBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getRPSBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getRunnerClassName() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getRunnerClassName() - -Method in class compbio.metadata.PresetManager -
      -
    getRunnerClassName() - -Method in class compbio.metadata.RunnerConfig -
      -
    getRunnerLimits(Class<V>) - -Static method in class compbio.engine.client.ConfExecutable -
    This method should be executed once and result of its execution reused. -
    GetRunnerOptions - Class in compbio.data.msa.jaxws
     
    GetRunnerOptions() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptions -
      -
    getRunnerOptions() - -Method in interface compbio.data.msa.Metadata -
    Get options supported by a web service -
    getRunnerOptions(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ClustalOWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ClustalWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.GenericMetadataService -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MafftWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MuscleWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
     
    GetRunnerOptionsResponse() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getRunnerPresets(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getRuntime() - -Method in class compbio.stat.collector.JobStat -
      -
    getSchema(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getScoreByMethod(Enum<?>) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScoreByMethod(String) - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    getScores() - -Method in class compbio.data.sequence.Score -
    The column scores for the alignment -
    getSeqNumber() - -Method in class compbio.metadata.Limit -
      -
    getSequence() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of sequence -
    getSequenceLenghtActual() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtActual() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequenceLenghtAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequences() - -Method in class compbio.data.sequence.Alignment -
      -
    getService() - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    getService(String) - -Static method in enum compbio.ws.client.Services -
      -
    getServiceByJobDirectory(File) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceByRunner(Class<? extends Executable>) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    GetServiceCategories - Class in compbio.data.msa.jaxws
     
    GetServiceCategories() - -Constructor for class compbio.data.msa.jaxws.GetServiceCategories -
      -
    getServiceCategories() - -Method in interface compbio.data.msa.RegistryWS -
    Gets the list of services per category. -
    getServiceCategories() - -Method in class compbio.ws.server.RegistryWS -
      -
    GetServiceCategoriesResponse - Class in compbio.data.msa.jaxws
     
    GetServiceCategoriesResponse() - -Constructor for class compbio.data.msa.jaxws.GetServiceCategoriesResponse -
      -
    GetServiceDescription - Class in compbio.data.msa.jaxws
     
    GetServiceDescription() - -Constructor for class compbio.data.msa.jaxws.GetServiceDescription -
      -
    getServiceDescription(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Gives the description of the service. -
    getServiceDescription(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    GetServiceDescriptionResponse - Class in compbio.data.msa.jaxws
     
    GetServiceDescriptionResponse() - -Constructor for class compbio.data.msa.jaxws.GetServiceDescriptionResponse -
      -
    getServiceImpl(Services) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceInfo() - -Method in enum compbio.ws.client.Services -
      -
    getServices() - -Method in class compbio.data.msa.Category -
      -
    getServices(String) - -Static method in class compbio.ws.client.Jws2Client -
      -
    getSession() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getSingleWSStat(Services) - -Method in class compbio.stat.collector.StatProcessor -
      -
    getSize() - -Method in class compbio.data.sequence.Alignment -
      -
    getSMERFSColumnScore(String) - -Static method in enum compbio.data.sequence.SMERFSConstraints -
      -
    getStart() - -Method in class compbio.stat.collector.JobStat -
      -
    getStartTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getStatFile() - -Static method in class compbio.runner.conservation.AACon -
      -
    getStatFile() - -Static method in class compbio.runner.disorder.Jronn -
      -
    getStatFile() - -Static method in class compbio.runner.msa.ClustalO -
      -
    getStatFile() - -Static method in class compbio.runner.msa.ClustalW -
      -
    getStatFile() - -Static method in class compbio.runner.msa.Muscle -
      -
    getStatistics(JobInfo) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getStatLogger(Services, WebServiceContext) - -Static method in class compbio.ws.server._WSLogger -
    Deprecated.   -
    getStats(int) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    getStats(Date) - -Static method in class compbio.stat.servlet.util.StatCollection -
      -
    getStatus() - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    getSubmissionTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getSupportedOptions(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getSupportedRuntimes() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getSupportedRuntimes() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getSupportedRuntimes(Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    GetSupportedServices - Class in compbio.data.msa.jaxws
     
    GetSupportedServices() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServices -
      -
    getSupportedServices() - -Method in interface compbio.data.msa.RegistryWS -
    List of services that are functioning on the server. -
    getSupportedServices() - -Method in class compbio.ws.server.RegistryWS -
      -
    GetSupportedServicesResponse - Class in compbio.data.msa.jaxws
     
    GetSupportedServicesResponse() - -Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse -
      -
    getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getSyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    getTaskDirectory(Class<?>) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getTaskId() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getTaskId() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getTaskId() - -Method in class compbio.engine.Job -
      -
    getTestArgs() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestArgs() - -Method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Ronn -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getTestParams() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated. 0 - unlimited -
    getTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getTmhmm2Runnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getTotal() - -Method in class compbio.stat.servlet.util.Totals -
      -
    getTotalJobsCount(Timestamp, Timestamp) - -Method in class compbio.stat.collector.StatDB -
      -
    getTotalRuntime() - -Method in class compbio.stat.collector.StatProcessor -
      -
    getType() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getType() - -Method in class compbio.metadata.ValueConstrain -
      -
    getType() - -Method in class compbio.runner.conservation.AACon -
      -
    getType() - -Method in class compbio.runner.disorder.Disembl -
      -
    getType() - -Method in class compbio.runner.disorder.GlobPlot -
      -
    getType() - -Method in class compbio.runner.disorder.IUPred -
      -
    getType() - -Method in class compbio.runner.disorder.Jronn -
      -
    getType() - -Method in class compbio.runner.msa.ClustalO -
      -
    getType() - -Method in class compbio.runner.msa.ClustalW -
      -
    getType() - -Method in class compbio.runner.msa.Mafft -
      -
    getType() - -Method in class compbio.runner.msa.Muscle -
      -
    getType() - -Method in class compbio.runner.msa.Probcons -
      -
    getType() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getUsedSysTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getUsedUserTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getValidator(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidator(Schema) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidValue() - -Method in class compbio.metadata.Parameter -
      -
    getVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getWebService() - -Method in class compbio.stat.collector.JobStat -
      -
    getWorkDirectory(String) - -Method in interface compbio.engine.AsyncExecutor -
      -
    getWorkDirectory() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getWorkDirectory() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getWorkDirectory(String) - -Static method in class compbio.engine.Configurator -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.local.LocalRunner -
      -
    getWorkDirectory() - -Method in interface compbio.engine.SyncExecutor -
      -
    GlobPlot - Class in compbio.runner.disorder
    ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame - - FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' - Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' - - Hard-coded values are 10 15 74 4 5.
    GlobPlot() - -Constructor for class compbio.runner.disorder.GlobPlot -
      -
    GLOBPLOT_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    GlobPlotWS - Class in compbio.ws.server
     
    GlobPlotWS() - -Constructor for class compbio.ws.server.GlobPlotWS -
      -
    -
    - - - - - - - - - - - - - - - -
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    hasDump() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasExited() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hashCode() - -Method in class compbio.data.msa.Category -
      -
    hashCode() - -Method in class compbio.data.sequence.Alignment -
      -
    hashCode() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    hashCode() - -Method in class compbio.data.sequence.FastaSequence -
      -
    hashCode() - -Method in class compbio.data.sequence.Range -
      -
    hashCode() - -Method in class compbio.data.sequence.Score -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager -
      -
    hashCode() - -Method in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    hashCode() - -Method in class compbio.engine.client.CommandBuilder -
      -
    hashCode() - -Method in class compbio.engine.client.RunConfiguration -
      -
    hashCode() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    hashCode() - -Method in class compbio.engine.ClusterJobId -
      -
    hashCode() - -Method in class compbio.engine.conf._Key -
    Deprecated.   -
    hashCode() - -Method in class compbio.engine.FilePuller -
      -
    hashCode() - -Method in class compbio.engine.Job -
      -
    hashCode() - -Method in class compbio.metadata.ChunkHolder -
      -
    hashCode() - -Method in class compbio.metadata.Limit -
      -
    hashCode() - -Method in class compbio.metadata.Option -
      -
    hashCode() - -Method in class compbio.metadata.Parameter -
      -
    hashCode() - -Method in class compbio.metadata.Preset -
      -
    hashCode() - -Method in class compbio.metadata.ValueConstrain -
      -
    hashCode() - -Method in class compbio.pipeline._jpred.Hit -
      -
    hashCode() - -Method in class compbio.pipeline._jpred.PScore -
      -
    hashCode() - -Method in class compbio.stat.collector.JobStat -
      -
    hashCode() - -Method in class compbio.stat.servlet.ServiceTestResult -
      -
    hashCode() - -Method in class compbio.stat.servlet.util.StatCollection -
      -
    hasMoreData() - -Method in class compbio.engine.FilePuller -
      -
    hasNext() - -Method in class compbio.data.sequence.FastaReader -
    -
    hasParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    hasResult() - -Method in class compbio.stat.collector.JobStat -
      -
    hasSignaled() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasStarted() - -Method in class compbio.stat.collector.JobStat -
      -
    hasTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    Deprecated.   -
    Hit - Class in compbio.pipeline._jpred
     
    Hit() - -Constructor for class compbio.pipeline._jpred.Hit -
      -
    Hit.EvalueComporator - Class in compbio.pipeline._jpred
     
    Hit.EvalueComporator() - -Constructor for class compbio.pipeline._jpred.Hit.EvalueComporator -
      -
    Hit.NumberComporator - Class in compbio.pipeline._jpred
     
    Hit.NumberComporator() - -Constructor for class compbio.pipeline._jpred.Hit.NumberComporator -
      -
    HttpCodeResponseServiceStatus - Class in compbio.stat.servlet
    This servlet checks the webservice coming as pathinfo and returns http code - as a reply.
    HttpCodeResponseServiceStatus() - -Constructor for class compbio.stat.servlet.HttpCodeResponseServiceStatus -
      -
    -
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    -
    -
    id - -Variable in class compbio.data.sequence.ScoreManager.ScoreHolder -
      -
    initPull() - -Method in class compbio.engine.FilePuller -
      -
    INPUT - -Static variable in class compbio.engine.client.SkeletalExecutable -
      -
    InputFilter - Class in compbio.stat.collector
     
    InputFilter() - -Constructor for class compbio.stat.collector.InputFilter -
      -
    IOHelper - Class in compbio.ws.client
     
    IOHelper() - -Constructor for class compbio.ws.client.IOHelper -
      -
    IS_CLUSTER_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    IS_LOCAL_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    isAbsolutePath(String) - -Static method in class compbio.engine.client.PathValidator -
    Whether a certain path is absolute or not is operation system dependent! -
    isAmbiguosProtein(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Check whether the sequence confirms to amboguous protein sequence -
    isClusterJob() - -Method in class compbio.stat.collector.JobStat -
      -
    isDefault() - -Method in class compbio.metadata.Limit -
      -
    isExceeded(List<FastaSequence>) - -Method in class compbio.metadata.Limit -
    Checks if the number of sequences or their average length in the dataset - exceeds this limit. -
    isFileCreated() - -Method in class compbio.engine.FilePuller -
      -
    isJavaLibrary(Class<?>) - -Static method in class compbio.engine.client.Util -
    Returns true of executableName.jar.file property has some value in the - Executable.properties file, false otherwise. -
    isMarked(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    isNonAmbNucleotideSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -
    isNucleotideSequence(FastaSequence) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    IsOperating - Class in compbio.data.msa.jaxws
     
    IsOperating() - -Constructor for class compbio.data.msa.jaxws.IsOperating -
      -
    isOperating(Services) - -Method in interface compbio.data.msa.RegistryWS -
    Check whether a particular web service is working on this server -
    isOperating(Services) - -Method in class compbio.ws.server.RegistryWS -
      -
    IsOperatingResponse - Class in compbio.data.msa.jaxws
     
    IsOperatingResponse() - -Constructor for class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isRequired() - -Method in class compbio.metadata.Option -
    Flag that indicated that this option must be specified in the command - line for an executable to run -
    isReturn() - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    isReturn() - -Method in class compbio.data.msa.jaxws.IsOperatingResponse -
      -
    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Please note this method closes the input stream provided as a parameter -
    isValidDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidJobId(String) - -Static method in class compbio.engine.client.Util -
      -
    IUPred - Class in compbio.runner.disorder
    iupred sequenceFile - - Maximum sequence length is 40000 chars.
    IUPred() - -Constructor for class compbio.runner.disorder.IUPred -
      -
    IUPRED_INFO - -Static variable in enum compbio.ws.client.Services -
      -
    IUPredWS - Class in compbio.ws.server
     
    IUPredWS() - -Constructor for class compbio.ws.server.IUPredWS -
      -
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    compbio.data._structure 
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.msa.jaxws 
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods - that work on the objects of this model.
    compbio.engine 
    compbio.engine.client 
    compbio.engine.cluster.drmaa 
    compbio.engine.cluster.dundee 
    compbio.engine.conf 
    compbio.engine.local 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project.
    compbio.pipeline._jpred 
    compbio.runnerUtilities commonly used by all runners.
    compbio.runner._impl 
    compbio.runner._jpred 
    compbio.runner.conservation 
    compbio.runner.disorder 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa)
    compbio.stat.collector 
    compbio.stat.servlet 
    compbio.stat.servlet.util 
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services.
    compbio.ws.server 
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