From: pvtroshin Date: Wed, 7 Dec 2011 12:04:26 +0000 (+0000) Subject: remove old datamodel javadoc X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;p=jabaws.git remove old datamodel javadoc git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4789 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/dm_javadoc/allclasses-frame.html b/website/dm_javadoc/allclasses-frame.html deleted file mode 100644 index 2e66516..0000000 --- a/website/dm_javadoc/allclasses-frame.html +++ /dev/null @@ -1,215 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
AAConClient -
-Align -
-Alignment -
-AlignmentMetadata -
-AlignResponse -
-Analize -
-AnalizeResponse -
-Argument -
-CancelJob -
-CancelJobResponse -
-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 -
-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/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html deleted file mode 100644 index 628249d..0000000 --- a/website/dm_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,215 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
AAConClient -
-Align -
-Alignment -
-AlignmentMetadata -
-AlignResponse -
-Analize -
-AnalizeResponse -
-Argument -
-CancelJob -
-CancelJobResponse -
-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 -
-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/JABAService.html b/website/dm_javadoc/compbio/data/msa/JABAService.html deleted file mode 100644 index 72b0491..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 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
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 c8e526c..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(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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 65733b3..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(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/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html deleted file mode 100644 index 303f784..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
- 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/dm_javadoc/compbio/data/msa/RegistryWS.html b/website/dm_javadoc/compbio/data/msa/RegistryWS.html deleted file mode 100644 index 601c1f4..0000000 --- a/website/dm_javadoc/compbio/data/msa/RegistryWS.html +++ /dev/null @@ -1,373 +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.
- DategetLastTestedOn(Services service) - -
-          The date and time the service has been verified to work last time
- 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.
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 228b45c..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
- 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/dm_javadoc/compbio/data/msa/class-use/JABAService.html b/website/dm_javadoc/compbio/data/msa/class-use/JABAService.html deleted file mode 100644 index 86701d0..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/JABAService.html +++ /dev/null @@ -1,230 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JABAService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-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(String host, - Services service) - -
-          Connects to a web service by the host and the service name web service - type
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html b/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html deleted file mode 100644 index 94b3610..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/JManagement.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.JManagement - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-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
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html b/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html deleted file mode 100644 index fac4b45..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/Metadata.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.Metadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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   -  - - - -
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html deleted file mode 100644 index 838168a..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.MsaWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.MsaWS

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - 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 be3d0ee..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(String host) - -
-          Get a connection of JABAWS registry
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html b/website/dm_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html deleted file mode 100644 index cb58108..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/SequenceAnnotation.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.SequenceAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - 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 34dc7f0..0000000 --- a/website/dm_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/dm_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/AlignResponse.html deleted file mode 100644 index cd5d7f0..0000000 --- a/website/dm_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/dm_javadoc/compbio/data/msa/jaxws/Analize.html b/website/dm_javadoc/compbio/data/msa/jaxws/Analize.html deleted file mode 100644 index e3ba140..0000000 --- a/website/dm_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
- -

-Analize

-
-public Analize()
-
-
- - - - - - - - -
-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 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html deleted file mode 100644 index 577ec9b..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/AnalizeResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -AnalizeResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/dm_javadoc/compbio/data/msa/jaxws/CancelJob.html deleted file mode 100644 index 6284435..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CancelJob.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJob - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html deleted file mode 100644 index eabec1d..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJobResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/dm_javadoc/compbio/data/msa/jaxws/CustomAlign.html deleted file mode 100644 index 1d15277..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CustomAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -CustomAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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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
-
-
-
- -

-getOptions

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

-setOptions

-
-public void setOptions(List<Option> options)
-
-
-
Parameters:
options - the value for the options 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/dm_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html deleted file mode 100644 index 3739a07..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CustomAlignResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/jaxws/CustomAnalize.html b/website/dm_javadoc/compbio/data/msa/jaxws/CustomAnalize.html deleted file mode 100644 index 9e175bb..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CustomAnalize.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -CustomAnalize - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/jaxws/CustomAnalizeResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/CustomAnalizeResponse.html deleted file mode 100644 index ddfae19..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/CustomAnalizeResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CustomAnalizeResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/jaxws/GetAnnotation.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetAnnotation.html deleted file mode 100644 index 40f4510..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetAnnotation.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/jaxws/GetAnnotationResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html deleted file mode 100644 index 9cacedc..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetAnnotationResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetAnnotationResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.data.msa.jaxws -
-Class GetAnnotationResponse

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.GetAnnotationResponse
-
-
-
-
public class GetAnnotationResponse
extends 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/jaxws/GetJobStatus.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetJobStatus.html deleted file mode 100644 index eb0b927..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 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTested.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTested.html deleted file mode 100644 index bb0bc27..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTested.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTested - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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) - -
-           
-  - - - - - - - -
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()
-
-
- -
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/GetLastTestedOn.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedOn.html deleted file mode 100644 index 64c5785..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedOn.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTestedOn - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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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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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html deleted file mode 100644 index 40c7ef6..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedOnResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTestedOnResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html deleted file mode 100644 index 7bfd667..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLastTestedResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLastTestedResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLimit.html deleted file mode 100644 index 252ecb9..0000000 --- a/website/dm_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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html deleted file mode 100644 index f856db2..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetLimits.html deleted file mode 100644 index 0df5e62..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimits.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetLimits - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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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- - - 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 e3b3815..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/data/msa/jaxws/GetPresets.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetPresets.html deleted file mode 100644 index 047ec67..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 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 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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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetJobId() - -
-           
- voidsetJobId(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 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 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/dm_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html deleted file mode 100644 index 5c5f7fa..0000000 --- a/website/dm_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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- - - -
- -

- -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
-  -

- - - - - - - - -
-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/GetSupportedServices.html b/website/dm_javadoc/compbio/data/msa/jaxws/GetSupportedServices.html deleted file mode 100644 index f351d95..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 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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 3e873c9..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/IsOperating.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -IsOperating - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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
-
-
-
- -

-setMessage

-
-public void setMessage(String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html deleted file mode 100644 index 45ed271..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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) - -
-           
- 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 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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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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
-  -

- - - - - - - - -
-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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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalize.html b/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalize.html deleted file mode 100644 index e1dbe9b..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalize.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAnalize - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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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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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html deleted file mode 100644 index 5bd80bc..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PresetAnalizeResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -PresetAnalizeResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html b/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html deleted file mode 100644 index bce24ab..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PullExecStatistics - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html b/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html deleted file mode 100644 index 631f047..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -PullExecStatisticsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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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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- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html b/website/dm_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html deleted file mode 100644 index c4c6b20..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -ResultNotAvailableExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetMessage() - -
-           
- voidsetMessage(String message) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-ResultNotAvailableExceptionBean

-
-public ResultNotAvailableExceptionBean()
-
-
- - - - - - - - -
-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
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public class TestAllServices
extends Object
- - -

-

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- - - - - - - - - - - -
-Constructor Summary
TestAllServices() - -
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-  - - - - - - - -
-Method Summary
-  - - - - - - - -
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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-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
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestAllServicesResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
-           
- voidsetReturn(String _return) - -
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-  - - - - - - - -
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 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
-
-
-
-
public class TestService
extends Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestService() - -
-           
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-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
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- - - - - - - - -
-Constructor Detail
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-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 Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
TestServiceResponse() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
- StringgetReturn() - -
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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
- -

-TestServiceResponse

-
-public TestServiceResponse()
-
-
- - - - - - - - -
-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 UnsupportedRuntimeExceptionBean

-
-java.lang.Object
-  extended by compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
-
-
-
-
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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- - - - - - - - - - - -
-Constructor Summary
UnsupportedRuntimeExceptionBean() - -
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Methods inherited from class java.lang.Object
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-Constructor Detail
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-UnsupportedRuntimeExceptionBean

-
-public UnsupportedRuntimeExceptionBean()
-
-
- - - - - - - - -
-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 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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- - - - - - - - - - - -
-Constructor Summary
WrongParameterExceptionBean() - -
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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
- -

-WrongParameterExceptionBean

-
-public WrongParameterExceptionBean()
-
-
- - - - - - - - -
-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.Align

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compbio.data.msa.jaxws.AlignResponse

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compbio.data.msa.jaxws.Analize

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compbio.data.msa.jaxws.AnalizeResponse

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-

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compbio.data.msa.jaxws.CancelJob

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compbio.data.msa.jaxws.CancelJobResponse

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-

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compbio.data.msa.jaxws.CustomAlign

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compbio.data.msa.jaxws.CustomAlignResponse

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compbio.data.msa.jaxws.GetAnnotationResponse

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compbio.data.msa.jaxws.GetJobStatus

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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.GetLimits

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compbio.data.msa.jaxws.GetLimitsResponse

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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.GetSupportedServices

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compbio.data.msa.jaxws.GetSupportedServicesResponse

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compbio.data.msa.jaxws.IsOperating

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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 -
-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 2a208c8..0000000 --- a/website/dm_javadoc/compbio/data/msa/jaxws/package-summary.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -compbio.data.msa.jaxws - - - - - - - - - - - - -
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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 
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
- - - - diff --git a/website/dm_javadoc/compbio/data/msa/package-summary.html b/website/dm_javadoc/compbio/data/msa/package-summary.html deleted file mode 100644 index 7c01954..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,198 +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
-  - -

-

-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.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
JABAService - -
-          This is a marker interface, contains no methods
JManagement - -
-           
Metadata - -
-           
-  -

- - - - - - - - - - - - - - -
-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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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html deleted file mode 100644 index f7d53a9..0000000 --- a/website/dm_javadoc/compbio/data/sequence/Alignment.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Alignment - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - 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 af9e57a..0000000 --- a/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -AlignmentMetadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.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
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index fd91235..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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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- 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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 7a7b854..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:
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/dm_javadoc/compbio/data/sequence/DisorderMethod.html b/website/dm_javadoc/compbio/data/sequence/DisorderMethod.html deleted file mode 100644 index 0029155..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:
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/dm_javadoc/compbio/data/sequence/FastaReader.html b/website/dm_javadoc/compbio/data/sequence/FastaReader.html deleted file mode 100644 index ff4b7f3..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:
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/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index 00d1300..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 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/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index e849381..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:
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/dm_javadoc/compbio/data/sequence/Range.html b/website/dm_javadoc/compbio/data/sequence/Range.html deleted file mode 100644 index 05cb2f8..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:
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/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/dm_javadoc/compbio/data/sequence/SMERFSConstraints.html deleted file mode 100644 index 61f386c..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:
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/dm_javadoc/compbio/data/sequence/Score.html b/website/dm_javadoc/compbio/data/sequence/Score.html deleted file mode 100644 index bd2db3b..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:
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>
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 f755ac1..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 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/dm_javadoc/compbio/data/sequence/ScoreManager.html b/website/dm_javadoc/compbio/data/sequence/ScoreManager.html deleted file mode 100644 index c97c0cd..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 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/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index 94308d4..0000000 --- a/website/dm_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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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/data/sequence/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html deleted file mode 100644 index 5cf30ca..0000000 --- a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - -UnknownFileFormatException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index bdac1a6..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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-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-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(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.
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html deleted file mode 100644 index c2950e9..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.AlignmentMetadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-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) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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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 7377442..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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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

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

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ConservationMethod.html b/website/dm_javadoc/compbio/data/sequence/class-use/ConservationMethod.html deleted file mode 100644 index f8d591b..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/ConservationMethod.html +++ /dev/null @@ -1,198 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.ConservationMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
-
-

-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/dm_javadoc/compbio/data/sequence/class-use/DisorderMethod.html b/website/dm_javadoc/compbio/data/sequence/class-use/DisorderMethod.html deleted file mode 100644 index 2e463f6..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/DisorderMethod.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.DisorderMethod - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-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.
-  -

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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

-
- - - - - - - - - - - - - - - - - - - - - -
-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
- 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.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) - -
-           
-  -

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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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-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
- 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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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(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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-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
- 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.
-  -

-

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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. 
-  -

- - - - - -
-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) - -
-           
-  -

-

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compbio.data.sequence.SequenceUtil

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

-

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-

-Uses of Class
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. 
-  -

- - - - - -
-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
-  -

-

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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 8bc97dc..0000000 --- a/website/dm_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,256 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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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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- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/package-tree.html b/website/dm_javadoc/compbio/data/sequence/package-tree.html deleted file mode 100644 index 38b2b26..0000000 --- a/website/dm_javadoc/compbio/data/sequence/package-tree.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - -compbio.data.sequence Class Hierarchy - - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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-Hierarchy For Package compbio.data.sequence -

-
-
-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Enum Hierarchy -

- -
- - - - - - - - - - - - - - - -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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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- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -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()
-
-
-
-
-
-
- -

-getDefaultValue

-
-String getDefaultValue()
-
-
-
-
-
-
- -

-getDescription

-
-String getDescription()
-
-
-
-
-
-
- -

-getName

-
-String getName()
-
-
-
-
-
-
- -

-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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html deleted file mode 100644 index a8bc319..0000000 --- a/website/dm_javadoc/compbio/metadata/ChunkHolder.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -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
- - - -
- -

- -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
-
-
- -

- - - - - - - - - - - -
-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()
-
-
-
-
-
-
- -

-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
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 39b1724..0000000 --- a/website/dm_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 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/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 702e9ab..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:
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/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index 37516c5..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:
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/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index e1147d1..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 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/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index 8df8034..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:
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/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index be6028b..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 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/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html deleted file mode 100644 index b766b8b..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 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/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index fa64862..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(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/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index b90fd64..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 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/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index 192067c..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 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
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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 d06f893..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:
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/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index 43dac79..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 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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    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index ffe5bde..0000000 --- a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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:
    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)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - 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 6e04bd5..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - -ValueConstrain.Type - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - 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
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 989474f..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
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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/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index fa9d8f7..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:
    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)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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    - - - -
    - - - 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 f612076..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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    - - - -
    -
    -

    -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 df6379d..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.ChunkHolder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -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(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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    -

    -Uses of Class
    compbio.metadata.JobExecutionException

    -
    -No usage of compbio.metadata.JobExecutionException -

    -

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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(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(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 b0afbfd..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
    - 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.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 3d9b576..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(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(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) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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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 23bb3d0..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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    -
    -

    -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
    - 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) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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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 a217dad..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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    -
    -

    -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 e1e5ccf..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
    - 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.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) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Parameter.html b/website/dm_javadoc/compbio/metadata/class-use/Parameter.html deleted file mode 100644 index f0ae514..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Parameter.html +++ /dev/null @@ -1,213 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.Parameter - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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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. 
    -  -

    - - - - - -
    -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
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Preset.html b/website/dm_javadoc/compbio/metadata/class-use/Preset.html deleted file mode 100644 index 49a12b9..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/Preset.html +++ /dev/null @@ -1,313 +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. 
    -  -

    - - - - - -
    -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) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -    		 - -
    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html b/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html deleted file mode 100644 index 6503e4d..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/PresetManager.html +++ /dev/null @@ -1,255 +0,0 @@ - - - - - - -Uses of Class compbio.metadata.PresetManager - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
    - - - -
    -
    -

    -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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    -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(String jobId) - -
    -          Return the result of the job.
    - AlignmentMsaWS.getResult(String jobId) - -
    -          Return the result of the job.
    -  -

    -

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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) - -
    -           
    - 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.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
    - 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.
    -  -

    -

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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(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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    -
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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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    compbio.metadata.WrongParameterException

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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. 
    -  -

    - - - - - -
    -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) - -
    -           
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    -Interfaces  - -
    -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 8cd2dc6..0000000 --- a/website/dm_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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    Package Hierarchies:
    All Packages
    -
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    -Class Hierarchy -

    - -

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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.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.
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - -
    - - - 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 7123695..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 
    -    		 - -
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    - 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 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(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 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/dm_javadoc/compbio/ws/client/IOHelper.html b/website/dm_javadoc/compbio/ws/client/IOHelper.html deleted file mode 100644 index 38097dd..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 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 67eb620..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 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/dm_javadoc/compbio/ws/client/MetadataHelper.html b/website/dm_javadoc/compbio/ws/client/MetadataHelper.html deleted file mode 100644 index 517e4bb..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 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 a4b2ec0..0000000 --- a/website/dm_javadoc/compbio/ws/client/Services.html +++ /dev/null @@ -1,508 +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 - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ServicesgetService(String servName) - -
    -           
    -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
    -
    -
    -
    -
    - - - - - - - - -
    -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)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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/ws/client/ServicesUtil.html b/website/dm_javadoc/compbio/ws/client/ServicesUtil.html deleted file mode 100644 index cdc6b40..0000000 --- a/website/dm_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 compbio.engine.client.Executable<?>>getRunnerByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesgetServiceByRunner(Class<compbio.engine.client.Executable<?>> runnerClassName) - -
    -           
    -static 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(Class<compbio.engine.client.Executable<?>> runnerClassName)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceImpl

    -
    -public static Class<? extends compbio.engine.client.Executable<?>> getServiceImpl(Services service)
    -
    -
    -
    -
    -
    -
    - -

    -getRunnerByJobDirectory

    -
    -public static Class<? extends compbio.engine.client.Executable<?>> getRunnerByJobDirectory(File jobdir)
    -
    -
    -
    -
    -
    -
    - -

    -getServiceByJobDirectory

    -
    -public static Services getServiceByJobDirectory(File jobdir)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html deleted file mode 100644 index 59e18de..0000000 --- a/website/dm_javadoc/compbio/ws/client/WSTester.html +++ /dev/null @@ -1,312 +0,0 @@ - - - - - - -WSTester - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    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 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
    -
    -
    - -

    - - - - - - - - - - - -
    -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
    -  -

    - - - - - - - - -
    -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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    -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
    - 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
    - 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() - -
    -           
    - 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) - -
    -           
    - 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.ws.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Services
    -static ServicesServices.getService(String servName) - -
    -           
    -static ServicesServicesUtil.getServiceByJobDirectory(File jobdir) - -
    -           
    -static ServicesServicesUtil.getServiceByRunner(Class<compbio.engine.client.Executable<?>> runnerClassName) - -
    -           
    -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 compbio.engine.client.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) - -
    -           
    -  -

    -

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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 -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -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

    -
    - - - - - - - - - - - - - - - - - -
    -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
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.client
    Services - -
    -          List of web services currently supported by JABAWS version 2
    -  -

    -

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    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.metadata.*
    - -

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    -public static final StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
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    -
    -
    AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Valid Amino acids -
    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
    asMap() - -Method in class compbio.data.sequence.ScoreManager -
      -
    asSet() - -Method in class compbio.data.sequence.ScoreManager -
      -
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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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    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 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
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    -
    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 -
      -
    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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    -
    -
    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.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<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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    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 -
      -
    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 -
    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 - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    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 -
    DisorderMethod - Enum in compbio.data.sequence
     
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    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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    -
    -
    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.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 -
    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.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<Executable<?>>) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    getServiceImpl(Services) - -Static method in class compbio.ws.client.ServicesUtil -
      -
    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 -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV LETTER  - NEXT LETTER - FRAMES   - NO FRAMES   -  - - - -
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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 -
      -
    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 -
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    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
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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 -
      -
    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.
    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.
    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services.
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