From 9d593e4828b2ce526a4e1fd1b11c8f78b112b5f5 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Fri, 12 Aug 2011 13:29:30 +0000 Subject: [PATCH] remove dm javadoc to update git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4505 e3abac25-378b-4346-85de-24260fe3988d --- website/dm_javadoc/allclasses-frame.html | 87 --- website/dm_javadoc/allclasses-noframe.html | 87 --- website/dm_javadoc/compbio/data/msa/MsaWS.html | 556 ------------- .../compbio/data/msa/class-use/MsaWS.html | 189 ----- .../dm_javadoc/compbio/data/msa/package-frame.html | 32 - .../compbio/data/msa/package-summary.html | 176 ----- .../dm_javadoc/compbio/data/msa/package-tree.html | 151 ---- .../dm_javadoc/compbio/data/msa/package-use.html | 171 ---- .../compbio/data/sequence/Alignment.html | 403 ---------- .../compbio/data/sequence/AlignmentMetadata.html | 329 -------- .../data/sequence/ClustalAlignmentUtil.html | 387 --------- .../compbio/data/sequence/FastaSequence.html | 471 ----------- 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c45a41e..0000000 --- a/website/dm_javadoc/allclasses-frame.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
Alignment -
-AlignmentMetadata -
-Argument -
-ChunkHolder -
-ClustalAlignmentUtil -
-FastaSequence -
-JobExecutionException -
-JobStatus -
-JobSubmissionException -
-Jws2Client -
-Limit -
-LimitExceededException -
-LimitsManager -
-MsaWS -
-Option -
-Parameter -
-Preset -
-PresetManager -
-Program -
-ResultNotAvailableException -
-RunnerConfig -
-SequenceUtil -
-Services -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WSTester -
-
- - - diff --git a/website/dm_javadoc/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html deleted file mode 100644 index 1120a19..0000000 --- a/website/dm_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
Alignment -
-AlignmentMetadata -
-Argument -
-ChunkHolder -
-ClustalAlignmentUtil -
-FastaSequence -
-JobExecutionException -
-JobStatus -
-JobSubmissionException -
-Jws2Client -
-Limit -
-LimitExceededException -
-LimitsManager -
-MsaWS -
-Option -
-Parameter -
-Preset -
-PresetManager -
-Program -
-ResultNotAvailableException -
-RunnerConfig -
-SequenceUtil -
-Services -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WSTester -
-
- - - 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 122814d..0000000 --- a/website/dm_javadoc/compbio/data/msa/MsaWS.html +++ /dev/null @@ -1,556 +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
-
-
-
public interface MsaWS<T>
- - -

-Multiple Sequence Alignment (MSA) Web Services Interface -

- -

-

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

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Stringalign(List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- booleancancelJob(String jobId) - -
-          Stop running the job jobId but leave its output untouched
- StringcustomAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- JobStatusgetJobStatus(String jobId) - -
-          Return the status of the job.
- 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
- AlignmentgetResult(String jobId) - -
-          Return the result of the job.
- RunnerConfig<T>getRunnerOptions() - -
-          Get options supported by a web service
- StringpresetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
- ChunkHolderpullExecStatistics(String jobId, - long position) - -
-          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
-  -

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

-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
-
-
-
- -

-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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - 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 2fd76ec..0000000 --- a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.data.msa.MsaWS - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.data.msa.MsaWS

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

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

- - - - - - - - - -
Methods in compbio.ws.client that return MsaWS
-static - - - - -
-<T> MsaWS<T>
-		Jws2Client.connect(String host, - Services service) - -
-          Connects to a web service by the host and the service name
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/package-frame.html b/website/dm_javadoc/compbio/data/msa/package-frame.html deleted file mode 100644 index 6228fea..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-frame.html +++ /dev/null @@ -1,32 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - -compbio.data.msa - - - - -
-Interfaces  - -
-MsaWS
- - - - 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 26b6877..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
- - - -
-

-Package compbio.data.msa -

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

-See: -
-          Description -

- - - - - - - - - -
-Interface Summary
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
-  - -

-

-Package compbio.data.msa Description -

- -

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

- -

-

-
Version:
-
1.0 April 2010
-
Author:
-
Peter Troshin
-
-
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/dm_javadoc/compbio/data/msa/package-tree.html b/website/dm_javadoc/compbio/data/msa/package-tree.html deleted file mode 100644 index 70a3ef3..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-tree.html +++ /dev/null @@ -1,151 +0,0 @@ - - - - - - -compbio.data.msa Class Hierarchy - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Hierarchy For Package compbio.data.msa -

-
-
-
Package Hierarchies:
All Packages
-
-

-Interface Hierarchy -

- -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/msa/package-use.html b/website/dm_javadoc/compbio/data/msa/package-use.html deleted file mode 100644 index 43e7f7c..0000000 --- a/website/dm_javadoc/compbio/data/msa/package-use.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - -Uses of Package compbio.data.msa - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Package
compbio.data.msa

-
- - - - - - - - - -
-Packages that use compbio.data.msa
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.ws.client
MsaWS - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - 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 5f14d30..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 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- 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
clone, finalize, 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
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html deleted file mode 100644 index 62c0b14..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 
-		 - -
- 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
clone, finalize, 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 
-		 - -
- 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/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index 3cbace7..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 
-		 - -
- 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(OutputStream outStream, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  - - - - - - - -
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-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(OutputStream outStream,
-                                         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:
outStream -
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/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index f7ead48..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
clone, finalize, 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 909a998..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
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-CLUSTAL

-
-public static final Program CLUSTAL
-
-
ClustalW -

-

-
-
-
- -

-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/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index de2bd93..0000000 --- a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,673 +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 -

- -

-

-
Version:
-
1.0
-
Author:
-
Petr 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 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>readFasta(InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-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
clone, equals, finalize, 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
-
-
-
- -

-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
-
-
-
- -

-closeSilently

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

-

-
Parameters:
log -
stream -
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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 6163110..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 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-UnknownFileFormatException

-
-public UnknownFileFormatException()
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(File file,
-                                  Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(String message,
-                                  Throwable cause)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(String message)
-
-
-
- -

-UnknownFileFormatException

-
-public UnknownFileFormatException(Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- 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 cfddffa..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- 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.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.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(OutputStream outStream, - Alignment alignment) - -
-          Write Clustal formatted alignment Limitations: does not record the - consensus.
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - 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 48f1339..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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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - 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 3fa8980..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 - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html deleted file mode 100644 index 4b31821..0000000 --- a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.FastaSequence - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.data.sequence.FastaSequence

-
- - - - - - - - - - - - - - - - - -
-Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
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.
- StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
-          Align a list of sequences with options.
- StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
-  -

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

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
- List<FastaSequence>Alignment.getSequences() - -
-           
-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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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

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

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

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that throw UnknownFileFormatException
-static AlignmentClustalAlignmentUtil.readClustalFile(File file) - -
-           
-static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) - -
-          Read Clustal formatted alignment.
-  -

-

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-Classes  - -
-Alignment -
-AlignmentMetadata -
-ClustalAlignmentUtil -
-FastaSequence -
-SequenceUtil
- - - - - - -
-Enums  - -
-Program
- - - - - - -
-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 1609e36..0000000 --- a/website/dm_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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-

-Package compbio.data.sequence -

-A data model for multiple sequence alignment web services and utility methods - that work on the objects of this model. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
AlignmentMultiple sequence alignment.
AlignmentMetadataAlignment metadata e.g.
ClustalAlignmentUtilTools to read and write clustal formated files
FastaSequenceA FASTA formatted sequence.
SequenceUtilUtility class for operations on sequences
-  - -

- - - - - - - - - -
-Enum Summary
ProgramThe list of programmes that can produce alignments
-  - -

- - - - - - - - - -
-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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-Hierarchy For Package compbio.data.sequence -

-
-
-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Enum Hierarchy -

- -
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-Uses of Package
compbio.data.sequence

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

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.sequence
Alignment - -
-          Multiple sequence alignment.
AlignmentMetadata - -
-          Alignment metadata e.g.
FastaSequence - -
-          A FASTA formatted sequence.
Program - -
-          The list of programmes that can produce alignments
UnknownFileFormatException - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.metadata
FastaSequence - -
-          A FASTA formatted sequence.
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/dm_javadoc/compbio/metadata/Argument.html b/website/dm_javadoc/compbio/metadata/Argument.html deleted file mode 100644 index b500d00..0000000 --- a/website/dm_javadoc/compbio/metadata/Argument.html +++ /dev/null @@ -1,327 +0,0 @@ - - - - - - -Argument - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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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
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- 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 c898bcc..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
clone, finalize, 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
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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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/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 1e83666..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
clone, equals, finalize, 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 8728f80..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
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-PENDING

-
-public static final JobStatus PENDING
-
-
Jobs which are in the queue and awaiting execution reported for cluster - jobs only -

-

-
-
-
- -

-RUNNING

-
-public static final JobStatus RUNNING
-
-
Jobs that are running -

-

-
-
-
- -

-CANCELLED

-
-public static final JobStatus CANCELLED
-
-
Jobs that has been cancelled -

-

-
-
-
- -

-FINISHED

-
-public static final JobStatus FINISHED
-
-
Finished jobs -

-

-
-
-
- -

-FAILED

-
-public static final JobStatus FAILED
-
-
Failed jobs -

-

-
-
-
- -

-UNDEFINED

-
-public static final JobStatus UNDEFINED
-
-
Represents jobs with unknown status -

-

-
-
-
- -

-STARTED

-
-public static final JobStatus STARTED
-
-
Job calculation has been started. First status reported by the local - engine -

-

-
-
-
- -

-SUBMITTED

-
-public static final JobStatus SUBMITTED
-
-
Job has been submitted. This status is only set for cluster jobs -

-

-
-
-
- -

-COLLECTED

-
-public static final JobStatus COLLECTED
-
-
Results has been collected -

-

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

-values

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

-

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

-valueOf

-
-public static JobStatus valueOf(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 59f457e..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
clone, equals, finalize, 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 51efd54..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
clone, finalize, 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 9fbf007..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
clone, equals, finalize, 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 52a8aaf..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
clone, equals, finalize, 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 7fc0e28..0000000 --- a/website/dm_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,822 +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
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-protected  StringdefaultValue - -
-           
-protected  Stringdescription - -
-           
-protected  URLfurtherDetails - -
-           
-protected  booleanisRequired - -
-           
-protected  Stringname - -
-           
-  - - - - - - - - - - -
-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
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
-  -

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

-description

-
-protected String description
-
-
-
-
-
- -

-name

-
-protected String name
-
-
-
-
-
- -

-isRequired

-
-protected boolean isRequired
-
-
-
-
-
- -

-furtherDetails

-
-protected URL furtherDetails
-
-
-
-
-
- -

-defaultValue

-
-protected String defaultValue
-
-
-
-
- - - - - - - - -
-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 7a54dc1..0000000 --- a/website/dm_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,590 +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
-
- -

- - - - - - - -
-Field Summary
-  - - - - - - - -
Fields inherited from class compbio.metadata.Option
defaultValue, description, furtherDetails, isRequired, name
-  - - - - - - - - - - -
-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
clone, finalize, 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 e42c70d..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
clone, finalize, 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 5ecd88a..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
clone, equals, finalize, 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 423c8b1..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
clone, equals, finalize, 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 0e8948a..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
clone, finalize, 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 dd5739b..0000000 --- a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.metadata -
    -Class UnsupportedRuntimeException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.UnsupportedRuntimeException
-
    -
    -
    All Implemented Interfaces:
    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
    clone, equals, finalize, 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 fbbe56c..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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    - - - -
    - -

    - -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
    clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -Integer

    -
    -public static final ValueConstrain.Type Integer
    -
    -
    -
    -
    -
    - -

    -Float

    -
    -public static final ValueConstrain.Type Float
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

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

    -

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

    -valueOf

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

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    IllegalArgumentException - if this enum type has no constant -with the specified name -
    NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 5968d9e..0000000 --- a/website/dm_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -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
    - - - -
    - -

    - -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
    clone, finalize, 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 f8703fe..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
    clone, equals, finalize, 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   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index 59618f6..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 c36b0c5..0000000 --- a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,182 +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. 
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa that return ChunkHolder
    - ChunkHolderMsaWS.pullExecStatistics(String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - - - - - - - - - - - -
    -Packages that use JobStatus
    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 JobStatus in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return JobStatus
    - JobStatusMsaWS.getJobStatus(String jobId) - -
    -          Return the status of the job.
    -  -

    - - - - - -
    -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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    - - - - - - - - - - - - - -
    -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.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

    - - - - - -
    -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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    -Uses of Class
    compbio.metadata.Limit

    -
    - - - - - - - - - - - - - -
    -Packages that use Limit
    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 Limit in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return Limit
    - Limit<T>MsaWS.getLimit(String presetName) - -
    -          Get a Limit for a preset.
    -  -

    - - - - - -
    -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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    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.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

    - - - - - -
    -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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    -Uses of Class
    compbio.metadata.LimitsManager

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa that return LimitsManager
    - LimitsManager<T>MsaWS.getLimits() - -
    -          List Limits supported by a web service.
    -  -

    -

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    -Packages that use Option
    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 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.
    -  -

    - - - - - -
    -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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    -
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    -Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    -  -

    - - - - - -
    -Uses of Parameter in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Parameter
    - 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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    -Uses of Class
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    -
    - - - - - - - - - - - - - -
    -Packages that use Preset
    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 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.
    -  -

    - - - - - -
    -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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    -Uses of Class
    compbio.metadata.PresetManager

    -
    - - - - - - - - - - - - - -
    -Packages that use PresetManager
    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 PresetManager in compbio.data.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa that return PresetManager
    - PresetManager<T>MsaWS.getPresets() - -
    -          Get presets supported by a web service
    -  -

    - - - - - -
    -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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    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.ResultNotAvailableException

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa that throw ResultNotAvailableException
    - 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.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>MsaWS.getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

    - - - - - -
    -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. 
    -  -

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    -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.
    - StringMsaWS.customAlign(List<FastaSequence> sequences, - List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

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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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    -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.
    - StringMsaWS.presetAlign(List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

    - - - - - -
    -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 6256e43..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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    - - - diff --git a/website/dm_javadoc/compbio/metadata/package-tree.html b/website/dm_javadoc/compbio/metadata/package-tree.html deleted file mode 100644 index 6de85dc..0000000 --- a/website/dm_javadoc/compbio/metadata/package-tree.html +++ /dev/null @@ -1,178 +0,0 @@ - - - - - - -compbio.metadata Class Hierarchy - - - - - - - - - - - - -
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    -Hierarchy For Package compbio.metadata -

    -
    -
    -
    Package Hierarchies:
    All Packages
    -
    -

    -Class Hierarchy -

    - -

    -Interface 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.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.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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    - - - -
    - -

    - -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 - - - - -
    -<T> MsaWS<T>
    -    		connect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name
    -static StringgetHost(String[] cmd) - -
    -          Extracts host name from the command line
    -static StringgetServiceName(String[] cmd) - -
    -          Extracts service name from the command line
    -static voidmain(String[] args) - -
    -          Starts command line client, if no parameter are supported print help.
    -static booleanvalidURL(String urlstr) - -
    -          Attempt to construct the URL object from the string
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -getServiceName

    -
    -public static String getServiceName(String[] cmd)
    -
    -
    Extracts service name from the command line -

    -

    -
    Parameters:
    cmd - command line options -
    Returns:
    service name or null if it is not defined
    -
    -
    -
    - -

    -getHost

    -
    -public static String getHost(String[] cmd)
    -
    -
    Extracts host name from the command line -

    -

    -
    Parameters:
    cmd - command line options -
    Returns:
    host name or null if it is not defined
    -
    -
    -
    - -

    -connect

    -
    -public static <T> MsaWS<T> connect(String host,
-                                   Services service)
-                        throws WebServiceException
    -
    -
    Connects to a web service by the host and the service name -

    -

    -
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - -
    Returns:
    MsaWS -
    Throws: -
    WebServiceException
    -
    -
    -
    - -

    -main

    -
    -public static void main(String[] args)
    -
    -
    Starts command line client, if no parameter are supported print help. Two - parameters are required for successfull 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!
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
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    - -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 1 -

    - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    ClustalWS - -
    -           
    MafftWS - -
    -           
    MuscleWS - -
    -           
    ProbconsWS - -
    -           
    TcoffeeWS - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static ServicesgetService(Class wsImplClass) - -
    -           
    -static ServicesgetService(String servName) - -
    -           
    -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
    clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -MafftWS

    -
    -public static final Services MafftWS
    -
    -
    -
    -
    -
    - -

    -MuscleWS

    -
    -public static final Services MuscleWS
    -
    -
    -
    -
    -
    - -

    -ClustalWS

    -
    -public static final Services ClustalWS
    -
    -
    -
    -
    -
    - -

    -TcoffeeWS

    -
    -public static final Services TcoffeeWS
    -
    -
    -
    -
    -
    - -

    -ProbconsWS

    -
    -public static final Services ProbconsWS
    -
    -
    -
    -
    - - - - - - - - -
    -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)
    -
    -
    -
    -
    -
    -
    - -

    -getService

    -
    -public static Services getService(Class wsImplClass)
    -
    -
    -
    -
    -
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    - - - -
    - - - diff --git a/website/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html deleted file mode 100644 index ce5d917..0000000 --- a/website/dm_javadoc/compbio/ws/client/WSTester.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -WSTester - - - - - - - - - - - - -
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    - -compbio.ws.client -
    -Class WSTester

    -
    -java.lang.Object
-  extended by compbio.ws.client.WSTester
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    public class WSTester
    extends Object
    - - -

    -Class for testing web services -

    - -

    -

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    Version:
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    1.0 February 2010
    -
    Author:
    -
    pvtroshin
    -
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    -Constructor Summary
    WSTester() - -
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-                 throws IOException
    -
    -
    Test JWS2 web services -

    -

    -
    Type Parameters:
    T - web service type
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    args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested -
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    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

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    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Services
    -static ServicesServices.getService(Class wsImplClass) - -
    -           
    -static ServicesServices.getService(String servName) - -
    -           
    -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 with parameters of type Services
    -static - - - - -
    -<T> MsaWS<T>
    -    		Jws2Client.connect(String host, - Services service) - -
    -          Connects to a web service by the host and the service name
    -  -

    -

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    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - -
    -Class Summary
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    WSTesterClass for testing web services
    -  - -

    - - - - - - - - - -
    -Enum Summary
    ServicesList of web services currently supported by JABAWS version 1
    -  - -

    -

    -Package compbio.ws.client Description -

    - -

    -A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. -

    - -

    -

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    1.0 April 2010
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    compbio.ws.clientA command line client and web services testing client for - JAva Bioinformatics Analysis Web Services. 
    -  -

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    AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Valid Amino acids -
    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(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 -
      -
    AMBIGUOUS_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Same as AA pattern but with two additional letters - XU -
    AMBIGUOUS_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Ambiguous nucleotide -
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
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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 -
      -
    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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    -
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    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 -
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    -
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    -
    name - -Variable in class compbio.metadata.Option -
      -
    newLimitExceeded(Limit<?>, List<FastaSequence>) - -Static method in exception compbio.metadata.LimitExceededException -
      -
    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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    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(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with preset. -
    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(String, long) - -Method in interface compbio.data.msa.MsaWS -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. -
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    readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Read Clustal formatted alignment. -
    readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    readFasta(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -
    Reads fasta sequences from inStream into the list of FastaSequence - objects -
    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 -
      -
    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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    -
    -
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 1
    setDefaultValue(String) - -Method in class compbio.metadata.Option -
    Sets one of the values defined in optionList as default. -
    setDefaultValue(String) - -Method in class compbio.metadata.Parameter -
      -
    setDescription(String) - -Method in class compbio.metadata.Option -
      -
    setDescription(String) - -Method in class compbio.metadata.Preset -
      -
    setFurtherDetails(URL) - -Method in class compbio.metadata.Option -
      -
    setMax(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setMin(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setName(String) - -Method in class compbio.metadata.Option -
      -
    setName(String) - -Method in class compbio.metadata.Preset -
      -
    setOptionName(String) - -Method in class compbio.metadata.Parameter -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Option -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setOptions(List<String>) - -Method in class compbio.metadata.Preset -
      -
    setOptions(List<Option<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Adds the list of options or parameters to the internal list of options -
    setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -
    Sets the list of parameters as internal list -
    setPossibleValues(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setPresets(List<Preset<T>>) - -Method in class compbio.metadata.PresetManager -
      -
    setPrmSeparator(String) - -Method in class compbio.metadata.RunnerConfig -
    Sets name value separator character -
    setRequired(boolean) - -Method in class compbio.metadata.Option -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.PresetManager -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.RunnerConfig -
    Set the name of a runner class -
    setType(ValueConstrain.Type) - -Method in class compbio.metadata.ValueConstrain -
      -
    setValidValue(ValueConstrain) - -Method in class compbio.metadata.Parameter -
      -
    setValue(String) - -Method in interface compbio.metadata.Argument -
    Set default values for the parameter or an option -
    setValue(String) - -Method in class compbio.metadata.Option -
      -
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    -
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    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.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 -
      -
    -
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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 -
      -
    -
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    -
    -
    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.Program -
    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.Program -
    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(String) - -Method in interface compbio.data.msa.MsaWS -
    Stop running the job jobId but leave its output untouched -
    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 -
      -
    cleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all whitespace chars in the sequence string -
    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 -
      -
    compbio.data.msa - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.ws.client - package compbio.ws.client
    A command line client and web services testing client for - JAva Bioinformatics Analysis Web Services.
    connect(String, Services) - -Static method in class compbio.ws.client.Jws2Client -
    Connects to a web service by the host and the service name -
    copyAndValidateRConfig(RunnerConfig<?>) - -Method in class compbio.metadata.RunnerConfig -
      -
    countMatchesInSequence(String, String) - -Static method in class compbio.data.sequence.FastaSequence -
      -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with options. -
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    WHITE_SPACE - -Static variable in class compbio.data.sequence.SequenceUtil -
    A whitespace character: [\t\n\x0B\f\r] -
    writeClustalAlignment(OutputStream, 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 -
      -
    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 -
      -
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - -Constructor for class compbio.ws.client.WSTester -
      -
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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 -
    defaultValue - -Variable in class compbio.metadata.Option -
      -
    description - -Variable in class compbio.metadata.Option -
      -
    DIGIT - -Static variable in class compbio.data.sequence.SequenceUtil -
    A digit -
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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.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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    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 -
    furtherDetails - -Variable in class compbio.metadata.Option -
      -
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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 exception compbio.metadata.LimitExceededException -
      -
    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 -
      -
    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 -
      -
    getHost(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Extracts host name from the command line -
    getId() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of id -
    getJobStatus(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the status of the job. -
    getLength() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getLimit(String) - -Method in interface compbio.data.msa.MsaWS -
    Get a Limit for a preset. -
    getLimitByName(String) - -Method in class compbio.metadata.LimitsManager -
      -
    getLimits() - -Method in interface compbio.data.msa.MsaWS -
    List Limits supported by a web service. -
    getLimits() - -Method in class compbio.metadata.LimitsManager -
      -
    getMax() - -Method in class compbio.metadata.ValueConstrain -
      -
    getMetadata() - -Method in class compbio.data.sequence.Alignment -
      -
    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 -
      -
    getNumberOfSequencesAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getOnelineFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getOptionName() - -Method in class compbio.metadata.Parameter -
      -
    getOptionNames() - -Method in class compbio.metadata.Option -
      -
    getOptions() - -Method in class compbio.metadata.Preset -
      -
    getOptions() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of the Options supported by the executable of type T -
    getParameters() - -Method in class compbio.metadata.RunnerConfig -
    Returns the list of parameters supported executable of type T. -
    getPossibleValues() - -Method in interface compbio.metadata.Argument -
      -
    getPossibleValues() - -Method in class compbio.metadata.Option -
    List of possible optionNames -
    getPossibleValues() - -Method in class compbio.metadata.Parameter -
    List is more convenient to work with -
    getPreset() - -Method in class compbio.metadata.Limit -
      -
    getPresetByName(String) - -Method in class compbio.metadata.PresetManager -
      -
    getPresets() - -Method in interface compbio.data.msa.MsaWS -
    Get presets supported by a web service -
    getPresets() - -Method in class compbio.metadata.PresetManager -
      -
    getPrmSeparator() - -Method in class compbio.metadata.RunnerConfig -
      -
    getProgram() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    getResult(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the result of the job. -
    getRunnerClassName() - -Method in class compbio.metadata.PresetManager -
      -
    getRunnerClassName() - -Method in class compbio.metadata.RunnerConfig -
      -
    getRunnerOptions() - -Method in interface compbio.data.msa.MsaWS -
    Get options supported by a web service -
    getSeqNumber() - -Method in class compbio.metadata.Limit -
      -
    getSequence() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of sequence -
    getSequenceLenghtActual() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequenceLenghtAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequences() - -Method in class compbio.data.sequence.Alignment -
      -
    getService(String) - -Static method in enum compbio.ws.client.Services -
      -
    getService(Class) - -Static method in enum compbio.ws.client.Services -
      -
    getServiceName(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Extracts service name from the command line -
    getSize() - -Method in class compbio.data.sequence.Alignment -
      -
    getType() - -Method in class compbio.metadata.ValueConstrain -
      -
    getValidValue() - -Method in class compbio.metadata.Parameter -
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    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.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 -
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    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 -
      -
    isProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isRequired - -Variable in class compbio.metadata.Option -
      -
    isRequired() - -Method in class compbio.metadata.Option -
    Flag that indicated that this option must be specified in the command - line for an executable to run -
    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Please note this method closes the input stream provided as a parameter -
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    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 -
      -
    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.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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    -Package compbio.data.sequence
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    -Class compbio.data.sequence.UnknownFileFormatException extends Exception implements Serializable
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    -Class compbio.metadata.JobSubmissionException extends Exception implements Serializable
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    -Class compbio.metadata.ResultNotAvailableException extends Exception implements Serializable
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    -Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
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