From: pvtroshin Date: Fri, 12 Aug 2011 13:02:22 +0000 (+0000) Subject: delete old javadoc to update X-Git-Url: http://source.jalview.org/gitweb/?p=jabaws.git;a=commitdiff_plain;h=5ca8c6a56369ea884670666cddcc5f1d3a09bc10 delete old javadoc to update git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4504 e3abac25-378b-4346-85de-24260fe3988d --- diff --git a/website/full_javadoc/allclasses-frame.html b/website/full_javadoc/allclasses-frame.html deleted file mode 100644 index 16054f8..0000000 --- a/website/full_javadoc/allclasses-frame.html +++ /dev/null @@ -1,309 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
Align -
-Alignment -
-AlignmentMetadata -
-AlignResponse -
-Argument -
-AsyncExecutor -
-AsyncJobRunner -
-AsyncLocalRunner -
-BlastAll -
-BlastParameters -
-BlastParser -
-CancelJob -
-CancelJobResponse -
-ChunkHolder -
-Cleaner -
-ClustalAlignmentUtil -
-ClustalW -
-ClustalWS -
-ClusterJobId -
-ClusterNativeSpecExecutable -
-ClusterSession -
-ClusterUtil -
-CommandBuilder -
-ConfExecutable -
-Configurator -
-ConfiguredExecutable -
-CustomAlign -
-CustomAlignResponse -
-DirectoryManager -
-Disembl -
-Environment -
-EnvVariableProcessor -
-Executable -
-Executable.ExecProvider -
-ExecutableWrapper -
-FastaSequence -
-FilePuller -
-GetJobStatus -
-GetJobStatusResponse -
-GetLimit -
-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetProgress -
-GetProgressResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-JnetAnnotation -
-Job -
-JobExecutionException -
-JobExecutionExceptionBean -
-JobRunner -
-JobStatus -
-JobSubmissionException -
-JobSubmissionExceptionBean -
-Jpred4 -
-JpredAnnotation -
-JpredResult -
-Jws2Client -
-Jws2Client.Services -
-Limit -
-LimitExceededException -
-LimitExceededExceptionBean -
-LimitsManager -
-LoadBalancer -
-LocalEngineUtil -
-LocalExecutorService -
-LocalRunner -
-Mafft -
-MafftWS -
-Mcl -
-MsaWS -
-Muscle -
-MuscleWS -
-NetNglyc -
-OB -
-Option -
-OptionCombinator -
-Pairwise -
-Parameter -
-PathValidator -
-PipedExecutable -
-Preset -
-PresetAlign -
-PresetAlignResponse -
-PresetManager -
-Probcons -
-ProbconsWS -
-Program -
-ProgressGetter -
-PropertyHelperManager -
-PScore -
-PSIBlast -
-PsiBlast -
-PulledFileCache -
-PullExecStatistics -
-PullExecStatisticsResponse -
-PullFile -
-PullFileResponse -
-ResultNotAvailableException -
-ResultNotAvailableExceptionBean -
-Ronn -
-RPSBlast -
-RunConfiguration -
-RunnerConfig -
-RunnerConfigMarshaller -
-Runners -
-SequenceUtil -
-SimpleWSPublisher -
-SkeletalExecutable -
-StatisticManager -
-StreamGobbler -
-SubmissionManager -
-SyncExecutor -
-Tcoffee -
-TcoffeeWS -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-UnsupportedRuntimeExceptionBean -
-Util -
-Util -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WrongParameterExceptionBean -
-WSTester -
-WSUtil -
-_DrmaaExample -
-_JobStatus -
-_Jpred -
-_Key -
-_NativeSpecHelper -
-_Queue -
-_QueueConstraints -
-_SkeletalCommandBuilder -
-_TrackingExecutor -
-
- - - diff --git a/website/full_javadoc/allclasses-noframe.html b/website/full_javadoc/allclasses-noframe.html deleted file mode 100644 index bad8588..0000000 --- a/website/full_javadoc/allclasses-noframe.html +++ /dev/null @@ -1,309 +0,0 @@ - - - - - - -All Classes - - - - - - - - - - - -All Classes -
- - - - - -
Align -
-Alignment -
-AlignmentMetadata -
-AlignResponse -
-Argument -
-AsyncExecutor -
-AsyncJobRunner -
-AsyncLocalRunner -
-BlastAll -
-BlastParameters -
-BlastParser -
-CancelJob -
-CancelJobResponse -
-ChunkHolder -
-Cleaner -
-ClustalAlignmentUtil -
-ClustalW -
-ClustalWS -
-ClusterJobId -
-ClusterNativeSpecExecutable -
-ClusterSession -
-ClusterUtil -
-CommandBuilder -
-ConfExecutable -
-Configurator -
-ConfiguredExecutable -
-CustomAlign -
-CustomAlignResponse -
-DirectoryManager -
-Disembl -
-Environment -
-EnvVariableProcessor -
-Executable -
-Executable.ExecProvider -
-ExecutableWrapper -
-FastaSequence -
-FilePuller -
-GetJobStatus -
-GetJobStatusResponse -
-GetLimit -
-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetProgress -
-GetProgressResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-JnetAnnotation -
-Job -
-JobExecutionException -
-JobExecutionExceptionBean -
-JobRunner -
-JobStatus -
-JobSubmissionException -
-JobSubmissionExceptionBean -
-Jpred4 -
-JpredAnnotation -
-JpredResult -
-Jws2Client -
-Jws2Client.Services -
-Limit -
-LimitExceededException -
-LimitExceededExceptionBean -
-LimitsManager -
-LoadBalancer -
-LocalEngineUtil -
-LocalExecutorService -
-LocalRunner -
-Mafft -
-MafftWS -
-Mcl -
-MsaWS -
-Muscle -
-MuscleWS -
-NetNglyc -
-OB -
-Option -
-OptionCombinator -
-Pairwise -
-Parameter -
-PathValidator -
-PipedExecutable -
-Preset -
-PresetAlign -
-PresetAlignResponse -
-PresetManager -
-Probcons -
-ProbconsWS -
-Program -
-ProgressGetter -
-PropertyHelperManager -
-PScore -
-PSIBlast -
-PsiBlast -
-PulledFileCache -
-PullExecStatistics -
-PullExecStatisticsResponse -
-PullFile -
-PullFileResponse -
-ResultNotAvailableException -
-ResultNotAvailableExceptionBean -
-Ronn -
-RPSBlast -
-RunConfiguration -
-RunnerConfig -
-RunnerConfigMarshaller -
-Runners -
-SequenceUtil -
-SimpleWSPublisher -
-SkeletalExecutable -
-StatisticManager -
-StreamGobbler -
-SubmissionManager -
-SyncExecutor -
-Tcoffee -
-TcoffeeWS -
-UnknownFileFormatException -
-UnsupportedRuntimeException -
-UnsupportedRuntimeExceptionBean -
-Util -
-Util -
-ValueConstrain -
-ValueConstrain.Type -
-WrongParameterException -
-WrongParameterExceptionBean -
-WSTester -
-WSUtil -
-_DrmaaExample -
-_JobStatus -
-_Jpred -
-_Key -
-_NativeSpecHelper -
-_Queue -
-_QueueConstraints -
-_SkeletalCommandBuilder -
-_TrackingExecutor -
-
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html deleted file mode 100644 index 7afbc88..0000000 --- a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JnetAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data._structure -
-Enum JnetAnnotation

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

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
JNETCONF - -
-           
JNETHMM - -
-           
jnetpred - -
-           
JNETPROPE - -
-           
JNETPROPH - -
-           
JNETSOL0 - -
-           
JNETSOL25 - -
-           
JNETSOL5 - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JnetAnnotationvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static JnetAnnotation[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-jnetpred

-
-public static final JnetAnnotation jnetpred
-
-
-
-
-
- -

-JNETCONF

-
-public static final JnetAnnotation JNETCONF
-
-
-
-
-
- -

-JNETSOL25

-
-public static final JnetAnnotation JNETSOL25
-
-
-
-
-
- -

-JNETSOL5

-
-public static final JnetAnnotation JNETSOL5
-
-
-
-
-
- -

-JNETSOL0

-
-public static final JnetAnnotation JNETSOL0
-
-
-
-
-
- -

-JNETHMM

-
-public static final JnetAnnotation JNETHMM
-
-
-
-
-
- -

-JNETPROPH

-
-public static final JnetAnnotation JNETPROPH
-
-
-
-
-
- -

-JNETPROPE

-
-public static final JnetAnnotation JNETPROPE
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

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

-

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

-valueOf

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

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html deleted file mode 100644 index d72000f..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html +++ /dev/null @@ -1,418 +0,0 @@ - - - - - - -JpredAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data._structure -
-Enum JpredAnnotation

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

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
JNETCONF - -
-           
JNETHMM - -
-           
jnetpred - -
-           
JNETPROPE - -
-           
JNETPROPH - -
-           
JNETSOL0 - -
-           
JNETSOL25 - -
-           
JNETSOL5 - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JpredAnnotationvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static JpredAnnotation[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-jnetpred

-
-public static final JpredAnnotation jnetpred
-
-
-
-
-
- -

-JNETCONF

-
-public static final JpredAnnotation JNETCONF
-
-
-
-
-
- -

-JNETSOL25

-
-public static final JpredAnnotation JNETSOL25
-
-
-
-
-
- -

-JNETSOL5

-
-public static final JpredAnnotation JNETSOL5
-
-
-
-
-
- -

-JNETSOL0

-
-public static final JpredAnnotation JNETSOL0
-
-
-
-
-
- -

-JNETHMM

-
-public static final JpredAnnotation JNETHMM
-
-
-
-
-
- -

-JNETPROPH

-
-public static final JpredAnnotation JNETPROPH
-
-
-
-
-
- -

-JNETPROPE

-
-public static final JpredAnnotation JNETPROPE
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

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

-

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

-valueOf

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

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/JpredResult.html b/website/full_javadoc/compbio/data/_structure/JpredResult.html deleted file mode 100644 index 904c222..0000000 --- a/website/full_javadoc/compbio/data/_structure/JpredResult.html +++ /dev/null @@ -1,260 +0,0 @@ - - - - - - -JpredResult - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data._structure -
-Class JpredResult

-
-java.lang.Object
-  extended by compbio.data._structure.JpredResult
-
-
-
-
public class JpredResult
extends java.lang.Object
- - -

-Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784, -

- -

-

-
Author:
-
pvtroshin
-
-
- -

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

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

-JpredResult

-
-public JpredResult()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html deleted file mode 100644 index db95c3b..0000000 --- a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Class compbio.data._structure.JnetAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.data._structure.JnetAnnotation

-
- - - - - - - - - -
-Packages that use JnetAnnotation
compbio.data._structure  
-  -

- - - - - -
-Uses of JnetAnnotation in compbio.data._structure
-  -

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html deleted file mode 100644 index fcae915..0000000 --- a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Class compbio.data._structure.JpredAnnotation - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.data._structure.JpredAnnotation

-
- - - - - - - - - -
-Packages that use JpredAnnotation
compbio.data._structure  
-  -

- - - - - -
-Uses of JpredAnnotation in compbio.data._structure
-  -

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

-

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-Package compbio.data._structure -

- - - - - - - - - -
-Class Summary
JpredResultJnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
-  - -

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-Enum Summary
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- -

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

-
-
Type Parameters:
T - executable type / web service type
-
-
All Known Implementing Classes:
ClustalWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
-
-
-
-
public interface MsaWS<T>
- - -

-Multiple Sequence Alignment (MSA) Web Services Interface -

- -

-

-
Author:
-
pvtroshin - - Date September 2009
-
-
- -

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

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

-align

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

-

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

-customAlign

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

-

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

-presetAlign

-
-java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                             Preset<T> preset)
-                             throws UnsupportedRuntimeException,
-                                    LimitExceededException,
-                                    JobSubmissionException,
-                                    WrongParameterException
-
-
Align a list of sequences with preset. @see 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. - This - exception is thrown when the job could not be submitted due - to the following reasons: 1) The number of sequences in the - submission or their average length is greater then defined by - the default Limit. 2) Any problems on the server side e.g. it - is misconfigured or malfunction, is reported via this - exception. In the first case the information on the limit - could be obtained from an exception. -
WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty -
UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JABAWS is deployed on Windows and Mafft - service is called -
LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
JobSubmissionException
-
-
-
- -

-getResult

-
-Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
-
-
Return the result of the job. -

-

-
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 is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException. -
java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format
-
-
-
- -

-cancelJob

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

-

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

-getJobStatus

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

-

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

-pullExecStatistics

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

-

-
Parameters:
jobId - - unique job identifier
position - - next position within the file to read -
Returns:
ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read -
Throws: -
java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in - invalid format and also if the position value is negative
-
-
-
- -

-getRunnerOptions

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

-

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

-getPresets

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

-

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

-getLimit

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

-

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

-getLimits

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

-

-
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:
LimitManager
-
-
- -
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-Uses of Interface
compbio.data.msa.MsaWS

-
- - - - - - - - - - - - - -
-Packages that use MsaWS
compbio.ws.client  
compbio.ws.server  
-  -

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

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

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

- - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.ws.server that implement MsaWS
- classClustalWS - -
-           
- classMafftWS - -
-           
- classMuscleWS - -
-           
- classProbconsWS - -
-           
- classTcoffeeWS - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html deleted file mode 100644 index b4181e3..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/Align.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -Align - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.msa.jaxws -
-Class Align

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

-

- -

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

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

-Align

-
-public Align()
-
-
- - - - - - - - -
-Method Detail
- -

-getFastaSequences

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

-setFastaSequences

-
-public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
-
-
-
Parameters:
fastaSequences - the value for the fastaSequences property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html deleted file mode 100644 index 1a50071..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -AlignResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class AlignResponse

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

-

- -

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

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

-AlignResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html deleted file mode 100644 index e858d81..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJob - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class CancelJob

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

-

- -

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

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

-CancelJob

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

-getJobId

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

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html deleted file mode 100644 index 69785d5..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CancelJobResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class CancelJobResponse

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

-

- -

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

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

-CancelJobResponse

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

-isReturn

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

-setReturn

-
-public void setReturn(boolean _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html deleted file mode 100644 index 838e512..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -CustomAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

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

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

-

- -

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

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

-CustomAlign

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

-getFastaSequences

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

-setFastaSequences

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

-getOptions

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

-setOptions

-
-public void setOptions(java.util.List<Option> options)
-
-
-
Parameters:
options - the value for the options property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html deleted file mode 100644 index a7d5cfe..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -CustomAlignResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class CustomAlignResponse

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

-

- -

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

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

-CustomAlignResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html deleted file mode 100644 index e4f1719..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetJobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetJobStatus

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

-

- -

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

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

-GetJobStatus

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

-getJobId

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

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html deleted file mode 100644 index 401d145..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetJobStatusResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetJobStatusResponse

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

-

- -

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

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

-GetJobStatusResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(JobStatus _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html deleted file mode 100644 index 3433200..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimit - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimit

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

-

- -

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

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

-GetLimit

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

-getPresetName

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

-setPresetName

-
-public void setPresetName(java.lang.String presetName)
-
-
-
Parameters:
presetName - the value for the presetName property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html deleted file mode 100644 index 5def54c..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class GetLimitResponse

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

-

- -

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

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

-GetLimitResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(Limit _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html deleted file mode 100644 index aa83b59..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - -GetLimits - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

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

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

-

- -

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

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

-GetLimits

-
-public GetLimits()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html deleted file mode 100644 index 04d2e7a..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetLimitsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetLimitsResponse

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

-

- -

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

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

-GetLimitsResponse

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

-getReturn

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

-setReturn

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

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

-

- -

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

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

-GetPresets

-
-public GetPresets()
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html deleted file mode 100644 index f5f62bb..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetPresetsResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

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

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

-

- -

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

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

-GetPresetsResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(PresetManager _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html deleted file mode 100644 index 97f3af9..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetProgress - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class GetProgress

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

-

- -

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

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

-GetProgress

-
-public GetProgress()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

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

-setJobId

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

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

-

- -

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

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

-GetProgressResponse

-
-public GetProgressResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

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

-setReturn

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

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

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

-

- -

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

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

-GetResult

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

-getJobId

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

-setJobId

-
-public void setJobId(java.lang.String jobId)
-
-
-
Parameters:
jobId - the value for the jobId property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html deleted file mode 100644 index e5da690..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -GetResultResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -compbio.data.msa.jaxws -
-Class GetResultResponse

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

-

- -

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

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

-GetResultResponse

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

-getReturn

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

-setReturn

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

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

-

- -

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

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

-GetRunnerOptions

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

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

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

-

- -

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

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

-GetRunnerOptionsResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(RunnerConfig _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html deleted file mode 100644 index 90a42af..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -JobExecutionExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- -

- -compbio.data.msa.jaxws -
-Class JobExecutionExceptionBean

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-JobExecutionExceptionBean

-
-public JobExecutionExceptionBean()
-
-
- - - - - - - - -
-Method Detail
- -

-getMessage

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

-setMessage

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

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

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-JobSubmissionExceptionBean

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

-getMessage

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

-setMessage

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

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

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-LimitExceededExceptionBean

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

-getActualNumberofSequences

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

-setActualNumberofSequences

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

-getMessage

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

-setMessage

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

-getNumberOfSequencesAllowed

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

-setNumberOfSequencesAllowed

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

-getSequenceLenghtActual

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

-setSequenceLenghtActual

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

-getSequenceLenghtAllowed

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

-setSequenceLenghtAllowed

-
-public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
-
-
-
Parameters:
sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html deleted file mode 100644 index 57cf5af..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PresetAlign - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

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

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

-

- -

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

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

-PresetAlign

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

-getFastaSequences

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

-setFastaSequences

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

-getPreset

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

-setPreset

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

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

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

-

- -

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

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

-PresetAlignResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(java.lang.String _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html deleted file mode 100644 index 1ab6ead..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PullExecStatistics - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

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

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

-

- -

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

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

-PullExecStatistics

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

-getJobId

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

-setJobId

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

-getPosition

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

-setPosition

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

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

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

-

- -

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

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

-PullExecStatisticsResponse

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

-getReturn

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

-setReturn

-
-public void setReturn(ChunkHolder _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html deleted file mode 100644 index ff92d78..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html +++ /dev/null @@ -1,311 +0,0 @@ - - - - - - -PullFile - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class PullFile

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

-

- -

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

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

-PullFile

-
-public PullFile()
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

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

-setJobId

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

-getPosition

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

-setPosition

-
-public void setPosition(long position)
-
-
-
Parameters:
position - the value for the position property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html deleted file mode 100644 index 966917b..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html +++ /dev/null @@ -1,272 +0,0 @@ - - - - - - -PullFileResponse - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class PullFileResponse

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

-

- -

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

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

-PullFileResponse

-
-public PullFileResponse()
-
-
- - - - - - - - -
-Method Detail
- -

-getReturn

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

-setReturn

-
-public void setReturn(ChunkHolder _return)
-
-
-
Parameters:
_return - the value for the _return property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html deleted file mode 100644 index 9f89492..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -ResultNotAvailableExceptionBean - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class ResultNotAvailableExceptionBean

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-ResultNotAvailableExceptionBean

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

-getMessage

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

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html deleted file mode 100644 index 1660fdf..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -UnsupportedRuntimeExceptionBean - - - - - - - - - - - - -
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- - - -
- -

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

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-UnsupportedRuntimeExceptionBean

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

-getMessage

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

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html deleted file mode 100644 index ecf51ab..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -WrongParameterExceptionBean - - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.msa.jaxws -
-Class WrongParameterExceptionBean

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

-This class was generated by the JAX-WS RI. - JAX-WS RI 2.1.7-hudson-48- - Generated source version: 2.1.7 -

- -

-

- -

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

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

-WrongParameterExceptionBean

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

-getMessage

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

-setMessage

-
-public void setMessage(java.lang.String message)
-
-
-
Parameters:
message - the value for the message property
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html deleted file mode 100644 index 63a3520..0000000 --- a/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.data.msa.jaxws.Align - - - - - - - - - - - - -
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-Uses of Class
compbio.data.msa.jaxws.Align

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

-

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

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

-

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compbio.data.msa.jaxws.CancelJob

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

-

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

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Class
compbio.data.msa.jaxws.CustomAlign

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

-

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

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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-Uses of Class
compbio.data.msa.jaxws.GetJobStatus

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

-

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

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

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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compbio.data.msa.jaxws.GetLimit

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

-

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compbio.data.msa.jaxws.GetLimitResponse

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

-

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

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

-

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compbio.data.msa.jaxws.GetLimitsResponse

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

-

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compbio.data.msa.jaxws.GetPresets

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

-

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compbio.data.msa.jaxws.GetPresetsResponse

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

-

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compbio.data.msa.jaxws.PullExecStatistics

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compbio.data.msa.jaxws.PullExecStatisticsResponse

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compbio.data.msa.jaxws.PullFile

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compbio.data.msa.jaxws.PullFileResponse

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-Classes  - -
-Align -
-AlignResponse -
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-CustomAlign -
-CustomAlignResponse -
-GetJobStatus -
-GetJobStatusResponse -
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-GetLimitResponse -
-GetLimits -
-GetLimitsResponse -
-GetPresets -
-GetPresetsResponse -
-GetProgress -
-GetProgressResponse -
-GetResult -
-GetResultResponse -
-GetRunnerOptions -
-GetRunnerOptionsResponse -
-JobExecutionExceptionBean -
-JobSubmissionExceptionBean -
-LimitExceededExceptionBean -
-PresetAlign -
-PresetAlignResponse -
-PullExecStatistics -
-PullExecStatisticsResponse -
-PullFile -
-PullFileResponse -
-ResultNotAvailableExceptionBean -
-UnsupportedRuntimeExceptionBean -
-WrongParameterExceptionBean
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-Package compbio.data.msa.jaxws -

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-Class Summary
Align 
AlignResponse 
CancelJob 
CancelJobResponse 
CustomAlign 
CustomAlignResponse 
GetJobStatus 
GetJobStatusResponse 
GetLimit 
GetLimitResponse 
GetLimits 
GetLimitsResponse 
GetPresets 
GetPresetsResponse 
GetProgress 
GetProgressResponse 
GetResult 
GetResultResponse 
GetRunnerOptions 
GetRunnerOptionsResponse 
JobExecutionExceptionBeanThis class was generated by the JAX-WS RI.
JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
PresetAlign 
PresetAlignResponse 
PullExecStatistics 
PullExecStatisticsResponse 
PullFile 
PullFileResponse 
ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
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- - - - diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html deleted file mode 100644 index 3cb53ac..0000000 --- a/website/full_javadoc/compbio/data/msa/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.data.msa - - - - - - - - - - - - -
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-Package compbio.data.msa -

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

-

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-Uses of Package
compbio.data.msa

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- - - - - - - - - - - - - -
-Packages that use compbio.data.msa
compbio.ws.client  
compbio.ws.server  
-  -

- - - - - - - - -
-Classes in compbio.data.msa used by compbio.ws.client
MsaWS - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
-  -

- - - - - - - - -
-Classes in compbio.data.msa used by compbio.ws.server
MsaWS - -
-          Multiple Sequence Alignment (MSA) Web Services Interface
-  -

-

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- - - diff --git a/website/full_javadoc/compbio/data/sequence/Alignment.html b/website/full_javadoc/compbio/data/sequence/Alignment.html deleted file mode 100644 index 8cad073..0000000 --- a/website/full_javadoc/compbio/data/sequence/Alignment.html +++ /dev/null @@ -1,381 +0,0 @@ - - - - - - -Alignment - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class Alignment

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

-Multiple sequence alignment. - - Does not give any guarantees on the content of individual FastaSequece - records. That is it does not guarantee that the neither the names of - sequences or the sequences themselves are unique. -

- -

-

-
Author:
-
pvtroshin - - Date September 2009
-
See Also:
FastaSequence, -AlignmentMetadata
-
- -

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

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

-Alignment

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

-Alignment

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

-getSequences

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

-getSize

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

-getMetadata

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

-toString

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

-equals

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

-

-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html deleted file mode 100644 index 6650404..0000000 --- a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html +++ /dev/null @@ -1,329 +0,0 @@ - - - - - - -AlignmentMetadata - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class AlignmentMetadata

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

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

- -

-

-
Author:
-
pvtroshin - - Date September 2009
-
-
- -

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

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

-AlignmentMetadata

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

-getProgram

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

-getGapchar

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

-equals

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

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
- -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html deleted file mode 100644 index c7fb25a..0000000 --- a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html +++ /dev/null @@ -1,385 +0,0 @@ - - - - - - -ClustalAlignmentUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.sequence -
-Class ClustalAlignmentUtil

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

-Tools to read and write clustal formated files -

- -

-

-
Author:
-
Petr Troshin based on jimp class - - Date September 2009
-
-
- -

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

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

-gapchar

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

-

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

-ClustalAlignmentUtil

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

-readClustalFile

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

-

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

-isValidClustalFile

-
-public static boolean isValidClustalFile(java.io.InputStream input)
-
-
-
Parameters:
input - -
Returns:
true if the file is recognised as Clustal formatted alignment, - false otherwise
-
-
-
- -

-writeClustalAlignment

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

-

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

-readClustalFile

-
-public static Alignment readClustalFile(java.io.File file)
-                                 throws UnknownFileFormatException,
-                                        java.io.IOException
-
-
- -
Throws: -
UnknownFileFormatException -
java.io.IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html deleted file mode 100644 index 07a1dcf..0000000 --- a/website/full_javadoc/compbio/data/sequence/FastaSequence.html +++ /dev/null @@ -1,448 +0,0 @@ - - - - - - -FastaSequence - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class FastaSequence

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

-A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it store 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 -

- -

-

-
Author:
-
pvtroshin - - Date September 2009
-
-
- -

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

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

-FastaSequence

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

-

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

-getId

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

-

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

-getSequence

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

-

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

-countMatchesInSequence

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

-getFormattedFasta

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

-getOnelineFasta

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

-getFormatedSequence

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

-

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

-getLength

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

-toString

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

-

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

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/Program.html b/website/full_javadoc/compbio/data/sequence/Program.html deleted file mode 100644 index 4c68bca..0000000 --- a/website/full_javadoc/compbio/data/sequence/Program.html +++ /dev/null @@ -1,388 +0,0 @@ - - - - - - -Program - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.data.sequence -
-Enum Program

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

-Programmes that can produce alignments -

- -

-

-
Author:
-
pvtroshin
-
-
- -

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

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

-CLUSTAL

-
-public static final Program CLUSTAL
-
-
ClustalW -

-

-
-
-
- -

-MAFFT

-
-public static final Program MAFFT
-
-
Mafft -

-

-
-
-
- -

-MUSCLE

-
-public static final Program MUSCLE
-
-
Muscle -

-

-
-
-
- -

-Tcoffee

-
-public static final Program Tcoffee
-
-
Tcoffee -

-

-
-
-
- -

-Probcons

-
-public static final Program Probcons
-
-
Probcons -

-

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

-values

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

-

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

-valueOf

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

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html deleted file mode 100644 index a7bdf1a..0000000 --- a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html +++ /dev/null @@ -1,624 +0,0 @@ - - - - - - -SequenceUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.data.sequence -
-Class SequenceUtil

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

-Utility class for operations on sequences -

- -

-

-
Author:
-
pvtroshin - - Date September 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static java.util.regex.PatternAA - -
-          Valid Amino acids
-static java.util.regex.PatternAMBIGUOUS_AA - -
-          Same as AA pattern but with two additional letters - XU
-static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE - -
-          Ambiguous nucleotide
-static java.util.regex.PatternDIGIT - -
-          A digit
-static java.util.regex.PatternNON_AA - -
-          inversion of AA pattern
-static java.util.regex.PatternNON_NUCLEOTIDE - -
-          Non nucleotide
-static java.util.regex.PatternNONWORD - -
-          Non word
-static java.util.regex.PatternNUCLEOTIDE - -
-          Nucleotides a, t, g, c, u
-static java.util.regex.PatternWHITE_SPACE - -
-          A whitespace character: [\t\n\x0B\f\r]
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static java.lang.StringcleanSequence(java.lang.String sequence) - -
-          Removes all whitespace chars in the sequence string
-static java.lang.StringdeepCleanSequence(java.lang.String sequence) - -
-          Removes all special characters and digits as well as whitespace chars - from the sequence
-static booleanisAmbiguosProtein(java.lang.String sequence) - -
-          Check whether the sequence confirms to amboguous protein sequence
-static booleanisNonAmbNucleotideSequence(java.lang.String sequence) - -
-          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char
-static booleanisNucleotideSequence(FastaSequence s) - -
-           
-static booleanisProteinSequence(java.lang.String sequence) - -
-           
-static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-static voidwriteFasta(java.io.OutputStream os, - java.util.List<FastaSequence> sequences) - -
-          Writes FastaSequence in the file, each sequence will take one line only
-static voidwriteFasta(java.io.OutputStream outstream, - java.util.List<FastaSequence> sequences, - int width) - -
-          Writes list of FastaSequeces into the outstream formatting the sequence - so that it contains width chars on each line
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-WHITE_SPACE

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

-

-
-
-
- -

-DIGIT

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

-

-
-
-
- -

-NONWORD

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

-

-
-
-
- -

-AA

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

-

-
-
-
- -

-NON_AA

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

-

-
-
-
- -

-AMBIGUOUS_AA

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

-

-
-
-
- -

-NUCLEOTIDE

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

-

-
-
-
- -

-AMBIGUOUS_NUCLEOTIDE

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

-

-
-
-
- -

-NON_NUCLEOTIDE

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

-

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

-isNucleotideSequence

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

-isNonAmbNucleotideSequence

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

-

-
-
-
-
- -

-cleanSequence

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

-

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

-deepCleanSequence

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

-

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

-isProteinSequence

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

-isAmbiguosProtein

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

-

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

-writeFasta

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

-

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

-readFasta

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

-

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

-writeFasta

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

-

-
Parameters:
os -
sequences - -
Throws: -
java.io.IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html deleted file mode 100644 index d45a4ea..0000000 --- a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - -UnknownFileFormatException - - - - - - - - - - - - -
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- - - - - - - - - - - - -
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- - - -
- -

- -compbio.data.sequence -
-Class UnknownFileFormatException

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

-

-
See Also:
Serialized Form
-
- -

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

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

-UnknownFileFormatException

-
-public UnknownFileFormatException()
-
-
-
- -

-UnknownFileFormatException

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

-UnknownFileFormatException

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

-UnknownFileFormatException

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

-UnknownFileFormatException

-
-public UnknownFileFormatException(java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html deleted file mode 100644 index af197d7..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html +++ /dev/null @@ -1,433 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Alignment - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-
-

-Uses of Class
compbio.data.sequence.Alignment

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Alignment
compbio.data.msa  
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.server  
-  -

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

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

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

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

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

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

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

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

- - - - - -
-Uses of Alignment in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return Alignment
-static AlignmentUtil.readClustalFile(java.lang.String workDirectory, - java.lang.String clustFile) - -
-           
-  -

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

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner.msa that return Alignment
- AlignmentTcoffee.getResults(java.lang.String workDirectory) - -
-           
- AlignmentClustalW.getResults(java.lang.String workDirectory) - -
-           
- AlignmentProbcons.getResults(java.lang.String workDirectory) - -
-           
- AlignmentMuscle.getResults(java.lang.String workDirectory) - -
-           
- AlignmentMafft.getResults(java.lang.String workDirectory) - -
-           
-  -

- - - - - -
-Uses of Alignment in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.ws.server that return Alignment
- AlignmentTcoffeeWS.getResult(java.lang.String jobId) - -
-           
- AlignmentProbconsWS.getResult(java.lang.String jobId) - -
-           
- AlignmentMuscleWS.getResult(java.lang.String jobId) - -
-           
- AlignmentMafftWS.getResult(java.lang.String jobId) - -
-           
- AlignmentClustalWS.getResult(java.lang.String jobId) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html deleted file mode 100644 index efa449b..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html +++ /dev/null @@ -1,196 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.AlignmentMetadata - - - - - - - - - - - - -
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- - - - - - - - - - - - -
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-		 - -
- 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 - Classes in this package have no dependencies to other sources in the project. 
-  -

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

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

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

-

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-Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

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

-

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

-Uses of Class
compbio.data.sequence.FastaSequence

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use FastaSequence
compbio.data.msa  
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.engine  
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.pipeline._jpred  
compbio.runnerUtilities commonly used by all runners. 
compbio.ws.server  
-  -

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

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.data.msa with type arguments of type FastaSequence
- java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
-          Align a list of sequences with default settings.
- java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
-          Align a list of sequences with options.
- java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
-          Align a list of sequences with preset.
-  -

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

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

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

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

- - - - - - - - - - - - - -
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
- java.util.List<FastaSequence>Alignment.getSequences() - -
-           
-static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.InputStream inStream) - -
-          Reads fasta sequences from inStream into the list of FastaSequence - objects
-  -

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

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

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

- - - - - -
-Uses of FastaSequence in compbio.engine
-  -

- - - - - - - - - - - - - -
Method parameters in compbio.engine with type arguments of type FastaSequence
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-  -

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

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

- - - - - -
-Uses of FastaSequence in compbio.pipeline._jpred
-  -

- - - - - - - - -
Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence
Pairwise(java.util.List<FastaSequence> sequences) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.runner
-  -

- - - - - - - - - -
Method parameters in compbio.runner with type arguments of type FastaSequence
-static voidUtil.writeInput(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
-           
-  -

- - - - - -
-Uses of FastaSequence in compbio.ws.server
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.ws.server with type arguments of type FastaSequence
- java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) - -
-           
- java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) - -
-           
- java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) - -
-           
- java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) - -
-           
- java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) - -
-           
-static - - - - -
-<T> java.lang.String
-		WSUtil.align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
-           
- java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
-           
- java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
-           
- java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
-           
- java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
-           
- java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
-           
- java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
-           
- java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
-           
- java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
-           
- java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
-           
- java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
-           
-static voidWSUtil.validateFastaInput(java.util.List<FastaSequence> sequences) - -
-           
-  -

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-Uses of Class
compbio.data.sequence.Program

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

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

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

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

-

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compbio.data.sequence.SequenceUtil

-
-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 - Classes in this package have no dependencies to other sources in the project. 
compbio.runnerUtilities commonly used by all runners. 
-  -

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

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

- - - - - -
-Uses of UnknownFileFormatException in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that throw UnknownFileFormatException
-static AlignmentUtil.readClustalFile(java.lang.String workDirectory, - java.lang.String clustFile) - -
-           
-  -

-

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-Classes  - -
-Alignment -
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-ClustalAlignmentUtil -
-FastaSequence -
-SequenceUtil
- - - - - - -
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- - - - - - -
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-UnknownFileFormatException
- - - - diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html deleted file mode 100644 index 04cec6a..0000000 --- a/website/full_javadoc/compbio/data/sequence/package-summary.html +++ /dev/null @@ -1,223 +0,0 @@ - - - - - - -compbio.data.sequence - - - - - - - - - - - - -
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-Package compbio.data.sequence -

-A data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. -

-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
ProgramProgrammes that can produce alignments
-  - -

- - - - - - - - - -
-Exception Summary
UnknownFileFormatException 
-  - -

-

-Package compbio.data.sequence Description -

- -

-A 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 Jalview Web Services v2. -

- -

-

-
Author:
-
Petr Troshin - - Date January 2010
-
-
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-Hierarchy For Package compbio.data.sequence -

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Package Hierarchies:
All Packages
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-Class Hierarchy -

- -

-Enum Hierarchy -

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-Uses of Package
compbio.data.sequence

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use compbio.data.sequence
compbio.data.msa  
compbio.data.msa.jaxws  
compbio.data.sequenceA data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.engine  
compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
compbio.pipeline._jpred  
compbio.runnerUtilities commonly used by all runners. 
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.ws.server  
-  -

- - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
-  -

- - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.data.msa.jaxws
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 - -
-          Programmes that can produce alignments
UnknownFileFormatException - -
-           
-  -

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

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

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

- - - - - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
UnknownFileFormatException - -
-           
-  -

- - - - - - - - -
-Classes in compbio.data.sequence used by compbio.runner.msa
Alignment - -
-          Multiple sequence alignment.
-  -

- - - - - - - - - - - -
-Classes in compbio.data.sequence used by compbio.ws.server
Alignment - -
-          Multiple sequence alignment.
FastaSequence - -
-          A FASTA formatted sequence.
-  -

-

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

- -compbio.engine -
-Interface AsyncExecutor

-
-
All Known Implementing Classes:
AsyncJobRunner, AsyncLocalRunner
-
-
-
-
public interface AsyncExecutor
- - -

-An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface. - Implementation agnostic. Executables can be run either locally to the JVM or on the cluster. -

- -

-

-
Author:
-
pvtroshin - Date October 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(java.lang.String jobId) - -
-          Stop running job.
- booleancleanup(java.lang.String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(java.lang.String jobId) - -
-          Query the status of the job
- ConfiguredExecutable<?>getResults(java.lang.String jobId) - -
-          Retrieve the results of the job.
- java.lang.StringgetWorkDirectory(java.lang.String jobId) - -
-           
- java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  -

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

-submitJob

-
-java.lang.String submitJob(ConfiguredExecutable<?> executable)
-                           throws JobSubmissionException
-
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-getResults

-
-ConfiguredExecutable<?> getResults(java.lang.String jobId)
-                                   throws ResultNotAvailableException
-
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Parameters:
jobId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
-
- -

-getWorkDirectory

-
-java.lang.String getWorkDirectory(java.lang.String jobId)
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
-
- -

-cleanup

-
-boolean cleanup(java.lang.String jobId)
-
-
Remove all files and a job directory for a jobid. -

-

-
Parameters:
jobId - -
Returns:
true if job directory was successfully removed, false otherwise.
-
-
-
- -

-cancelJob

-
-boolean cancelJob(java.lang.String jobId)
-
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

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

-

-
Parameters:
String - jobId - unique job identifier -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/Cleaner.html b/website/full_javadoc/compbio/engine/Cleaner.html deleted file mode 100644 index f5a3e89..0000000 --- a/website/full_javadoc/compbio/engine/Cleaner.html +++ /dev/null @@ -1,278 +0,0 @@ - - - - - - -Cleaner - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class Cleaner

-
-java.lang.Object
-  extended by compbio.engine.Cleaner
-
-
-
-
public class Cleaner
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Cleaner() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static booleandeleteAllFiles(java.lang.String directory) - -
-           
-static booleandeleteFiles(ConfiguredExecutable<?> exec) - -
-          This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-Cleaner

-
-public Cleaner()
-
-
- - - - - - - - -
-Method Detail
- -

-deleteFiles

-
-public static boolean deleteFiles(ConfiguredExecutable<?> exec)
-
-
This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -

-

-
Parameters:
workDirectory -
files - -
Returns:
-
-
-
- -

-deleteAllFiles

-
-public static boolean deleteAllFiles(java.lang.String directory)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html deleted file mode 100644 index cedced1..0000000 --- a/website/full_javadoc/compbio/engine/ClusterJobId.html +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - -ClusterJobId - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class ClusterJobId

-
-java.lang.Object
-  extended by compbio.engine.ClusterJobId
-
-
-
-
@Immutable
-public class ClusterJobId
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ClusterJobId(java.lang.String jobId) - -
-           
-  - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetJobId() - -
-           
- inthashCode() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait
-  -

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

-ClusterJobId

-
-public ClusterJobId(java.lang.String jobId)
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

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

-hashCode

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

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html deleted file mode 100644 index 61bbed4..0000000 --- a/website/full_javadoc/compbio/engine/Configurator.html +++ /dev/null @@ -1,538 +0,0 @@ - - - - - - -Configurator - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class Configurator

-
-java.lang.Object
-  extended by compbio.engine.Configurator
-
-
-
-
public class Configurator
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static java.lang.StringCLUSTER_WORK_DIRECTORY - -
-           
-static booleanIS_CLUSTER_ENGINE_ENABLED - -
-           
-static booleanIS_LOCAL_ENGINE_ENABLED - -
-           
-static java.lang.StringLOCAL_WORK_DIRECTORY - -
-           
-  - - - - - - - - - - -
-Constructor Summary
Configurator() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		configureExecutable(Executable<T> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorgetAsyncEngine(java.lang.String taskId) - -
-           
-static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static java.lang.StringgetWorkDirectory(java.lang.String taskId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-IS_LOCAL_ENGINE_ENABLED

-
-public static final boolean IS_LOCAL_ENGINE_ENABLED
-
-
-
-
-
- -

-IS_CLUSTER_ENGINE_ENABLED

-
-public static final boolean IS_CLUSTER_ENGINE_ENABLED
-
-
-
-
-
- -

-LOCAL_WORK_DIRECTORY

-
-public static final java.lang.String LOCAL_WORK_DIRECTORY
-
-
-
-
-
- -

-CLUSTER_WORK_DIRECTORY

-
-public static final java.lang.String CLUSTER_WORK_DIRECTORY
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-Configurator

-
-public Configurator()
-
-
- - - - - - - - -
-Method Detail
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              java.util.List<FastaSequence> dataSet)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-configureExecutable

-
-public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
-                                                              Executable.ExecProvider provider)
-                                                   throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable,
-                                           Executable.ExecProvider provider)
-
-
-
-
-
-
- -

-getSyncEngine

-
-public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable,
-                                         Executable.ExecProvider provider)
-                                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable)
-
-
-
-
-
-
- -

-getAsyncEngine

-
-public static AsyncExecutor getAsyncEngine(java.lang.String taskId)
-
-
-
-
-
-
- -

-getSyncEngine

-
-public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
-                                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getWorkDirectory

-
-public static java.lang.String getWorkDirectory(java.lang.String taskId)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/FilePuller.html b/website/full_javadoc/compbio/engine/FilePuller.html deleted file mode 100644 index 5a017ae..0000000 --- a/website/full_javadoc/compbio/engine/FilePuller.html +++ /dev/null @@ -1,551 +0,0 @@ - - - - - - -FilePuller - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class FilePuller

-
-java.lang.Object
-  extended by compbio.engine.FilePuller
-
-
-
All Implemented Interfaces:
java.lang.Comparable<java.util.concurrent.Delayed>, java.util.concurrent.Delayed
-
-
-
-
public class FilePuller
extends java.lang.Object
implements java.util.concurrent.Delayed
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(java.util.concurrent.Delayed o) - -
-           
- voiddisconnect() - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- longgetDelay(java.util.concurrent.TimeUnit unit) - -
-           
- java.lang.StringgetFile() - -
-           
- bytegetProgress() - -
-           
- inthashCode() - -
-           
- booleanhasMoreData() - -
-           
- voidinitPull() - -
-           
- booleanisFileCreated() - -
-           
-static FilePullernewFilePuller(java.lang.String file, - int chunkSize) - -
-           
-static FilePullernewProgressPuller(java.lang.String file) - -
-          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
- ChunkHolderpull(long position) - -
-           
- java.lang.StringtoString() - -
-           
- voidwaitForFile(long maxWaitSeconds) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-newFilePuller

-
-public static FilePuller newFilePuller(java.lang.String file,
-                                       int chunkSize)
-
-
-
-
-
-
-
-
-
- -

-newProgressPuller

-
-public static FilePuller newProgressPuller(java.lang.String file)
-
-
Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. Intended to be used in conjunction with a tool - which output progress as a percent value from 0 to 100. In any cases - progress could not be more than the largest byte value 255. -

-

-
-
-
-
Parameters:
file - -
Returns:
-
-
-
- -

-pull

-
-public ChunkHolder pull(long position)
-                 throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-initPull

-
-public void initPull()
-
-
-
-
-
-
-
-
-
- -

-getFile

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

-isFileCreated

-
-public boolean isFileCreated()
-
-
-
-
-
-
-
-
-
- -

-waitForFile

-
-public void waitForFile(long maxWaitSeconds)
-
-
-
-
-
-
-
-
-
- -

-hasMoreData

-
-public boolean hasMoreData()
-                    throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-compareTo

-
-public int compareTo(java.util.concurrent.Delayed o)
-
-
-
Specified by:
compareTo in interface java.lang.Comparable<java.util.concurrent.Delayed>
-
-
-
-
-
-
- -

-getDelay

-
-public long getDelay(java.util.concurrent.TimeUnit unit)
-
-
-
Specified by:
getDelay in interface java.util.concurrent.Delayed
-
-
-
-
-
-
- -

-disconnect

-
-public void disconnect()
-
-
-
-
-
-
-
-
-
- -

-toString

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

-equals

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

-hashCode

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

-getProgress

-
-public byte getProgress()
-                 throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/Job.html b/website/full_javadoc/compbio/engine/Job.html deleted file mode 100644 index dc4790d..0000000 --- a/website/full_javadoc/compbio/engine/Job.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - -Job - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class Job

-
-java.lang.Object
-  extended by compbio.engine.Job
-
-
-
-
@Immutable
-public final class Job
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Job(java.lang.String taskId, - java.lang.String jobId, - ConfiguredExecutable<?> cexecutable) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
-static JobgetByJobId(java.lang.String jobId, - java.util.List<Job> jobs) - -
-           
-static JobgetByTaskId(java.lang.String taskId, - java.util.List<Job> jobs) - -
-           
- ConfiguredExecutable<?>getConfExecutable() - -
-           
- ClusterJobIdgetJobId() - -
-           
- java.lang.StringgetTaskId() - -
-           
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-Job

-
-public Job(java.lang.String taskId,
-           java.lang.String jobId,
-           ConfiguredExecutable<?> cexecutable)
-
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public ClusterJobId getJobId()
-
-
-
-
-
-
- -

-getTaskId

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

-getConfExecutable

-
-public ConfiguredExecutable<?> getConfExecutable()
-
-
-
-
-
-
- -

-hashCode

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

-equals

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

-toString

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

-getByTaskId

-
-public static Job getByTaskId(java.lang.String taskId,
-                              java.util.List<Job> jobs)
-
-
-
-
-
-
- -

-getByJobId

-
-public static Job getByJobId(java.lang.String jobId,
-                             java.util.List<Job> jobs)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/LoadBalancer.html b/website/full_javadoc/compbio/engine/LoadBalancer.html deleted file mode 100644 index eb3b1d9..0000000 --- a/website/full_javadoc/compbio/engine/LoadBalancer.html +++ /dev/null @@ -1,247 +0,0 @@ - - - - - - -LoadBalancer - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine -
-Class LoadBalancer

-
-java.lang.Object
-  extended by compbio.engine.LoadBalancer
-
-
-
-
public class LoadBalancer
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - - - - - - -
-Method Summary
-static Executable.ExecProvidergetEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		getEngine(Executable<V> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-getEngine

-
-public static Executable.ExecProvider getEngine(Executable<?> executable)
-
-
-
-
-
-
- -

-getEngine

-
-public static <T,V> Executable.ExecProvider getEngine(Executable<V> executable,
-                                                      java.util.List<FastaSequence> dataSet)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/ProgressGetter.html b/website/full_javadoc/compbio/engine/ProgressGetter.html deleted file mode 100644 index 93c4cd3..0000000 --- a/website/full_javadoc/compbio/engine/ProgressGetter.html +++ /dev/null @@ -1,273 +0,0 @@ - - - - - - -ProgressGetter - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine -
-Class ProgressGetter

-
-java.lang.Object
-  extended by compbio.engine.ProgressGetter
-
-
-
-
public class ProgressGetter
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
ProgressGetter() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static bytegetProgress(java.lang.String progressFile) - -
-           
-static ChunkHolderpull(java.lang.String file, - long position) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-ProgressGetter

-
-public ProgressGetter()
-
-
- - - - - - - - -
-Method Detail
- -

-pull

-
-public static final ChunkHolder pull(java.lang.String file,
-                                     long position)
-
-
-
-
-
-
- -

-getProgress

-
-public static final byte getProgress(java.lang.String progressFile)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/PulledFileCache.html b/website/full_javadoc/compbio/engine/PulledFileCache.html deleted file mode 100644 index 0d11dcf..0000000 --- a/website/full_javadoc/compbio/engine/PulledFileCache.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - -PulledFileCache - - - - - - - - - - - - -
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- -

- -compbio.engine -
-Class PulledFileCache

-
-java.lang.Object
-  extended by compbio.engine.PulledFileCache
-
-
-
-
public final class PulledFileCache
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PulledFileCache() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static FilePullerget(java.lang.String fileName) - -
-           
-static booleanput(FilePuller fpuller) - -
-          This method allows duplicates to be added.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-PulledFileCache

-
-public PulledFileCache()
-
-
- - - - - - - - -
-Method Detail
- -

-get

-
-public static FilePuller get(java.lang.String fileName)
-
-
-
-
-
-
- -

-put

-
-public static boolean put(FilePuller fpuller)
-
-
This method allows duplicates to be added. This is a responsibility of - the called to ensure this will not happen! -

-

-
Parameters:
fpuller - -
Returns:
-
-
- -
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- - - diff --git a/website/full_javadoc/compbio/engine/SubmissionManager.html b/website/full_javadoc/compbio/engine/SubmissionManager.html deleted file mode 100644 index 9a83cd7..0000000 --- a/website/full_javadoc/compbio/engine/SubmissionManager.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -SubmissionManager - - - - - - - - - - - - -
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- -

- -compbio.engine -
-Class SubmissionManager

-
-java.lang.Object
-  extended by compbio.engine.SubmissionManager
-
-
-
-
public class SubmissionManager
extends java.lang.Object
- - -

-Submit jobs for execution -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static voidaddTask(ConfiguredExecutable<?> executable, - java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
-           
-static java.util.concurrent.Future<ConfiguredExecutable<?>>getTask(java.lang.String taskId) - -
-           
-static voidremoveTask(ConfiguredExecutable<?> executable) - -
-           
-static voidremoveTask(java.lang.String key) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-addTask

-
-public static void addTask(ConfiguredExecutable<?> executable,
-                           java.util.concurrent.Future<ConfiguredExecutable<?>> future)
-
-
-
-
-
-
- -

-getTask

-
-public static java.util.concurrent.Future<ConfiguredExecutable<?>> getTask(java.lang.String taskId)
-
-
-
-
-
-
- -

-removeTask

-
-public static void removeTask(ConfiguredExecutable<?> executable)
-
-
-
-
-
-
- -

-removeTask

-
-public static void removeTask(java.lang.String key)
-
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- -

- -compbio.engine -
-Interface SyncExecutor

-
-
All Known Implementing Classes:
JobRunner, LocalRunner
-
-
-
-
public interface SyncExecutor
- - -

-Synchronous executor, is an engine to run the Executable synchronously. -

- -

-

-
Author:
-
pvtroshin - Date October 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- voidexecuteJob() - -
-          Execute the job
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- java.lang.StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  -

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

-executeJob

-
-void executeJob()
-                throws JobSubmissionException
-
-
Execute the job -

-

- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-cleanup

-
-boolean cleanup()
-
-
Clean up after the job -

-

- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
-
- -

-waitForResult

-
-ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

- -
Returns:
object from wich the result can be obtained -
Throws: -
JobExecutionException
-
-
-
- -

-getWorkDirectory

-
-java.lang.String getWorkDirectory()
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-cancelJob

-
-boolean cancelJob()
-
-
Stops running job. - Clean up is not performed. -

-

- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-JobStatus getJobStatus()
-
-
Query the status of the job by its id. -

-

- -
Returns:
- JobStatus
-
-
- -
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-Uses of Interface
compbio.engine.AsyncExecutor

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use AsyncExecutor
compbio.engine  
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
compbio.ws.server  
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return AsyncExecutor
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(java.lang.String taskId) - -
-           
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Classes in compbio.engine.cluster.drmaa that implement AsyncExecutor
- classAsyncJobRunner - -
-          Single cluster job runner class
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.engine.local
-  -

- - - - - - - - - -
Classes in compbio.engine.local that implement AsyncExecutor
- classAsyncLocalRunner - -
-           
-  -

- - - - - -
-Uses of AsyncExecutor in compbio.ws.server
-  -

- - - - - - - - - -
Methods in compbio.ws.server that return AsyncExecutor
-static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
-           
-  -

-

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compbio.engine.Cleaner

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-No usage of compbio.engine.Cleaner -

-

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compbio.engine.ClusterJobId

-
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-Packages that use ClusterJobId
compbio.engine  
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
-  -

- - - - - -
-Uses of ClusterJobId in compbio.engine
-  -

- - - - - - - - - -
Methods in compbio.engine that return ClusterJobId
- ClusterJobIdJob.getJobId() - -
-           
-  -

- - - - - -
-Uses of ClusterJobId in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return ClusterJobId
-static ClusterJobIdClusterSession.getClusterJobId(java.lang.String taskId) - -
-           
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ClusterJobId
- intClusterSession.getJobStatus(ClusterJobId jobId) - -
-          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
-  -

-

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compbio.engine.Configurator

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-No usage of compbio.engine.Configurator -

-

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compbio.engine.FilePuller

-
- - - - - - - - - -
-Packages that use FilePuller
compbio.engine  
-  -

- - - - - -
-Uses of FilePuller in compbio.engine
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return FilePuller
-static FilePullerPulledFileCache.get(java.lang.String fileName) - -
-           
-static FilePullerFilePuller.newFilePuller(java.lang.String file, - int chunkSize) - -
-           
-static FilePullerFilePuller.newProgressPuller(java.lang.String file) - -
-          Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more.
-  -

- - - - - - - - - -
Methods in compbio.engine with parameters of type FilePuller
-static booleanPulledFileCache.put(FilePuller fpuller) - -
-          This method allows duplicates to be added.
-  -

-

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compbio.engine.Job

-
- - - - - - - - - -
-Packages that use Job
compbio.engine  
-  -

- - - - - -
-Uses of Job in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return Job
-static JobJob.getByJobId(java.lang.String jobId, - java.util.List<Job> jobs) - -
-           
-static JobJob.getByTaskId(java.lang.String taskId, - java.util.List<Job> jobs) - -
-           
-  -

- - - - - - - - - - - - - -
Method parameters in compbio.engine with type arguments of type Job
-static JobJob.getByJobId(java.lang.String jobId, - java.util.List<Job> jobs) - -
-           
-static JobJob.getByTaskId(java.lang.String taskId, - java.util.List<Job> jobs) - -
-           
-  -

-

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compbio.engine.LoadBalancer

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-

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compbio.engine.ProgressGetter

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-No usage of compbio.engine.ProgressGetter -

-

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-Uses of Class
compbio.engine.PulledFileCache

-
-No usage of compbio.engine.PulledFileCache -

-

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-Uses of Class
compbio.engine.SubmissionManager

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-

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-Uses of Interface
compbio.engine.SyncExecutor

-
- - - - - - - - - - - - - - - - - -
-Packages that use SyncExecutor
compbio.engine  
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return SyncExecutor
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Classes in compbio.engine.cluster.drmaa that implement SyncExecutor
- classJobRunner - -
-          Single cluster job runner class
-  -

- - - - - -
-Uses of SyncExecutor in compbio.engine.local
-  -

- - - - - - - - - -
Classes in compbio.engine.local that implement SyncExecutor
- classLocalRunner - -
-           
-  -

-

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

- -compbio.engine.client -
-Interface ClusterNativeSpecExecutable<T>

-
-
All Superinterfaces:
Executable<T>
-
-
-
All Known Implementing Classes:
Tcoffee
-
-
-
-
public interface ClusterNativeSpecExecutable<T>
extends Executable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetNativeSpecs() - -
-           
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
-  -

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

-getNativeSpecs

-
-java.lang.String getNativeSpecs()
-
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-
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- -
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- - - diff --git a/website/full_javadoc/compbio/engine/client/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/CommandBuilder.html deleted file mode 100644 index a717442..0000000 --- a/website/full_javadoc/compbio/engine/client/CommandBuilder.html +++ /dev/null @@ -1,582 +0,0 @@ - - - - - - -CommandBuilder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.client -
-Class CommandBuilder<T>

-
-java.lang.Object
-  extended by compbio.engine.client.CommandBuilder<T>
-
-
-
-
public class CommandBuilder<T>
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
CommandBuilder(java.lang.String nameValueSeparator) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidaddParams(java.util.List<java.lang.String> params) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- java.util.List<java.lang.String>getCommands() - -
-           
- java.lang.StringgetCommandString() - -
-           
- java.lang.StringgetParamValue(java.lang.String paramName) - -
-           
- inthashCode() - -
-           
- booleanhasParam(java.lang.String paramName) - -
-           
-static - - - - -
-<T> CommandBuilder<T>
-		newCommandBuilder(java.util.List<? extends Option<T>> arguments, - java.lang.String nameValueSeparator) - -
-          This produces the same result as getCommands method.
- booleanremoveParam(java.lang.String paramName) - -
-           
- booleansetFirst(java.lang.String param) - -
-           
- booleansetLast(java.lang.String paramName) - -
-           
- booleansetLast(java.lang.String paramName, - java.lang.String paramValue) - -
-           
- booleansetParam(java.lang.String param) - -
-           
- booleansetParam(java.lang.String paramName, - java.lang.String paramValue) - -
-           
- voidsetParams(java.util.List<java.lang.String> params) - -
-           
- intsize() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-CommandBuilder

-
-public CommandBuilder(java.lang.String nameValueSeparator)
-
-
- - - - - - - - -
-Method Detail
- -

-addParams

-
-public void addParams(java.util.List<java.lang.String> params)
-
-
-
-
-
-
- -

-setParams

-
-public void setParams(java.util.List<java.lang.String> params)
-
-
-
-
-
-
- -

-hasParam

-
-public boolean hasParam(java.lang.String paramName)
-
-
-
-
-
-
- -

-setFirst

-
-public boolean setFirst(java.lang.String param)
-
-
-
-
-
-
- -

-setParam

-
-public boolean setParam(java.lang.String param)
-
-
-
-
-
-
- -

-setLast

-
-public boolean setLast(java.lang.String paramName)
-
-
-
-
-
-
- -

-setLast

-
-public boolean setLast(java.lang.String paramName,
-                       java.lang.String paramValue)
-
-
-
-
-
-
- -

-getParamValue

-
-public java.lang.String getParamValue(java.lang.String paramName)
-
-
-
-
-
-
- -

-removeParam

-
-public boolean removeParam(java.lang.String paramName)
-
-
-
-
-
-
- -

-setParam

-
-public boolean setParam(java.lang.String paramName,
-                        java.lang.String paramValue)
-
-
-
-
-
-
- -

-getCommands

-
-public java.util.List<java.lang.String> getCommands()
-
-
-
-
-
-
- -

-getCommandString

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

-newCommandBuilder

-
-public static <T> CommandBuilder<T> newCommandBuilder(java.util.List<? extends Option<T>> arguments,
-                                                      java.lang.String nameValueSeparator)
-
-
This produces the same result as getCommands method. The only difference - is that it accepts a List of Options as an input -

-

-
Parameters:
arguments - -
Returns:
-
-
-
- -

-size

-
-public int size()
-
-
-
-
-
-
- -

-hashCode

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

-equals

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

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html deleted file mode 100644 index a6ea5cc..0000000 --- a/website/full_javadoc/compbio/engine/client/ConfExecutable.html +++ /dev/null @@ -1,1000 +0,0 @@ - - - - - - -ConfExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.engine.client -
-Class ConfExecutable<T>

-
-java.lang.Object
-  extended by compbio.engine.client.ConfExecutable<T>
-
-
-
All Implemented Interfaces:
ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>
-
-
-
-
public class ConfExecutable<T>
extends java.lang.Object
implements ConfiguredExecutable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - -
-Field Summary
-static java.lang.StringCLUSTER_TASK_ID_PREFIX - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ConfExecutable(Executable<T> executable, - java.lang.String taskDirectory) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(java.util.List<java.lang.String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- java.lang.StringgetCommand(Executable.ExecProvider provider) - -
-           
- java.util.List<java.lang.String>getCreatedFiles() - -
-           
- java.util.Map<java.lang.String,java.lang.String>getEnvironment() - -
-           
- java.lang.StringgetError() - -
-           
- Executable.ExecProvidergetExecProvider() - -
-           
- Executable<T>getExecutable() - -
-           
- java.lang.StringgetInput() - -
-          Not all input paths are relative! Input path could be absolute!
- Limit<T>getLimit(java.lang.String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- java.lang.StringgetOutput() - -
-           
- CommandBuilder<T>getParameters() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
- - - - - -
-<V> V
-		getResults() - -
-           
- - - - - -
-<V> V
-		getResults(java.lang.String directory) - -
-           
- RunConfigurationgetRunConfiguration() - -
-           
-static - - - - -
-<V> LimitsManager<V>
-		getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) - -
-          This method should be executed once and result of its execution reused.
-static - - - - -
-<V> RunnerConfig<V>
-		getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) - -
-           
-static - - - - -
-<V> PresetManager<V>
-		getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) - -
-           
- Executable.ExecProvidergetSupportedRuntimes() - -
-           
- java.lang.StringgetTaskId() - -
-           
- java.lang.StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) - -
-           
- booleansaveRunConfiguration() - -
-           
- voidsetExecProvider(Executable.ExecProvider provider) - -
-           
- voidsetWorkDirectory(java.lang.String workDirectory) - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-CLUSTER_TASK_ID_PREFIX

-
-public static final java.lang.String CLUSTER_TASK_ID_PREFIX
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ConfExecutable

-
-public ConfExecutable(Executable<T> executable,
-                      java.lang.String taskDirectory)
-
-
- - - - - - - - -
-Method Detail
- -

-getExecProvider

-
-public Executable.ExecProvider getExecProvider()
-
-
-
Specified by:
getExecProvider in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-setExecProvider

-
-public void setExecProvider(Executable.ExecProvider provider)
-
-
-
-
-
-
-
-
-
- -

-getCommand

-
-public java.lang.String getCommand(Executable.ExecProvider provider)
-                            throws UnsupportedRuntimeException
-
-
-
Specified by:
getCommand in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
UnsupportedRuntimeException
-
-
-
- -

-getSupportedRuntimes

-
-public Executable.ExecProvider getSupportedRuntimes()
-
-
-
Specified by:
getSupportedRuntimes in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getLimit

-
-public Limit<T> getLimit(java.lang.String presetName)
-
-
-
Specified by:
getLimit in interface Executable<T>
-
-
-
-
-
-
- -

-getLimits

-
-public LimitsManager<T> getLimits()
-
-
-
Specified by:
getLimits in interface Executable<T>
-
-
-
-
-
-
- -

-getTaskId

-
-public java.lang.String getTaskId()
-
-
-
Specified by:
getTaskId in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-setWorkDirectory

-
-public void setWorkDirectory(java.lang.String workDirectory)
-
-
-
Specified by:
setWorkDirectory in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getWorkDirectory

-
-public java.lang.String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-addParameters

-
-public Executable<T> addParameters(java.util.List<java.lang.String> parameters)
-
-
Description copied from interface: Executable
-
Adds parameter to the list of parameters for a native executable -

-

-
Specified by:
addParameters in interface Executable<T>
-
-
- -
Returns:
this Executable
-
-
-
- -

-getOutput

-
-public java.lang.String getOutput()
-
-
-
Specified by:
getOutput in interface Executable<T>
-
-
-
-
-
-
- -

-getError

-
-public java.lang.String getError()
-
-
-
Specified by:
getError in interface Executable<T>
-
-
-
-
-
-
- -

-getCreatedFiles

-
-public java.util.List<java.lang.String> getCreatedFiles()
-
-
-
Specified by:
getCreatedFiles in interface Executable<T>
-
-
-
-
-
-
- -

-getInput

-
-public java.lang.String getInput()
-
-
Not all input paths are relative! Input path could be absolute! -

-

-
Specified by:
getInput in interface Executable<T>
-
-
-
See Also:
compbio.engine.client.Executable#getInputFiles()
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters()
-
-
-
Specified by:
getParameters in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
Specified by:
getParameters in interface Executable<T>
-
-
-
-
-
-
- -

-getExecutable

-
-public Executable<T> getExecutable()
-
-
-
Specified by:
getExecutable in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-getResults

-
-public <V> V getResults()
-             throws ResultNotAvailableException
-
-
-
Specified by:
getResults in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getResults

-
-public <V> V getResults(java.lang.String directory)
-             throws ResultNotAvailableException
-
-
-
Specified by:
getResults in interface Executable<T>
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getRunnerOptions

-
-public static <V> RunnerConfig<V> getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
-                                        throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-getRunnerPresets

-
-public static <V> PresetManager<V> getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
-                                         throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-getRunnerLimits

-
-public static <V> LimitsManager<V> getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz)
-                                        throws java.io.IOException
-
-
This method should be executed once and result of its execution reused. - If not used carefully it could slow down the system! -

-

-
-
-
-
Type Parameters:
V -
Parameters:
clazz - -
Returns:
-
Throws: -
java.io.IOException
-
-
-
- -

-getEnvironment

-
-public java.util.Map<java.lang.String,java.lang.String> getEnvironment()
-
-
-
Specified by:
getEnvironment in interface ConfiguredExecutable<T>
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)
-
-
-
Specified by:
loadRunConfiguration in interface Executable<T>
-
-
-
-
-
-
- -

-newConfExecutable

-
-public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)
-
-
-
-
-
-
-
-
-
- -

-saveRunConfiguration

-
-public boolean saveRunConfiguration()
-                             throws java.io.IOException
-
-
-
Specified by:
saveRunConfiguration in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-getRunConfiguration

-
-public RunConfiguration getRunConfiguration()
-
-
-
-
-
-
-
-
-
- -

-loadRunConfiguration

-
-public ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
-                                             throws java.io.IOException
-
-
-
Specified by:
loadRunConfiguration in interface ConfiguredExecutable<T>
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html deleted file mode 100644 index 1a59a09..0000000 --- a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html +++ /dev/null @@ -1,504 +0,0 @@ - - - - - - -ConfiguredExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Interface ConfiguredExecutable<T>

-
-
All Superinterfaces:
Executable<T>, PipedExecutable<T>
-
-
-
All Known Implementing Classes:
ConfExecutable
-
-
-
-
public interface ConfiguredExecutable<T>
extends Executable<T>, PipedExecutable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetCommand(Executable.ExecProvider provider) - -
-           
- java.util.Map<java.lang.String,java.lang.String>getEnvironment() - -
-           
- Executable.ExecProvidergetExecProvider() - -
-           
- Executable<T>getExecutable() - -
-           
- CommandBuilder<T>getParameters() - -
-           
- - - - - -
-<V> V
-		getResults() - -
-           
- Executable.ExecProvidergetSupportedRuntimes() - -
-           
- java.lang.StringgetTaskId() - -
-           
- java.lang.StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) - -
-           
- booleansaveRunConfiguration() - -
-           
- voidsetWorkDirectory(java.lang.String workDirectory) - -
-           
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
-  -

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

-getEnvironment

-
-java.util.Map<java.lang.String,java.lang.String> getEnvironment()
-
-
-
-
-
-
-
-
-
- -

-getTaskId

-
-java.lang.String getTaskId()
-
-
-
-
-
-
-
-
-
- -

-getCommand

-
-java.lang.String getCommand(Executable.ExecProvider provider)
-                            throws JobSubmissionException
-
-
-
-
-
- -
Throws: -
JobSubmissionException
-
-
-
- -

-getSupportedRuntimes

-
-Executable.ExecProvider getSupportedRuntimes()
-
-
-
-
-
-
-
-
-
- -

-getWorkDirectory

-
-java.lang.String getWorkDirectory()
-
-
-
-
-
-
-
-
-
- -

-setWorkDirectory

-
-void setWorkDirectory(java.lang.String workDirectory)
-
-
-
-
-
-
-
-
-
- -

-getResults

-
-<V> V getResults()
-             throws ResultNotAvailableException
-
-
-
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-getExecutable

-
-Executable<T> getExecutable()
-
-
-
-
-
-
-
-
-
- -

-getParameters

-
-CommandBuilder<T> getParameters()
-
-
-
-
-
-
-
-
-
- -

-saveRunConfiguration

-
-boolean saveRunConfiguration()
-                             throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-loadRunConfiguration

-
-ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
-                                             throws java.io.IOException
-
-
-
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-getExecProvider

-
-Executable.ExecProvider getExecProvider()
-
-
-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html deleted file mode 100644 index 096638b..0000000 --- a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -EnvVariableProcessor - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class EnvVariableProcessor

-
-java.lang.Object
-  extended by compbio.engine.client.EnvVariableProcessor
-
-
-
-
public class EnvVariableProcessor
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringPATH - -
-          Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable
-  - - - - - - - - - - -
-Constructor Summary
EnvVariableProcessor() - -
-           
-  - - - - - - - - - - - -
-Method Summary
-static java.util.Map<java.lang.String,java.lang.String>getEnvVariables(java.lang.String property, - java.lang.Class<?> clazz) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-PATH

-
-public static final java.lang.String PATH
-
-
Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -

-

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

-EnvVariableProcessor

-
-public EnvVariableProcessor()
-
-
- - - - - - - - -
-Method Detail
- -

-getEnvVariables

-
-public static java.util.Map<java.lang.String,java.lang.String> getEnvVariables(java.lang.String property,
-                                                                               java.lang.Class<?> clazz)
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html deleted file mode 100644 index 085b7fc..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html +++ /dev/null @@ -1,341 +0,0 @@ - - - - - - -Executable.ExecProvider - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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.engine.client -
-Enum Executable.ExecProvider

-
-java.lang.Object
-  extended by java.lang.Enum<Executable.ExecProvider>
-      extended by compbio.engine.client.Executable.ExecProvider
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<Executable.ExecProvider>
-
-
-
Enclosing interface:
Executable<T>
-
-
-
-
public static enum Executable.ExecProvider
extends java.lang.Enum<Executable.ExecProvider>
- - -

-

- -

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

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

-Local

-
-public static final Executable.ExecProvider Local
-
-
-
-
-
- -

-Cluster

-
-public static final Executable.ExecProvider Cluster
-
-
-
-
-
- -

-Any

-
-public static final Executable.ExecProvider Any
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

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

-

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

-valueOf

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

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Executable.html b/website/full_javadoc/compbio/engine/client/Executable.html deleted file mode 100644 index 9f7254f..0000000 --- a/website/full_javadoc/compbio/engine/client/Executable.html +++ /dev/null @@ -1,423 +0,0 @@ - - - - - - -Executable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Interface Executable<T>

-
-
Type Parameters:
T -
-
-
All Known Subinterfaces:
ClusterNativeSpecExecutable<T>, ConfiguredExecutable<T>, PipedExecutable<T>
-
-
-
All Known Implementing Classes:
_SkeletalCommandBuilder, BlastAll, ClustalW, ConfExecutable, Disembl, Mafft, Mcl, Muscle, NetNglyc, OB, Probcons, PsiBlast, PSIBlast, Ronn, RPSBlast, SkeletalExecutable, Tcoffee
-
-
-
-
public interface Executable<T>
- - -

-Interface to a native executable. -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Nested Class Summary
-static classExecutable.ExecProvider - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(java.util.List<java.lang.String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- java.util.List<java.lang.String>getCreatedFiles() - -
-           
- java.lang.StringgetError() - -
-           
- java.lang.StringgetInput() - -
-           
- Limit<T>getLimit(java.lang.String presetName) - -
-           
- LimitsManager<T>getLimits() - -
-           
- java.lang.StringgetOutput() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
- - - - - -
-<V> V
-		getResults(java.lang.String directory) - -
-           
- Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

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

-addParameters

-
-Executable<T> addParameters(java.util.List<java.lang.String> parameters)
-
-
Adds parameter to the list of parameters for a native executable -

-

-
Parameters:
parameters - -
Returns:
this Executable
-
-
-
- -

-getCreatedFiles

-
-java.util.List<java.lang.String> getCreatedFiles()
-
-
-
-
-
-
- -

-getInput

-
-java.lang.String getInput()
-
-
-
-
-
-
- -

-getOutput

-
-java.lang.String getOutput()
-
-
-
-
-
-
- -

-getError

-
-java.lang.String getError()
-
-
-
-
-
-
- -

-getParameters

-
-CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
-
-
-
- -

-getResults

-
-<V> V getResults(java.lang.String directory)
-             throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
-
- -

-loadRunConfiguration

-
-Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
-
-
-
-
-
- -

-getLimit

-
-Limit<T> getLimit(java.lang.String presetName)
-
-
-
-
-
-
- -

-getLimits

-
-LimitsManager<T> getLimits()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/PathValidator.html b/website/full_javadoc/compbio/engine/client/PathValidator.html deleted file mode 100644 index d83660e..0000000 --- a/website/full_javadoc/compbio/engine/client/PathValidator.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - -PathValidator - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class PathValidator

-
-java.lang.Object
-  extended by compbio.engine.client.PathValidator
-
-
-
-
public final class PathValidator
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
PathValidator() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleanisAbsolutePath(java.lang.String path) - -
-          Whether a certain path is absolute or not is operation system dependent!
-static booleanisValidDirectory(java.lang.String directory) - -
-           
-static booleanisValidExecutable(java.lang.String command) - -
-           
-static voidvalidateDirectory(java.lang.String workDirectory) - -
-           
-static voidvalidateExecutable(java.lang.String command) - -
-           
-static voidvalidatePathNames(java.util.List<java.lang.String> filenames, - java.lang.String type) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-PathValidator

-
-public PathValidator()
-
-
- - - - - - - - -
-Method Detail
- -

-isValidExecutable

-
-public static boolean isValidExecutable(java.lang.String command)
-
-
-
-
-
-
- -

-validateExecutable

-
-public static void validateExecutable(java.lang.String command)
-                               throws java.lang.IllegalArgumentException
-
-
- -
Throws: -
java.lang.IllegalArgumentException
-
-
-
- -

-isValidDirectory

-
-public static boolean isValidDirectory(java.lang.String directory)
-
-
-
-
-
-
- -

-validatePathNames

-
-public static void validatePathNames(java.util.List<java.lang.String> filenames,
-                                     java.lang.String type)
-                              throws java.lang.IllegalArgumentException
-
-
-
Parameters:
filenames -
type - - merely a string to be added to error message to explain what - type of files are lacking -
Throws: -
java.lang.IllegalArgumentException
-
-
-
- -

-isAbsolutePath

-
-public static boolean isAbsolutePath(java.lang.String path)
-
-
Whether a certain path is absolute or not is operation system dependent! -

-

-
Parameters:
path - -
Returns:
-
-
-
- -

-validateDirectory

-
-public static void validateDirectory(java.lang.String workDirectory)
-                              throws java.lang.IllegalArgumentException
-
-
- -
Throws: -
java.lang.IllegalArgumentException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/PipedExecutable.html deleted file mode 100644 index e3e7f54..0000000 --- a/website/full_javadoc/compbio/engine/client/PipedExecutable.html +++ /dev/null @@ -1,228 +0,0 @@ - - - - - - -PipedExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Interface PipedExecutable<T>

-
-
Type Parameters:
T -
-
-
All Superinterfaces:
Executable<T>
-
-
-
All Known Subinterfaces:
ConfiguredExecutable<T>
-
-
-
All Known Implementing Classes:
ConfExecutable, Mafft, Probcons, Tcoffee
-
-
-
-
public interface PipedExecutable<T>
extends Executable<T>
- - -

-This is a marker interface to indicate that the output of the process must be - captured. It is in generally better for the process to manage its own - streams, but some executables are not capable of this thus require different - handling -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
-  -

- -

- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/RunConfiguration.html deleted file mode 100644 index 56783a6..0000000 --- a/website/full_javadoc/compbio/engine/client/RunConfiguration.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -RunConfiguration - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class RunConfiguration

-
-java.lang.Object
-  extended by compbio.engine.client.RunConfiguration
-
-
-
-
public class RunConfiguration
extends java.lang.Object
- - -

-Value class for persisting ConfExecutable instances -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringrconfigFile - -
-           
-  - - - - - - - - - - - - - -
-Constructor Summary
RunConfiguration() - -
-           
RunConfiguration(ConfExecutable<?> cexec) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetError() - -
-           
- java.lang.StringgetInput() - -
-           
- java.lang.StringgetOutput() - -
-           
- CommandBuilder<?>getParameters() - -
-           
- java.lang.StringgetRunnerClassName() - -
-           
- inthashCode() - -
-           
-static RunConfigurationload(java.io.InputStream input) - -
-           
- voidsetError(java.lang.String error) - -
-           
- voidsetInput(java.lang.String input) - -
-           
- voidsetOutput(java.lang.String output) - -
-           
- voidsetParameters(CommandBuilder<?> parameters) - -
-           
- java.lang.StringtoString() - -
-           
-static booleanwrite(RunConfiguration rconf) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-rconfigFile

-
-public static final java.lang.String rconfigFile
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-RunConfiguration

-
-public RunConfiguration()
-
-
-
- -

-RunConfiguration

-
-public RunConfiguration(ConfExecutable<?> cexec)
-
-
- - - - - - - - -
-Method Detail
- -

-write

-
-public static boolean write(RunConfiguration rconf)
-                     throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-load

-
-public static RunConfiguration load(java.io.InputStream input)
-                             throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-setOutput

-
-public void setOutput(java.lang.String output)
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<?> getParameters()
-
-
-
-
-
-
- -

-setParameters

-
-public void setParameters(CommandBuilder<?> parameters)
-
-
-
-
-
-
- -

-getOutput

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

-setError

-
-public void setError(java.lang.String error)
-
-
-
-
-
-
- -

-getError

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

-getInput

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

-setInput

-
-public void setInput(java.lang.String input)
-
-
-
-
-
-
- -

-getRunnerClassName

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

-equals

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

-hashCode

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

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html deleted file mode 100644 index bc14f0c..0000000 --- a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html +++ /dev/null @@ -1,641 +0,0 @@ - - - - - - -SkeletalExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class SkeletalExecutable<T>

-
-java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<T>
-
-
-
All Implemented Interfaces:
Executable<T>
-
-
-
Direct Known Subclasses:
ClustalW, Mafft, Muscle, Probcons, PsiBlast, Tcoffee
-
-
-
-
public abstract class SkeletalExecutable<T>
extends java.lang.Object
implements Executable<T>
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from interface compbio.engine.client.Executable
Executable.ExecProvider
-  - - - - - - - - - - - - - - -
-Constructor Summary
SkeletalExecutable() - -
-           
SkeletalExecutable(java.lang.String parameterKeyValueDelimiter) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Executable<T>addParameters(java.util.List<java.lang.String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetClusterSettings() - -
-           
- java.util.List<java.lang.String>getCreatedFiles() - -
-          This method cannot really tell whether the files has actually been - created or not.
- java.lang.StringgetError() - -
-           
- java.lang.StringgetInput() - -
-           
- java.lang.StringgetOutput() - -
-           
- CommandBuilder<T>getParameters(Executable.ExecProvider provider) - -
-           
-abstract  java.lang.Class<? extends Executable<?>>getType() - -
-           
- inthashCode() - -
-           
- Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
-           
- SkeletalExecutable<T>setError(java.lang.String errFile) - -
-           
- SkeletalExecutable<T>setInput(java.lang.String inFile) - -
-           
- SkeletalExecutable<T>setOutput(java.lang.String outFile) - -
-           
- Executable<T>setParameter(java.lang.String parameter) - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  - - - - - - - -
Methods inherited from interface compbio.engine.client.Executable
getLimit, getLimits, getResults
-  -

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

-SkeletalExecutable

-
-public SkeletalExecutable()
-
-
-
- -

-SkeletalExecutable

-
-public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)
-
-
- - - - - - - - -
-Method Detail
- -

-setInput

-
-public SkeletalExecutable<T> setInput(java.lang.String inFile)
-
-
-
-
-
-
-
-
-
- -

-setOutput

-
-public SkeletalExecutable<T> setOutput(java.lang.String outFile)
-
-
-
-
-
-
-
-
-
- -

-setError

-
-public SkeletalExecutable<T> setError(java.lang.String errFile)
-
-
-
-
-
-
-
-
-
- -

-getParameters

-
-public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
-
-
-
Specified by:
getParameters in interface Executable<T>
-
-
-
-
-
-
- -

-addParameters

-
-public Executable<T> addParameters(java.util.List<java.lang.String> parameters)
-
-
Description copied from interface: Executable
-
Adds parameter to the list of parameters for a native executable -

-

-
Specified by:
addParameters in interface Executable<T>
-
-
- -
Returns:
this Executable
-
-
-
- -

-setParameter

-
-public Executable<T> setParameter(java.lang.String parameter)
-
-
-
-
-
-
-
-
-
- -

-getCreatedFiles

-
-public java.util.List<java.lang.String> getCreatedFiles()
-
-
This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

-

-
Specified by:
getCreatedFiles in interface Executable<T>
-
-
-
See Also:
Executable.getCreatedFiles()
-
-
-
- -

-getInput

-
-public java.lang.String getInput()
-
-
-
Specified by:
getInput in interface Executable<T>
-
-
-
-
-
-
- -

-getOutput

-
-public java.lang.String getOutput()
-
-
-
Specified by:
getOutput in interface Executable<T>
-
-
-
-
-
-
- -

-getError

-
-public java.lang.String getError()
-
-
-
Specified by:
getError in interface Executable<T>
-
-
-
-
-
-
- -

-toString

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

-loadRunConfiguration

-
-public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
-
-
-
Specified by:
loadRunConfiguration in interface Executable<T>
-
-
-
-
-
-
- -

-equals

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

-hashCode

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

-getClusterSettings

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

-getType

-
-public abstract java.lang.Class<? extends Executable<?>> getType()
-
-
-
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html deleted file mode 100644 index 5574f03..0000000 --- a/website/full_javadoc/compbio/engine/client/Util.html +++ /dev/null @@ -1,505 +0,0 @@ - - - - - - -Util - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.client -
-Class Util

-
-java.lang.Object
-  extended by compbio.engine.client.Util
-
-
-
-
public final class Util
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
Util() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static java.lang.StringconvertToAbsolute(java.lang.String relativePath) - -
-           
-static java.lang.StringgetCommand(Executable.ExecProvider provider, - java.lang.Class<?> clazz) - -
-           
-static java.lang.StringgetExecProperty(java.lang.String propertySpec, - java.lang.Class<?> clazz) - -
-           
-static java.lang.StringgetExecProperty(java.lang.String propertySpec, - Executable<?> exec) - -
-           
-static java.lang.StringgetFullPath(java.lang.String workDirectory, - java.lang.String fileName) - -
-           
-static Executable.ExecProvidergetSupportedRuntimes(java.lang.Class<?> clazz) - -
-           
-static booleanisMarked(java.lang.String workDirectory, - JobStatus marker) - -
-           
-static booleanisValidJobId(java.lang.String key) - -
-           
-static ConfiguredExecutable<?>loadExecutable(java.lang.String taskId) - -
-           
-static java.util.Map<java.lang.String,java.lang.String>mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, - java.util.Map<java.lang.String,java.lang.String> variables) - -
-           
-static voidwriteFile(java.lang.String workDirectory, - java.lang.String fileAndEventName, - java.lang.String content, - boolean override) - -
-           
-static booleanwriteMarker(java.lang.String workDirectory, - JobStatus fileType) - -
-           
-static voidwriteStatFile(java.lang.String workDirectory, - java.lang.String fileAndEventName) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-Util

-
-public Util()
-
-
- - - - - - - - -
-Method Detail
- -

-isValidJobId

-
-public static boolean isValidJobId(java.lang.String key)
-
-
-
-
-
-
- -

-writeStatFile

-
-public static void writeStatFile(java.lang.String workDirectory,
-                                 java.lang.String fileAndEventName)
-
-
-
-
-
-
- -

-writeFile

-
-public static void writeFile(java.lang.String workDirectory,
-                             java.lang.String fileAndEventName,
-                             java.lang.String content,
-                             boolean override)
-
-
-
-
-
-
- -

-writeMarker

-
-public static final boolean writeMarker(java.lang.String workDirectory,
-                                        JobStatus fileType)
-
-
-
-
-
-
- -

-isMarked

-
-public static boolean isMarked(java.lang.String workDirectory,
-                               JobStatus marker)
-
-
-
-
-
-
- -

-mergeEnvVariables

-
-public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
-                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)
-
-
-
-
-
-
- -

-convertToAbsolute

-
-public static java.lang.String convertToAbsolute(java.lang.String relativePath)
-
-
-
-
-
-
- -

-getExecProperty

-
-public static java.lang.String getExecProperty(java.lang.String propertySpec,
-                                               Executable<?> exec)
-
-
-
-
-
-
- -

-getExecProperty

-
-public static java.lang.String getExecProperty(java.lang.String propertySpec,
-                                               java.lang.Class<?> clazz)
-
-
-
-
-
-
- -

-getFullPath

-
-public static java.lang.String getFullPath(java.lang.String workDirectory,
-                                           java.lang.String fileName)
-
-
-
-
-
-
- -

-getCommand

-
-public static java.lang.String getCommand(Executable.ExecProvider provider,
-                                          java.lang.Class<?> clazz)
-
-
-
-
-
-
- -

-getSupportedRuntimes

-
-public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)
-
-
-
-
-
-
- -

-loadExecutable

-
-public static ConfiguredExecutable<?> loadExecutable(java.lang.String taskId)
-                                              throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html deleted file mode 100644 index d57b7bd..0000000 --- a/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Interface compbio.engine.client.ClusterNativeSpecExecutable - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Interface
compbio.engine.client.ClusterNativeSpecExecutable

-
- - - - - - - - - -
-Packages that use ClusterNativeSpecExecutable
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of ClusterNativeSpecExecutable in compbio.runner.msa
-  -

- - - - - - - - - -
Classes in compbio.runner.msa that implement ClusterNativeSpecExecutable
- classTcoffee - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html deleted file mode 100644 index 663f217..0000000 --- a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html +++ /dev/null @@ -1,339 +0,0 @@ - - - - - - -Uses of Class compbio.engine.client.CommandBuilder - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Class
compbio.engine.client.CommandBuilder

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use CommandBuilder
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of CommandBuilder in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return CommandBuilder
- CommandBuilder<T>ConfiguredExecutable.getParameters() - -
-           
- CommandBuilder<T>ConfExecutable.getParameters() - -
-           
- CommandBuilder<?>RunConfiguration.getParameters() - -
-           
- CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> CommandBuilder<T>
-		CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, - java.lang.String nameValueSeparator) - -
-          This produces the same result as getCommands method.
-  -

- - - - - - - - - -
Methods in compbio.engine.client with parameters of type CommandBuilder
- voidRunConfiguration.setParameters(CommandBuilder<?> parameters) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return CommandBuilder
- CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner._impl
-  -

- - - - - - - - - -
Methods in compbio.runner._impl that return CommandBuilder
- CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of CommandBuilder in compbio.runner.msa
-  -

- - - - - - - - - -
Methods in compbio.runner.msa that return CommandBuilder
- CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
-           
-  -

-

- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-Uses of Class
compbio.engine.client.ConfExecutable

-
- - - - - - - - - -
-Packages that use ConfExecutable
compbio.engine.clientClasses and interfaces representing an input for engines. 
-  -

- - - - - -
-Uses of ConfExecutable in compbio.engine.client
-  -

- - - - - - - - -
Constructors in compbio.engine.client with parameters of type ConfExecutable
RunConfiguration(ConfExecutable<?> cexec) - -
-           
-  -

-

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-Uses of Interface
compbio.engine.client.ConfiguredExecutable

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use ConfiguredExecutable
compbio.engine  
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
compbio.runnerUtilities commonly used by all runners. 
compbio.ws.server  
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine that return ConfiguredExecutable
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - java.util.List<FastaSequence> dataSet) - -
-           
- ConfiguredExecutable<?>Job.getConfExecutable() - -
-           
- ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.String jobId) - -
-          Retrieve the results of the job.
- ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  -

- - - - - - - - - -
Methods in compbio.engine that return types with arguments of type ConfiguredExecutable
-static java.util.concurrent.Future<ConfiguredExecutable<?>>SubmissionManager.getTask(java.lang.String taskId) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type ConfiguredExecutable
-static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
-           
-static booleanCleaner.deleteFiles(ConfiguredExecutable<?> exec) - -
-          This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty)
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static voidSubmissionManager.removeTask(ConfiguredExecutable<?> executable) - -
-           
- java.lang.StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  -

- - - - - - - - - -
Method parameters in compbio.engine with type arguments of type ConfiguredExecutable
-static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, - java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine with parameters of type ConfiguredExecutable
Job(java.lang.String taskId, - java.lang.String jobId, - ConfiguredExecutable<?> cexecutable) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.client
-  -

- - - - - - - - - -
Classes in compbio.engine.client that implement ConfiguredExecutable
- classConfExecutable<T> - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return ConfiguredExecutable
-static ConfiguredExecutable<?>Util.loadExecutable(java.lang.String taskId) - -
-           
- ConfiguredExecutable<?>ConfiguredExecutable.loadRunConfiguration(java.io.InputStream input) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(java.io.InputStream input) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable
- ConfiguredExecutable<?>ClusterSession.getResults(java.lang.String taskId) - -
-           
- ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) - -
-           
- ConfiguredExecutable<?>JobRunner.waitForResult() - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
-static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
-           
- java.lang.StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
JobRunner(ConfiguredExecutable<?> confExec) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.engine.local
-  -

- - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.local that return ConfiguredExecutable
- ConfiguredExecutable<?>ExecutableWrapper.call() - -
-          It is vital that output and error streams are captured immediately for - this call() to succeed.
-static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String taskId) - -
-           
- ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) - -
-           
- ConfiguredExecutable<?>LocalRunner.waitForResult() - -
-           
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.local with parameters of type ConfiguredExecutable
-static booleanLocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable) - -
-           
- java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable
-static booleanLocalEngineUtil.cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String workDirectory) - -
-           
-static JobStatusLocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
-           
-static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String taskId) - -
-           
-  -

- - - - - - - - - - - -
Constructors in compbio.engine.local with parameters of type ConfiguredExecutable
ExecutableWrapper(ConfiguredExecutable<?> executable, - java.lang.String workDirectory) - -
-           
LocalRunner(ConfiguredExecutable<?> executable) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type ConfiguredExecutable
-static voidUtil.writeInput(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
-           
-  -

- - - - - -
-Uses of ConfiguredExecutable in compbio.ws.server
-  -

- - - - - - - - - - - - - -
Methods in compbio.ws.server with parameters of type ConfiguredExecutable
-static - - - - -
-<T> java.lang.String
-		WSUtil.align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
-           
-static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.EnvVariableProcessor

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-Uses of Class
compbio.engine.client.Executable.ExecProvider

-
- - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Executable.ExecProvider
compbio.engine  
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.engine
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine that return Executable.ExecProvider
-static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type Executable.ExecProvider
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return Executable.ExecProvider
- Executable.ExecProviderConfiguredExecutable.getExecProvider() - -
-           
- Executable.ExecProviderConfExecutable.getExecProvider() - -
-           
- Executable.ExecProviderConfiguredExecutable.getSupportedRuntimes() - -
-           
- Executable.ExecProviderConfExecutable.getSupportedRuntimes() - -
-           
-static Executable.ExecProviderUtil.getSupportedRuntimes(java.lang.Class<?> clazz) - -
-           
-static Executable.ExecProviderExecutable.ExecProvider.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static Executable.ExecProvider[]Executable.ExecProvider.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client with parameters of type Executable.ExecProvider
- java.lang.StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
-           
-static java.lang.StringUtil.getCommand(Executable.ExecProvider provider, - java.lang.Class<?> clazz) - -
-           
- CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) - -
-           
- CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) - -
-           
- voidConfExecutable.setExecProvider(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type Executable.ExecProvider
- CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner._impl
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner._impl with parameters of type Executable.ExecProvider
- java.lang.StringMcl.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringBlastAll.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringRPSBlast.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringRonn.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringPSIBlast.getCommand(Executable.ExecProvider provider) - -
-           
- java.lang.StringDisembl.getCommand(Executable.ExecProvider provider) - -
-           
- CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
-           
-  -

- - - - - -
-Uses of Executable.ExecProvider in compbio.runner.msa
-  -

- - - - - - - - - -
Methods in compbio.runner.msa with parameters of type Executable.ExecProvider
- CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
-           
-  -

-

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-Uses of Interface
compbio.engine.client.Executable

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use Executable
compbio.engine  
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.engine.confClasses commonly used by both engines. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.runner.psiblast  
-  -

- - - - - -
-Uses of Executable in compbio.engine
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine with parameters of type Executable
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
-           
-static - - - - -
-<T> ConfiguredExecutable<T>
-		Configurator.configureExecutable(Executable<T> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) - -
-           
-static - - - - -
-<T,V> Executable.ExecProvider
-		LoadBalancer.getEngine(Executable<V> executable, - java.util.List<FastaSequence> dataSet) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - -
Subinterfaces of Executable in compbio.engine.client
- interfaceClusterNativeSpecExecutable<T> - -
-           
- interfaceConfiguredExecutable<T> - -
-           
- interfacePipedExecutable<T> - -
-          This is a marker interface to indicate that the output of the process must be - captured.
-  -

- - - - - - - - - - - - - -
Classes in compbio.engine.client that implement Executable
- classConfExecutable<T> - -
-           
- classSkeletalExecutable<T> - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return Executable
- Executable<T>SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters) - -
-           
- Executable<T>Executable.addParameters(java.util.List<java.lang.String> parameters) - -
-          Adds parameter to the list of parameters for a native executable
- Executable<T>ConfExecutable.addParameters(java.util.List<java.lang.String> parameters) - -
-           
- Executable<T>ConfiguredExecutable.getExecutable() - -
-           
- Executable<T>ConfExecutable.getExecutable() - -
-           
- Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<T>SkeletalExecutable.setParameter(java.lang.String parameter) - -
-           
-  -

- - - - - - - - - -
Methods in compbio.engine.client that return types with arguments of type Executable
-abstract  java.lang.Class<? extends Executable<?>>SkeletalExecutable.getType() - -
-           
-  -

- - - - - - - - - -
Methods in compbio.engine.client with parameters of type Executable
-static java.lang.StringUtil.getExecProperty(java.lang.String propertySpec, - Executable<?> exec) - -
-           
-  -

- - - - - - - - - - - - - - - - - -
Method parameters in compbio.engine.client with type arguments of type Executable
-static - - - - -
-<V> LimitsManager<V>
-		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) - -
-          This method should be executed once and result of its execution reused.
-static - - - - -
-<V> RunnerConfig<V>
-		ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) - -
-           
-static - - - - -
-<V> PresetManager<V>
-		ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) - -
-           
-  -

- - - - - - - - -
Constructors in compbio.engine.client with parameters of type Executable
ConfExecutable(Executable<T> executable, - java.lang.String taskDirectory) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.engine.conf
-  -

- - - - - - - - - -
Methods in compbio.engine.conf that return types with arguments of type Executable
-static java.lang.Class<Executable<?>>DirectoryManager.getClass(java.lang.String taskId) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner
-  -

- - - - - - - - - -
Classes in compbio.runner that implement Executable
- class_SkeletalCommandBuilder - -
-           
-  -

- - - - - - - - - -
Methods in compbio.runner that return Executable
- Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - -
Method parameters in compbio.runner with type arguments of type Executable
-static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
-           
-static - - - - -
-<T> LimitsManager<T>
-		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) - -
-          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then
-static - - - - -
-<T> PresetManager<T>
-		Util.getPresets(java.lang.Class<? extends Executable<T>> clazz) - -
-           
-static - - - - -
-<T> RunnerConfig<T>
-		Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) - -
-           
-  -

- - - - - - - - -
Constructor parameters in compbio.runner with type arguments of type Executable
OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner._impl
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.runner._impl that implement Executable
- classBlastAll - -
-           
- classDisembl - -
-           
- classMcl - -
-           
- classNetNglyc - -
-           
- classOB - -
-          TODO this needs fixing! Executable does not work
- classPSIBlast - -
-           
- classRonn - -
-           
- classRPSBlast - -
-           
-  -

- - - - - - - - - -
Methods in compbio.runner._impl that return Executable
- Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Classes in compbio.runner.msa that implement Executable
- classClustalW - -
-           
- classMafft - -
-           
- classMuscle - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.runner.msa that return types with arguments of type Executable
- java.lang.Class<? extends Executable<?>>Tcoffee.getType() - -
-           
- java.lang.Class<? extends Executable<?>>ClustalW.getType() - -
-           
- java.lang.Class<? extends Executable<?>>Probcons.getType() - -
-           
- java.lang.Class<? extends Executable<?>>Muscle.getType() - -
-           
- java.lang.Class<? extends Executable<?>>Mafft.getType() - -
-           
-  -

- - - - - -
-Uses of Executable in compbio.runner.psiblast
-  -

- - - - - - - - - -
Classes in compbio.runner.psiblast that implement Executable
- classPsiBlast - -
-           
-  -

- - - - - - - - - -
Methods in compbio.runner.psiblast that return types with arguments of type Executable
- java.lang.Class<? extends Executable<?>>PsiBlast.getType() - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.PathValidator

-
-No usage of compbio.engine.client.PathValidator -

-

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-Uses of Interface
compbio.engine.client.PipedExecutable

-
- - - - - - - - - - - - - -
-Packages that use PipedExecutable
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
-  -

- - - - - -
-Uses of PipedExecutable in compbio.engine.client
-  -

- - - - - - - - - -
Subinterfaces of PipedExecutable in compbio.engine.client
- interfaceConfiguredExecutable<T> - -
-           
-  -

- - - - - - - - - -
Classes in compbio.engine.client that implement PipedExecutable
- classConfExecutable<T> - -
-           
-  -

- - - - - -
-Uses of PipedExecutable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - -
Classes in compbio.runner.msa that implement PipedExecutable
- classMafft - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.RunConfiguration

-
- - - - - - - - - - - - - - - - - -
-Packages that use RunConfiguration
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
-  -

- - - - - -
-Uses of RunConfiguration in compbio.engine.client
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.client that return RunConfiguration
- RunConfigurationConfExecutable.getRunConfiguration() - -
-           
-static RunConfigurationRunConfiguration.load(java.io.InputStream input) - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client with parameters of type RunConfiguration
- Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) - -
-           
- ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) - -
-           
-static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) - -
-           
-static booleanRunConfiguration.write(RunConfiguration rconf) - -
-           
-  -

- - - - - -
-Uses of RunConfiguration in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner with parameters of type RunConfiguration
- Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

- - - - - -
-Uses of RunConfiguration in compbio.runner._impl
-  -

- - - - - - - - - -
Methods in compbio.runner._impl with parameters of type RunConfiguration
- Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) - -
-           
-  -

-

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-Uses of Class
compbio.engine.client.SkeletalExecutable

-
- - - - - - - - - - - - - - - - - -
-Packages that use SkeletalExecutable
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.runner.psiblast  
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.engine.client
-  -

- - - - - - - - - - - - - - - - - -
Methods in compbio.engine.client that return SkeletalExecutable
- SkeletalExecutable<T>SkeletalExecutable.setError(java.lang.String errFile) - -
-           
- SkeletalExecutable<T>SkeletalExecutable.setInput(java.lang.String inFile) - -
-           
- SkeletalExecutable<T>SkeletalExecutable.setOutput(java.lang.String outFile) - -
-           
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.runner.msa
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Subclasses of SkeletalExecutable in compbio.runner.msa
- classClustalW - -
-           
- classMafft - -
-           
- classMuscle - -
-           
- classProbcons - -
-           
- classTcoffee - -
-           
-  -

- - - - - -
-Uses of SkeletalExecutable in compbio.runner.psiblast
-  -

- - - - - - - - - -
Subclasses of SkeletalExecutable in compbio.runner.psiblast
- classPsiBlast - -
-           
-  -

-

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compbio.engine.client.Util

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-

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-Interfaces  - -
-ClusterNativeSpecExecutable -
-ConfiguredExecutable -
-Executable -
-PipedExecutable
- - - - - - -
-Classes  - -
-CommandBuilder -
-ConfExecutable -
-EnvVariableProcessor -
-PathValidator -
-RunConfiguration -
-SkeletalExecutable -
-Util
- - - - - - -
-Enums  - -
-Executable.ExecProvider
- - - - diff --git a/website/full_javadoc/compbio/engine/client/package-summary.html b/website/full_javadoc/compbio/engine/client/package-summary.html deleted file mode 100644 index 8ce82d7..0000000 --- a/website/full_javadoc/compbio/engine/client/package-summary.html +++ /dev/null @@ -1,242 +0,0 @@ - - - - - - -compbio.engine.client - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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-

-Package compbio.engine.client -

-Classes and interfaces representing an input for engines. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - -
-Interface Summary
ClusterNativeSpecExecutable<T> 
ConfiguredExecutable<T> 
Executable<T>Interface to a native executable.
PipedExecutable<T>This is a marker interface to indicate that the output of the process must be - captured.
-  - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
CommandBuilder<T> 
ConfExecutable<T> 
EnvVariableProcessor 
PathValidator 
RunConfigurationValue class for persisting ConfExecutable instances
SkeletalExecutable<T> 
Util 
-  - -

- - - - - - - - - -
-Enum Summary
Executable.ExecProvider 
-  - -

-

-Package compbio.engine.client Description -

- -

-Classes and interfaces representing an input for engines. These classes are known to runners, - which form the next layer of the JABAWS hierarchy. -

- -

-

-
Author:
-
Petr Troshin - - Date January 2010
-
-
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-Hierarchy For Package compbio.engine.client -

-
-
-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Interface Hierarchy -

- -

-Enum Hierarchy -

- -
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compbio.engine.client

-
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Packages that use compbio.engine.client
compbio.engine  
compbio.engine.clientClasses and interfaces representing an input for engines. 
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
compbio.engine.confClasses commonly used by both engines. 
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
compbio.runnerUtilities commonly used by all runners. 
compbio.runner._impl  
compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
compbio.runner.psiblast  
compbio.ws.server  
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine
ConfiguredExecutable - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.client
CommandBuilder - -
-           
ConfExecutable - -
-           
ConfiguredExecutable - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
PipedExecutable - -
-          This is a marker interface to indicate that the output of the process must be - captured.
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
SkeletalExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.cluster.drmaa
ConfiguredExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.conf
Executable - -
-          Interface to a native executable.
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.engine.local
ConfiguredExecutable - -
-           
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
-  -

- - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner._impl
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
RunConfiguration - -
-          Value class for persisting ConfExecutable instances
-  -

- - - - - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner.msa
ClusterNativeSpecExecutable - -
-           
CommandBuilder - -
-           
Executable - -
-          Interface to a native executable.
Executable.ExecProvider - -
-           
PipedExecutable - -
-          This is a marker interface to indicate that the output of the process must be - captured.
SkeletalExecutable - -
-           
-  -

- - - - - - - - - - - -
-Classes in compbio.engine.client used by compbio.runner.psiblast
Executable - -
-          Interface to a native executable.
SkeletalExecutable - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.client used by compbio.ws.server
ConfiguredExecutable - -
-           
-  -

-

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- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class AsyncJobRunner

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.AsyncJobRunner
-
-
-
All Implemented Interfaces:
AsyncExecutor
-
-
-
-
public class AsyncJobRunner
extends java.lang.Object
implements AsyncExecutor
- - -

-Single cluster job runner class -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
AsyncJobRunner() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(java.lang.String jobId) - -
-          Stop running job.
- booleancleanup(java.lang.String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(java.lang.String jobId) - -
-          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
- ConfiguredExecutable<?>getResults(java.lang.String jobId) - -
-          Retrieve the results of the job.
- java.lang.StringgetWorkDirectory(java.lang.String jobId) - -
-           
- java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-AsyncJobRunner

-
-public AsyncJobRunner()
-
-
- - - - - - - - -
-Method Detail
- -

-submitJob

-
-public java.lang.String submitJob(ConfiguredExecutable<?> executable)
-                           throws JobSubmissionException
-
-
Description copied from interface: AsyncExecutor
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

-
Specified by:
submitJob in interface AsyncExecutor
-
-
- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-cancelJob

-
-public boolean cancelJob(java.lang.String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

-
Specified by:
cancelJob in interface AsyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus(java.lang.String jobId)
-
-
This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. Cancelled jobs needs to be - tracked manually! -

-

-
Specified by:
getJobStatus in interface AsyncExecutor
-
-
- -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
-
- -

-cleanup

-
-public boolean cleanup(java.lang.String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Remove all files and a job directory for a jobid. -

-

-
Specified by:
cleanup in interface AsyncExecutor
-
-
- -
Returns:
true if job directory was successfully removed, false otherwise.
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(java.lang.String jobId)
-                                   throws ResultNotAvailableException
-
-
Description copied from interface: AsyncExecutor
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Specified by:
getResults in interface AsyncExecutor
-
-
-
Parameters:
jobId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
-
- -

-getWorkDirectory

-
-public java.lang.String getWorkDirectory(java.lang.String jobId)
-
-
-
Specified by:
getWorkDirectory in interface AsyncExecutor
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html deleted file mode 100644 index 51b0e22..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html +++ /dev/null @@ -1,471 +0,0 @@ - - - - - - -ClusterSession - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class ClusterSession

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterSession
-
-
-
-
public final class ClusterSession
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringJOBID - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidclose() - -
-           
-static ClusterJobIdgetClusterJobId(java.lang.String taskId) - -
-           
- intgetJobStatus(ClusterJobId jobId) - -
-          Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed.
-static java.lang.StringgetJobStatus(int status) - -
-          Deprecated. 
- ConfiguredExecutable<?>getResults(java.lang.String taskId) - -
-           
- org.ggf.drmaa.SessiongetSession() - -
-           
-static StatisticManagergetStatistics(org.ggf.drmaa.JobInfo status) - -
-           
- voidremoveJob(java.lang.String taskId) - -
-           
- org.ggf.drmaa.JobInfowaitForJob(java.lang.String taskId) - -
-           
- org.ggf.drmaa.JobInfowaitForJob(java.lang.String jobId, - long waitingTime) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-JOBID

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

-getSession

-
-public org.ggf.drmaa.Session getSession()
-
-
-
-
-
-
- -

-close

-
-public void close()
-
-
-
-
-
-
- -

-removeJob

-
-public void removeJob(java.lang.String taskId)
-
-
-
-
-
-
- -

-waitForJob

-
-public org.ggf.drmaa.JobInfo waitForJob(java.lang.String taskId)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        java.io.IOException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
java.io.IOException
-
-
-
- -

-getClusterJobId

-
-public static ClusterJobId getClusterJobId(java.lang.String taskId)
-                                    throws java.io.IOException
-
-
- -
Throws: -
java.io.IOException
-
-
-
- -

-waitForJob

-
-public org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId,
-                                        long waitingTime)
-                                 throws org.ggf.drmaa.DrmaaException,
-                                        java.io.IOException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
java.io.IOException
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(java.lang.String taskId)
-                                   throws org.ggf.drmaa.DrmaaException,
-                                          ResultNotAvailableException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException -
ResultNotAvailableException
-
-
-
- -

-getStatistics

-
-public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
-                                      throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getJobStatus

-
-public int getJobStatus(ClusterJobId jobId)
-                 throws org.ggf.drmaa.DrmaaException,
-                        org.ggf.drmaa.InvalidJobException
-
-
Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -

-

- -
Throws: -
org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it - will throw this exception for all finished or cancelled jobs -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getJobStatus

-
-@Deprecated
-public static java.lang.String getJobStatus(int status)
-                                     throws org.ggf.drmaa.DrmaaException
-
-
Deprecated.  -

-

Method for getting jobs status by quering the cluster, It returns status - in therms of a Sessions, not a JobStatus Should only be used for testing! -

-

-
Parameters:
status - -
Returns:
-
Throws: -
org.ggf.drmaa.DrmaaException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html deleted file mode 100644 index ad68763..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html +++ /dev/null @@ -1,314 +0,0 @@ - - - - - - -ClusterUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class ClusterUtil

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.ClusterUtil
-
-
-
-
public class ClusterUtil
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.text.NumberFormatCLUSTER_STAT_IN_SEC - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ClusterUtil() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static booleancancelJob(java.lang.String jobId, - ClusterSession csession) - -
-           
-static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, - java.lang.String jobId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-CLUSTER_STAT_IN_SEC

-
-public static final java.text.NumberFormat CLUSTER_STAT_IN_SEC
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-ClusterUtil

-
-public ClusterUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-public static final boolean cancelJob(java.lang.String jobId,
-                                      ClusterSession csession)
-
-
-
-
-
-
- -

-waitForResult

-
-public static final org.ggf.drmaa.JobInfo waitForResult(ClusterSession csession,
-                                                        java.lang.String jobId)
-                                                 throws JobExecutionException
-
-
- -
Throws: -
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
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html deleted file mode 100644 index da7c2e3..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html +++ /dev/null @@ -1,487 +0,0 @@ - - - - - - -JobRunner - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class JobRunner

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.JobRunner
-
-
-
All Implemented Interfaces:
SyncExecutor
-
-
-
-
public class JobRunner
extends java.lang.Object
implements SyncExecutor
- - -

-Single cluster job runner class -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
JobRunner(ConfiguredExecutable<?> confExec) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- booleandeepClean() - -
-           
- voidexecuteJob() - -
-          Execute the job
-static JobRunnergetInstance(ConfiguredExecutable<?> executable) - -
-           
- org.ggf.drmaa.JobInfogetJobInfo() - -
-          This method will block before the calculation has completed and then - return the object containing a job execution statistics
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- java.lang.StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-JobRunner

-
-public JobRunner(ConfiguredExecutable<?> confExec)
-          throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
- - - - - - - - -
-Method Detail
- -

-deepClean

-
-public boolean deepClean()
-
-
-
-
-
-
-
-
-
- -

-cleanup

-
-public boolean cleanup()
-
-
Description copied from interface: SyncExecutor
-
Clean up after the job -

-

-
Specified by:
cleanup in interface SyncExecutor
-
-
- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
-
- -

-cancelJob

-
-public boolean cancelJob()
-
-
Description copied from interface: SyncExecutor
-
Stops running job. - Clean up is not performed. -

-

-
Specified by:
cancelJob in interface SyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getWorkDirectory

-
-public java.lang.String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface SyncExecutor
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-executeJob

-
-public void executeJob()
-                throws JobSubmissionException
-
-
Description copied from interface: SyncExecutor
-
Execute the job -

-

-
Specified by:
executeJob in interface SyncExecutor
-
-
- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-getJobInfo

-
-public org.ggf.drmaa.JobInfo getJobInfo()
-                                 throws JobExecutionException
-
-
This method will block before the calculation has completed and then - return the object containing a job execution statistics -

-

-
-
-
- -
Returns:
-
Throws: -
JobExecutionException
-
-
-
- -

-waitForResult

-
-public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Description copied from interface: SyncExecutor
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

-
Specified by:
waitForResult in interface SyncExecutor
-
-
- -
Returns:
object from wich the result can be obtained -
Throws: -
JobExecutionException
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus()
-
-
Description copied from interface: SyncExecutor
-
Query the status of the job by its id. -

-

-
Specified by:
getJobStatus in interface SyncExecutor
-
-
- -
Returns:
- JobStatus
-
-
-
- -

-getInstance

-
-public static JobRunner getInstance(ConfiguredExecutable<?> executable)
-                             throws JobSubmissionException
-
-
-
-
-
- -
Throws: -
JobSubmissionException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html deleted file mode 100644 index da1ad93..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html +++ /dev/null @@ -1,759 +0,0 @@ - - - - - - -StatisticManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class StatisticManager

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa.StatisticManager
-
-
-
-
public class StatisticManager
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
StatisticManager(org.ggf.drmaa.JobInfo status) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetAllStats() - -
-           
- java.lang.StringgetCalculationTime() - -
-           
- java.lang.StringgetCPUTimeStat() - -
-           
- java.lang.StringgetCPUUsageTime() - -
-           
- java.lang.StringgetDataTransfered() - -
-           
- java.lang.StringgetEndTime() - -
-           
- java.lang.StringgetExecutionStat() - -
-           
- java.lang.StringgetExitStatus() - -
-           
- java.lang.StringgetIOWait() - -
-           
- java.lang.StringgetJobId() - -
-           
- java.lang.StringgetJobPriority() - -
-           
- java.lang.StringgetMaxVMem() - -
-           
- java.lang.StringgetMemoryStat() - -
-           
- java.util.Map<java.lang.String,java.lang.String>getRawUsage() - -
-           
- java.lang.StringgetStartTime() - -
-           
- java.lang.StringgetSubmissionTime() - -
-           
- java.lang.StringgetTimeStat() - -
-           
- java.lang.StringgetUsedSysTime() - -
-           
- java.lang.StringgetUsedUserTime() - -
-           
- java.lang.StringgetVMem() - -
-           
- booleanhasDump() - -
-           
- booleanhasExited() - -
-           
- booleanhasSignaled() - -
-           
- java.lang.StringtermSignal() - -
-           
- java.lang.StringtoString() - -
-           
- booleanwasAborted() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-StatisticManager

-
-public StatisticManager(org.ggf.drmaa.JobInfo status)
-                 throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
- - - - - - - - -
-Method Detail
- -

-getJobId

-
-public java.lang.String getJobId()
-                          throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasExited

-
-public boolean hasExited()
-                  throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasSignaled

-
-public boolean hasSignaled()
-                    throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-hasDump

-
-public boolean hasDump()
-                throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-termSignal

-
-public java.lang.String termSignal()
-                            throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-wasAborted

-
-public boolean wasAborted()
-                   throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getSubmissionTime

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

-getVMem

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

-getMaxVMem

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

-getUsedSysTime

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

-getUsedUserTime

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

-getCalculationTime

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

-getEndTime

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

-getStartTime

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

-getIOWait

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

-getCPUUsageTime

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

-getDataTransfered

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

-getJobPriority

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

-getExitStatus

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

-getAllStats

-
-public java.lang.String getAllStats()
-                             throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getExecutionStat

-
-public java.lang.String getExecutionStat()
-                                  throws org.ggf.drmaa.DrmaaException
-
-
- -
Throws: -
org.ggf.drmaa.DrmaaException
-
-
-
- -

-getMemoryStat

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

-getCPUTimeStat

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

-getTimeStat

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

-getRawUsage

-
-public java.util.Map<java.lang.String,java.lang.String> getRawUsage()
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
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- -compbio.engine.cluster.drmaa -
-Class _DrmaaExample

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa._DrmaaExample
-
-
-
-
public class _DrmaaExample
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
_DrmaaExample() - -
-           
-  - - - - - - - - - - - -
-Method Summary
-static voidmain(java.lang.String[] args) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-_DrmaaExample

-
-public _DrmaaExample()
-
-
- - - - - - - - -
-Method Detail
- -

-main

-
-public static void main(java.lang.String[] args)
-                 throws java.lang.Exception
-
-
- -
Throws: -
java.lang.Exception
-
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- - - -
- -

- -compbio.engine.cluster.drmaa -
-Class _JobStatus

-
-java.lang.Object
-  extended by compbio.engine.cluster.drmaa._JobStatus
-
-
-
-
public class _JobStatus
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
_JobStatus() - -
-           
-  - - - - - - - - - - - -
-Method Summary
-static voidmain(java.lang.String[] args) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-_JobStatus

-
-public _JobStatus()
-
-
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-Method Detail
- -

-main

-
-public static void main(java.lang.String[] args)
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-Uses of Class
compbio.engine.cluster.drmaa.ClusterSession

-
- - - - - - - - - -
-Packages that use ClusterSession
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
-  -

- - - - - -
-Uses of ClusterSession in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - - - - - -
Methods in compbio.engine.cluster.drmaa with parameters of type ClusterSession
-static booleanClusterUtil.cancelJob(java.lang.String jobId, - ClusterSession csession) - -
-           
-static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - java.lang.String jobId) - -
-           
-  -

-

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compbio.engine.cluster.drmaa.ClusterUtil

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-

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-Uses of Class
compbio.engine.cluster.drmaa.JobRunner

-
- - - - - - - - - -
-Packages that use JobRunner
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
-  -

- - - - - -
-Uses of JobRunner in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return JobRunner
-static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
-           
-  -

-

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-Uses of Class
compbio.engine.cluster.drmaa.StatisticManager

-
- - - - - - - - - -
-Packages that use StatisticManager
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
-  -

- - - - - -
-Uses of StatisticManager in compbio.engine.cluster.drmaa
-  -

- - - - - - - - - -
Methods in compbio.engine.cluster.drmaa that return StatisticManager
-static StatisticManagerClusterSession.getStatistics(org.ggf.drmaa.JobInfo status) - -
-           
-  -

-

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compbio.engine.cluster.drmaa._DrmaaExample

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-No usage of compbio.engine.cluster.drmaa._DrmaaExample -

-

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compbio.engine.cluster.drmaa._JobStatus

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-

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-Classes  - -
-_DrmaaExample -
-_JobStatus -
-AsyncJobRunner -
-ClusterSession -
-ClusterUtil -
-JobRunner -
-StatisticManager
- - - - diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html deleted file mode 100644 index a995ad5..0000000 --- a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - -compbio.engine.cluster.drmaa - - - - - - - - - - - - -
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-Package compbio.engine.cluster.drmaa -

-An cluster engine classes responsible for execution of Executables on the clusters. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
_DrmaaExample 
_JobStatus 
AsyncJobRunnerSingle cluster job runner class
ClusterSession 
ClusterUtil 
JobRunnerSingle cluster job runner class
StatisticManager 
-  - -

-

-Package compbio.engine.cluster.drmaa Description -

- -

-An cluster engine classes responsible for execution of Executables on the clusters. - Implementation uses DRMAA library. - Classes in this package depend on the data model classes. - They form a second layer of Jalview Web Services v2. -

- -

-

-
Author:
-
Petr Troshin - - Date January 2010
-
-
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-Hierarchy For Package compbio.engine.cluster.drmaa -

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Package Hierarchies:
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-Class Hierarchy -

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-Uses of Package
compbio.engine.cluster.drmaa

-
- - - - - - - - - -
-Packages that use compbio.engine.cluster.drmaa
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine.cluster.drmaa used by compbio.engine.cluster.drmaa
ClusterSession - -
-           
JobRunner - -
-          Single cluster job runner class
StatisticManager - -
-           
-  -

-

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- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.engine.cluster.dundee -
-Enum _Queue

-
-java.lang.Object
-  extended by java.lang.Enum<_Queue>
-      extended by compbio.engine.cluster.dundee._Queue
-
-
-
All Implemented Interfaces:
java.io.Serializable, java.lang.Comparable<_Queue>
-
-
-
-
public enum _Queue
extends java.lang.Enum<_Queue>
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
BIGINT - -
-           
BIGMEM - -
-           
BIT64 - -
-           
DEVEL - -
-          Order of the constraint reflect the priority of the queue
PRIBIT64 - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetMemoryLimit() - -
-          return max memory limit in Mb
-static _QueuegetQueue(int maxMemory, - int timeLimitInHours) - -
-           
- _QueuegetQueue(java.lang.String queueName) - -
-           
-static _QueuegetQueueByMemoryRequirements(int maxMemory) - -
-           
- intgetTimeLimit() - -
-          0 - unlimited
- booleanhasTimeLimit() - -
-           
- java.lang.StringtoString() - -
-           
-static _QueuevalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static _Queue[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-DEVEL

-
-public static final _Queue DEVEL
-
-
Order of the constraint reflect the priority of the queue -

-

-
-
-
- -

-PRIBIT64

-
-public static final _Queue PRIBIT64
-
-
-
-
-
- -

-BIT64

-
-public static final _Queue BIT64
-
-
-
-
-
- -

-BIGINT

-
-public static final _Queue BIGINT
-
-
-
-
-
- -

-BIGMEM

-
-public static final _Queue BIGMEM
-
-
-
-
- - - - - - - - -
-Method Detail
- -

-values

-
-public static _Queue[] 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 (_Queue c : _Queue.values())
-    System.out.println(c);
-
-

-

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

-valueOf

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

-

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

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Enum<_Queue>
-
-
-
-
-
-
- -

-getTimeLimit

-
-public int getTimeLimit()
-
-
0 - unlimited -

-

- -
Returns:
max runtime in hours
-
-
-
- -

-hasTimeLimit

-
-public boolean hasTimeLimit()
-
-
- -
Returns:
true if the queue has time limit, false overwise
-
-
-
- -

-getMemoryLimit

-
-public int getMemoryLimit()
-
-
return max memory limit in Mb -

-

- -
Returns:
-
-
-
- -

-getQueueByMemoryRequirements

-
-public static _Queue getQueueByMemoryRequirements(int maxMemory)
-
-
-
-
-
-
- -

-getQueue

-
-public static _Queue getQueue(int maxMemory,
-                              int timeLimitInHours)
-
-
-
-
-
-
- -

-getQueue

-
-public _Queue getQueue(java.lang.String queueName)
-
-
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-
-
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html deleted file mode 100644 index f951552..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html +++ /dev/null @@ -1,281 +0,0 @@ - - - - - - -_QueueConstraints - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.cluster.dundee -
-Class _QueueConstraints

-
-java.lang.Object
-  extended by compbio.engine.cluster.dundee._QueueConstraints
-
-
-
-
public final class _QueueConstraints
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - - - - - - - - - - - - - -
-Field Summary
-static intFIRST_MEMORY_LIMIT - -
-           
-static intLONG_TIME_LIMIT - -
-           
-static intMAX_MEMORY_LIMIT - -
-           
-static intSHORT_TIME_LIMIT - -
-           
-  - - - - - - - -
-Method Summary
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-SHORT_TIME_LIMIT

-
-public static final int SHORT_TIME_LIMIT
-
-
-
See Also:
Constant Field Values
-
-
- -

-LONG_TIME_LIMIT

-
-public static final int LONG_TIME_LIMIT
-
-
-
See Also:
Constant Field Values
-
-
- -

-FIRST_MEMORY_LIMIT

-
-public static final int FIRST_MEMORY_LIMIT
-
-
-
See Also:
Constant Field Values
-
-
- -

-MAX_MEMORY_LIMIT

-
-public static final int MAX_MEMORY_LIMIT
-
-
-
See Also:
Constant Field Values
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html deleted file mode 100644 index d5b990c..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - -Uses of Class compbio.engine.cluster.dundee._Queue - - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
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-
-

-Uses of Class
compbio.engine.cluster.dundee._Queue

-
- - - - - - - - - - - - - -
-Packages that use _Queue
compbio.engine.cluster.dundee  
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - -
-Uses of _Queue in compbio.engine.cluster.dundee
-  -

- - - - - - - - - - - - - - - - - - - - - - - - - -
Methods in compbio.engine.cluster.dundee that return _Queue
-static _Queue_Queue.getQueue(int maxMemory, - int timeLimitInHours) - -
-           
- _Queue_Queue.getQueue(java.lang.String queueName) - -
-           
-static _Queue_Queue.getQueueByMemoryRequirements(int maxMemory) - -
-           
-static _Queue_Queue.valueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static _Queue[]_Queue.values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  -

- - - - - -
-Uses of _Queue in compbio.runner
-  -

- - - - - - - - - -
Methods in compbio.runner that return _Queue
- _Queue_NativeSpecHelper.getApproprieteQueue() - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html deleted file mode 100644 index 233b459..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.engine.cluster.dundee._QueueConstraints - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.cluster.dundee._QueueConstraints

-
-No usage of compbio.engine.cluster.dundee._QueueConstraints -

-

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-Classes  - -
-_QueueConstraints
- - - - - - -
-Enums  - -
-_Queue
- - - - diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html deleted file mode 100644 index 5cbb529..0000000 --- a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - -compbio.engine.cluster.dundee - - - - - - - - - - - - -
- - - - - - - - - - - - - - - -
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-		 - -
- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
- - - -
-

-Package compbio.engine.cluster.dundee -

- - - - - - - - - -
-Class Summary
_QueueConstraints 
-  - -

- - - - - - - - - -
-Enum Summary
_Queue 
-  - -

-

-
-
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-Hierarchy For Package compbio.engine.cluster.dundee -

-
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-
Package Hierarchies:
All Packages
-
-

-Class Hierarchy -

- -

-Enum Hierarchy -

- -
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- - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- PREV  - NEXT - FRAMES   - NO FRAMES   -  - - - -
- - - -
-
-

-Uses of Package
compbio.engine.cluster.dundee

-
- - - - - - - - - - - - - -
-Packages that use compbio.engine.cluster.dundee
compbio.engine.cluster.dundee  
compbio.runnerUtilities commonly used by all runners. 
-  -

- - - - - - - - -
-Classes in compbio.engine.cluster.dundee used by compbio.engine.cluster.dundee
_Queue - -
-           
-  -

- - - - - - - - -
-Classes in compbio.engine.cluster.dundee used by compbio.runner
_Queue - -
-           
-  -

-

- - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html deleted file mode 100644 index f4e425b..0000000 --- a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html +++ /dev/null @@ -1,307 +0,0 @@ - - - - - - -DirectoryManager - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.conf -
-Class DirectoryManager

-
-java.lang.Object
-  extended by compbio.engine.conf.DirectoryManager
-
-
-
-
public class DirectoryManager
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringDELIM - -
-           
-  - - - - - - - - - - -
-Constructor Summary
DirectoryManager() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static java.lang.Class<Executable<?>>getClass(java.lang.String taskId) - -
-           
-static java.lang.StringgetTaskDirectory(java.lang.Class<?> clazz) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-DELIM

-
-public static final java.lang.String DELIM
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-DirectoryManager

-
-public DirectoryManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getTaskDirectory

-
-public static java.lang.String getTaskDirectory(java.lang.Class<?> clazz)
-
-
-
-
-
-
- -

-getClass

-
-public static java.lang.Class<Executable<?>> getClass(java.lang.String taskId)
-
-
-
-
-
- -
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html deleted file mode 100644 index d4816f8..0000000 --- a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html +++ /dev/null @@ -1,332 +0,0 @@ - - - - - - -PropertyHelperManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.conf -
-Class PropertyHelperManager

-
-java.lang.Object
-  extended by compbio.engine.conf.PropertyHelperManager
-
-
-
-
public final class PropertyHelperManager
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringconfDir - -
-           
-  - - - - - - - - - - -
-Constructor Summary
PropertyHelperManager() - -
-           
-  - - - - - - - - - - - - - - - -
-Method Summary
-static java.lang.StringgetLocalPath() - -
-          Method return the absolute path to the project root directory.
-static compbio.util.PropertyHelpergetPropertyHelper() - -
-          Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-confDir

-
-public static final java.lang.String confDir
-
-
-
-
- - - - - - - - -
-Constructor Detail
- -

-PropertyHelperManager

-
-public PropertyHelperManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getPropertyHelper

-
-public static compbio.util.PropertyHelper getPropertyHelper()
-
-
Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. Then prepend this absolute path to the rest of - paths pros: no input from user cons: relocation of the source may cause - problems 2) Require users to add configuration directories to the class - path and then load entries from it. pros: cons: Many paths needs to be - added. Put significant burden on the user. Hard to tell web appl server - to add these entries to its class path. 3) Ask for project source - directory explicitly in the configuration. pros cons: similar to 1, but - this initial configuration file must reside in well known location! Why - ask users what can be found automatically? 4) Have everything in the - location already in class path for tomcat. cons: only classes and - lib/*.jar are added, eclipse will remove non classses from classes dir. - - Try 1 - succeed. -

-

- -
Returns:
-
-
-
- -

-getLocalPath

-
-public static java.lang.String getLocalPath()
-
-
Method return the absolute path to the project root directory. It assumes - the following structure of the project project root conf settings - binaries WEB-INF classes compbio engine conf If the structure changes it - must be reflected in this method -

-

- -
Returns:
-
Throws: -
javax.naming.ConfigurationException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html deleted file mode 100644 index 6457ed8..0000000 --- a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html +++ /dev/null @@ -1,507 +0,0 @@ - - - - - - -RunnerConfigMarshaller - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.conf -
-Class RunnerConfigMarshaller<T>

-
-java.lang.Object
-  extended by compbio.engine.conf.RunnerConfigMarshaller<T>
-
-
-
-
public class RunnerConfigMarshaller<T>
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - - - - -
-Constructor Summary
RunnerConfigMarshaller(java.lang.Class<?> rootClass) - -
-           
RunnerConfigMarshaller(java.lang.Class<?> rootClass, - java.lang.Class<?>... classes) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static javax.xml.validation.SchemagetSchema(java.lang.String schemafile) - -
-           
-static javax.xml.validation.ValidatorgetValidator(javax.xml.validation.Schema schema) - -
-           
-static javax.xml.validation.ValidatorgetValidator(java.lang.String schemafile) - -
-           
- - - - - -
-<V> V
-		read(java.io.InputStream instream, - java.lang.Class<V> resultElemType) - -
-           
- - - - - -
-<V> V
-		read(java.io.InputStream instream, - java.lang.Class<V> resultElemType, - java.lang.Class<?>... classes) - -
-           
- - - - - -
-<V> V
-		readAndValidate(java.io.InputStream document, - java.lang.Class<V> resultElemType) - -
-           
-static booleanvalidate(javax.xml.validation.Validator validator, - java.lang.String document) - -
-           
- voidwrite(java.lang.Object xmlRootElement, - java.io.OutputStream out) - -
-           
- voidwriteAndValidate(java.lang.Object xmlRootElement, - java.lang.String schemafile, - java.io.OutputStream out) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-RunnerConfigMarshaller

-
-public RunnerConfigMarshaller(java.lang.Class<?> rootClass)
-                       throws javax.xml.bind.JAXBException
-
-
- -
Throws: -
javax.xml.bind.JAXBException
-
-
- -

-RunnerConfigMarshaller

-
-public RunnerConfigMarshaller(java.lang.Class<?> rootClass,
-                              java.lang.Class<?>... classes)
-                       throws javax.xml.bind.JAXBException
-
-
- -
Throws: -
javax.xml.bind.JAXBException
-
- - - - - - - - -
-Method Detail
- -

-write

-
-public void write(java.lang.Object xmlRootElement,
-                  java.io.OutputStream out)
-           throws javax.xml.bind.JAXBException,
-                  java.io.IOException
-
-
- -
Throws: -
javax.xml.bind.JAXBException -
java.io.IOException
-
-
-
- -

-writeAndValidate

-
-public void writeAndValidate(java.lang.Object xmlRootElement,
-                             java.lang.String schemafile,
-                             java.io.OutputStream out)
-                      throws javax.xml.bind.JAXBException,
-                             java.io.IOException,
-                             org.xml.sax.SAXException
-
-
- -
Throws: -
javax.xml.bind.JAXBException -
java.io.IOException -
org.xml.sax.SAXException
-
-
-
- -

-getSchema

-
-public static javax.xml.validation.Schema getSchema(java.lang.String schemafile)
-                                             throws org.xml.sax.SAXException
-
-
- -
Throws: -
org.xml.sax.SAXException
-
-
-
- -

-getValidator

-
-public static javax.xml.validation.Validator getValidator(java.lang.String schemafile)
-                                                   throws org.xml.sax.SAXException
-
-
- -
Returns:
-
Throws: -
org.xml.sax.SAXException
-
-
-
- -

-getValidator

-
-public static javax.xml.validation.Validator getValidator(javax.xml.validation.Schema schema)
-                                                   throws org.xml.sax.SAXException
-
-
- -
Throws: -
org.xml.sax.SAXException
-
-
-
- -

-validate

-
-public static boolean validate(javax.xml.validation.Validator validator,
-                               java.lang.String document)
-                        throws java.io.IOException,
-                               org.xml.sax.SAXException
-
-
- -
Throws: -
java.io.IOException -
org.xml.sax.SAXException
-
-
-
- -

-readAndValidate

-
-public <V> V readAndValidate(java.io.InputStream document,
-                             java.lang.Class<V> resultElemType)
-                  throws javax.xml.bind.JAXBException,
-                         java.io.IOException,
-                         org.xml.sax.SAXException
-
-
- -
Throws: -
javax.xml.bind.JAXBException -
java.io.IOException -
org.xml.sax.SAXException
-
-
-
- -

-read

-
-public <V> V read(java.io.InputStream instream,
-                  java.lang.Class<V> resultElemType)
-       throws javax.xml.bind.JAXBException
-
-
- -
Throws: -
javax.xml.bind.JAXBException
-
-
-
- -

-read

-
-public <V> V read(java.io.InputStream instream,
-                  java.lang.Class<V> resultElemType,
-                  java.lang.Class<?>... classes)
-       throws javax.xml.bind.JAXBException
-
-
- -
Throws: -
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-
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- -compbio.engine.conf -
-Class _Key

-
-java.lang.Object
-  extended by compbio.engine.conf._Key
-
-
-
-
public final class _Key
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringDELIM - -
-           
-  - - - - - - - - - - -
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_Key(java.lang.Class<?> clazz) - -
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-  - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
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-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-DELIM

-
-public static final java.lang.String DELIM
-
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See Also:
Constant Field Values
-
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-Constructor Detail
- -

-_Key

-
-public _Key(java.lang.Class<?> clazz)
-
-
- - - - - - - - -
-Method Detail
- -

-equals

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

-toString

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

-hashCode

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

-parse

-
-public static _Key parse(java.lang.String key)
-
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compbio.engine.conf.DirectoryManager

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-

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-

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-Uses of Class
compbio.engine.conf._Key

-
- - - - - - - - - -
-Packages that use _Key
compbio.engine.confClasses commonly used by both engines. 
-  -

- - - - - -
-Uses of _Key in compbio.engine.conf
-  -

- - - - - - - - - -
Methods in compbio.engine.conf that return _Key
-static _Key_Key.parse(java.lang.String key) - -
-           
-  -

-

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-Classes  - -
-_Key -
-DirectoryManager -
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- - - - diff --git a/website/full_javadoc/compbio/engine/conf/package-summary.html b/website/full_javadoc/compbio/engine/conf/package-summary.html deleted file mode 100644 index 7dc8a3b..0000000 --- a/website/full_javadoc/compbio/engine/conf/package-summary.html +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - -compbio.engine.conf - - - - - - - - - - - - -
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- PREV PACKAGE  - NEXT PACKAGE - FRAMES   - NO FRAMES   -  - - - -
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-

-Package compbio.engine.conf -

-Classes commonly used by both engines. -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - -
-Class Summary
_Key 
DirectoryManager 
PropertyHelperManager 
RunnerConfigMarshaller<T> 
-  - -

-

-Package compbio.engine.conf Description -

- -

-Classes commonly used by both engines. -

- -

-

-
Author:
-
Petr Troshin - - Date January 2010
-
-
- - - - - - - - - - - - - - - -
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-Hierarchy For Package compbio.engine.conf -

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-Class Hierarchy -

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compbio.engine.conf

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compbio.engine.confClasses commonly used by both engines. 
-  -

- - - - - - - - -
-Classes in compbio.engine.conf used by compbio.engine.conf
_Key - -
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-

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- - - -
- -

- -compbio.engine.local -
-Class AsyncLocalRunner

-
-java.lang.Object
-  extended by compbio.engine.local.AsyncLocalRunner
-
-
-
All Implemented Interfaces:
AsyncExecutor
-
-
-
-
public final class AsyncLocalRunner
extends java.lang.Object
implements AsyncExecutor
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
AsyncLocalRunner() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob(java.lang.String jobId) - -
-          Stop running job.
- booleancleanup(java.lang.String jobId) - -
-          Remove all files and a job directory for a jobid.
- JobStatusgetJobStatus(java.lang.String jobId) - -
-          Query the status of the job
- ConfiguredExecutable<?>getResults(java.lang.String taskId) - -
-          Retrieve the results of the job.
- java.lang.StringgetWorkDirectory(java.lang.String jobId) - -
-           
- java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) - -
-          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-AsyncLocalRunner

-
-public AsyncLocalRunner()
-
-
- - - - - - - - -
-Method Detail
- -

-getWorkDirectory

-
-public java.lang.String getWorkDirectory(java.lang.String jobId)
-
-
-
Specified by:
getWorkDirectory in interface AsyncExecutor
-
-
-
Parameters:
jobId - unique job identifier -
Returns:
task working directory
-
-
-
- -

-cancelJob

-
-public boolean cancelJob(java.lang.String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. -

-

-
Specified by:
cancelJob in interface AsyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus(java.lang.String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Query the status of the job -

-

-
Specified by:
getJobStatus in interface AsyncExecutor
-
-
- -
Returns:
The JobStatus object representing the status of the job
See Also:
JobStatus
-
-
-
- -

-submitJob

-
-public java.lang.String submitJob(ConfiguredExecutable<?> executable)
-                           throws JobSubmissionException
-
-
Description copied from interface: AsyncExecutor
-
Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. - All it guarantees that the job will be eventually executed. - The start of execution will depend on the number of jobs in the queue. -

-

-
Specified by:
submitJob in interface AsyncExecutor
-
-
- -
Returns:
unique job identifier -
Throws: -
JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
-
-
-
- -

-cleanup

-
-public boolean cleanup(java.lang.String jobId)
-
-
Description copied from interface: AsyncExecutor
-
Remove all files and a job directory for a jobid. -

-

-
Specified by:
cleanup in interface AsyncExecutor
-
-
-
Parameters:
jobId - -
Returns:
-
-
-
- -

-getResults

-
-public ConfiguredExecutable<?> getResults(java.lang.String taskId)
-                                   throws ResultNotAvailableException
-
-
Description copied from interface: AsyncExecutor
-
Retrieve the results of the job. Please not that current implementations of this method - blocks if the task is running until the end of the calculation. -

-

-
Specified by:
getResults in interface AsyncExecutor
-
-
-
Parameters:
taskId - job identifier obtained at the job submission -
Returns:
ConfiguredExecutable object from which result can be obtained -
Throws: -
ResultNotAvailableException - if the result is not available for whatever reason. - Could be due to execution failure, or due to the results being removed from the server at - the time of request.
-
-
- -
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- - - -
- -

- -compbio.engine.local -
-Class ExecutableWrapper

-
-java.lang.Object
-  extended by compbio.engine.local.ExecutableWrapper
-
-
-
All Implemented Interfaces:
java.util.concurrent.Callable<ConfiguredExecutable<?>>
-
-
-
-
@Immutable
-public final class ExecutableWrapper
extends java.lang.Object
implements java.util.concurrent.Callable<ConfiguredExecutable<?>>
- - -

-

- -

- - - - - - - - - - - - - - - -
-Field Summary
-static java.lang.StringPROC_ERR_FILE - -
-           
-static java.lang.StringPROC_OUT_FILE - -
-           
-  - - - - - - - - - - -
-Constructor Summary
ExecutableWrapper(ConfiguredExecutable<?> executable, - java.lang.String workDirectory) - -
-           
-  - - - - - - - - - - - -
-Method Summary
- ConfiguredExecutable<?>call() - -
-          It is vital that output and error streams are captured immediately for - this call() to succeed.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-PROC_OUT_FILE

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

-PROC_ERR_FILE

-
-public static final java.lang.String PROC_ERR_FILE
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-ExecutableWrapper

-
-public ExecutableWrapper(ConfiguredExecutable<?> executable,
-                         java.lang.String workDirectory)
-                  throws JobSubmissionException
-
-
- -
Throws: -
JobSubmissionException
-
- - - - - - - - -
-Method Detail
- -

-call

-
-public ConfiguredExecutable<?> call()
-                             throws java.io.IOException
-
-
It is vital that output and error streams are captured immediately for - this call() to succeed. Thus each instance if ExecutableWrapper has 2 its - own thread ready to capture the output. If executor could not execute - capture immediately this could lead to the call method to stale, as - execution could not proceed without output being captured. Every call to - call() method will use 2 threads -

-

-
Specified by:
call in interface java.util.concurrent.Callable<ConfiguredExecutable<?>>
-
-
- -
Throws: -
java.io.IOException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html deleted file mode 100644 index a4edf4a..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - -LocalEngineUtil - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.local -
-Class LocalEngineUtil

-
-java.lang.Object
-  extended by compbio.engine.local.LocalEngineUtil
-
-
-
-
public final class LocalEngineUtil
extends java.lang.Object
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LocalEngineUtil() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static booleancancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String workDirectory) - -
-           
-static booleancleanup(ConfiguredExecutable<?> confExecutable) - -
-           
-static JobStatusgetJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
-           
-static JobStatusgetRecordedJobStatus(java.lang.String jobId) - -
-           
-static ConfiguredExecutable<?>getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String taskId) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-LocalEngineUtil

-
-public LocalEngineUtil()
-
-
- - - - - - - - -
-Method Detail
- -

-cancelJob

-
-public static boolean cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
-                                java.lang.String workDirectory)
-
-
-
-
-
-
- -

-getJobStatus

-
-public static JobStatus getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future)
-
-
-
-
-
-
- -

-getRecordedJobStatus

-
-public static JobStatus getRecordedJobStatus(java.lang.String jobId)
-
-
-
-
-
-
- -

-cleanup

-
-public static boolean cleanup(ConfiguredExecutable<?> confExecutable)
-
-
-
-
-
-
- -

-getResults

-
-public static ConfiguredExecutable<?> getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
-                                                 java.lang.String taskId)
-                                          throws ResultNotAvailableException
-
-
- -
Throws: -
ResultNotAvailableException
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html deleted file mode 100644 index 9cf5fd7..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html +++ /dev/null @@ -1,310 +0,0 @@ - - - - - - -LocalExecutorService - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.local -
-Class LocalExecutorService

-
-java.lang.Object
-  extended by java.util.concurrent.AbstractExecutorService
-      extended by java.util.concurrent.ThreadPoolExecutor
-          extended by compbio.engine.local.LocalExecutorService
-
-
-
All Implemented Interfaces:
java.util.concurrent.Executor, java.util.concurrent.ExecutorService
-
-
-
-
public final class LocalExecutorService
extends java.util.concurrent.ThreadPoolExecutor
- - -

-

- -

- - - - - - - -
-Nested Class Summary
-  - - - - - - - -
Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor
java.util.concurrent.ThreadPoolExecutor.AbortPolicy, java.util.concurrent.ThreadPoolExecutor.CallerRunsPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardOldestPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardPolicy
-  - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancanAcceptMoreWork() - -
-          If the Executor queue is empty
-static LocalExecutorServicegetExecutor() - -
-          This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally
-static voidshutDown() - -
-          This stops all executing processes via interruption.
-  - - - - - - - -
Methods inherited from class java.util.concurrent.ThreadPoolExecutor
allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow
-  - - - - - - - -
Methods inherited from class java.util.concurrent.AbstractExecutorService
invokeAll, invokeAll, invokeAny, invokeAny, submit, submit, submit
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-getExecutor

-
-public static LocalExecutorService getExecutor()
-
-
This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -

-

- -
Returns:
-
-
-
- -

-shutDown

-
-public static void shutDown()
-
-
This stops all executing processes via interruption. Thus it is vital - that all processes that use this service respond to interruption -

-

-
-
-
-
- -

-canAcceptMoreWork

-
-public boolean canAcceptMoreWork()
-
-
If the Executor queue is empty -

-

- -
Returns:
true is not all threads are busy, false overwise
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html deleted file mode 100644 index b64d9db..0000000 --- a/website/full_javadoc/compbio/engine/local/LocalRunner.html +++ /dev/null @@ -1,398 +0,0 @@ - - - - - - -LocalRunner - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.local -
-Class LocalRunner

-
-java.lang.Object
-  extended by compbio.engine.local.LocalRunner
-
-
-
All Implemented Interfaces:
SyncExecutor
-
-
-
-
public final class LocalRunner
extends java.lang.Object
implements SyncExecutor
- - -

-

- -

- - - - - - - - - - - -
-Constructor Summary
LocalRunner(ConfiguredExecutable<?> executable) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleancancelJob() - -
-          Stops running job.
- booleancleanup() - -
-          Clean up after the job
- voidexecuteJob() - -
-          Execute the job
- JobStatusgetJobStatus() - -
-          Query the status of the job by its id.
- java.lang.StringgetWorkDirectory() - -
-           
- ConfiguredExecutable<?>waitForResult() - -
-          Call to this method block for as long as it is required for an executable to finish its job.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-LocalRunner

-
-public LocalRunner(ConfiguredExecutable<?> executable)
-
-
- - - - - - - - -
-Method Detail
- -

-getWorkDirectory

-
-public java.lang.String getWorkDirectory()
-
-
-
Specified by:
getWorkDirectory in interface SyncExecutor
-
-
- -
Returns:
working directory if the task
-
-
-
- -

-cancelJob

-
-public boolean cancelJob()
-
-
Description copied from interface: SyncExecutor
-
Stops running job. - Clean up is not performed. -

-

-
Specified by:
cancelJob in interface SyncExecutor
-
-
- -
Returns:
true if job was cancelled successfully, false otherwise
-
-
-
- -

-getJobStatus

-
-public JobStatus getJobStatus()
-
-
Description copied from interface: SyncExecutor
-
Query the status of the job by its id. -

-

-
Specified by:
getJobStatus in interface SyncExecutor
-
-
- -
Returns:
- JobStatus
-
-
-
- -

-executeJob

-
-public void executeJob()
-                throws JobSubmissionException
-
-
Description copied from interface: SyncExecutor
-
Execute the job -

-

-
Specified by:
executeJob in interface SyncExecutor
-
-
- -
Throws: -
JobSubmissionException - if submission fails
-
-
-
- -

-waitForResult

-
-public ConfiguredExecutable<?> waitForResult()
-                                      throws JobExecutionException
-
-
Description copied from interface: SyncExecutor
-
Call to this method block for as long as it is required for an executable to finish its job. - If the calculation has been completed already, the this method returns results immediately. - This could return the result directly, but that would be type unsafe -

-

-
Specified by:
waitForResult in interface SyncExecutor
-
-
- -
Returns:
object from wich the result can be obtained -
Throws: -
java.util.concurrent.CancellationException -
JobExecutionException
-
-
-
- -

-cleanup

-
-public boolean cleanup()
-
-
Description copied from interface: SyncExecutor
-
Clean up after the job -

-

-
Specified by:
cleanup in interface SyncExecutor
-
-
- -
Returns:
true if all the files created by this job have been removed successfully, false otherwise
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html deleted file mode 100644 index 4ddf4c6..0000000 --- a/website/full_javadoc/compbio/engine/local/StreamGobbler.html +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - -StreamGobbler - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- - - -
- -

- -compbio.engine.local -
-Class StreamGobbler

-
-java.lang.Object
-  extended by compbio.engine.local.StreamGobbler
-
-
-
All Implemented Interfaces:
java.lang.Runnable
-
-
-
-
@ThreadSafe
-public class StreamGobbler
extends java.lang.Object
implements java.lang.Runnable
- - -

-

- -

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

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

-run

-
-public void run()
-
-
-
Specified by:
run in interface java.lang.Runnable
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html deleted file mode 100644 index e10952d..0000000 --- a/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html +++ /dev/null @@ -1,427 +0,0 @@ - - - - - - -_TrackingExecutor - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
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- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.engine.local -
-Class _TrackingExecutor

-
-java.lang.Object
-  extended by java.util.concurrent.AbstractExecutorService
-      extended by compbio.engine.local._TrackingExecutor
-
-
-
All Implemented Interfaces:
java.util.concurrent.Executor, java.util.concurrent.ExecutorService
-
-
-
-
public class _TrackingExecutor
extends java.util.concurrent.AbstractExecutorService
- - -

-This executor extends standard Java ExecutorService by adding the method to - obtain all Runnables which were running and did not complete upon executor - termination. For this to work properly Runnables must propagate an - Interruption exceptions, not swallow them, which a good Runnable should do - anyway. - - TODO it may be better to persists task from different place -

- -

-

-
Author:
-
pvtroshin
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
_TrackingExecutor(java.util.concurrent.ExecutorService executor) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanawaitTermination(long timeout, - java.util.concurrent.TimeUnit unit) - -
-           
- voidexecute(java.lang.Runnable runnable) - -
-           
- java.util.ListgetCancelledTasks() - -
-           
- booleanisShutdown() - -
-           
- booleanisTerminated() - -
-           
- voidshutdown() - -
-           
- java.util.List<java.lang.Runnable>shutdownNow() - -
-           
- - - - - -
-<T> java.util.concurrent.Future<T>
-		submit(java.util.concurrent.Callable<T> task) - -
-           
-  - - - - - - - -
Methods inherited from class java.util.concurrent.AbstractExecutorService
invokeAll, invokeAll, invokeAny, invokeAny, submit, submit
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-  -

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

-_TrackingExecutor

-
-public _TrackingExecutor(java.util.concurrent.ExecutorService executor)
-
-
- - - - - - - - -
-Method Detail
- -

-getCancelledTasks

-
-public java.util.List getCancelledTasks()
-
-
-
-
-
-
- -

-execute

-
-public void execute(java.lang.Runnable runnable)
-
-
-
-
-
-
- -

-submit

-
-public <T> java.util.concurrent.Future<T> submit(java.util.concurrent.Callable<T> task)
-
-
-
Specified by:
submit in interface java.util.concurrent.ExecutorService
Overrides:
submit in class java.util.concurrent.AbstractExecutorService
-
-
-
-
-
-
- -

-awaitTermination

-
-public boolean awaitTermination(long timeout,
-                                java.util.concurrent.TimeUnit unit)
-                         throws java.lang.InterruptedException
-
-
- -
Throws: -
java.lang.InterruptedException
-
-
-
- -

-isShutdown

-
-public boolean isShutdown()
-
-
-
-
-
-
- -

-isTerminated

-
-public boolean isTerminated()
-
-
-
-
-
-
- -

-shutdown

-
-public void shutdown()
-
-
-
-
-
-
- -

-shutdownNow

-
-public java.util.List<java.lang.Runnable> shutdownNow()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html deleted file mode 100644 index a5689d9..0000000 --- a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.engine.local.AsyncLocalRunner - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.local.AsyncLocalRunner

-
-No usage of compbio.engine.local.AsyncLocalRunner -

-

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compbio.engine.local.ExecutableWrapper

-
-No usage of compbio.engine.local.ExecutableWrapper -

-

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-Uses of Class
compbio.engine.local.LocalEngineUtil

-
-No usage of compbio.engine.local.LocalEngineUtil -

-

- - - - - - - - - - - - - - - -
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-Uses of Class
compbio.engine.local.LocalExecutorService

-
- - - - - - - - - -
-Packages that use LocalExecutorService
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
-  -

- - - - - -
-Uses of LocalExecutorService in compbio.engine.local
-  -

- - - - - - - - - -
Methods in compbio.engine.local that return LocalExecutorService
-static LocalExecutorServiceLocalExecutorService.getExecutor() - -
-          This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally
-  -

-

- - - - - - - - - - - - - - - -
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- - - - - - - - - - - - -
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-Uses of Class
compbio.engine.local.LocalRunner

-
-No usage of compbio.engine.local.LocalRunner -

-

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-Uses of Class
compbio.engine.local.StreamGobbler

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-Classes  - -
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-AsyncLocalRunner -
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-Package compbio.engine.local -

-An local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). -

-See: -
-          Description -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
_TrackingExecutorThis executor extends standard Java ExecutorService by adding the method to - obtain all Runnables which were running and did not complete upon executor - termination.
AsyncLocalRunner 
ExecutableWrapper 
LocalEngineUtil 
LocalExecutorService 
LocalRunner 
StreamGobbler 
-  - -

-

-Package compbio.engine.local Description -

- -

-An local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). - Implementation uses Java 6 Executor framework to execute native programmes in parallel in different threads. - Classes in this package depend on the data model classes. - They form a second layer of Jalview Web Services v2. -

- -

-

-
Author:
-
Petr Troshin - - Date January 2010
-
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-Uses of Package
compbio.engine.local

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- - - - - - - - - -
-Packages that use compbio.engine.local
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
-  -

- - - - - - - - -
-Classes in compbio.engine.local used by compbio.engine.local
LocalExecutorService - -
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-Interfaces  - -
-AsyncExecutor -
-SyncExecutor
- - - - - - -
-Classes  - -
-Cleaner -
-ClusterJobId -
-Configurator -
-FilePuller -
-Job -
-LoadBalancer -
-ProgressGetter -
-PulledFileCache -
-SubmissionManager
- - - - diff --git a/website/full_javadoc/compbio/engine/package-summary.html b/website/full_javadoc/compbio/engine/package-summary.html deleted file mode 100644 index da7acf2..0000000 --- a/website/full_javadoc/compbio/engine/package-summary.html +++ /dev/null @@ -1,208 +0,0 @@ - - - - - - -compbio.engine - - - - - - - - - - - - -
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-Package compbio.engine -

- - - - - - - - - - - - - -
-Interface Summary
AsyncExecutorAn asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
SyncExecutorSynchronous executor, is an engine to run the Executable synchronously.
-  - -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Class Summary
Cleaner 
ClusterJobId 
Configurator 
FilePuller 
Job 
LoadBalancer 
ProgressGetter 
PulledFileCache 
SubmissionManagerSubmit jobs for execution
-  - -

-

-
-
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Package Hierarchies:
All Packages
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-Class Hierarchy -

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-Interface Hierarchy -

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-Uses of Package
compbio.engine

-
- - - - - - - - - - - - - - - - - - - - - -
-Packages that use compbio.engine
compbio.engine  
compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
compbio.ws.server  
-  -

- - - - - - - - - - - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
ClusterJobId - -
-           
FilePuller - -
-           
Job - -
-           
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine.cluster.drmaa
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
ClusterJobId - -
-           
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - - - - -
-Classes in compbio.engine used by compbio.engine.local
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
SyncExecutor - -
-          Synchronous executor, is an engine to run the Executable synchronously.
-  -

- - - - - - - - -
-Classes in compbio.engine used by compbio.ws.server
AsyncExecutor - -
-          An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
-  -

-

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- -compbio.metadata -
-Interface Argument<T>

-
-
Type Parameters:
T - executable type
-
-
All Known Implementing Classes:
Option, Parameter
-
-
-
-
public interface Argument<T>
- - -

-An unmodifiable view for the options and parameters, with one exception - it - allows to set a value -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Parameter, -Option
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.lang.StringgetDefaultValue() - -
-           
- java.lang.StringgetDescription() - -
-           
- java.net.URLgetFurtherDetails() - -
-           
- java.lang.StringgetName() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-           
- voidsetValue(java.lang.String defaultValue) - -
-          Set default values for the parameter or an option
-  -

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

-getFurtherDetails

-
-java.net.URL getFurtherDetails()
-
-
-
-
-
-
- -

-getDefaultValue

-
-java.lang.String getDefaultValue()
-
-
-
-
-
-
- -

-getDescription

-
-java.lang.String getDescription()
-
-
-
-
-
-
- -

-getName

-
-java.lang.String getName()
-
-
-
-
-
-
- -

-getPossibleValues

-
-java.util.List<java.lang.String> getPossibleValues()
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-void setValue(java.lang.String defaultValue)
-              throws WrongParameterException
-
-
Set default values for the parameter or an option -

-

-
Parameters:
defaultValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
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- - - diff --git a/website/full_javadoc/compbio/metadata/ChunkHolder.html b/website/full_javadoc/compbio/metadata/ChunkHolder.html deleted file mode 100644 index 9b66ead..0000000 --- a/website/full_javadoc/compbio/metadata/ChunkHolder.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - -ChunkHolder - - - - - - - - - - - - -
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- - - -
- -

- -compbio.metadata -
-Class ChunkHolder

-
-java.lang.Object
-  extended by compbio.metadata.ChunkHolder
-
-
-
-
public class ChunkHolder
extends java.lang.Object
- - -

-Represents a chunk of string data together with the position in a file from - where corresponding to of the data. -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
ChunkHolder(java.lang.String chunk, - long position) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetChunk() - -
-           
- longgetNextPosition() - -
-           
- inthashCode() - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-ChunkHolder

-
-public ChunkHolder(java.lang.String chunk,
-                   long position)
-
-
- - - - - - - - -
-Method Detail
- -

-getChunk

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

-getNextPosition

-
-public long getNextPosition()
-
-
-
-
-
-
- -

-equals

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

-toString

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

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class java.lang.Object
-
-
-
-
-
- -
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- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html deleted file mode 100644 index 6e1b992..0000000 --- a/website/full_javadoc/compbio/metadata/JobExecutionException.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - -JobExecutionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
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Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- - - -
- -

- -compbio.metadata -
-Class JobExecutionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobExecutionException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class JobExecutionException
extends java.lang.Exception
- - -

-JobExecutionException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides DrmaaException -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
See Also:
Serialized Form
-
- -

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

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

-JobExecutionException

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

-JobExecutionException

-
-public JobExecutionException(java.lang.Throwable cause)
-
-
-
- -

-JobExecutionException

-
-public JobExecutionException(java.lang.String message,
-                             java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html deleted file mode 100644 index 7d716e8..0000000 --- a/website/full_javadoc/compbio/metadata/JobStatus.html +++ /dev/null @@ -1,465 +0,0 @@ - - - - - - -JobStatus - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- -

- -compbio.metadata -
-Enum JobStatus

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

-The status of the job. -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
-
- -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Enum Constant Summary
CANCELLED - -
-          Jobs that has been cancelled
COLLECTED - -
-          Results has been collected
FAILED - -
-          Failed jobs
FINISHED - -
-          Finished jobs
PENDING - -
-          Jobs which are in the queue and awaiting execution reported for cluster - jobs only
RUNNING - -
-          Jobs that are running
STARTED - -
-          Job calculation has been started.
SUBMITTED - -
-          Job has been submitted.
UNDEFINED - -
-          Represents jobs with unknown status
-  - - - - - - - - - - - - - - - -
-Method Summary
-static JobStatusvalueOf(java.lang.String name) - -
-          Returns the enum constant of this type with the specified name.
-static JobStatus[]values() - -
-          Returns an array containing the constants of this enum type, in -the order they are declared.
-  - - - - - - - -
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-PENDING

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

-

-
-
-
- -

-RUNNING

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

-

-
-
-
- -

-CANCELLED

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

-

-
-
-
- -

-FINISHED

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

-

-
-
-
- -

-FAILED

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

-

-
-
-
- -

-UNDEFINED

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

-

-
-
-
- -

-STARTED

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

-

-
-
-
- -

-SUBMITTED

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

-

-
-
-
- -

-COLLECTED

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

-

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

-values

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

-

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

-valueOf

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

-

-
Parameters:
name - the name of the enum constant to be returned. -
Returns:
the enum constant with the specified name -
Throws: -
java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
java.lang.NullPointerException - if the argument is null
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/JobSubmissionException.html deleted file mode 100644 index c290dba..0000000 --- a/website/full_javadoc/compbio/metadata/JobSubmissionException.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -JobSubmissionException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class JobSubmissionException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
-
-
-
-
public class JobSubmissionException
extends java.lang.Exception
- - -

-Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException. If - this exception is thrown the task has not been calculated -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Serialized Form
-
- -

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

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

-JobSubmissionException

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

-JobSubmissionException

-
-public JobSubmissionException(java.lang.Throwable cause)
-
-
-
- -

-JobSubmissionException

-
-public JobSubmissionException(java.lang.String message,
-                              java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html deleted file mode 100644 index f2f4095..0000000 --- a/website/full_javadoc/compbio/metadata/Limit.html +++ /dev/null @@ -1,459 +0,0 @@ - - - - - - -Limit - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Limit<T>

-
-java.lang.Object
-  extended by compbio.metadata.Limit<T>
-
-
-
Type Parameters:
T - the type of an executable for which this limit is defined.
-
-
-
public class Limit<T>
extends java.lang.Object
- - -

-A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. -

- -

-

-
Author:
-
pvtroshin - - Date January 2010
-
See Also:
LimitsManager
-
- -

- - - - - - - - - - - - - - -
-Constructor Summary
Limit(int seqNumber, - int seqLength, - java.lang.String preset) - -
-           
Limit(int seqNumber, - int seqLength, - java.lang.String preset, - boolean isDefault) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- intgetAvgSeqLength() - -
-           
-static intgetAvgSequenceLength(java.util.List<FastaSequence> data) - -
-          Calculates an average sequence length of the dataset
- java.lang.StringgetPreset() - -
-           
- intgetSeqNumber() - -
-           
- inthashCode() - -
-           
- booleanisDefault() - -
-           
- booleanisExceeded(java.util.List<FastaSequence> data) - -
-          Checks if the number of sequences or their average length in the dataset - exceeds limits the values defined by this Limit
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             java.lang.String preset)
-
-
-
- -

-Limit

-
-public Limit(int seqNumber,
-             int seqLength,
-             java.lang.String preset,
-             boolean isDefault)
-
-
- - - - - - - - -
-Method Detail
- -

-getPreset

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

-getAvgSeqLength

-
-public int getAvgSeqLength()
-
-
-
-
-
-
- -

-getSeqNumber

-
-public int getSeqNumber()
-
-
-
-
-
-
- -

-isDefault

-
-public boolean isDefault()
-
-
-
-
-
-
- -

-hashCode

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

-equals

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

-toString

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

-isExceeded

-
-public boolean isExceeded(java.util.List<FastaSequence> data)
-
-
Checks if the number of sequences or their average length in the dataset - exceeds limits the values defined by this Limit -

-

-
Parameters:
data - -
Returns:
true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise.
-
-
-
- -

-getAvgSequenceLength

-
-public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
-
-
Calculates an average sequence length of the dataset -

-

-
Parameters:
data - -
Returns:
an average sequence length in the input dataset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/LimitExceededException.html b/website/full_javadoc/compbio/metadata/LimitExceededException.html deleted file mode 100644 index 910baa8..0000000 --- a/website/full_javadoc/compbio/metadata/LimitExceededException.html +++ /dev/null @@ -1,357 +0,0 @@ - - - - - - -LimitExceededException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class LimitExceededException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.LimitExceededException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class LimitExceededException
extends JobSubmissionException
- - -

-Thrown if the task larger in size that the limit that applies to the - calculation. -

- -

-

-
Author:
-
pvtroshin - - Date February 2010
-
See Also:
Limit, -Serialized Form
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitExceededException(java.lang.String message) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intgetActualNumberofSequences() - -
-           
- intgetNumberOfSequencesAllowed() - -
-           
- intgetSequenceLenghtActual() - -
-           
- intgetSequenceLenghtAllowed() - -
-           
-static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-LimitExceededException

-
-public LimitExceededException(java.lang.String message)
-
-
- - - - - - - - -
-Method Detail
- -

-newLimitExceeded

-
-public static LimitExceededException newLimitExceeded(Limit<?> limit,
-                                                      java.util.List<FastaSequence> seqs)
-
-
-
-
-
-
- -

-getNumberOfSequencesAllowed

-
-public int getNumberOfSequencesAllowed()
-
-
-
-
-
-
- -

-getActualNumberofSequences

-
-public int getActualNumberofSequences()
-
-
-
-
-
-
- -

-getSequenceLenghtAllowed

-
-public int getSequenceLenghtAllowed()
-
-
-
-
-
-
- -

-getSequenceLenghtActual

-
-public int getSequenceLenghtActual()
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/LimitsManager.html b/website/full_javadoc/compbio/metadata/LimitsManager.html deleted file mode 100644 index 88195c6..0000000 --- a/website/full_javadoc/compbio/metadata/LimitsManager.html +++ /dev/null @@ -1,363 +0,0 @@ - - - - - - -LimitsManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class LimitsManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.LimitsManager<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class LimitsManager<T>
extends java.lang.Object
- - -

-A collection of Limits -

- -

-

-
Author:
-
pvtroshin - - Date January 2010
-
See Also:
Limit
-
- -

- - - - - - - - - - - -
-Constructor Summary
LimitsManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Limit<T>getDefaultLimit() - -
-           
- Limit<T>getLimitByName(java.lang.String presetName) - -
-           
- java.util.List<Limit<T>>getLimits() - -
-           
- java.lang.StringtoString() - -
-           
- voidvalidate(PresetManager<T> presets) - -
-          Validate Limits
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-LimitsManager

-
-public LimitsManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getLimits

-
-public java.util.List<Limit<T>> getLimits()
-
-
- -
Returns:
all limits defined for an executable T
-
-
-
- -

-toString

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

-getLimitByName

-
-public Limit<T> getLimitByName(java.lang.String presetName)
-
-
-
Parameters:
presetName - -
Returns:
Limit defined for the executable T and presetName. If no limit is - defined for the presetName then default Limit is returned. If - presetName is empty or null than the default Limit will be - returned. If not limit defined for the type T than NULL will be - returned
-
-
-
- -

-getDefaultLimit

-
-public Limit<T> getDefaultLimit()
-
-
- -
Returns:
the default Limit for an executable type T
-
-
-
- -

-validate

-
-public void validate(PresetManager<T> presets)
-              throws javax.xml.bind.ValidationException
-
-
Validate Limits -

-

-
Parameters:
presets - -
Throws: -
javax.xml.bind.ValidationException - if any of the Limit defined is found to be invalid. That is - when - - 1) No default limit is defined - - 2) More than 1 default limit is defined - - 3) Limit's preset name does not match any presets for type T
See Also:
Limit, -Preset
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Option.html b/website/full_javadoc/compbio/metadata/Option.html deleted file mode 100644 index 1bb99d9..0000000 --- a/website/full_javadoc/compbio/metadata/Option.html +++ /dev/null @@ -1,714 +0,0 @@ - - - - - - -Option - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Option<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-
-
-
Type Parameters:
T - type of executable
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
Direct Known Subclasses:
Parameter
-
-
-
-
public class Option<T>
extends java.lang.Object
implements Argument<T>
- - -

-Command line option/flag or multiple exclusive options with no value. Example - -protein, -dna, -auto -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
Option(java.lang.String name, - java.lang.String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) - -
-          Adds an option to the optionName list
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetDefaultValue() - -
-          A default value of the option.
- java.lang.StringgetDescription() - -
-          A long description of the Option
- java.net.URLgetFurtherDetails() - -
-          The URL where further details about the option can be found
- java.lang.StringgetName() - -
-          Human readable name of the option
- java.util.List<java.lang.String>getOptionNames() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-          List of possible optionNames
- inthashCode() - -
-           
- booleanisRequired() - -
-          Flag that indicated that this option must be specified in the command - line for an executable to run
- voidsetDefaultValue(java.lang.String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetDescription(java.lang.String description) - -
-           
- voidsetFurtherDetails(java.net.URL furtherDetails) - -
-           
- voidsetName(java.lang.String name) - -
-           
- voidsetOptionNames(java.util.Set<java.lang.String> optionNames) - -
-           
- voidsetRequired(boolean isRequired) - -
-           
- voidsetValue(java.lang.String dValue) - -
-          Set default values for the parameter or an option
- java.lang.StringtoCommand(java.lang.String nameValueSeparator) - -
-          Convert the option to the command string.
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-Option

-
-public Option(java.lang.String name,
-              java.lang.String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getName

-
-public java.lang.String getName()
-
-
Human readable name of the option -

-

-
Specified by:
getName in interface Argument<T>
-
-
-
-
-
-
- -

-setName

-
-public void setName(java.lang.String name)
-
-
-
-
-
-
-
-
-
- -

-getDescription

-
-public java.lang.String getDescription()
-
-
A long description of the Option -

-

-
Specified by:
getDescription in interface Argument<T>
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(java.lang.String description)
-
-
-
-
-
-
-
-
-
- -

-getFurtherDetails

-
-public java.net.URL getFurtherDetails()
-
-
The URL where further details about the option can be found -

-

-
Specified by:
getFurtherDetails in interface Argument<T>
-
-
-
-
-
-
- -

-setFurtherDetails

-
-public void setFurtherDetails(java.net.URL furtherDetails)
-
-
-
-
-
-
-
-
-
- -

-getDefaultValue

-
-public java.lang.String getDefaultValue()
-
-
A default value of the option. Defaults to command line argument name - e.g. -auto -

-

-
Specified by:
getDefaultValue in interface Argument<T>
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(java.lang.String defaultVal)
-                     throws WrongParameterException
-
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
-
-
-
Parameters:
defaultVal - -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
-
- -

-isRequired

-
-public boolean isRequired()
-
-
Flag that indicated that this option must be specified in the command - line for an executable to run -

-

-
-
-
- -
Returns:
true is the option is required, false otherwise
-
-
-
- -

-setRequired

-
-public void setRequired(boolean isRequired)
-
-
-
-
-
-
-
-
-
- -

-getOptionNames

-
-public java.util.List<java.lang.String> getOptionNames()
-
-
-
-
-
- -
Returns:
List of option names
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(java.util.Set<java.lang.String> optionNames)
-
-
-
-
-
-
-
-
-
- -

-addOptionNames

-
-public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
-
-
Adds an option to the optionName list -

-

-
-
-
-
Parameters:
value - -
Returns:
modified optionName list
-
-
-
- -

-toString

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

-toCommand

-
-public java.lang.String toCommand(java.lang.String nameValueSeparator)
-
-
Convert the option to the command string. -

-

-
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

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

-hashCode

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

-getPossibleValues

-
-public java.util.List<java.lang.String> getPossibleValues()
-
-
List of possible optionNames -

-

-
Specified by:
getPossibleValues in interface Argument<T>
-
-
- -
Returns:
List of values allowed for an Argument
-
-
-
- -

-setValue

-
-public void setValue(java.lang.String dValue)
-              throws WrongParameterException
-
-
Description copied from interface: Argument
-
Set default values for the parameter or an option -

-

-
Specified by:
setValue in interface Argument<T>
-
-
-
Parameters:
dValue - the value to be set -
Throws: -
WrongParameterException - - when the value to be set is illegal. Wrong value for - numeric parameter is the value defined outside it , for - string type parameter, wrong value is the one which is not - listed in possible values list
See Also:
ValueConstrain
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Parameter.html b/website/full_javadoc/compbio/metadata/Parameter.html deleted file mode 100644 index 45505e0..0000000 --- a/website/full_javadoc/compbio/metadata/Parameter.html +++ /dev/null @@ -1,572 +0,0 @@ - - - - - - -Parameter - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Parameter<T>

-
-java.lang.Object
-  extended by compbio.metadata.Option<T>
-      extended by compbio.metadata.Parameter<T>
-
-
-
All Implemented Interfaces:
Argument<T>
-
-
-
-
public class Parameter<T>
extends Option<T>
- - -

-A single value containing option supported by the web service e.g. - seqType=protein. Where seqType is a optionName and protein is one of - possibleValues -

- -

-

-
Author:
-
pvtroshin - - Date November 2009
-
See Also:
Option, -Argument
-
- -

- - - - - - - - - - - -
-Constructor Summary
Parameter(java.lang.String name, - java.lang.String description) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) - -
-          Adds an option to the optionName list
- java.util.Set<java.lang.String>addPossibleValues(java.lang.String... value) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- java.lang.StringgetOptionName() - -
-           
- java.util.List<java.lang.String>getPossibleValues() - -
-          List is more convenient to work with
- ValueConstraingetValidValue() - -
-           
- inthashCode() - -
-           
- voidsetDefaultValue(java.lang.String defaultVal) - -
-          Sets one of the values defined in optionList as default.
- voidsetOptionName(java.lang.String optionName) - -
-           
- voidsetOptionNames(java.util.Set<java.lang.String> optionName) - -
-           
- voidsetPossibleValues(java.util.Set<java.lang.String> possibleValues) - -
-           
- voidsetValidValue(ValueConstrain validValue) - -
-           
- java.lang.StringtoCommand(java.lang.String nameValueSeparator) - -
-          Convert the option to the command string.
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class compbio.metadata.Option
getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-Parameter

-
-public Parameter(java.lang.String name,
-                 java.lang.String description)
-
-
- - - - - - - - -
-Method Detail
- -

-getValidValue

-
-public ValueConstrain getValidValue()
-
-
-
-
-
-
- -

-setValidValue

-
-public void setValidValue(ValueConstrain validValue)
-
-
-
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class Option<T>
-
-
-
-
-
-
- -

-toCommand

-
-public java.lang.String toCommand(java.lang.String nameValueSeparator)
-
-
Description copied from class: Option
-
Convert the option to the command string. -

-

-
Overrides:
toCommand in class Option<T>
-
-
- -
Returns:
If only one optionName is defined, than it is returned, if many - option names are defined, then the defaultValue is returned. - Option must have a default value if there are many optionNames to - be valid.
-
-
-
- -

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class Option<T>
-
-
-
-
-
-
- -

-getPossibleValues

-
-public java.util.List<java.lang.String> getPossibleValues()
-
-
List is more convenient to work with -

-

-
Specified by:
getPossibleValues in interface Argument<T>
Overrides:
getPossibleValues in class Option<T>
-
-
- -
Returns:
List of String
-
-
-
- -

-setPossibleValues

-
-public void setPossibleValues(java.util.Set<java.lang.String> possibleValues)
-
-
-
-
-
-
- -

-addPossibleValues

-
-public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
-
-
-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Option<T>
-
-
-
-
-
-
- -

-setOptionNames

-
-public void setOptionNames(java.util.Set<java.lang.String> optionName)
-
-
-
Overrides:
setOptionNames in class Option<T>
-
-
-
-
-
-
- -

-addOptionNames

-
-public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
-
-
Description copied from class: Option
-
Adds an option to the optionName list -

-

-
Overrides:
addOptionNames in class Option<T>
-
-
- -
Returns:
modified optionName list
-
-
-
- -

-getOptionName

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

-setOptionName

-
-public void setOptionName(java.lang.String optionName)
-
-
-
-
-
-
- -

-setDefaultValue

-
-public void setDefaultValue(java.lang.String defaultVal)
-                     throws WrongParameterException
-
-
Description copied from class: Option
-
Sets one of the values defined in optionList as default. Attempting set - the value not listed there will result in WrongParameter exception -

-

-
Overrides:
setDefaultValue in class Option<T>
-
-
- -
Throws: -
WrongParameterException - is thrown if the defaultValue is not found in optionList
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/Preset.html b/website/full_javadoc/compbio/metadata/Preset.html deleted file mode 100644 index 2995b06..0000000 --- a/website/full_javadoc/compbio/metadata/Preset.html +++ /dev/null @@ -1,455 +0,0 @@ - - - - - - -Preset - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class Preset<T>

-
-java.lang.Object
-  extended by compbio.metadata.Preset<T>
-
-
-
Type Parameters:
T - executable type
-
-
-
public class Preset<T>
extends java.lang.Object
- - -

-Collection of Options and Parameters with their values -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
See Also:
Option, -Parameter
-
- -

- - - - - - - - - - - -
-Constructor Summary
Preset() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- booleanequals(java.lang.Object obj) - -
-           
- java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) - -
-          Converts list of options as String to type Option
- java.lang.StringgetDescription() - -
-           
- java.lang.StringgetName() - -
-           
- java.util.List<java.lang.String>getOptions() - -
-           
- inthashCode() - -
-           
- voidsetDescription(java.lang.String description) - -
-           
- voidsetName(java.lang.String name) - -
-           
- voidsetOptions(java.util.List<java.lang.String> option) - -
-           
- java.lang.StringtoString() - -
-           
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

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

-Preset

-
-public Preset()
-
-
- - - - - - - - -
-Method Detail
- -

-setOptions

-
-public void setOptions(java.util.List<java.lang.String> option)
-
-
-
-
-
-
- -

-setName

-
-public void setName(java.lang.String name)
-
-
-
-
-
-
- -

-setDescription

-
-public void setDescription(java.lang.String description)
-
-
-
-
-
-
- -

-getOptions

-
-public java.util.List<java.lang.String> getOptions()
-
-
- -
Returns:
a List of Options as a String
-
-
-
- -

-getName

-
-public java.lang.String getName()
-
-
- -
Returns:
- name of the Preset
-
-
-
- -

-getDescription

-
-public java.lang.String getDescription()
-
-
- -
Returns:
- a long description of the Preset
-
-
-
- -

-getArguments

-
-public java.util.List<Option<T>> getArguments(RunnerConfig<T> rconfig)
-                                       throws WrongParameterException
-
-
Converts list of options as String to type Option -

-

-
Parameters:
rconfig - -
Returns:
List of Options -
Throws: -
WrongParameterException - if the value of the parameter is invalid @see - Parameter
-
-
-
- -

-toString

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

-hashCode

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

-equals

-
-public boolean equals(java.lang.Object obj)
-
-
-
Overrides:
equals in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/PresetManager.html b/website/full_javadoc/compbio/metadata/PresetManager.html deleted file mode 100644 index 17b792a..0000000 --- a/website/full_javadoc/compbio/metadata/PresetManager.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - -PresetManager - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class PresetManager<T>

-
-java.lang.Object
-  extended by compbio.metadata.PresetManager<T>
-
-
-
Type Parameters:
T - type of executable.
-
-
-
public class PresetManager<T>
extends java.lang.Object
- - -

-Collection of presets and methods to manipulate them @see Preset -

- -

-

-
Author:
-
pvtroshin - - Date December 2009
-
-
- -

- - - - - - - - - - - -
-Field Summary
-static java.lang.StringLOCAL_ENGINE_LIMIT_PRESET - -
-           
-  - - - - - - - - - - -
-Constructor Summary
PresetManager() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- Preset<T>getPresetByName(java.lang.String presetName) - -
-           
- java.util.List<Preset<T>>getPresets() - -
-           
- java.lang.StringgetRunnerClassName() - -
-           
- voidsetPresets(java.util.List<Preset<T>> presets) - -
-           
- voidsetRunnerClassName(java.lang.String runnerClassName) - -
-           
- java.lang.StringtoString() - -
-           
- voidvalidate(RunnerConfig<T> options) - -
-          Checks whether preset option and parameter are defined in RunnerConfig - object.
-  - - - - - - - -
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-LOCAL_ENGINE_LIMIT_PRESET

-
-public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
-
-
-
See Also:
Constant Field Values
-
- - - - - - - - -
-Constructor Detail
- -

-PresetManager

-
-public PresetManager()
-
-
- - - - - - - - -
-Method Detail
- -

-getPresets

-
-public java.util.List<Preset<T>> getPresets()
-
-
-
-
-
-
- -

-setPresets

-
-public void setPresets(java.util.List<Preset<T>> presets)
-
-
-
-
-
-
- -

-getRunnerClassName

-
-public java.lang.String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name of type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(java.lang.String runnerClassName)
-
-
-
-
-
-
- -

-getPresetByName

-
-public Preset<T> getPresetByName(java.lang.String presetName)
-
-
-
Parameters:
presetName - -
Returns:
preset by its name, null if no preset found
-
-
-
- -

-validate

-
-public void validate(RunnerConfig<T> options)
-              throws javax.xml.bind.ValidationException
-
-
Checks whether preset option and parameter are defined in RunnerConfig - object. - - TODO handle parameters with values properly! -

-

- -
Throws: -
javax.xml.bind.ValidationException - if preset is found to be invalid.
-
-
-
- -

-toString

-
-public java.lang.String toString()
-
-
-
Overrides:
toString in class java.lang.Object
-
-
-
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html deleted file mode 100644 index c0d8b57..0000000 --- a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html +++ /dev/null @@ -1,280 +0,0 @@ - - - - - - -ResultNotAvailableException - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class ResultNotAvailableException

-
-java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.ResultNotAvailableException
-
-
-
All Implemented Interfaces:
java.io.Serializable
-
-
-
-
public class ResultNotAvailableException
extends java.lang.Exception
- - -

-ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained. For cluster execution it hides lower level exceptions - like DrmaaException -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
See Also:
Serialized Form
-
- -

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

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

-ResultNotAvailableException

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

-ResultNotAvailableException

-
-public ResultNotAvailableException(java.lang.Throwable cause)
-
-
-
- -

-ResultNotAvailableException

-
-public ResultNotAvailableException(java.lang.String message,
-                                   java.lang.Throwable cause)
-
-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - - diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html deleted file mode 100644 index 7f59fd8..0000000 --- a/website/full_javadoc/compbio/metadata/RunnerConfig.html +++ /dev/null @@ -1,640 +0,0 @@ - - - - - - -RunnerConfig - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- -

- -compbio.metadata -
-Class RunnerConfig<T>

-
-java.lang.Object
-  extended by compbio.metadata.RunnerConfig<T>
-
-
-
Type Parameters:
T - type of an Executable
-
-
-
@NotThreadSafe
-public class RunnerConfig<T>
extends java.lang.Object
- - -

-The list of Parameters and Options supported by executable. -

- -

-

-
Author:
-
pvtroshin - - Date October 2009
-
-
- -

- - - - - - - - - - - -
-Constructor Summary
RunnerConfig() - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- voidaddOption(Option<T> option) - -
-           
- voidaddParameter(Parameter<T> param) - -
-           
- RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
-           
- booleanequals(java.lang.Object obj) - -
-           
- Option<T>getArgument(java.lang.String name) - -
-          Returns the argument by its name if found, NULL otherwise
- Option<T>getArgumentByOptionName(java.lang.String optionName) - -
-          Returns the argument by option name, NULL if the argument is not found
- java.util.List<Option<T>>getArguments() - -
-           
- java.util.List<Option<T>>getOptions() - -
-           
- java.util.List<Parameter<T>>getParameters() - -
-           
- java.lang.StringgetPrmSeparator() - -
-           
- java.lang.StringgetRunnerClassName() - -
-           
- booleanremoveArgument(java.lang.String name) - -
-          Removes the argument Argument if found.
- booleanremoveArgumentByOptionName(java.lang.String optionName) - -
-          Removes the argument
- voidsetOptions(java.util.List<Option<T>> parameters) - -
-           
- voidsetParameters(java.util.List<Parameter<T>> parameters) - -
-           
- voidsetPrmSeparator(java.lang.String prmSeparator) - -
-           
- voidsetRunnerClassName(java.lang.String runnerClassName) - -
-           
- java.lang.StringtoString() - -
-           
- voidvalidate() - -
-          Validate the arguments
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, wait
-  -

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

-RunnerConfig

-
-public RunnerConfig()
-
-
- - - - - - - - -
-Method Detail
- -

-copyAndValidateRConfig

-
-public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
-
-
-
-
-
-
- -

-getOptions

-
-public java.util.List<Option<T>> getOptions()
-
-
- -
Returns:
list of Option supported by type T
-
-
-
- -

-addParameter

-
-public void addParameter(Parameter<T> param)
-
-
-
-
-
-
- -

-addOption

-
-public void addOption(Option<T> option)
-
-
-
-
-
-
- -

-getArguments

-
-public java.util.List<Option<T>> getArguments()
-
-
- -
Returns:
list of Option and Parameter supported by type T
-
-
-
- -

-getPrmSeparator

-
-public java.lang.String getPrmSeparator()
-
-
- -
Returns:
name value separator character
-
-
-
- -

-setPrmSeparator

-
-public void setPrmSeparator(java.lang.String prmSeparator)
-
-
-
-
-
-
- -

-setOptions

-
-public void setOptions(java.util.List<Option<T>> parameters)
-
-
-
-
-
-
- -

-getRunnerClassName

-
-public java.lang.String getRunnerClassName()
-
-
- -
Returns:
fully qualified class name for type T
-
-
-
- -

-setRunnerClassName

-
-public void setRunnerClassName(java.lang.String runnerClassName)
-
-
-
-
-
-
- -

-setParameters

-
-public void setParameters(java.util.List<Parameter<T>> parameters)
-
-
-
-
-
-
- -

-getParameters

-
-public java.util.List<Parameter<T>> getParameters()
-
-
- -
Returns:
List of Parameter supported by type T.
-
-
-
- -

-toString

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

-equals

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

-getArgument

-
-public Option<T> getArgument(java.lang.String name)
-
-
Returns the argument by its name if found, NULL otherwise -

-

-
Parameters:
name - -
Returns:
Argument
-
-
-
- -

-removeArgument

-
-public boolean removeArgument(java.lang.String name)
-
-
Removes the argument Argument if found. -

-

-
Parameters:
name - of the argument -
Returns:
true if argument was removed, false otherwise
-
-
-
- -

-getArgumentByOptionName

-
-public Option<T> getArgumentByOptionName(java.lang.String optionName)
-
-
Returns the argument by option name, NULL if the argument is not found -

-

-
Parameters:
optionName - - the name of the option -
Returns:
Option
-
-
-
- -

-removeArgumentByOptionName

-
-public boolean removeArgumentByOptionName(java.lang.String optionName)
-
-
Removes the argument -

-

-
Parameters:
optionName - -
Returns:
true if argument with optionName exists and was removed, false - otherwise
-
-
-
- -

-validate

-
-public void validate()
-              throws javax.xml.bind.ValidationException
-
-
Validate the arguments -

-

- -
Throws: -
javax.xml.bind.ValidationException - if any of the arguments found invalid which is when -
-
  • Parameter value outside ValueConstrain boundary
    • -
  • Parameter name is not listed in possible values
    • -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html deleted file mode 100644 index b7d4950..0000000 --- a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -UnsupportedRuntimeException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class UnsupportedRuntimeException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.JobSubmissionException
-              extended by compbio.metadata.UnsupportedRuntimeException
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable
    -
    -
    -
    -
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    - - -

    -Indicates that the server could not execute native executables. e.g. If Mafft - (unix executable) is asked to be run on Windows. In context of JABAWS this - exception indicates that the service is deployed but is not able to run. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date February 2010
    -
    See Also:
    Serialized Form
    -
    - -

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

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

    -UnsupportedRuntimeException

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

    -UnsupportedRuntimeException

    -
    -public UnsupportedRuntimeException(java.lang.Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html deleted file mode 100644 index 62a7160..0000000 --- a/website/full_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:
    java.io.Serializable, java.lang.Comparable<ValueConstrain.Type>
    -
    -
    -
    Enclosing class:
    ValueConstrain
    -
    -
    -
    -
    public static enum ValueConstrain.Type
    extends java.lang.Enum<ValueConstrain.Type>
    - - -

    -

    - -

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

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

    -Integer

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

    -Float

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

    -values

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

    -

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

    -valueOf

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

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
    java.lang.NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html deleted file mode 100644 index 0d924f6..0000000 --- a/website/full_javadoc/compbio/metadata/ValueConstrain.html +++ /dev/null @@ -1,440 +0,0 @@ - - - - - - -ValueConstrain - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class ValueConstrain

    -
    -java.lang.Object
-  extended by compbio.metadata.ValueConstrain
-
    -
    -
    -
    public class ValueConstrain
    extends java.lang.Object
    - - -

    -The type and the lower and upper boundaries for numerical value. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date November 2009
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classValueConstrain.Type - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ValueConstrain() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - booleanequals(java.lang.Object obj) - -
    -           
    - java.lang.NumbergetMax() - -
    -           
    - java.lang.NumbergetMin() - -
    -           
    - ValueConstrain.TypegetType() - -
    -           
    - inthashCode() - -
    -           
    - voidsetMax(java.lang.String max) - -
    -           
    - voidsetMin(java.lang.String min) - -
    -           
    - voidsetType(ValueConstrain.Type type) - -
    -           
    - java.lang.StringtoString() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -ValueConstrain

    -
    -public ValueConstrain()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getType

    -
    -public ValueConstrain.Type getType()
    -
    -
    -
    -
    -
    -
    - -

    -setType

    -
    -public void setType(ValueConstrain.Type type)
    -
    -
    -
    -
    -
    -
    - -

    -getMax

    -
    -public java.lang.Number getMax()
    -
    -
    -
    -
    -
    -
    - -

    -setMax

    -
    -public void setMax(java.lang.String max)
    -
    -
    -
    -
    -
    -
    - -

    -getMin

    -
    -public java.lang.Number getMin()
    -
    -
    -
    -
    -
    -
    - -

    -setMin

    -
    -public void setMin(java.lang.String min)
    -
    -
    -
    -
    -
    -
    - -

    -equals

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

    -toString

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

    -hashCode

    -
    -public int hashCode()
    -
    -
    -
    Overrides:
    hashCode in class java.lang.Object
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html deleted file mode 100644 index 9d95892..0000000 --- a/website/full_javadoc/compbio/metadata/WrongParameterException.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - -WrongParameterException - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.metadata -
    -Class WrongParameterException

    -
    -java.lang.Object
-  extended by java.lang.Throwable
-      extended by java.lang.Exception
-          extended by compbio.metadata.WrongParameterException
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable
    -
    -
    -
    -
    public class WrongParameterException
    extends java.lang.Exception
    - - -

    -WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value. -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date October 2009
    -
    See Also:
    Serialized Form
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Constructor Summary
    WrongParameterException(Option<?> option) - -
    -           
    WrongParameterException(java.lang.String message) - -
    -           
    WrongParameterException(java.lang.String message, - java.lang.Throwable cause) - -
    -           
    WrongParameterException(java.lang.Throwable cause) - -
    -           
    -  - - - - - - - -
    -Method Summary
    -  - - - - - - - -
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    -  -

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

    -WrongParameterException

    -
    -public WrongParameterException(Option<?> option)
    -
    -
    -
    - -

    -WrongParameterException

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

    -WrongParameterException

    -
    -public WrongParameterException(java.lang.Throwable cause)
    -
    -
    -
    - -

    -WrongParameterException

    -
    -public WrongParameterException(java.lang.String message,
-                               java.lang.Throwable cause)
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/Argument.html b/website/full_javadoc/compbio/metadata/class-use/Argument.html deleted file mode 100644 index 11f5c1a..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/Argument.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - -Uses of Interface compbio.metadata.Argument - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Interface
    compbio.metadata.Argument

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

    - - - - - -
    -Uses of Argument in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Classes in compbio.metadata that implement Argument
    - classOption<T> - -
    -          Command line option/flag or multiple exclusive options with no value.
    - classParameter<T> - -
    -          A single value containing option supported by the web service e.g.
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    - - - diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html deleted file mode 100644 index 30abc70..0000000 --- a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html +++ /dev/null @@ -1,356 +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.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.ws.server  
    -  -

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

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

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

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return ChunkHolder
    - ChunkHolderPullFileResponse.getReturn() - -
    -           
    - ChunkHolderPullExecStatisticsResponse.getReturn() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    - voidPullFileResponse.setReturn(ChunkHolder _return) - -
    -           
    - voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return ChunkHolder
    - ChunkHolderFilePuller.pull(long position) - -
    -           
    -static ChunkHolderProgressGetter.pull(java.lang.String file, - long position) - -
    -           
    -  -

    - - - - - -
    -Uses of ChunkHolder in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return ChunkHolder
    - ChunkHolderTcoffeeWS.pullExecStatistics(java.lang.String jobId, - long position) - -
    -           
    - ChunkHolderProbconsWS.pullExecStatistics(java.lang.String jobId, - long position) - -
    -           
    - ChunkHolderMuscleWS.pullExecStatistics(java.lang.String jobId, - long position) - -
    -           
    - ChunkHolderMafftWS.pullExecStatistics(java.lang.String jobId, - long position) - -
    -           
    - ChunkHolderClustalWS.pullExecStatistics(java.lang.String jobId, - long position) - -
    -           
    -static ChunkHolderWSUtil.pullFile(java.lang.String jobId, - long position) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.JobExecutionException

    -
    - - - - - - - - - - - - - - - - - -
    -Packages that use JobExecutionException
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw JobExecutionException
    - ConfiguredExecutable<?>SyncExecutor.waitForResult() - -
    -          Call to this method block for as long as it is required for an executable to finish its job.
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobExecutionException
    - org.ggf.drmaa.JobInfoJobRunner.getJobInfo() - -
    -          This method will block before the calculation has completed and then - return the object containing a job execution statistics
    - ConfiguredExecutable<?>JobRunner.waitForResult() - -
    -           
    -static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, - java.lang.String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobExecutionException in compbio.engine.local
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.local that throw JobExecutionException
    - ConfiguredExecutable<?>LocalRunner.waitForResult() - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.JobStatus

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use JobStatus
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

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

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return JobStatus
    - JobStatusGetJobStatusResponse.getReturn() - -
    -           
    -  -

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

    - - - - - -
    -Uses of JobStatus in compbio.engine
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine that return JobStatus
    - JobStatusSyncExecutor.getJobStatus() - -
    -          Query the status of the job by its id.
    - JobStatusAsyncExecutor.getJobStatus(java.lang.String jobId) - -
    -          Query the status of the job
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.client with parameters of type JobStatus
    -static booleanUtil.isMarked(java.lang.String workDirectory, - JobStatus marker) - -
    -           
    -static booleanUtil.writeMarker(java.lang.String workDirectory, - JobStatus fileType) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that return JobStatus
    - JobStatusJobRunner.getJobStatus() - -
    -           
    - JobStatusAsyncJobRunner.getJobStatus(java.lang.String jobId) - -
    -          This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed.
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.engine.local
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.local that return JobStatus
    - JobStatusLocalRunner.getJobStatus() - -
    -           
    -static JobStatusLocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) - -
    -           
    - JobStatusAsyncLocalRunner.getJobStatus(java.lang.String jobId) - -
    -           
    -static JobStatusLocalEngineUtil.getRecordedJobStatus(java.lang.String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of JobStatus in compbio.metadata
    -  -

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

    - - - - - -
    -Uses of JobStatus in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return JobStatus
    -static JobStatusWSUtil.getJobStatus(java.lang.String jobId) - -
    -           
    - JobStatusTcoffeeWS.getJobStatus(java.lang.String jobId) - -
    -           
    - JobStatusProbconsWS.getJobStatus(java.lang.String jobId) - -
    -           
    - JobStatusMuscleWS.getJobStatus(java.lang.String jobId) - -
    -           
    - JobStatusMafftWS.getJobStatus(java.lang.String jobId) - -
    -           
    - JobStatusClustalWS.getJobStatus(java.lang.String jobId) - -
    -           
    -  -

    -

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    compbio.metadata.JobSubmissionException

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    -Packages that use JobSubmissionException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    -  -

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

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw JobSubmissionException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine that throw JobSubmissionException
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - Executable.ExecProvider provider) - -
    -           
    -static - - - - -
    -<T> ConfiguredExecutable<T>
    -    		Configurator.configureExecutable(Executable<T> executable, - java.util.List<FastaSequence> dataSet) - -
    -           
    - voidSyncExecutor.executeJob() - -
    -          Execute the job
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) - -
    -           
    -static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, - Executable.ExecProvider provider) - -
    -           
    - java.lang.StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) - -
    -          Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw JobSubmissionException
    - java.lang.StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException
    - voidJobRunner.executeJob() - -
    -           
    -static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) - -
    -           
    - java.lang.StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
    JobRunner(ConfiguredExecutable<?> confExec) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw JobSubmissionException
    - voidLocalRunner.executeJob() - -
    -           
    - java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.engine.local that throw JobSubmissionException
    ExecutableWrapper(ConfiguredExecutable<?> executable, - java.lang.String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Subclasses of JobSubmissionException in compbio.metadata
    - classLimitExceededException - -
    -          Thrown if the task larger in size that the limit that applies to the - calculation.
    - classUnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - -
    -Uses of JobSubmissionException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw JobSubmissionException
    - java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) - -
    -           
    - java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) - -
    -           
    - java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) - -
    -           
    - java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) - -
    -           
    - java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) - -
    -           
    -static - - - - -
    -<T> java.lang.String
    -    		WSUtil.align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
    -           
    - java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
    -           
    - java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
    -           
    - java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
    -           
    - java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
    -           
    - java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
    -           
    - java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.Limit

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Limit
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    -  -

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

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Limit
    - LimitGetLimitResponse.getReturn() - -
    -           
    -  -

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

    - - - - - -
    -Uses of Limit in compbio.engine.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return Limit
    - Limit<T>Executable.getLimit(java.lang.String presetName) - -
    -           
    - Limit<T>ConfExecutable.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.metadata
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Limit
    - Limit<T>LimitsManager.getDefaultLimit() - -
    -           
    - Limit<T>LimitsManager.getLimitByName(java.lang.String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Limit
    - java.util.List<Limit<T>>LimitsManager.getLimits() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Limit
    -static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, - java.util.List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return Limit
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Limit
    - Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Limit
    - Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) - -
    -           
    - Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Probcons>Probcons.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Muscle>Muscle.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Mafft>Mafft.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.runner.psiblast
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.psiblast that return Limit
    - Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - -
    -Uses of Limit in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return Limit
    - Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Probcons>ProbconsWS.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Muscle>MuscleWS.getLimit(java.lang.String presetName) - -
    -           
    - Limit<Mafft>MafftWS.getLimit(java.lang.String presetName) - -
    -           
    - Limit<ClustalW>ClustalWS.getLimit(java.lang.String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Limit
    -static - - - - -
    -<T> java.lang.String
    -    		WSUtil.align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.LimitExceededException

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

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

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw LimitExceededException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringMsaWS.presetAlign(java.util.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, - java.util.List<FastaSequence> seqs) - -
    -           
    -  -

    - - - - - -
    -Uses of LimitExceededException in compbio.ws.server
    -  -

    - - - - - - - - - -
    Methods in compbio.ws.server that throw LimitExceededException
    -static - - - - -
    -<T> java.lang.String
    -    		WSUtil.align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
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    -Uses of Class
    compbio.metadata.LimitsManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use LimitsManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    -  -

    - - - - - -
    -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.
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return LimitsManager
    - LimitsManagerGetLimitsResponse.getReturn() - -
    -           
    -  -

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

    - - - - - -
    -Uses of LimitsManager in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that return LimitsManager
    - LimitsManager<T>Executable.getLimits() - -
    -           
    - LimitsManager<T>ConfExecutable.getLimits() - -
    -           
    -static - - - - -
    -<V> LimitsManager<V>
    -    		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) - -
    -          This method should be executed once and result of its execution reused.
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner that return LimitsManager
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -           
    -static - - - - -
    -<T> LimitsManager<T>
    -    		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) - -
    -          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return LimitsManager
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    -  -

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

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return LimitsManager
    - LimitsManager<Tcoffee>Tcoffee.getLimits() - -
    -           
    - LimitsManager<ClustalW>ClustalW.getLimits() - -
    -           
    - LimitsManager<Probcons>Probcons.getLimits() - -
    -           
    - LimitsManager<Muscle>Muscle.getLimits() - -
    -           
    - LimitsManager<Mafft>Mafft.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.runner.psiblast
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.psiblast that return LimitsManager
    - LimitsManager<PsiBlast>PsiBlast.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of LimitsManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return LimitsManager
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.Option

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use Option
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

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

    - - - - - - - - - -
    Method parameters in compbio.data.msa with type arguments of type Option
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    - java.util.List<Option>CustomAlign.getOptions() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    - voidCustomAlign.setOptions(java.util.List<Option> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.engine.client
    -  -

    - - - - - - - - - -
    Method parameters in compbio.engine.client with type arguments of type Option
    -static - - - - -
    -<T> CommandBuilder<T>
    -    		CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, - java.lang.String nameValueSeparator) - -
    -          This produces the same result as getCommands method.
    -  -

    - - - - - -
    -Uses of Option in compbio.metadata
    -  -

    - - - - - - - - - -
    Subclasses of Option in compbio.metadata
    - classParameter<T> - -
    -          A single value containing option supported by the web service e.g.
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.metadata that return Option
    - Option<T>RunnerConfig.getArgument(java.lang.String name) - -
    -          Returns the argument by its name if found, NULL otherwise
    - Option<T>RunnerConfig.getArgumentByOptionName(java.lang.String optionName) - -
    -          Returns the argument by option name, NULL if the argument is not found
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Option
    - java.util.List<Option<T>>RunnerConfig.getArguments() - -
    -           
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - java.util.List<Option<T>>RunnerConfig.getOptions() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Option
    - voidRunnerConfig.addOption(Option<T> option) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Option
    - voidRunnerConfig.setOptions(java.util.List<Option<T>> parameters) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Option
    - java.util.List<Option<?>>OptionCombinator.getAllOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Option
    - java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments) - -
    -           
    -static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - java.util.List<java.lang.String>OptionCombinator.optionsToCommandString(java.util.List<Option<?>> options) - -
    -           
    -  -

    - - - - - -
    -Uses of Option in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Option
    - java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
    -           
    - java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
    -           
    - java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
    -           
    - java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
    -           
    - java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
    -           
    -static - - - - -
    -<T> java.util.List<java.lang.String>
    -    		WSUtil.getCommands(java.util.List<Option<T>> options, - java.lang.String keyValueSeparator) - -
    -           
    -  -

    -

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    compbio.metadata.Parameter

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

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

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Parameter
    - java.util.List<Parameter<T>>RunnerConfig.getParameters() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type Parameter
    - voidRunnerConfig.addParameter(Parameter<T> param) - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Parameter
    - voidRunnerConfig.setParameters(java.util.List<Parameter<T>> parameters) - -
    -           
    -  -

    - - - - - -
    -Uses of Parameter in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type Parameter
    - java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithRandomValues() - -
    -           
    - java.util.List<Parameter<?>>OptionCombinator.getAllParameters() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.runner with type arguments of type Parameter
    - java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, - java.util.Map<Parameter<?>,java.lang.String> prmValue) - -
    -           
    - java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, - java.util.Map<Parameter<?>,java.lang.String> prmValue) - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.Preset

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa with parameters of type Preset
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return Preset
    - PresetPresetAlign.getPreset() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    - voidPresetAlign.setPreset(Preset preset) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return Preset
    - Preset<T>PresetManager.getPresetByName(java.lang.String presetName) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return types with arguments of type Preset
    - java.util.List<Preset<T>>PresetManager.getPresets() - -
    -           
    -  -

    - - - - - - - - - -
    Method parameters in compbio.metadata with type arguments of type Preset
    - voidPresetManager.setPresets(java.util.List<Preset<T>> presets) - -
    -           
    -  -

    - - - - - -
    -Uses of Preset in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server with parameters of type Preset
    - java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.PresetManager

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use PresetManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

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

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

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return PresetManager
    - PresetManagerGetPresetsResponse.getReturn() - -
    -           
    -  -

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

    - - - - - -
    -Uses of PresetManager in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return PresetManager
    -static - - - - -
    -<V> PresetManager<V>
    -    		ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type PresetManager
    - voidLimitsManager.validate(PresetManager<T> presets) - -
    -          Validate Limits
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return PresetManager
    -static - - - - -
    -<T> PresetManager<T>
    -    		Util.getPresets(java.lang.Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of PresetManager in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return PresetManager
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    -  -

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    -Uses of Class
    compbio.metadata.ResultNotAvailableException

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    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use ResultNotAvailableException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    -  -

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

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

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine
    -  -

    - - - - - - - - - -
    Methods in compbio.engine that throw ResultNotAvailableException
    - ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.String jobId) - -
    -          Retrieve the results of the job.
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.client
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.engine.client that throw ResultNotAvailableException
    - - - - - -
    -<V> V
    -    		ConfiguredExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults() - -
    -           
    - - - - - -
    -<V> V
    -    		Executable.getResults(java.lang.String directory) - -
    -           
    - - - - - -
    -<V> V
    -    		ConfExecutable.getResults(java.lang.String directory) - -
    -           
    -static ConfiguredExecutable<?>Util.loadExecutable(java.lang.String taskId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.cluster.drmaa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.cluster.drmaa that throw ResultNotAvailableException
    - ConfiguredExecutable<?>ClusterSession.getResults(java.lang.String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.engine.local
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.engine.local that throw ResultNotAvailableException
    -static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, - java.lang.String taskId) - -
    -           
    - ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) - -
    -           
    -  -

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

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that throw ResultNotAvailableException
    - AlignmentTcoffee.getResults(java.lang.String workDirectory) - -
    -           
    - AlignmentClustalW.getResults(java.lang.String workDirectory) - -
    -           
    - AlignmentProbcons.getResults(java.lang.String workDirectory) - -
    -           
    - AlignmentMuscle.getResults(java.lang.String workDirectory) - -
    -           
    - AlignmentMafft.getResults(java.lang.String workDirectory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.runner.psiblast
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.psiblast that throw ResultNotAvailableException
    - - - - - -
    -<V> V
    -    		PsiBlast.getResults(java.lang.String directory) - -
    -           
    -  -

    - - - - - -
    -Uses of ResultNotAvailableException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw ResultNotAvailableException
    - AlignmentTcoffeeWS.getResult(java.lang.String jobId) - -
    -           
    - AlignmentProbconsWS.getResult(java.lang.String jobId) - -
    -           
    - AlignmentMuscleWS.getResult(java.lang.String jobId) - -
    -           
    - AlignmentMafftWS.getResult(java.lang.String jobId) - -
    -           
    - AlignmentClustalWS.getResult(java.lang.String jobId) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.RunnerConfig

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use RunnerConfig
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa that return RunnerConfig
    - RunnerConfig<T>MsaWS.getRunnerOptions() - -
    -          Get options supported by a web service
    -  -

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

    - - - - - - - - - -
    Methods in compbio.data.msa.jaxws that return RunnerConfig
    - RunnerConfigGetRunnerOptionsResponse.getReturn() - -
    -           
    -  -

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

    - - - - - -
    -Uses of RunnerConfig in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that return RunnerConfig
    -static - - - - -
    -<V> RunnerConfig<V>
    -    		ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata with parameters of type RunnerConfig
    - RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) - -
    -           
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidPresetManager.validate(RunnerConfig<T> options) - -
    -          Checks whether preset option and parameter are defined in RunnerConfig - object.
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.runner
    -  -

    - - - - - - - - - -
    Methods in compbio.runner that return RunnerConfig
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.runner with parameters of type RunnerConfig
    -static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - - - - -
    Constructors in compbio.runner with parameters of type RunnerConfig
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  -

    - - - - - -
    -Uses of RunnerConfig in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return RunnerConfig
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.UnsupportedRuntimeException

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    -Packages that use UnsupportedRuntimeException
    compbio.data.msa  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    -  -

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

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    - java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<T> preset) - -
    -          Align a list of sequences with preset.
    -  -

    - - - - - -
    -Uses of UnsupportedRuntimeException in compbio.engine.client
    -  -

    - - - - - - - - - -
    Methods in compbio.engine.client that throw UnsupportedRuntimeException
    - java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) - -
    -           
    -  -

    -

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

    - - - - - -
    -Uses of ValueConstrain.Type in compbio.metadata
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain.Type
    - ValueConstrain.TypeValueConstrain.getType() - -
    -           
    -static ValueConstrain.TypeValueConstrain.Type.valueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static ValueConstrain.Type[]ValueConstrain.Type.values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    - voidValueConstrain.setType(ValueConstrain.Type type) - -
    -           
    -  -

    -

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    -Uses of Class
    compbio.metadata.ValueConstrain

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

    - - - - - -
    -Uses of ValueConstrain in compbio.metadata
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata that return ValueConstrain
    - ValueConstrainParameter.getValidValue() - -
    -           
    -  -

    - - - - - - - - - -
    Methods in compbio.metadata with parameters of type ValueConstrain
    - voidParameter.setValidValue(ValueConstrain validValue) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.metadata.WrongParameterException

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

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

    - - - - - - - - - - - - - -
    Methods in compbio.data.msa that throw WrongParameterException
    - java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<T>> options) - -
    -          Align a list of sequences with options.
    - java.lang.StringMsaWS.presetAlign(java.util.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
    - java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) - -
    -          Converts list of options as String to type Option
    - voidParameter.setDefaultValue(java.lang.String defaultVal) - -
    -           
    - voidOption.setDefaultValue(java.lang.String defaultVal) - -
    -          Sets one of the values defined in optionList as default.
    - voidArgument.setValue(java.lang.String defaultValue) - -
    -          Set default values for the parameter or an option
    - voidOption.setValue(java.lang.String dValue) - -
    -           
    -  -

    - - - - - -
    -Uses of WrongParameterException in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that throw WrongParameterException
    - java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
    -           
    - java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
    -           
    - java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
    -           
    - java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
    -           
    - java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
    -           
    - java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    - java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    - java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    - java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    - java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

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    - - - - diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html deleted file mode 100644 index 5f5b66b..0000000 --- a/website/full_javadoc/compbio/metadata/package-summary.html +++ /dev/null @@ -1,286 +0,0 @@ - - - - - - -compbio.metadata - - - - - - - - - - - - -
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    -Package compbio.metadata -

    -A meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. -

    -See: -
    -          Description -

    - - - - - - - - - -
    -Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    -  - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ChunkHolderRepresents a chunk of string data together with the position in a file from - where corresponding to of the data.
    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 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.
    LimitExceededExceptionThrown 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 Jalview Web Services v2. -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
    -
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    -Hierarchy For Package compbio.metadata -

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    Package Hierarchies:
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    -Uses of Package
    compbio.metadata

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Packages that use compbio.metadata
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder - -
    -          Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
    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 - -
    -          Thrown if the task larger in size that the limit that applies to the - calculation.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.data.msa.jaxws
    ChunkHolder - -
    -          Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
    JobStatus - -
    -          The status of the job.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine
    ChunkHolder - -
    -          Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.client
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException - -
    -          Indicates that the server could not execute native executables.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.cluster.drmaa
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.engine.local
    JobExecutionException - -
    -          JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.metadata
    Argument - -
    -          An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    JobStatus - -
    -          The status of the job.
    JobSubmissionException - -
    -          Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitExceededException - -
    -          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 option supported by the web service e.g.
    Preset - -
    -          Collection of Options and Parameters with their values
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    ValueConstrain - -
    -          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type - -
    -           
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    Option - -
    -          Command line option/flag or multiple exclusive options with no value.
    Parameter - -
    -          A single value containing option supported by the web service e.g.
    PresetManager - -
    -          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig - -
    -          The list of Parameters and Options supported by executable.
    -  -

    - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner._impl
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.msa
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.runner.psiblast
    Limit - -
    -          A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    LimitsManager - -
    -          A collection of Limits
    ResultNotAvailableException - -
    -          ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.metadata used by compbio.ws.server
    ChunkHolder - -
    -          Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
    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 - -
    -          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.
    WrongParameterException - -
    -          WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    -  -

    -

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    - -compbio.pipeline._jpred -
    -Class BlastParser

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.BlastParser
-
    -
    -
    -
    public class BlastParser
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    BlastParser() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(java.lang.String[] args) - -
    -          args[0] is assumed to be the name of a Blast output file
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -BlastParser

    -
    -public BlastParser()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
-                 throws java.io.FileNotFoundException,
-                        javax.xml.stream.XMLStreamException
    -
    -
    args[0] is assumed to be the name of a Blast output file -

    -

    - -
    Throws: -
    javax.xml.stream.XMLStreamException -
    java.io.FileNotFoundException
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html deleted file mode 100644 index 8669156..0000000 --- a/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - -Jpred4 - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.pipeline._jpred -
    -Class Jpred4

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Jpred4
-
    -
    -
    -
    public class Jpred4
    extends java.lang.Object
    - - -

    -jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying. Default: uniref90 ( - /homes/www-jpred/databases/uniref90.filt) Please note that database must be - psi-blast indexed - - [--pred-nohits] Toggle allowing Jpred to make predictions even when there are - no PSI-BLAST hits. - - [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help] -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Jpred4() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    - voidrunPsiBlast() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -Jpred4

    -
    -public Jpred4()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -runPsiBlast

    -
    -public void runPsiBlast()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - -compbio.pipeline._jpred -
    -Class PScore

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.PScore
-
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    -
    public class PScore
    extends java.lang.Object
    - - -

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    -Constructor Summary
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    - booleanequals(java.lang.Object obj) - -
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    Methods inherited from class java.lang.Object
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    -PScore

    -
    -public PScore()
    -
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    -Method Detail
    - -

    -equals

    -
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    -
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    Overrides:
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    - -compbio.pipeline._jpred -
    -Class Pairwise

    -
    -java.lang.Object
-  extended by compbio.pipeline._jpred.Pairwise
-
    -
    -
    -
    public class Pairwise
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    Pairwise(java.util.List<FastaSequence> sequences) - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(java.lang.String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -Pairwise

    -
    -public Pairwise(java.util.List<FastaSequence> sequences)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static final void main(java.lang.String[] args)
-                       throws java.io.FileNotFoundException,
-                              java.io.IOException
    -
    -
    - -
    Throws: -
    java.io.FileNotFoundException -
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    -
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    -Classes  - -
    -BlastParser -
    -Jpred4 -
    -Pairwise -
    -PScore
    - - - - diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html deleted file mode 100644 index 06bf2f8..0000000 --- a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - -compbio.pipeline._jpred - - - - - - - - - - - - -
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    -Package compbio.pipeline._jpred -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    BlastParser 
    Jpred4jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Pairwise 
    PScore 
    -  - -

    -

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    - -compbio.runner -
    -Class OptionCombinator

    -
    -java.lang.Object
-  extended by compbio.runner.OptionCombinator
-
    -
    -
    -
    @Immutable
-public final class OptionCombinator
    extends java.lang.Object
    - - -

    -This class solve the following problems. Given the RunnerConfig - - 1) generate a valid option string with all options and parameters in it - - 2) Permute all possible combinations of options order and parameters values -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments) - -
    -           
    -static java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments, - RunnerConfig<? extends Executable<?>> rconfig) - -
    -           
    - java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithBorderValues(boolean minValue) - -
    -           
    - java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithRandomValues() - -
    -           
    - java.util.List<Option<?>>getAllOptions() - -
    -           
    - java.util.List<Parameter<?>>getAllParameters() - -
    -           
    - java.util.List<java.lang.String>getOptionsAtRandom() - -
    -           
    - java.util.List<java.lang.String>optionsToCommandString(java.util.List<Option<?>> options) - -
    -           
    - java.util.List<java.lang.String>parametersToCommandString(java.util.List<Parameter<?>> orderedList, - java.util.Map<Parameter<?>,java.lang.String> prmValue) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -OptionCombinator

    -
    -public OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -optionsToCommandString

    -
    -public java.util.List<java.lang.String> optionsToCommandString(java.util.List<Option<?>> options)
    -
    -
    -
    -
    -
    -
    - -

    -getOptionsAtRandom

    -
    -public java.util.List<java.lang.String> getOptionsAtRandom()
    -
    -
    -
    -
    -
    -
    - -

    -getAllOptions

    -
    -public java.util.List<Option<?>> getAllOptions()
    -
    -
    -
    -
    -
    -
    - -

    -getAllParameters

    -
    -public java.util.List<Parameter<?>> getAllParameters()
    -
    -
    -
    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments)
    -
    -
    -
    -
    -
    -
    - -

    -argumentsToCommandString

    -
    -public static java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments,
-                                                                        RunnerConfig<? extends Executable<?>> rconfig)
    -
    -
    -
    -
    -
    -
    - -

    -parametersToCommandString

    -
    -public java.util.List<java.lang.String> parametersToCommandString(java.util.List<Parameter<?>> orderedList,
-                                                                  java.util.Map<Parameter<?>,java.lang.String> prmValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithBorderValues

    -
    -public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithBorderValues(boolean minValue)
    -
    -
    -
    -
    -
    -
    - -

    -getAllConstrainedParametersWithRandomValues

    -
    -public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithRandomValues()
    -
    -
    -
    -
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    - -
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    - -compbio.runner -
    -Class Util

    -
    -java.lang.Object
-  extended by compbio.runner.Util
-
    -
    -
    -
    public final class Util
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringSPACE - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Util() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> LimitsManager<T>
    -    		getLimits(java.lang.Class<? extends Executable<T>> clazz) - -
    -          For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then
    -static - - - - -
    -<T> PresetManager<T>
    -    		getPresets(java.lang.Class<? extends Executable<T>> clazz) - -
    -           
    -static - - - - -
    -<T> RunnerConfig<T>
    -    		getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) - -
    -           
    -static AlignmentreadClustalFile(java.lang.String workDirectory, - java.lang.String clustFile) - -
    -           
    -static voidwriteInput(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<?> exec) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -SPACE

    -
    -public static final java.lang.String SPACE
    -
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    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Util

    -
    -public Util()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getLimits

    -
    -public static <T> LimitsManager<T> getLimits(java.lang.Class<? extends Executable<T>> clazz)
    -
    -
    For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -

    -

    -
    Parameters:
    rconfig - -
    Returns:
    public static List toOptionString(RunnerConfig - rconfig) { String option = ""; List options = new - ArrayList(); for (Parameter par : - rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) - { option = par.getOptionName(); } else { option = - par.getOptionName() + "=" + par.getPossibleValues().get(0); } // - separate options options.add(option); } return options; }
    -
    -
    -
    - -

    -getSupportedOptions

    -
    -public static <T> RunnerConfig<T> getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -getPresets

    -
    -public static <T> PresetManager<T> getPresets(java.lang.Class<? extends Executable<T>> clazz)
    -
    -
    -
    -
    -
    -
    - -

    -readClustalFile

    -
    -public static final Alignment readClustalFile(java.lang.String workDirectory,
-                                              java.lang.String clustFile)
-                                       throws UnknownFileFormatException,
-                                              java.io.IOException,
-                                              java.io.FileNotFoundException,
-                                              java.lang.NullPointerException
    -
    -
    - -
    Throws: -
    UnknownFileFormatException -
    java.io.IOException -
    java.io.FileNotFoundException -
    java.lang.NullPointerException
    -
    -
    -
    - -

    -writeInput

    -
    -public static void writeInput(java.util.List<FastaSequence> sequences,
-                              ConfiguredExecutable<?> exec)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html deleted file mode 100644 index 05a5ca7..0000000 --- a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html +++ /dev/null @@ -1,347 +0,0 @@ - - - - - - -_NativeSpecHelper - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner -
    -Class _NativeSpecHelper

    -
    -java.lang.Object
-  extended by compbio.runner._NativeSpecHelper
-
    -
    -
    -
    public class _NativeSpecHelper
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - -
    -Constructor Summary
    _NativeSpecHelper(int requiredMemory) - -
    -           
    _NativeSpecHelper(int requiredMemory, - int maxCalculationTime) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _QueuegetApproprieteQueue() - -
    -           
    - java.lang.StringgetNativeSpec() - -
    -           
    - java.lang.StringgetQueue() - -
    -           
    - voidsetQueue(java.lang.String queue) - -
    -           
    - voidsetRequiredMemory(int memory) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory)
    -
    -
    -
    - -

    -_NativeSpecHelper

    -
    -public _NativeSpecHelper(int requiredMemory,
-                         int maxCalculationTime)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setRequiredMemory

    -
    -public void setRequiredMemory(int memory)
    -
    -
    -
    -
    -
    -
    - -

    -setQueue

    -
    -public void setQueue(java.lang.String queue)
    -
    -
    -
    -
    -
    -
    - -

    -getQueue

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

    -getNativeSpec

    -
    -public java.lang.String getNativeSpec()
-                               throws java.net.UnknownServiceException
    -
    -
    - -
    Throws: -
    java.net.UnknownServiceException
    -
    -
    -
    - -

    -getApproprieteQueue

    -
    -public _Queue getApproprieteQueue()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html deleted file mode 100644 index ff0efa8..0000000 --- a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html +++ /dev/null @@ -1,586 +0,0 @@ - - - - - - -_SkeletalCommandBuilder - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner -
    -Class _SkeletalCommandBuilder

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    Direct Known Subclasses:
    BlastAll, Disembl, Mcl, OB, PSIBlast, Ronn, RPSBlast
    -
    -
    -
    -
    public abstract class _SkeletalCommandBuilder
    extends java.lang.Object
    implements Executable<_SkeletalCommandBuilder>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    _SkeletalCommandBuilder() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - _SkeletalCommandBuilderaddParameter(java.lang.String parameter) - -
    -           
    - _SkeletalCommandBuilderaddParameters(java.util.List<java.lang.String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - _SkeletalCommandBuilderaddParameters(java.lang.String[] parameters) - -
    -           
    - java.lang.StringgetEmail() - -
    -           
    - java.lang.StringgetError() - -
    -           
    - Limit<_SkeletalCommandBuilder>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<_SkeletalCommandBuilder>getLimits() - -
    -           
    - java.lang.StringgetName() - -
    -           
    - java.lang.StringgetOutput() - -
    -           
    - CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(java.lang.String directory) - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    - _SkeletalCommandBuildersetEmail(java.lang.String email) - -
    -           
    - _SkeletalCommandBuildersetName(java.lang.String name) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getInput
    -  -

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

    -_SkeletalCommandBuilder

    -
    -public _SkeletalCommandBuilder()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setEmail

    -
    -public _SkeletalCommandBuilder setEmail(java.lang.String email)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -setName

    -
    -public _SkeletalCommandBuilder setName(java.lang.String name)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getName

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

    -getEmail

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

    -addParameters

    -
    -public _SkeletalCommandBuilder addParameters(java.lang.String[] parameters)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public _SkeletalCommandBuilder addParameters(java.util.List<java.lang.String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -addParameter

    -
    -public _SkeletalCommandBuilder addParameter(java.lang.String parameter)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public <V> V getResults(java.lang.String directory)
    -
    -
    -
    Specified by:
    getResults in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
    -
    Specified by:
    loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getOutput

    -
    -public java.lang.String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getError

    -
    -public java.lang.String getError()
    -
    -
    -
    Specified by:
    getError in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<_SkeletalCommandBuilder> getLimit(java.lang.String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<_SkeletalCommandBuilder> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/BlastAll.html deleted file mode 100644 index 2faddc5..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastAll.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -BlastAll - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class BlastAll

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.BlastAll
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class BlastAll
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    BlastAll(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    - booleanremoveOutput(java.lang.String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -BlastAll

    -
    -public BlastAll(java.lang.String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -removeOutput

    -
    -public boolean removeOutput(java.lang.String outfile)
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

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

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public java.lang.String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html deleted file mode 100644 index 0dfb3cf..0000000 --- a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html +++ /dev/null @@ -1,200 +0,0 @@ - - - - - - -BlastParameters - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class BlastParameters

    -
    -java.lang.Object
-  extended by compbio.runner._impl.BlastParameters
-
    -
    -
    -
    public class BlastParameters
    extends java.lang.Object
    - - -

    -Utility class for common Blast parameters -

    - -

    -

    -
    Author:
    -
    pvtroshin - TODO
    -
    -
    - -

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

    - -

    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Disembl.html b/website/full_javadoc/compbio/runner/_impl/Disembl.html deleted file mode 100644 index 9c5d600..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Disembl.html +++ /dev/null @@ -1,379 +0,0 @@ - - - - - - -Disembl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class Disembl

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Disembl
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Disembl
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Disembl(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    -static java.util.List<java.lang.String>getTestArgs() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -Disembl

    -
    -public Disembl(java.lang.String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTestArgs

    -
    -public static java.util.List<java.lang.String> getTestArgs()
    -
    -
    -
    -
    -
    -
    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

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

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public java.lang.String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html deleted file mode 100644 index bc7399c..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Environment.html +++ /dev/null @@ -1,265 +0,0 @@ - - - - - - -Environment - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class Environment

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Environment
-
    -
    -
    -
    public final class Environment
    extends java.lang.Object
    - - -

    -This is utility class to encapsulate environmental variables like directory paths -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static java.lang.StringgetBlastBinDir() - -
    -           
    -static java.lang.StringgetBlastDatabasesDir() - -
    -           
    -static java.lang.StringgetRPSBlastDatabasesDir() - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -getBlastBinDir

    -
    -public static java.lang.String getBlastBinDir()
    -
    -
    -
    -
    -
    -
    - -

    -getBlastDatabasesDir

    -
    -public static final java.lang.String getBlastDatabasesDir()
    -
    -
    -
    -
    -
    -
    - -

    -getRPSBlastDatabasesDir

    -
    -public static final java.lang.String getRPSBlastDatabasesDir()
    -
    -
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    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html deleted file mode 100644 index c5c546f..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Mcl.html +++ /dev/null @@ -1,379 +0,0 @@ - - - - - - -Mcl - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Mcl

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Mcl
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Mcl
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Mcl(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    -static java.util.List<java.lang.String>getTestParams() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -Mcl

    -
    -public Mcl(java.lang.String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getTestParams

    -
    -public static java.util.List<java.lang.String> getTestParams()
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    -
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    -
    -
    -
    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
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    -
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    -
    -
    -
    - -

    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
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    -getCommandName

    -
    -public java.lang.String getCommandName()
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    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
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    -getInput

    -
    -public java.lang.String getInput()
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    -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html deleted file mode 100644 index 418085d..0000000 --- a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html +++ /dev/null @@ -1,552 +0,0 @@ - - - - - - -NetNglyc - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class NetNglyc

    -
    -java.lang.Object
-  extended by compbio.runner._impl.NetNglyc
-
    -
    -
    All Implemented Interfaces:
    Executable<NetNglyc>
    -
    -
    -
    -
    public class NetNglyc
    extends java.lang.Object
    implements Executable<NetNglyc>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    NetNglyc() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - NetNglycaddParameters(java.util.List<java.lang.String> parameters) - -
    -          Adds parameter to the list of parameters for a native executable
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetError() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    - Limit<NetNglyc>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<NetNglyc>getLimits() - -
    -           
    - java.lang.StringgetOutput() - -
    -           
    - CommandBuilder<NetNglyc>getParameters(Executable.ExecProvider provider) - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(java.lang.String directory) - -
    -           
    -static java.util.List<java.lang.String>getTestArgs() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    - Executable<?>loadRunConfiguration(RunConfiguration rconfig) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -NetNglyc

    -
    -public NetNglyc()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getParameters

    -
    -public CommandBuilder<NetNglyc> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<NetNglyc>
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    - -

    -getTestArgs

    -
    -public static java.util.List<java.lang.String> getTestArgs()
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    -
    - -

    -addParameters

    -
    -public NetNglyc addParameters(java.util.List<java.lang.String> parameters)
    -
    -
    Description copied from interface: Executable
    -
    Adds parameter to the list of parameters for a native executable -

    -

    -
    Specified by:
    addParameters in interface Executable<NetNglyc>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
    -
    -
    -
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    -
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    -
    -
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    - -

    -getCommandName

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

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    -
    Specified by:
    getCreatedFiles in interface Executable<NetNglyc>
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public java.lang.String getInput()
    -
    -
    -
    Specified by:
    getInput in interface Executable<NetNglyc>
    -
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    -
    -
    -
    - -

    -getResults

    -
    -public <V> V getResults(java.lang.String directory)
    -
    -
    -
    Specified by:
    getResults in interface Executable<NetNglyc>
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    -
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    -loadRunConfiguration

    -
    -public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    -
    -
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    Specified by:
    loadRunConfiguration in interface Executable<NetNglyc>
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    -getOutput

    -
    -public java.lang.String getOutput()
    -
    -
    -
    Specified by:
    getOutput in interface Executable<NetNglyc>
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    -getError

    -
    -public java.lang.String getError()
    -
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    Specified by:
    getError in interface Executable<NetNglyc>
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    -getLimit

    -
    -public Limit<NetNglyc> getLimit(java.lang.String presetName)
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    Specified by:
    getLimit in interface Executable<NetNglyc>
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    -getLimits

    -
    -public LimitsManager<NetNglyc> getLimits()
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    Specified by:
    getLimits in interface Executable<NetNglyc>
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    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html deleted file mode 100644 index 55d1730..0000000 --- a/website/full_javadoc/compbio/runner/_impl/OB.html +++ /dev/null @@ -1,382 +0,0 @@ - - - - - - -OB - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class OB

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.OB
-
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    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
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    -
    public class OB
    extends _SkeletalCommandBuilder
    - - -

    -TODO this needs fixing! Executable does not work -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - - - - -
    -Constructor Summary
    OB() - -
    -           
    OB(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    - java.util.List<java.lang.String>getTestArgs() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    -static voidmain(java.lang.String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
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    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -OB

    -
    -public OB()
    -
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    - -

    -OB

    -
    -public OB(java.lang.String workDirectory)
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    -Method Detail
    - -

    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
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    -getTestArgs

    -
    -public java.util.List<java.lang.String> getTestArgs()
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    -main

    -
    -public static void main(java.lang.String[] args)
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    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
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    -getInput

    -
    -public java.lang.String getInput()
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html deleted file mode 100644 index b14bdb4..0000000 --- a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -PSIBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class PSIBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.PSIBlast
-
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    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
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    -
    public class PSIBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
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    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
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    -Constructor Summary
    PSIBlast(java.lang.String workDirectory) - -
    -           
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    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    - booleanremoveOutput(java.lang.String outfile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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    - - - - - - - - -
    -Constructor Detail
    - -

    -PSIBlast

    -
    -public PSIBlast(java.lang.String workDirectory)
    -
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    -Method Detail
    - -

    -removeOutput

    -
    -public boolean removeOutput(java.lang.String outfile)
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    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
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    -getCommandName

    -
    -public java.lang.String getCommandName()
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    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
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    -getInput

    -
    -public java.lang.String getInput()
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    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html deleted file mode 100644 index 64cecfd..0000000 --- a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -RPSBlast - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner._impl -
    -Class RPSBlast

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.RPSBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class RPSBlast
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    RPSBlast(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    -static java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -RPSBlast

    -
    -public RPSBlast(java.lang.String workDirectory)
    -
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    - - - - - - - - -
    -Method Detail
    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
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    -
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    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
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    -getCommandName

    -
    -public static java.lang.String getCommandName()
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    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
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    -getInput

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    - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html deleted file mode 100644 index d5f9998..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Ronn.html +++ /dev/null @@ -1,360 +0,0 @@ - - - - - - -Ronn - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Ronn

    -
    -java.lang.Object
-  extended by compbio.runner._SkeletalCommandBuilder
-      extended by compbio.runner._impl.Ronn
-
    -
    -
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    -
    -
    -
    -
    public class Ronn
    extends _SkeletalCommandBuilder
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    Ronn(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.StringgetCommand(Executable.ExecProvider provider) - -
    -           
    - java.lang.StringgetCommandName() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -           
    - java.lang.StringgetInput() - -
    -           
    -static java.lang.StringgetTestCommand() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -Ronn

    -
    -public Ronn(java.lang.String workDirectory)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getCommand

    -
    -public java.lang.String getCommand(Executable.ExecProvider provider)
    -
    -
    -
    -
    -
    -
    - -

    -getTestCommand

    -
    -public static java.lang.String getTestCommand()
    -
    -
    -
    -
    -
    -
    - -

    -getCommandName

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

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    -
    -
    -
    -
    - -

    -getInput

    -
    -public java.lang.String getInput()
    -
    -
    -
    -
    -
    - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html deleted file mode 100644 index 3a3978d..0000000 --- a/website/full_javadoc/compbio/runner/_impl/Runners.html +++ /dev/null @@ -1,371 +0,0 @@ - - - - - - -Runners - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.runner._impl -
    -Class Runners

    -
    -java.lang.Object
-  extended by compbio.runner._impl.Runners
-
    -
    -
    -
    public final class Runners
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static BlastAllgetBlastAllRunnable(java.lang.String workDirectory) - -
    -           
    -static DisemblgetDisemblRunnable(java.lang.String workDirectory) - -
    -           
    -static MclgetMclRunnable(java.lang.String workDirectory) - -
    -           
    -static NetNglycgetNetNglycRunnable(java.lang.String workDirectory) - -
    -           
    -static OBgetOBRunnable(java.lang.String workDirectory) - -
    -           
    -static PSIBlastgetPSIBlastRunnable(java.lang.String workDirectory) - -
    -           
    -static RonngetRonnRunnable(java.lang.String workDirectory) - -
    -           
    -static RPSBlastgetRPSBlastRunnable(java.lang.String workDirectory) - -
    -           
    -static compbio.runner._impl.Tmhmm2getTmhmm2Runnable(java.lang.String workDirectory) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -getMclRunnable

    -
    -public static Mcl getMclRunnable(java.lang.String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getOBRunnable

    -
    -public static OB getOBRunnable(java.lang.String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getDisemblRunnable

    -
    -public static Disembl getDisemblRunnable(java.lang.String workDirectory)
    -
    -
    -
    -
    -
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    - -

    -getNetNglycRunnable

    -
    -public static NetNglyc getNetNglycRunnable(java.lang.String workDirectory)
    -
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    -
    -
    -
    - -

    -getRonnRunnable

    -
    -public static Ronn getRonnRunnable(java.lang.String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getTmhmm2Runnable

    -
    -public static compbio.runner._impl.Tmhmm2 getTmhmm2Runnable(java.lang.String workDirectory)
    -
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    -
    -
    - -

    -getRPSBlastRunnable

    -
    -public static RPSBlast getRPSBlastRunnable(java.lang.String workDirectory)
    -
    -
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    -
    -
    -
    - -

    -getBlastAllRunnable

    -
    -public static BlastAll getBlastAllRunnable(java.lang.String workDirectory)
    -
    -
    -
    -
    -
    -
    - -

    -getPSIBlastRunnable

    -
    -public static PSIBlast getPSIBlastRunnable(java.lang.String workDirectory)
    -
    -
    -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html deleted file mode 100644 index 6389cd6..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.BlastAll - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.BlastAll

    -
    - - - - - - - - - -
    -Packages that use BlastAll
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of BlastAll in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return BlastAll
    -static BlastAllRunners.getBlastAllRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html deleted file mode 100644 index 8ebcce6..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html +++ /dev/null @@ -1,144 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.BlastParameters - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.BlastParameters

    -
    -No usage of compbio.runner._impl.BlastParameters -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html deleted file mode 100644 index 005572a..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.Disembl - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner._impl.Disembl

    -
    - - - - - - - - - -
    -Packages that use Disembl
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Disembl in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Disembl
    -static DisemblRunners.getDisemblRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Uses of Class
    compbio.runner._impl.Environment

    -
    -No usage of compbio.runner._impl.Environment -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html deleted file mode 100644 index d08bb98..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.Mcl - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner._impl.Mcl

    -
    - - - - - - - - - -
    -Packages that use Mcl
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Mcl in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Mcl
    -static MclRunners.getMclRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html deleted file mode 100644 index ecd9ab5..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.NetNglyc - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner._impl.NetNglyc

    -
    - - - - - - - - - -
    -Packages that use NetNglyc
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of NetNglyc in compbio.runner._impl
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return NetNglyc
    - NetNglycNetNglyc.addParameters(java.util.List<java.lang.String> parameters) - -
    -           
    -static NetNglycRunners.getNetNglycRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner._impl that return types with arguments of type NetNglyc
    - Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<NetNglyc>NetNglyc.getLimits() - -
    -           
    - CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    -

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

    -Uses of Class
    compbio.runner._impl.OB

    -
    - - - - - - - - - -
    -Packages that use OB
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of OB in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return OB
    -static OBRunners.getOBRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html deleted file mode 100644 index 8bc9956..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.PSIBlast - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner._impl.PSIBlast

    -
    - - - - - - - - - -
    -Packages that use PSIBlast
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of PSIBlast in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return PSIBlast
    -static PSIBlastRunners.getPSIBlastRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html deleted file mode 100644 index a1f52e3..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.RPSBlast - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.runner._impl.RPSBlast

    -
    - - - - - - - - - -
    -Packages that use RPSBlast
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of RPSBlast in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return RPSBlast
    -static RPSBlastRunners.getRPSBlastRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html deleted file mode 100644 index cc6975e..0000000 --- a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html +++ /dev/null @@ -1,180 +0,0 @@ - - - - - - -Uses of Class compbio.runner._impl.Ronn - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.runner._impl.Ronn

    -
    - - - - - - - - - -
    -Packages that use Ronn
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of Ronn in compbio.runner._impl
    -  -

    - - - - - - - - - -
    Methods in compbio.runner._impl that return Ronn
    -static RonnRunners.getRonnRunnable(java.lang.String workDirectory) - -
    -           
    -  -

    -

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    BlastAll 
    BlastParametersUtility class for common Blast parameters
    Disembl 
    EnvironmentThis is utility class to encapsulate environmental variables like directory paths
    Mcl 
    NetNglyc 
    OBTODO this needs fixing! Executable does not work
    PSIBlast 
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    compbio.runner._impl  
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    -Classes in compbio.runner._impl used by compbio.runner._impl
    BlastAll - -
    -           
    Disembl - -
    -           
    Mcl - -
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    NetNglyc - -
    -           
    OB - -
    -          TODO this needs fixing! Executable does not work
    PSIBlast - -
    -           
    Ronn - -
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    - -compbio.runner._jpred -
    -Class _Jpred

    -
    -java.lang.Object
-  extended by compbio.runner._jpred._Jpred
-
    -
    -
    -
    public class _Jpred
    extends java.lang.Object
    - - -

    -

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

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    -_Jpred

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    -Classes  - -
    -_Jpred
    - - - - diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html deleted file mode 100644 index f375d9f..0000000 --- a/website/full_javadoc/compbio/runner/_jpred/package-summary.html +++ /dev/null @@ -1,157 +0,0 @@ - - - - - - -compbio.runner._jpred - - - - - - - - - - - - -
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    -Class Summary
    _Jpred 
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    -Packages that use _SkeletalCommandBuilder
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner
    -  -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return _SkeletalCommandBuilder
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameter(java.lang.String parameter) - -
    -           
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.util.List<java.lang.String> parameters) - -
    -           
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.lang.String[] parameters) - -
    -           
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setEmail(java.lang.String email) - -
    -           
    - _SkeletalCommandBuilder_SkeletalCommandBuilder.setName(java.lang.String name) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner that return types with arguments of type _SkeletalCommandBuilder
    - Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() - -
    -           
    - CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of _SkeletalCommandBuilder in compbio.runner._impl
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    Subclasses of _SkeletalCommandBuilder in compbio.runner._impl
    - classBlastAll - -
    -           
    - classDisembl - -
    -           
    - classMcl - -
    -           
    - classOB - -
    -          TODO this needs fixing! Executable does not work
    - classPSIBlast - -
    -           
    - classRonn - -
    -           
    - classRPSBlast - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html deleted file mode 100644 index e2cbdb5..0000000 --- a/website/full_javadoc/compbio/runner/msa/ClustalW.html +++ /dev/null @@ -1,473 +0,0 @@ - - - - - - -ClustalW - - - - - - - - - - - - -
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    - -compbio.runner.msa -
    -Class ClustalW

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<ClustalW>
-      extended by compbio.runner.msa.ClustalW
-
    -
    -
    All Implemented Interfaces:
    Executable<ClustalW>
    -
    -
    -
    -
    public class ClustalW
    extends SkeletalExecutable<ClustalW>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    ClustalW() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - Limit<ClustalW>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<ClustalW>getLimits() - -
    -           
    - AlignmentgetResults(java.lang.String workDirectory) - -
    -           
    -static java.lang.StringgetStatFile() - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    - ClustalWsetInput(java.lang.String inFile) - -
    -           
    - ClustalWsetOutput(java.lang.String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -KEY_VALUE_SEPARATOR

    -
    -public static final java.lang.String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -ClustalW

    -
    -public ClustalW()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public ClustalW setOutput(java.lang.String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public ClustalW setInput(java.lang.String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<ClustalW>
    -
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    -
    -
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    - -

    -getResults

    -
    -public Alignment getResults(java.lang.String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<ClustalW>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<ClustalW>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static java.lang.String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalW> getLimit(java.lang.String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalW> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<ClustalW>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html deleted file mode 100644 index 0a6d12c..0000000 --- a/website/full_javadoc/compbio/runner/msa/Mafft.html +++ /dev/null @@ -1,448 +0,0 @@ - - - - - - -Mafft - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Mafft

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Mafft>
-      extended by compbio.runner.msa.Mafft
-
    -
    -
    All Implemented Interfaces:
    Executable<Mafft>, PipedExecutable<Mafft>
    -
    -
    -
    -
    public class Mafft
    extends SkeletalExecutable<Mafft>
    implements PipedExecutable<Mafft>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Mafft() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - MafftaddParameters(java.util.List<java.lang.String> parameters) - -
    -          Mafft input must always be the last parameter!
    - Limit<Mafft>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Mafft>getLimits() - -
    -           
    - AlignmentgetResults(java.lang.String workDirectory) - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    - MafftsetInput(java.lang.String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    equals, getClusterSettings, getCreatedFiles, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getError, getInput, getOutput, getParameters, loadRunConfiguration
    -  -

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

    -KEY_VALUE_SEPARATOR

    -
    -public static final java.lang.String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Mafft

    -
    -public Mafft()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(java.lang.String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Mafft>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -setInput

    -
    -public Mafft setInput(java.lang.String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Mafft>
    -
    -
    -
    -
    -
    -
    - -

    -addParameters

    -
    -public Mafft addParameters(java.util.List<java.lang.String> parameters)
    -
    -
    Mafft input must always be the last parameter! -

    -

    -
    Specified by:
    addParameters in interface Executable<Mafft>
    Overrides:
    addParameters in class SkeletalExecutable<Mafft>
    -
    -
    - -
    Returns:
    this Executable
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Mafft> getLimit(java.lang.String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<Mafft>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Mafft> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<Mafft>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Mafft>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html deleted file mode 100644 index 479eb57..0000000 --- a/website/full_javadoc/compbio/runner/msa/Muscle.html +++ /dev/null @@ -1,481 +0,0 @@ - - - - - - -Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Muscle

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Muscle>
-      extended by compbio.runner.msa.Muscle
-
    -
    -
    All Implemented Interfaces:
    Executable<Muscle>
    -
    -
    -
    -
    public class Muscle
    extends SkeletalExecutable<Muscle>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Muscle() - -
    -          Default options are - - -clwstrict - write output in clustal format
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - Limit<Muscle>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Muscle>getLimits() - -
    -           
    - AlignmentgetResults(java.lang.String workDirectory) - -
    -           
    -static java.lang.StringgetStatFile() - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    - MusclesetInput(java.lang.String inFile) - -
    -           
    - MusclesetOutput(java.lang.String outFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -KEY_VALUE_SEPARATOR

    -
    -public static final java.lang.String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Muscle

    -
    -public Muscle()
    -
    -
    Default options are - - -clwstrict - write output in clustal format -

    -

    -
    Parameters:
    workDirectory -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setOutput

    -
    -public Muscle setOutput(java.lang.String outFile)
    -
    -
    -
    Overrides:
    setOutput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -setInput

    -
    -public Muscle setInput(java.lang.String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(java.lang.String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Muscle>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Muscle>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -getStatFile

    -
    -public static java.lang.String getStatFile()
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Muscle> getLimit(java.lang.String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Muscle> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Muscle>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html deleted file mode 100644 index 74a2d6a..0000000 --- a/website/full_javadoc/compbio/runner/msa/Probcons.html +++ /dev/null @@ -1,452 +0,0 @@ - - - - - - -Probcons - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Probcons

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Probcons>
-      extended by compbio.runner.msa.Probcons
-
    -
    -
    All Implemented Interfaces:
    Executable<Probcons>, PipedExecutable<Probcons>
    -
    -
    -
    -
    public class Probcons
    extends SkeletalExecutable<Probcons>
    implements PipedExecutable<Probcons>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Probcons() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - Limit<Probcons>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Probcons>getLimits() - -
    -           
    - AlignmentgetResults(java.lang.String workDirectory) - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    - ProbconssetInput(java.lang.String inFile) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getError, getInput, getOutput, getParameters, loadRunConfiguration
    -  -

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

    -KEY_VALUE_SEPARATOR

    -
    -public static final java.lang.String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Probcons

    -
    -public Probcons()
    -
    -
    -
    Parameters:
    workDirectory -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public Alignment getResults(java.lang.String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Probcons>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Probcons>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Probcons>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setInput

    -
    -public Probcons setInput(java.lang.String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Probcons>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Probcons> getLimit(java.lang.String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<Probcons>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Probcons> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<Probcons>
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Probcons>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/Tcoffee.html deleted file mode 100644 index b35bcc1..0000000 --- a/website/full_javadoc/compbio/runner/msa/Tcoffee.html +++ /dev/null @@ -1,542 +0,0 @@ - - - - - - -Tcoffee - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.runner.msa -
    -Class Tcoffee

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<Tcoffee>
-      extended by compbio.runner.msa.Tcoffee
-
    -
    -
    All Implemented Interfaces:
    ClusterNativeSpecExecutable<Tcoffee>, Executable<Tcoffee>, PipedExecutable<Tcoffee>
    -
    -
    -
    -
    public class Tcoffee
    extends SkeletalExecutable<Tcoffee>
    implements PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Field Summary
    -static java.lang.StringKEY_VALUE_SEPARATOR - -
    -           
    -  - - - - - - - - - - -
    -Constructor Summary
    Tcoffee() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static intgetClusterCpuNum() - -
    -           
    - java.util.List<java.lang.String>getCreatedFiles() - -
    -          This method cannot really tell whether the files has actually been - created or not.
    - Limit<Tcoffee>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Tcoffee>getLimits() - -
    -           
    - java.lang.StringgetNativeSpecs() - -
    -           
    - CommandBuilder<Tcoffee>getParameters(Executable.ExecProvider provider) - -
    -           
    - AlignmentgetResults(java.lang.String workDirectory) - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    - TcoffeesetInput(java.lang.String inFile) - -
    -           
    - voidsetNCore(int ncoreNumber) - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  - - - - - - - -
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getError, getInput, getOutput, loadRunConfiguration
    -  -

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

    -KEY_VALUE_SEPARATOR

    -
    -public static final java.lang.String KEY_VALUE_SEPARATOR
    -
    -
    -
    See Also:
    Constant Field Values
    -
    - - - - - - - - -
    -Constructor Detail
    - -

    -Tcoffee

    -
    -public Tcoffee()
    -
    -
    -
    Parameters:
    workDirectory -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -setInput

    -
    -public Tcoffee setInput(java.lang.String inFile)
    -
    -
    -
    Overrides:
    setInput in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getResults

    -
    -public Alignment getResults(java.lang.String workDirectory)
-                     throws ResultNotAvailableException
    -
    -
    -
    Specified by:
    getResults in interface Executable<Tcoffee>
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getCreatedFiles

    -
    -public java.util.List<java.lang.String> getCreatedFiles()
    -
    -
    Description copied from class: SkeletalExecutable
    -
    This method cannot really tell whether the files has actually been - created or not. It must be overridden as required. -

    -

    -
    Specified by:
    getCreatedFiles in interface Executable<Tcoffee>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    See Also:
    Executable.getCreatedFiles()
    -
    -
    -
    - -

    -setNCore

    -
    -public void setNCore(int ncoreNumber)
    -
    -
    -
    -
    -
    -
    -
    -
    -
    - -

    -getParameters

    -
    -public CommandBuilder<Tcoffee> getParameters(Executable.ExecProvider provider)
    -
    -
    -
    Specified by:
    getParameters in interface Executable<Tcoffee>
    Overrides:
    getParameters in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Tcoffee> getLimit(java.lang.String presetName)
    -
    -
    -
    Specified by:
    getLimit in interface Executable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Tcoffee> getLimits()
    -
    -
    -
    Specified by:
    getLimits in interface Executable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getNativeSpecs

    -
    -public java.lang.String getNativeSpecs()
    -
    -
    -
    Specified by:
    getNativeSpecs in interface ClusterNativeSpecExecutable<Tcoffee>
    -
    -
    -
    -
    -
    -
    - -

    -getClusterCpuNum

    -
    -public static int getClusterCpuNum()
    -
    -
    -
    -
    -
    - -
    Returns:
    number of cpus to use on the cluster or 0 if the value is - undefined
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<Tcoffee>
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html deleted file mode 100644 index 5d5eecf..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.ClustalW - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.runner.msa.ClustalW

    -
    - - - - - - - - - - - - - -
    -Packages that use ClustalW
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return ClustalW
    - ClustalWClustalW.setInput(java.lang.String inFile) - -
    -           
    - ClustalWClustalW.setOutput(java.lang.String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type ClustalW
    - Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<ClustalW>ClustalW.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of ClustalW in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type ClustalW
    - Limit<ClustalW>ClustalWS.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<ClustalW>ClustalWS.getLimits() - -
    -           
    - PresetManager<ClustalW>ClustalWS.getPresets() - -
    -           
    - RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type ClustalW
    - java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
    -           
    - java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html deleted file mode 100644 index 65e6512..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Mafft - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
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    -
    -

    -Uses of Class
    compbio.runner.msa.Mafft

    -
    - - - - - - - - - - - - - -
    -Packages that use Mafft
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Mafft in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Mafft
    - MafftMafft.addParameters(java.util.List<java.lang.String> parameters) - -
    -          Mafft input must always be the last parameter!
    - MafftMafft.setInput(java.lang.String inFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Mafft
    - Limit<Mafft>Mafft.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Mafft>Mafft.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of Mafft in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Mafft
    - Limit<Mafft>MafftWS.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Mafft>MafftWS.getLimits() - -
    -           
    - PresetManager<Mafft>MafftWS.getPresets() - -
    -           
    - RunnerConfig<Mafft>MafftWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Mafft
    - java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
    -           
    - java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html deleted file mode 100644 index 2621067..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Muscle - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.runner.msa.Muscle

    -
    - - - - - - - - - - - - - -
    -Packages that use Muscle
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Muscle in compbio.runner.msa
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return Muscle
    - MuscleMuscle.setInput(java.lang.String inFile) - -
    -           
    - MuscleMuscle.setOutput(java.lang.String outFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Muscle
    - Limit<Muscle>Muscle.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Muscle>Muscle.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of Muscle in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Muscle
    - Limit<Muscle>MuscleWS.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Muscle>MuscleWS.getLimits() - -
    -           
    - PresetManager<Muscle>MuscleWS.getPresets() - -
    -           
    - RunnerConfig<Muscle>MuscleWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Muscle
    - java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
    -           
    - java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html deleted file mode 100644 index 3ffa0e0..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html +++ /dev/null @@ -1,283 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Probcons - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - -
    -
    -

    -Uses of Class
    compbio.runner.msa.Probcons

    -
    - - - - - - - - - - - - - -
    -Packages that use Probcons
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Probcons in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Probcons
    - ProbconsProbcons.setInput(java.lang.String inFile) - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Probcons
    - Limit<Probcons>Probcons.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Probcons>Probcons.getLimits() - -
    -           
    -  -

    - - - - - -
    -Uses of Probcons in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Probcons
    - Limit<Probcons>ProbconsWS.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Probcons>ProbconsWS.getLimits() - -
    -           
    - PresetManager<Probcons>ProbconsWS.getPresets() - -
    -           
    - RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Probcons
    - java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
    -           
    - java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html deleted file mode 100644 index 243fcd9..0000000 --- a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - -Uses of Class compbio.runner.msa.Tcoffee - - - - - - - - - - - - -
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    -

    -Uses of Class
    compbio.runner.msa.Tcoffee

    -
    - - - - - - - - - - - - - -
    -Packages that use Tcoffee
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.runner.msa
    -  -

    - - - - - - - - - -
    Methods in compbio.runner.msa that return Tcoffee
    - TcoffeeTcoffee.setInput(java.lang.String inFile) - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - -
    Methods in compbio.runner.msa that return types with arguments of type Tcoffee
    - Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Tcoffee>Tcoffee.getLimits() - -
    -           
    - CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) - -
    -           
    -  -

    - - - - - -
    -Uses of Tcoffee in compbio.ws.server
    -  -

    - - - - - - - - - - - - - - - - - - - - - -
    Methods in compbio.ws.server that return types with arguments of type Tcoffee
    - Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<Tcoffee>TcoffeeWS.getLimits() - -
    -           
    - PresetManager<Tcoffee>TcoffeeWS.getPresets() - -
    -           
    - RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() - -
    -           
    -  -

    - - - - - - - - - - - - - -
    Method parameters in compbio.ws.server with type arguments of type Tcoffee
    - java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
    -           
    - java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -           
    -  -

    -

    - - - - - - - - - - - - - - - -
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    -Classes  - -
    -ClustalW -
    -Mafft -
    -Muscle -
    -Probcons -
    -Tcoffee
    - - - - diff --git a/website/full_javadoc/compbio/runner/msa/package-summary.html b/website/full_javadoc/compbio/runner/msa/package-summary.html deleted file mode 100644 index 82e1c12..0000000 --- a/website/full_javadoc/compbio/runner/msa/package-summary.html +++ /dev/null @@ -1,192 +0,0 @@ - - - - - - -compbio.runner.msa - - - - - - - - - - - - -
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    -Package compbio.runner.msa -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ClustalW 
    Mafft 
    Muscle 
    Probcons 
    Tcoffee 
    -  - -

    -

    -Package compbio.runner.msa Description -

    - -

    -Wrappers for native executables for multiple sequence alignment (msa) -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
    -
    -
    - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/runner/msa/package-tree.html b/website/full_javadoc/compbio/runner/msa/package-tree.html deleted file mode 100644 index d790016..0000000 --- a/website/full_javadoc/compbio/runner/msa/package-tree.html +++ /dev/null @@ -1,159 +0,0 @@ - - - - - - -compbio.runner.msa Class Hierarchy - - - - - - - - - - - - -
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    -Class Hierarchy -

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    -Uses of Package
    compbio.runner.msa

    -
    - - - - - - - - - - - - - -
    -Packages that use compbio.runner.msa
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.runner.msa
    ClustalW - -
    -           
    Mafft - -
    -           
    Muscle - -
    -           
    Probcons - -
    -           
    Tcoffee - -
    -           
    -  -

    - - - - - - - - - - - - - - - - - - - - -
    -Classes in compbio.runner.msa used by compbio.ws.server
    ClustalW - -
    -           
    Mafft - -
    -           
    Muscle - -
    -           
    Probcons - -
    -           
    Tcoffee - -
    -           
    -  -

    -

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    -Classes  - -
    -_NativeSpecHelper -
    -_SkeletalCommandBuilder -
    -OptionCombinator -
    -Util
    - - - - diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html deleted file mode 100644 index e5f3a22..0000000 --- a/website/full_javadoc/compbio/runner/package-summary.html +++ /dev/null @@ -1,188 +0,0 @@ - - - - - - -compbio.runner - - - - - - - - - - - - -
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    -Package compbio.runner -

    -Utilities commonly used by all runners. -

    -See: -
    -          Description -

    - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    _NativeSpecHelper 
    _SkeletalCommandBuilder 
    OptionCombinatorThis class solve the following problems.
    Util 
    -  - -

    -

    -Package compbio.runner Description -

    - -

    -Utilities commonly used by all runners. -

    - -

    -

    -
    Author:
    -
    Petr Troshin - - Date January 2010
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    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
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    _SkeletalCommandBuilder - -
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    - - - -
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    - -compbio.runner.psiblast -
    -Class PsiBlast

    -
    -java.lang.Object
-  extended by compbio.engine.client.SkeletalExecutable<PsiBlast>
-      extended by compbio.runner.psiblast.PsiBlast
-
    -
    -
    All Implemented Interfaces:
    Executable<PsiBlast>
    -
    -
    -
    -
    public class PsiBlast
    extends SkeletalExecutable<PsiBlast>
    - - -

    -

    - -

    - - - - - - - -
    -Nested Class Summary
    -  - - - - - - - -
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    -  - - - - - - - - - - - -
    -Constructor Summary
    PsiBlast() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - Limit<PsiBlast>getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<PsiBlast>getLimits() - -
    -           
    - - - - - -
    -<V> V
    -    		getResults(java.lang.String directory) - -
    -           
    - java.lang.Class<? extends Executable<?>>getType() - -
    -           
    -  - - - - - - - -
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getCreatedFiles, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setInput, setOutput, setParameter, toString
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -PsiBlast

    -
    -public PsiBlast()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -getResults

    -
    -public <V> V getResults(java.lang.String directory)
-             throws ResultNotAvailableException
    -
    -
    - -
    Throws: -
    ResultNotAvailableException
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<PsiBlast> getLimit(java.lang.String presetName)
    -
    -
    -
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<PsiBlast> getLimits()
    -
    -
    -
    -
    -
    -
    - -

    -getType

    -
    -public java.lang.Class<? extends Executable<?>> getType()
    -
    -
    -
    Specified by:
    getType in class SkeletalExecutable<PsiBlast>
    -
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    -Uses of Class
    compbio.runner.psiblast.PsiBlast

    -
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    -Packages that use PsiBlast
    compbio.runner.psiblast  
    -  -

    - - - - - -
    -Uses of PsiBlast in compbio.runner.psiblast
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.runner.psiblast that return types with arguments of type PsiBlast
    - Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) - -
    -           
    - LimitsManager<PsiBlast>PsiBlast.getLimits() - -
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    -Package compbio.runner.psiblast -

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    PsiBlast 
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    compbio.runner.psiblast  
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    -Classes in compbio.runner.psiblast used by compbio.runner.psiblast
    PsiBlast - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html deleted file mode 100644 index 35584df..0000000 --- a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html +++ /dev/null @@ -1,377 +0,0 @@ - - - - - - -Jws2Client.Services - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.client -
    -Enum Jws2Client.Services

    -
    -java.lang.Object
-  extended by java.lang.Enum<Jws2Client.Services>
-      extended by compbio.ws.client.Jws2Client.Services
-
    -
    -
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Jws2Client.Services>
    -
    -
    -
    Enclosing class:
    Jws2Client
    -
    -
    -
    -
    public static enum Jws2Client.Services
    extends java.lang.Enum<Jws2Client.Services>
    - - -

    -List of web services currently supported by JWS2 -

    - -

    -

    - -

    - - - - - - - - - - - - - - - - - - - - - - -
    -Enum Constant Summary
    ClustalWS - -
    -           
    MafftWS - -
    -           
    MuscleWS - -
    -           
    ProbconsWS - -
    -           
    TcoffeeWS - -
    -           
    -  - - - - - - - - - - - - - - - -
    -Method Summary
    -static Jws2Client.ServicesvalueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Jws2Client.Services[]values() - -
    -          Returns an array containing the constants of this enum type, in -the order they are declared.
    -  - - - - - - - -
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    -  -

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

    -MafftWS

    -
    -public static final Jws2Client.Services MafftWS
    -
    -
    -
    -
    -
    - -

    -MuscleWS

    -
    -public static final Jws2Client.Services MuscleWS
    -
    -
    -
    -
    -
    - -

    -ClustalWS

    -
    -public static final Jws2Client.Services ClustalWS
    -
    -
    -
    -
    -
    - -

    -TcoffeeWS

    -
    -public static final Jws2Client.Services TcoffeeWS
    -
    -
    -
    -
    -
    - -

    -ProbconsWS

    -
    -public static final Jws2Client.Services ProbconsWS
    -
    -
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -values

    -
    -public static Jws2Client.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 (Jws2Client.Services c : Jws2Client.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 Jws2Client.Services valueOf(java.lang.String name)
    -
    -
    Returns the enum constant of this type with the specified name. -The string must match exactly an identifier used to declare an -enum constant in this type. (Extraneous whitespace characters are -not permitted.) -

    -

    -
    Parameters:
    name - the name of the enum constant to be returned. -
    Returns:
    the enum constant with the specified name -
    Throws: -
    java.lang.IllegalArgumentException - if this enum type has no constant -with the specified name -
    java.lang.NullPointerException - if the argument is null
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD -DETAIL: ENUM CONSTANTS | FIELD | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html deleted file mode 100644 index 97c55bf..0000000 --- a/website/full_javadoc/compbio/ws/client/Jws2Client.html +++ /dev/null @@ -1,375 +0,0 @@ - - - - - - -Jws2Client - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.client -
    -Class Jws2Client

    -
    -java.lang.Object
-  extended by compbio.ws.client.Jws2Client
-
    -
    -
    -
    public class Jws2Client
    extends java.lang.Object
    - - -

    -A command line client for Jalview Web Services version 2 -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Nested Class Summary
    -static classJws2Client.Services - -
    -          List of web services currently supported by JWS2
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> MsaWS<T>
    -    		connect(java.lang.String host, - Jws2Client.Services service) - -
    -          Connects to a web service by the host and the service name
    -static java.lang.StringgetHost(java.lang.String[] cmd) - -
    -          Extracts host name from the command line
    -static java.lang.StringgetServiceName(java.lang.String[] cmd) - -
    -          Extracts service name from the command line
    -static voidmain(java.lang.String[] args) - -
    -          Starts command line client, if no parameter are supported print help.
    -static booleanvalidURL(java.lang.String urlstr) - -
    -          Attempt to construct the URL object from the string
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -validURL

    -
    -public static boolean validURL(java.lang.String urlstr)
    -
    -
    Attempt to construct the URL object from the string -

    -

    -
    Parameters:
    urlstr - -
    Returns:
    true if it succeed false otherwise
    -
    -
    -
    - -

    -getServiceName

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

    -

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

    -getHost

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

    -

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

    -connect

    -
    -public static <T> MsaWS<T> connect(java.lang.String host,
-                                   Jws2Client.Services service)
-                        throws javax.xml.ws.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: -
    javax.xml.ws.WebServiceException
    -
    -
    -
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
    -
    -
    Starts command line client, if no parameter are supported print help. Two - parameters are required for 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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    - -compbio.ws.client -
    -Class SimpleWSClient

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

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    SimpleWSClient() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(java.lang.String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -SimpleWSClient

    -
    -public SimpleWSClient()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
-                 throws java.io.FileNotFoundException,
-                        java.io.IOException,
-                        JobSubmissionException,
-                        java.lang.InterruptedException,
-                        WrongParameterException
    -
    -
    - -
    Throws: -
    java.io.FileNotFoundException -
    java.io.IOException -
    JobSubmissionException -
    java.lang.InterruptedException -
    WrongParameterException
    -
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    - -compbio.ws.client -
    -Class WSTester

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

    -Class for testing web services -

    - -

    -

    -
    Author:
    -
    pvtroshin - - Date February 2010
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    WSTester() - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> void
    -    		main(java.lang.String[] args) - -
    -          Test JWS2 web services
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -WSTester

    -
    -public WSTester()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static <T> void main(java.lang.String[] args)
    -
    -
    Test JWS2 web services -

    -

    -
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= - - -s= which is optional. If service name is not - provided then all known JWS2 web services are tested
    -
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    compbio.ws.client.Jws2Client.Services

    -
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    -Packages that use Jws2Client.Services
    compbio.ws.client  
    -  -

    - - - - - -
    -Uses of Jws2Client.Services in compbio.ws.client
    -  -

    - - - - - - - - - - - - - -
    Methods in compbio.ws.client that return Jws2Client.Services
    -static Jws2Client.ServicesJws2Client.Services.valueOf(java.lang.String name) - -
    -          Returns the enum constant of this type with the specified name.
    -static Jws2Client.Services[]Jws2Client.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 Jws2Client.Services
    -static - - - - -
    -<T> MsaWS<T>
    -    		Jws2Client.connect(java.lang.String host, - Jws2Client.Services service) - -
    -          Connects to a web service by the host and the service name
    -  -

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    - - - - - - -
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    -

    -Package compbio.ws.client -

    - - - - - - - - - - - - - -
    -Class Summary
    Jws2ClientA command line client for Jalview Web Services version 2
    WSTesterClass for testing web services
    -  - -

    - - - - - - - - - -
    -Enum Summary
    Jws2Client.ServicesList of web services currently supported by JWS2
    -  - -

    -

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    -Packages that use compbio.ws.client
    compbio.ws.client  
    -  -

    - - - - - - - - -
    -Classes in compbio.ws.client used by compbio.ws.client
    Jws2Client.Services - -
    -          List of web services currently supported by JWS2
    -  -

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    - - - -
    - -

    - -compbio.ws.server -
    -Class ClustalWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ClustalWS
-
    -
    -
    All Implemented Interfaces:
    MsaWS<ClustalW>
    -
    -
    -
    -
    public class ClustalWS
    extends java.lang.Object
    implements MsaWS<ClustalW>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ClustalWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(java.lang.String jobId) - -
    -          Stop running job but leave its output untouched
    - java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<ClustalW>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    - Limit<ClustalW>getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<ClustalW>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<ClustalW>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(java.lang.String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<ClustalW>getRunnerOptions() - -
    -          Get options supported by a web service
    - java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<ClustalW> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -ClustalWS

    -
    -public ClustalWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

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

    -

    -
    Specified by:
    align in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException
    -
    -
    -
    - -

    -presetAlign

    -
    -public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                                    Preset<ClustalW> preset)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. @see Preset - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    -
    -
    -
    - -

    -customAlign

    -
    -public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                                    java.util.List<Option<ClustalW>> options)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<ClustalW> getRunnerOptions()
    -
    -
    Description copied from interface: MsaWS
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface MsaWS<ClustalW>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. -

    -

    -
    Specified by:
    getResult in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<ClustalW> getLimit(java.lang.String presetName)
    -
    -
    Description copied from interface: MsaWS
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<ClustalW> getLimits()
    -
    -
    Description copied from interface: MsaWS
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface MsaWS<ClustalW>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Stop running job but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface MsaWS<ClustalW>
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Return the status of the job. @see JobStatus -

    -

    -
    Specified by:
    getJobStatus in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<ClustalW> getPresets()
    -
    -
    Description copied from interface: MsaWS
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface MsaWS<ClustalW>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -pullExecStatistics

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

    -

    -
    Specified by:
    pullExecStatistics in interface MsaWS<ClustalW>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html deleted file mode 100644 index d419846..0000000 --- a/website/full_javadoc/compbio/ws/server/MafftWS.html +++ /dev/null @@ -1,599 +0,0 @@ - - - - - - -MafftWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class MafftWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MafftWS
-
    -
    -
    All Implemented Interfaces:
    MsaWS<Mafft>
    -
    -
    -
    -
    public class MafftWS
    extends java.lang.Object
    implements MsaWS<Mafft>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    MafftWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(java.lang.String jobId) - -
    -          Stop running job but leave its output untouched
    - java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Mafft>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    - Limit<Mafft>getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Mafft>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Mafft>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(java.lang.String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Mafft>getRunnerOptions() - -
    -          Get options supported by a web service
    - java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<Mafft> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -MafftWS

    -
    -public MafftWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

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

    -

    -
    Specified by:
    align in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException
    -
    -
    -
    - -

    -customAlign

    -
    -public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                                    java.util.List<Option<Mafft>> options)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                                    Preset<Mafft> preset)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. @see Preset - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Mafft> getLimit(java.lang.String presetName)
    -
    -
    Description copied from interface: MsaWS
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Mafft> getLimits()
    -
    -
    Description copied from interface: MsaWS
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface MsaWS<Mafft>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

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

    -

    -
    Specified by:
    pullExecStatistics in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Stop running job but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface MsaWS<Mafft>
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Return the status of the job. @see JobStatus -

    -

    -
    Specified by:
    getJobStatus in interface MsaWS<Mafft>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Mafft> getPresets()
    -
    -
    Description copied from interface: MsaWS
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface MsaWS<Mafft>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Mafft> getRunnerOptions()
    -
    -
    Description copied from interface: MsaWS
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface MsaWS<Mafft>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/MuscleWS.html b/website/full_javadoc/compbio/ws/server/MuscleWS.html deleted file mode 100644 index 0d9ec95..0000000 --- a/website/full_javadoc/compbio/ws/server/MuscleWS.html +++ /dev/null @@ -1,599 +0,0 @@ - - - - - - -MuscleWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class MuscleWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.MuscleWS
-
    -
    -
    All Implemented Interfaces:
    MsaWS<Muscle>
    -
    -
    -
    -
    public class MuscleWS
    extends java.lang.Object
    implements MsaWS<Muscle>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    MuscleWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(java.lang.String jobId) - -
    -          Stop running job but leave its output untouched
    - java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Muscle>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    - Limit<Muscle>getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Muscle>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Muscle>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(java.lang.String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Muscle>getRunnerOptions() - -
    -          Get options supported by a web service
    - java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<Muscle> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -MuscleWS

    -
    -public MuscleWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

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

    -

    -
    Specified by:
    align in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException
    -
    -
    -
    - -

    -customAlign

    -
    -public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                                    java.util.List<Option<Muscle>> options)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                                    Preset<Muscle> preset)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. @see Preset - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Muscle> getLimit(java.lang.String presetName)
    -
    -
    Description copied from interface: MsaWS
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Muscle> getLimits()
    -
    -
    Description copied from interface: MsaWS
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface MsaWS<Muscle>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

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

    -

    -
    Specified by:
    pullExecStatistics in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Stop running job but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface MsaWS<Muscle>
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Return the status of the job. @see JobStatus -

    -

    -
    Specified by:
    getJobStatus in interface MsaWS<Muscle>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Muscle> getPresets()
    -
    -
    Description copied from interface: MsaWS
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface MsaWS<Muscle>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Muscle> getRunnerOptions()
    -
    -
    Description copied from interface: MsaWS
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface MsaWS<Muscle>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/ProbconsWS.html deleted file mode 100644 index a97b8eb..0000000 --- a/website/full_javadoc/compbio/ws/server/ProbconsWS.html +++ /dev/null @@ -1,599 +0,0 @@ - - - - - - -ProbconsWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class ProbconsWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.ProbconsWS
-
    -
    -
    All Implemented Interfaces:
    MsaWS<Probcons>
    -
    -
    -
    -
    public class ProbconsWS
    extends java.lang.Object
    implements MsaWS<Probcons>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    ProbconsWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(java.lang.String jobId) - -
    -          Stop running job but leave its output untouched
    - java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Probcons>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    - Limit<Probcons>getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Probcons>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Probcons>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(java.lang.String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Probcons>getRunnerOptions() - -
    -          Get options supported by a web service
    - java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<Probcons> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -ProbconsWS

    -
    -public ProbconsWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

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

    -

    -
    Specified by:
    align in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException
    -
    -
    -
    - -

    -customAlign

    -
    -public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                                    java.util.List<Option<Probcons>> options)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                                    Preset<Probcons> preset)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. @see Preset - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Probcons> getLimit(java.lang.String presetName)
    -
    -
    Description copied from interface: MsaWS
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Probcons> getLimits()
    -
    -
    Description copied from interface: MsaWS
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface MsaWS<Probcons>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

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

    -

    -
    Specified by:
    pullExecStatistics in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Stop running job but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface MsaWS<Probcons>
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Return the status of the job. @see JobStatus -

    -

    -
    Specified by:
    getJobStatus in interface MsaWS<Probcons>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Probcons> getPresets()
    -
    -
    Description copied from interface: MsaWS
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface MsaWS<Probcons>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Probcons> getRunnerOptions()
    -
    -
    Description copied from interface: MsaWS
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface MsaWS<Probcons>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html deleted file mode 100644 index e4fd0ac..0000000 --- a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html +++ /dev/null @@ -1,263 +0,0 @@ - - - - - - -SimpleWSPublisher - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class SimpleWSPublisher

    -
    -java.lang.Object
-  extended by compbio.ws.server.SimpleWSPublisher
-
    -
    -
    -
    public class SimpleWSPublisher
    extends java.lang.Object
    - - -

    -This class publish a web service. This is not a production implementation. - Should be used only for during development and testing -

    - -

    -

    -
    Author:
    -
    pvtroshin
    -
    -
    - -

    - - - - - - - - - - - -
    -Constructor Summary
    SimpleWSPublisher(java.lang.Object exec, - java.lang.String context) - -
    -           
    -  - - - - - - - - - - - -
    -Method Summary
    -static voidmain(java.lang.String[] args) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -SimpleWSPublisher

    -
    -public SimpleWSPublisher(java.lang.Object exec,
-                         java.lang.String context)
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -main

    -
    -public static void main(java.lang.String[] args)
    -
    -
    -
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - - - diff --git a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html deleted file mode 100644 index bc9ed89..0000000 --- a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html +++ /dev/null @@ -1,599 +0,0 @@ - - - - - - -TcoffeeWS - - - - - - - - - - - - -
    - - - - - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    -    		 - -
    - PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
    - SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
    - - - -
    - -

    - -compbio.ws.server -
    -Class TcoffeeWS

    -
    -java.lang.Object
-  extended by compbio.ws.server.TcoffeeWS
-
    -
    -
    All Implemented Interfaces:
    MsaWS<Tcoffee>
    -
    -
    -
    -
    public class TcoffeeWS
    extends java.lang.Object
    implements MsaWS<Tcoffee>
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    TcoffeeWS() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    - java.lang.Stringalign(java.util.List<FastaSequence> sequences) - -
    -          Align a list of sequences with default settings.
    - booleancancelJob(java.lang.String jobId) - -
    -          Stop running job but leave its output untouched
    - java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, - java.util.List<Option<Tcoffee>> options) - -
    -          Align a list of sequences with options.
    - JobStatusgetJobStatus(java.lang.String jobId) - -
    -          Return the status of the job.
    - Limit<Tcoffee>getLimit(java.lang.String presetName) - -
    -          Get a Limit for a preset.
    - LimitsManager<Tcoffee>getLimits() - -
    -          List Limits supported by a web service.
    - PresetManager<Tcoffee>getPresets() - -
    -          Get presets supported by a web service
    - AlignmentgetResult(java.lang.String jobId) - -
    -          Return the result of the job.
    - RunnerConfig<Tcoffee>getRunnerOptions() - -
    -          Get options supported by a web service
    - java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, - Preset<Tcoffee> preset) - -
    -          Align a list of sequences with preset.
    - ChunkHolderpullExecStatistics(java.lang.String jobId, - long position) - -
    -          Reads 1kb chunk from the statistics file which is specific to a given web - service from the position.
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -TcoffeeWS

    -
    -public TcoffeeWS()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -align

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

    -

    -
    Specified by:
    align in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    JobSubmissionException
    -
    -
    -
    - -

    -customAlign

    -
    -public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
-                                    java.util.List<Option<Tcoffee>> options)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with options. -

    -

    -
    Specified by:
    customAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    options - A list of Options -
    Returns:
    jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be - permitted or denied
    -
    -
    -
    - -

    -presetAlign

    -
    -public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
-                                    Preset<Tcoffee> preset)
-                             throws JobSubmissionException,
-                                    WrongParameterException
    -
    -
    Description copied from interface: MsaWS
    -
    Align a list of sequences with preset. @see Preset - - Limit for a presetName is used whether the calculation will be permitted - or denied. If no Limit was defined for a presetName, than default limit - is used. -

    -

    -
    Specified by:
    presetAlign in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform - any sequence validity checks. Nor does it checks whether the - sequences names are unique. It is responsibility of the caller - to validate this information
    preset - A list of Options -
    Returns:
    String - jobId - unique identifier for the job -
    Throws: -
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a - given web service, e.g. JWS2 is deployed on Windows and Mafft - service is called -
    LimitExceededException - is throw if the input sequences number or average length - exceeds what is defined by the limit -
    WrongParameterException - is throws when 1) One of the Options provided is not - supported, 2) The value of the option is defined outside the - boundaries. In both cases exception object contain the - information on the violating Option. -
    JobSubmissionException
    -
    -
    -
    - -

    -getResult

    -
    -public Alignment getResult(java.lang.String jobId)
-                    throws ResultNotAvailableException
    -
    -
    Description copied from interface: MsaWS
    -
    Return the result of the job. -

    -

    -
    Specified by:
    getResult in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    jobId - a unique job identifier -
    Returns:
    Alignment -
    Throws: -
    ResultNotAvailableException - this exception is throw if the job execution was not - successful or the result of the execution could not be found. - (e.g. removed). Exception could also be thrown is dues to the - lower level problems on the server i.e. IOException, - FileNotFoundException problems as well as - UnknownFileFormatException.
    -
    -
    -
    - -

    -getLimit

    -
    -public Limit<Tcoffee> getLimit(java.lang.String presetName)
    -
    -
    Description copied from interface: MsaWS
    -
    Get a Limit for a preset. -

    -

    -
    Specified by:
    getLimit in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    presetName - the name of the preset. if no name is provided, then the - default preset is returned. If no limit for a particular - preset is defined then the default preset is returned -
    Returns:
    Limit
    -
    -
    -
    - -

    -getLimits

    -
    -public LimitsManager<Tcoffee> getLimits()
    -
    -
    Description copied from interface: MsaWS
    -
    List Limits supported by a web service. -

    -

    -
    Specified by:
    getLimits in interface MsaWS<Tcoffee>
    -
    -
    - -
    Returns:
    LimitManager
    -
    -
    -
    - -

    -pullExecStatistics

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

    -

    -
    Specified by:
    pullExecStatistics in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read -
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data - and a next position within the file from which no data has been - read
    -
    -
    -
    - -

    -cancelJob

    -
    -public boolean cancelJob(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Stop running job but leave its output untouched -

    -

    -
    Specified by:
    cancelJob in interface MsaWS<Tcoffee>
    -
    -
    - -
    Returns:
    true if job was cancelled successfully, false otherwise
    -
    -
    -
    - -

    -getJobStatus

    -
    -public JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    Description copied from interface: MsaWS
    -
    Return the status of the job. @see JobStatus -

    -

    -
    Specified by:
    getJobStatus in interface MsaWS<Tcoffee>
    -
    -
    -
    Parameters:
    jobId - - unique job identifier -
    Returns:
    JobStatus - status of the job
    -
    -
    -
    - -

    -getPresets

    -
    -public PresetManager<Tcoffee> getPresets()
    -
    -
    Description copied from interface: MsaWS
    -
    Get presets supported by a web service -

    -

    -
    Specified by:
    getPresets in interface MsaWS<Tcoffee>
    -
    -
    - -
    Returns:
    PresetManager the object contains information about presets - supported by a web service
    -
    -
    -
    - -

    -getRunnerOptions

    -
    -public RunnerConfig<Tcoffee> getRunnerOptions()
    -
    -
    Description copied from interface: MsaWS
    -
    Get options supported by a web service -

    -

    -
    Specified by:
    getRunnerOptions in interface MsaWS<Tcoffee>
    -
    -
    - -
    Returns:
    RunnerConfig the list of options and parameters supported by a - web service.
    -
    -
    - -
    - - - - - - - - - - - - - - - - - - - -
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    - - - diff --git a/website/full_javadoc/compbio/ws/server/WSUtil.html b/website/full_javadoc/compbio/ws/server/WSUtil.html deleted file mode 100644 index cb07ea7..0000000 --- a/website/full_javadoc/compbio/ws/server/WSUtil.html +++ /dev/null @@ -1,510 +0,0 @@ - - - - - - -WSUtil - - - - - - - - - - - - -
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    - - - -
    - -

    - -compbio.ws.server -
    -Class WSUtil

    -
    -java.lang.Object
-  extended by compbio.ws.server.WSUtil
-
    -
    -
    -
    public final class WSUtil
    extends java.lang.Object
    - - -

    -

    - -

    - - - - - - - - - - - -
    -Constructor Summary
    WSUtil() - -
    -           
    -  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Method Summary
    -static - - - - -
    -<T> java.lang.String
    -    		align(java.util.List<FastaSequence> sequences, - ConfiguredExecutable<T> confExec, - org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String callingMethod, - Limit<T> limit) - -
    -           
    -static booleancancelJob(java.lang.String jobId) - -
    -           
    -static - - - - -
    -<T> java.util.List<java.lang.String>
    -    		getCommands(java.util.List<Option<T>> options, - java.lang.String keyValueSeparator) - -
    -           
    -static AsyncExecutorgetEngine(ConfiguredExecutable<?> confClustal) - -
    -           
    -static JobStatusgetJobStatus(java.lang.String jobId) - -
    -           
    -static bytegetProgress(java.lang.String jobId) - -
    -           
    -static java.lang.StringgetRemoteAddress(javax.xml.ws.WebServiceContext wsContext) - -
    -           
    -static voidlog(org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String activity) - -
    -           
    -static voidlog(org.apache.log4j.Logger statLog, - javax.xml.ws.WebServiceContext wsContext, - java.lang.String jobId, - java.lang.String activity) - -
    -           
    -static ChunkHolderpullFile(java.lang.String jobId, - long position) - -
    -           
    -static voidvalidateFastaInput(java.util.List<FastaSequence> sequences) - -
    -           
    -static voidvalidateJobId(java.lang.String jobId) - -
    -           
    -  - - - - - - - -
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    -  -

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

    -WSUtil

    -
    -public WSUtil()
    -
    -
    - - - - - - - - -
    -Method Detail
    - -

    -log

    -
    -public static void log(org.apache.log4j.Logger statLog,
-                       javax.xml.ws.WebServiceContext wsContext,
-                       java.lang.String activity)
    -
    -
    -
    -
    -
    -
    - -

    -validateJobId

    -
    -public static final void validateJobId(java.lang.String jobId)
-                                throws java.security.InvalidParameterException
    -
    -
    - -
    Throws: -
    java.security.InvalidParameterException
    -
    -
    -
    - -

    -validateFastaInput

    -
    -public static final void validateFastaInput(java.util.List<FastaSequence> sequences)
-                                     throws java.security.InvalidParameterException
    -
    -
    - -
    Throws: -
    java.security.InvalidParameterException
    -
    -
    -
    - -

    -log

    -
    -public static void log(org.apache.log4j.Logger statLog,
-                       javax.xml.ws.WebServiceContext wsContext,
-                       java.lang.String jobId,
-                       java.lang.String activity)
    -
    -
    -
    -
    -
    -
    - -

    -getJobStatus

    -
    -public static JobStatus getJobStatus(java.lang.String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -pullFile

    -
    -public static ChunkHolder pullFile(java.lang.String jobId,
-                                   long position)
    -
    -
    -
    -
    -
    -
    - -

    -getProgress

    -
    -public static byte getProgress(java.lang.String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getEngine

    -
    -public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)
    -
    -
    -
    -
    -
    -
    - -

    -cancelJob

    -
    -public static boolean cancelJob(java.lang.String jobId)
    -
    -
    -
    -
    -
    -
    - -

    -getRemoteAddress

    -
    -public static java.lang.String getRemoteAddress(javax.xml.ws.WebServiceContext wsContext)
    -
    -
    -
    -
    -
    -
    - -

    -align

    -
    -public static <T> java.lang.String align(java.util.List<FastaSequence> sequences,
-                                         ConfiguredExecutable<T> confExec,
-                                         org.apache.log4j.Logger statLog,
-                                         javax.xml.ws.WebServiceContext wsContext,
-                                         java.lang.String callingMethod,
-                                         Limit<T> limit)
-                              throws LimitExceededException,
-                                     JobSubmissionException
    -
    -
    - -
    Throws: -
    LimitExceededException -
    JobSubmissionException
    -
    -
    -
    - -

    -getCommands

    -
    -public static final <T> java.util.List<java.lang.String> getCommands(java.util.List<Option<T>> options,
-                                                                     java.lang.String keyValueSeparator)
    -
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    -Uses of Class
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    -

    - - - - - - - - - - - - - - - -
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    -Package compbio.ws.server -

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -Class Summary
    ClustalWS 
    MafftWS 
    MuscleWS 
    ProbconsWS 
    SimpleWSPublisherThis class publish a web service.
    TcoffeeWS 
    WSUtil 
    -  - -

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    compbio.data.sequence.ClustalAlignmentUtil
    -public static final chargapchar45
    - -

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    -compbio.engine.*
    - -

    - - - - - - - - - - - - -
    compbio.engine.client.ConfExecutable<T>
    -public static final java.lang.StringCLUSTER_TASK_ID_PREFIX"@"
    - -

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    compbio.engine.client.EnvVariableProcessor
    -public static final java.lang.StringPATH"PATH"
    - -

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    compbio.engine.client.RunConfiguration
    -public static final java.lang.StringrconfigFile"RunnerConfig.xml"
    - -

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    compbio.engine.cluster.drmaa.ClusterSession
    -public static final java.lang.StringJOBID"JOBID"
    - -

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    compbio.engine.cluster.dundee._QueueConstraints
    -public static final intFIRST_MEMORY_LIMIT14000
    -public static final intLONG_TIME_LIMIT24
    -public static final intMAX_MEMORY_LIMIT30000
    -public static final intSHORT_TIME_LIMIT8
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    compbio.engine.conf._Key
    -public static final java.lang.StringDELIM"#"
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    compbio.engine.conf.DirectoryManager
    -public static final java.lang.StringDELIM"#"
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    compbio.engine.local.ExecutableWrapper
    -public static final java.lang.StringPROC_ERR_FILE"procError.txt"
    -public static final java.lang.StringPROC_OUT_FILE"procOutput.txt"
    - -

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    -compbio.metadata.*
    - -

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    -public static final java.lang.StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
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    -compbio.runner.*
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    -public static final java.lang.StringSPACE" "
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    -public static final java.lang.StringKEY_VALUE_SEPARATOR"="
    - -

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    compbio.runner.msa.Mafft
    -public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    - -

    - -

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    compbio.runner.msa.Muscle
    -public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    - -

    - -

    - - - - - - - - - - - - -
    compbio.runner.msa.Probcons
    -public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    - -

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    compbio.runner.msa.Tcoffee
    -public static final java.lang.StringKEY_VALUE_SEPARATOR"="
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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 -
      -
    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 -
      -
    addParameter(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    addParameters(List<String>) - -Method in class compbio.engine.client.ConfExecutable -
      -
    addParameters(List<String>) - -Method in interface compbio.engine.client.Executable -
    Adds parameter to the list of parameters for a native executable -
    addParameters(List<String>) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    addParameters(List<String>) - -Method in class compbio.runner._impl.NetNglyc -
      -
    addParameters(String[]) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    addParameters(List<String>) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    addParameters(List<String>) - -Method in class compbio.runner.msa.Mafft -
    Mafft input must always be the last parameter! -
    addParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    addPossibleValues(String...) - -Method in class compbio.metadata.Parameter -
      -
    addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.SubmissionManager -
      -
    Align - Class in compbio.data.msa.jaxws
     
    Align() - -Constructor for class compbio.data.msa.jaxws.Align -
      -
    align(List<FastaSequence>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with default settings. -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ClustalWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MafftWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.MuscleWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    align(List<FastaSequence>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, WebServiceContext, String, Limit<T>) - -Static method in class compbio.ws.server.WSUtil -
      -
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - -Constructor for class compbio.data.sequence.Alignment -
      -
    Alignment(List<FastaSequence>, AlignmentMetadata) - -Constructor for class compbio.data.sequence.Alignment -
      -
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - -Constructor for class compbio.data.sequence.AlignmentMetadata -
      -
    AlignResponse - Class in compbio.data.msa.jaxws
     
    AlignResponse() - -Constructor for class compbio.data.msa.jaxws.AlignResponse -
      -
    AMBIGUOUS_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    Same as AA pattern but with two additional letters - XU -
    AMBIGUOUS_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Ambiguous nucleotide -
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it - allows to set a value
    argumentsToCommandString(List<? extends Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - -Static method in class compbio.runner.OptionCombinator -
      -
    AsyncExecutor - Interface in compbio.engine
    An asynchronous executor engine, capable of running, cancelling, - obtaining results calculated by a native executable wrapper in Executable interface.
    AsyncJobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    AsyncJobRunner() - -Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    AsyncLocalRunner - Class in compbio.engine.local
     
    AsyncLocalRunner() - -Constructor for class compbio.engine.local.AsyncLocalRunner -
      -
    awaitTermination(long, TimeUnit) - -Method in class compbio.engine.local._TrackingExecutor -
      -
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    JnetAnnotation - Enum in compbio.data._structure
     
    Job - Class in compbio.engine
     
    Job(String, String, ConfiguredExecutable<?>) - -Constructor for class compbio.engine.Job -
      -
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation - cannot be obtained.
    JobExecutionException(String) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionException(String, Throwable) - -Constructor for exception compbio.metadata.JobExecutionException -
      -
    JobExecutionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobExecutionExceptionBean() - -Constructor for class compbio.data.msa.jaxws.JobExecutionExceptionBean -
      -
    JOBID - -Static variable in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    JobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    JobRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.cluster.drmaa.JobRunner -
      -
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a - wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionException(String, Throwable) - -Constructor for exception compbio.metadata.JobSubmissionException -
      -
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobSubmissionExceptionBean() - -Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    Jpred4 - Class in compbio.pipeline._jpred
    jpred --sequence OR --alignment [--db - ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] - - jpred4 --sequence The path to the sequence (in FASTA format) you - want to predict OR - - [--alignment ] The alignment which to use for prediction - - [--profile=] - - [--db ] Database to use for PSI-BLAST querying.
    Jpred4() - -Constructor for class compbio.pipeline._jpred.Jpred4 -
      -
    JpredAnnotation - Enum in compbio.data._structure
     
    JpredResult - Class in compbio.data._structure
    Jnet result - - jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H - ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, - -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- - , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, - 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 - 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 - , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- - , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- - ,B, - JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- - ,-,- - JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, - -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, - JNETHMM:-,H,H,H,H,H,H,H,H,H,H, - H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, - -,-,-,-,-,-,-,-,-,-,-,-,-,-,- - ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, - JNETPROPH:0.0110,0.1125,0.8552,0.0107 - ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 - ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 - ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, - JNETPROPE:0.0107,0.6245,0.3614,0.0120 - ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 - ,0.9586,0.0465,0.0094,0.9662,0.0433, - ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    JpredResult() - -Constructor for class compbio.data._structure.JpredResult -
      -
    Jws2Client - Class in compbio.ws.client
    A command line client for Jalview Web Services version 2
    Jws2Client.Services - Enum in compbio.ws.client
    List of web services currently supported by JWS2
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    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.ClustalW -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Mafft -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Muscle -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Probcons -
      -
    KEY_VALUE_SEPARATOR - -Static variable in class compbio.runner.msa.Tcoffee -
      -
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    -
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average - sequence length for a preset.
    Limit(int, int, String) - -Constructor for class compbio.metadata.Limit -
      -
    Limit(int, int, String, boolean) - -Constructor for class compbio.metadata.Limit -
      -
    LimitExceededException - Exception in compbio.metadata
    Thrown if the task larger in size that the limit that applies to the - calculation.
    LimitExceededException(String) - -Constructor for exception compbio.metadata.LimitExceededException -
      -
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    LimitExceededExceptionBean() - -Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - -Constructor for class compbio.metadata.LimitsManager -
      -
    load(InputStream) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    LoadBalancer - Class in compbio.engine
     
    loadExecutable(String) - -Static method in class compbio.engine.client.Util -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in class compbio.engine.client.ConfExecutable -
      -
    loadRunConfiguration(InputStream) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in interface compbio.engine.client.Executable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._impl.NetNglyc -
      -
    loadRunConfiguration(RunConfiguration) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    LOCAL_ENGINE_LIMIT_PRESET - -Static variable in class compbio.metadata.PresetManager -
      -
    LOCAL_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    LocalEngineUtil - Class in compbio.engine.local
     
    LocalEngineUtil() - -Constructor for class compbio.engine.local.LocalEngineUtil -
      -
    LocalExecutorService - Class in compbio.engine.local
     
    LocalRunner - Class in compbio.engine.local
     
    LocalRunner(ConfiguredExecutable<?>) - -Constructor for class compbio.engine.local.LocalRunner -
      -
    log(Logger, WebServiceContext, String) - -Static method in class compbio.ws.server.WSUtil -
      -
    log(Logger, WebServiceContext, String, String) - -Static method in class compbio.ws.server.WSUtil -
      -
    LONG_TIME_LIMIT - -Static variable in class compbio.engine.cluster.dundee._QueueConstraints -
      -
    -
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    -
    -
    Mafft - Class in compbio.runner.msa
     
    Mafft() - -Constructor for class compbio.runner.msa.Mafft -
      -
    MafftWS - Class in compbio.ws.server
     
    MafftWS() - -Constructor for class compbio.ws.server.MafftWS -
      -
    main(String[]) - -Static method in class compbio.engine.cluster.drmaa._DrmaaExample -
      -
    main(String[]) - -Static method in class compbio.engine.cluster.drmaa._JobStatus -
      -
    main(String[]) - -Static method in class compbio.pipeline._jpred.BlastParser -
    args[0] is assumed to be the name of a Blast output file -
    main(String[]) - -Static method in class compbio.pipeline._jpred.Pairwise -
      -
    main(String[]) - -Static method in class compbio.runner._impl.OB -
      -
    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 -
    main(String[]) - -Static method in class compbio.ws.server.SimpleWSPublisher -
      -
    MAX_MEMORY_LIMIT - -Static variable in class compbio.engine.cluster.dundee._QueueConstraints -
      -
    Mcl - Class in compbio.runner._impl
     
    Mcl(String) - -Constructor for class compbio.runner._impl.Mcl -
      -
    mergeEnvVariables(Map<String, String>, Map<String, String>) - -Static method in class compbio.engine.client.Util -
      -
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    Muscle - Class in compbio.runner.msa
     
    Muscle() - -Constructor for class compbio.runner.msa.Muscle -
    Default options are - - -clwstrict - write output in clustal format -
    MuscleWS - Class in compbio.ws.server
     
    MuscleWS() - -Constructor for class compbio.ws.server.MuscleWS -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    NetNglyc - Class in compbio.runner._impl
     
    NetNglyc() - -Constructor for class compbio.runner._impl.NetNglyc -
      -
    newCommandBuilder(List<? extends Option<T>>, String) - -Static method in class compbio.engine.client.CommandBuilder -
    This produces the same result as getCommands method. -
    newConfExecutable(RunConfiguration) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    newFilePuller(String, int) - -Static method in class compbio.engine.FilePuller -
      -
    newLimitExceeded(Limit<?>, List<FastaSequence>) - -Static method in exception compbio.metadata.LimitExceededException -
      -
    newProgressPuller(String) - -Static method in class compbio.engine.FilePuller -
    Progress Puller is designed to read 3 characters from the beginning of - the file, nothing more. -
    NON_AA - -Static variable in class compbio.data.sequence.SequenceUtil -
    inversion of AA pattern -
    NON_NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non nucleotide -
    NONWORD - -Static variable in class compbio.data.sequence.SequenceUtil -
    Non word -
    NUCLEOTIDE - -Static variable in class compbio.data.sequence.SequenceUtil -
    Nucleotides a, t, g, c, u -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    OB - Class in compbio.runner._impl
    TODO this needs fixing! Executable does not work
    OB() - -Constructor for class compbio.runner._impl.OB -
      -
    OB(String) - -Constructor for class compbio.runner._impl.OB -
      -
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - -Constructor for class compbio.metadata.Option -
      -
    OptionCombinator - Class in compbio.runner
    This class solve the following problems.
    OptionCombinator(RunnerConfig<? extends Executable<?>>) - -Constructor for class compbio.runner.OptionCombinator -
      -
    optionsToCommandString(List<Option<?>>) - -Method in class compbio.runner.OptionCombinator -
      -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    Pairwise - Class in compbio.pipeline._jpred
     
    Pairwise(List<FastaSequence>) - -Constructor for class compbio.pipeline._jpred.Pairwise -
      -
    Parameter<T> - Class in compbio.metadata
    A single value containing option supported by the web service e.g.
    Parameter(String, String) - -Constructor for class compbio.metadata.Parameter -
      -
    parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - -Method in class compbio.runner.OptionCombinator -
      -
    parse(String) - -Static method in class compbio.engine.conf._Key -
      -
    PATH - -Static variable in class compbio.engine.client.EnvVariableProcessor -
    Special variable keys Absolute path(s) will be merged with the content of - the system PATH variable -
    PathValidator - Class in compbio.engine.client
     
    PathValidator() - -Constructor for class compbio.engine.client.PathValidator -
      -
    PipedExecutable<T> - Interface in compbio.engine.client
    This is a marker interface to indicate that the output of the process must be - captured.
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - -Constructor for class compbio.metadata.Preset -
      -
    PresetAlign - Class in compbio.data.msa.jaxws
     
    PresetAlign() - -Constructor for class compbio.data.msa.jaxws.PresetAlign -
      -
    presetAlign(List<FastaSequence>, Preset<T>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with preset. -
    presetAlign(List<FastaSequence>, Preset<ClustalW>) - -Method in class compbio.ws.server.ClustalWS -
      -
    presetAlign(List<FastaSequence>, Preset<Mafft>) - -Method in class compbio.ws.server.MafftWS -
      -
    presetAlign(List<FastaSequence>, Preset<Muscle>) - -Method in class compbio.ws.server.MuscleWS -
      -
    presetAlign(List<FastaSequence>, Preset<Probcons>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    presetAlign(List<FastaSequence>, Preset<Tcoffee>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PresetAlignResponse - Class in compbio.data.msa.jaxws
     
    PresetAlignResponse() - -Constructor for class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - -Constructor for class compbio.metadata.PresetManager -
      -
    Probcons - Class in compbio.runner.msa
     
    Probcons() - -Constructor for class compbio.runner.msa.Probcons -
      -
    ProbconsWS - Class in compbio.ws.server
     
    ProbconsWS() - -Constructor for class compbio.ws.server.ProbconsWS -
      -
    PROC_ERR_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    PROC_OUT_FILE - -Static variable in class compbio.engine.local.ExecutableWrapper -
      -
    Program - Enum in compbio.data.sequence
    Programmes that can produce alignments
    ProgressGetter - Class in compbio.engine
     
    ProgressGetter() - -Constructor for class compbio.engine.ProgressGetter -
      -
    PropertyHelperManager - Class in compbio.engine.conf
     
    PropertyHelperManager() - -Constructor for class compbio.engine.conf.PropertyHelperManager -
      -
    PScore - Class in compbio.pipeline._jpred
     
    PScore() - -Constructor for class compbio.pipeline._jpred.PScore -
      -
    PSIBlast - Class in compbio.runner._impl
     
    PSIBlast(String) - -Constructor for class compbio.runner._impl.PSIBlast -
      -
    PsiBlast - Class in compbio.runner.psiblast
     
    PsiBlast() - -Constructor for class compbio.runner.psiblast.PsiBlast -
      -
    pull(long) - -Method in class compbio.engine.FilePuller -
      -
    pull(String, long) - -Static method in class compbio.engine.ProgressGetter -
      -
    PulledFileCache - Class in compbio.engine
     
    PulledFileCache() - -Constructor for class compbio.engine.PulledFileCache -
      -
    PullExecStatistics - Class in compbio.data.msa.jaxws
     
    PullExecStatistics() - -Constructor for class compbio.data.msa.jaxws.PullExecStatistics -
      -
    pullExecStatistics(String, long) - -Method in interface compbio.data.msa.MsaWS -
    Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ClustalWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MafftWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.MuscleWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.ProbconsWS -
      -
    pullExecStatistics(String, long) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
     
    PullExecStatisticsResponse() - -Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    PullFile - Class in compbio.data.msa.jaxws
     
    PullFile() - -Constructor for class compbio.data.msa.jaxws.PullFile -
      -
    pullFile(String, long) - -Static method in class compbio.ws.server.WSUtil -
      -
    PullFileResponse - Class in compbio.data.msa.jaxws
     
    PullFileResponse() - -Constructor for class compbio.data.msa.jaxws.PullFileResponse -
      -
    put(FilePuller) - -Static method in class compbio.engine.PulledFileCache -
    This method allows duplicates to be added. -
    -
    - - - - - - - - - - - - - - - -
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    -
    -
    rconfigFile - -Static variable in class compbio.engine.client.RunConfiguration -
      -
    read(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    read(InputStream, Class<V>, Class<?>...) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readAndValidate(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
    Read Clustal formatted alignment. -
    readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    readClustalFile(String, String) - -Static method in class compbio.runner.Util -
      -
    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 -
    removeJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.BlastAll -
      -
    removeOutput(String) - -Method in class compbio.runner._impl.PSIBlast -
      -
    removeParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    removeTask(ConfiguredExecutable<?>) - -Static method in class compbio.engine.SubmissionManager -
      -
    removeTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
    ResultNotAvailableException(String) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableException(String, Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -
      -
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    ResultNotAvailableExceptionBean() - -Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    Ronn - Class in compbio.runner._impl
     
    Ronn(String) - -Constructor for class compbio.runner._impl.Ronn -
      -
    RPSBlast - Class in compbio.runner._impl
     
    RPSBlast(String) - -Constructor for class compbio.runner._impl.RPSBlast -
      -
    run() - -Method in class compbio.engine.local.StreamGobbler -
      -
    RunConfiguration - Class in compbio.engine.client
    Value class for persisting ConfExecutable instances
    RunConfiguration() - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunConfiguration(ConfExecutable<?>) - -Constructor for class compbio.engine.client.RunConfiguration -
      -
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - -Constructor for class compbio.metadata.RunnerConfig -
      -
    RunnerConfigMarshaller<T> - Class in compbio.engine.conf
     
    RunnerConfigMarshaller(Class<?>) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    RunnerConfigMarshaller(Class<?>, Class<?>...) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -
      -
    Runners - Class in compbio.runner._impl
     
    runPsiBlast() - -Method in class compbio.pipeline._jpred.Jpred4 -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -S

    -
    -
    saveRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    saveRunConfiguration() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    setActualNumberofSequences(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setDefaultValue(String) - -Method in class compbio.metadata.Option -
    Sets one of the values defined in optionList as default. -
    setDefaultValue(String) - -Method in class compbio.metadata.Parameter -
      -
    setDescription(String) - -Method in class compbio.metadata.Option -
      -
    setDescription(String) - -Method in class compbio.metadata.Preset -
      -
    setEmail(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    setError(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setError(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setExecProvider(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.Align -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setFastaSequences(List<FastaSequence>) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setFirst(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setFurtherDetails(URL) - -Method in class compbio.metadata.Option -
      -
    setInput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setInput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setInput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setInput(String) - -Method in class compbio.runner.msa.Mafft -
      -
    setInput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setInput(String) - -Method in class compbio.runner.msa.Probcons -
      -
    setInput(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetProgress -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setJobId(String) - -Method in class compbio.data.msa.jaxws.PullFile -
      -
    setLast(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setLast(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setMax(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.JobExecutionExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    setMessage(String) - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    setMin(String) - -Method in class compbio.metadata.ValueConstrain -
      -
    setName(String) - -Method in class compbio.metadata.Option -
      -
    setName(String) - -Method in class compbio.metadata.Preset -
      -
    setName(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    setNCore(int) - -Method in class compbio.runner.msa.Tcoffee -
      -
    setNumberOfSequencesAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setOptionName(String) - -Method in class compbio.metadata.Parameter -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Option -
      -
    setOptionNames(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setOptions(List<Option>) - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    setOptions(List<String>) - -Method in class compbio.metadata.Preset -
      -
    setOptions(List<Option<T>>) - -Method in class compbio.metadata.RunnerConfig -
      -
    setOutput(String) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setOutput(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setOutput(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    setOutput(String) - -Method in class compbio.runner.msa.Muscle -
      -
    setParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParam(String, String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setParameter(String) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    setParameters(CommandBuilder<?>) - -Method in class compbio.engine.client.RunConfiguration -
      -
    setParameters(List<Parameter<T>>) - -Method in class compbio.metadata.RunnerConfig -
      -
    setParams(List<String>) - -Method in class compbio.engine.client.CommandBuilder -
      -
    setPosition(long) - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    setPosition(long) - -Method in class compbio.data.msa.jaxws.PullFile -
      -
    setPossibleValues(Set<String>) - -Method in class compbio.metadata.Parameter -
      -
    setPreset(Preset) - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    setPresetName(String) - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    setPresets(List<Preset<T>>) - -Method in class compbio.metadata.PresetManager -
      -
    setPrmSeparator(String) - -Method in class compbio.metadata.RunnerConfig -
      -
    setQueue(String) - -Method in class compbio.runner._NativeSpecHelper -
      -
    setRequired(boolean) - -Method in class compbio.metadata.Option -
      -
    setRequiredMemory(int) - -Method in class compbio.runner._NativeSpecHelper -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    setReturn(boolean) - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    setReturn(JobStatus) - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    setReturn(Limit) - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    setReturn(LimitsManager) - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    setReturn(PresetManager) - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    setReturn(byte) - -Method in class compbio.data.msa.jaxws.GetProgressResponse -
      -
    setReturn(Alignment) - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    setReturn(RunnerConfig) - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    setReturn(String) - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    setReturn(ChunkHolder) - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    setReturn(ChunkHolder) - -Method in class compbio.data.msa.jaxws.PullFileResponse -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.PresetManager -
      -
    setRunnerClassName(String) - -Method in class compbio.metadata.RunnerConfig -
      -
    setSequenceLenghtActual(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setSequenceLenghtAllowed(int) - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    setType(ValueConstrain.Type) - -Method in class compbio.metadata.ValueConstrain -
      -
    setValidValue(ValueConstrain) - -Method in class compbio.metadata.Parameter -
      -
    setValue(String) - -Method in interface compbio.metadata.Argument -
    Set default values for the parameter or an option -
    setValue(String) - -Method in class compbio.metadata.Option -
      -
    setWorkDirectory(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    setWorkDirectory(String) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    SHORT_TIME_LIMIT - -Static variable in class compbio.engine.cluster.dundee._QueueConstraints -
      -
    shutdown() - -Method in class compbio.engine.local._TrackingExecutor -
      -
    shutDown() - -Static method in class compbio.engine.local.LocalExecutorService -
    This stops all executing processes via interruption. -
    shutdownNow() - -Method in class compbio.engine.local._TrackingExecutor -
      -
    SimpleWSPublisher - Class in compbio.ws.server
    This class publish a web service.
    SimpleWSPublisher(Object, String) - -Constructor for class compbio.ws.server.SimpleWSPublisher -
      -
    size() - -Method in class compbio.engine.client.CommandBuilder -
      -
    SkeletalExecutable<T> - Class in compbio.engine.client
     
    SkeletalExecutable() - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SkeletalExecutable(String) - -Constructor for class compbio.engine.client.SkeletalExecutable -
      -
    SPACE - -Static variable in class compbio.runner.Util -
      -
    StatisticManager - Class in compbio.engine.cluster.drmaa
     
    StatisticManager(JobInfo) - -Constructor for class compbio.engine.cluster.drmaa.StatisticManager -
      -
    StreamGobbler - Class in compbio.engine.local
     
    SubmissionManager - Class in compbio.engine
    Submit jobs for execution
    submit(Callable<T>) - -Method in class compbio.engine.local._TrackingExecutor -
      -
    submitJob(ConfiguredExecutable<?>) - -Method in interface compbio.engine.AsyncExecutor -
    Submits job for the execution - Immediate execution is not guaranteed, this method puts the job in the queue. -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    submitJob(ConfiguredExecutable<?>) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    SyncExecutor - Interface in compbio.engine
    Synchronous executor, is an engine to run the Executable synchronously.
    -
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    Tcoffee - Class in compbio.runner.msa
     
    Tcoffee() - -Constructor for class compbio.runner.msa.Tcoffee -
      -
    TcoffeeWS - Class in compbio.ws.server
     
    TcoffeeWS() - -Constructor for class compbio.ws.server.TcoffeeWS -
      -
    termSignal() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    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.engine.client.CommandBuilder -
      -
    toString() - -Method in class compbio.engine.client.ConfExecutable -
      -
    toString() - -Method in class compbio.engine.client.RunConfiguration -
      -
    toString() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    toString() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    toString() - -Method in enum compbio.engine.cluster.dundee._Queue -
      -
    toString() - -Method in class compbio.engine.conf._Key -
      -
    toString() - -Method in class compbio.engine.FilePuller -
      -
    toString() - -Method in class compbio.engine.Job -
      -
    toString() - -Method in class compbio.metadata.ChunkHolder -
      -
    toString() - -Method in class compbio.metadata.Limit -
      -
    toString() - -Method in class compbio.metadata.LimitsManager -
      -
    toString() - -Method in class compbio.metadata.Option -
      -
    toString() - -Method in class compbio.metadata.Parameter -
      -
    toString() - -Method in class compbio.metadata.Preset -
      -
    toString() - -Method in class compbio.metadata.PresetManager -
      -
    toString() - -Method in class compbio.metadata.RunnerConfig -
      -
    toString() - -Method in class compbio.metadata.ValueConstrain -
      -
    toString() - -Method in class compbio.pipeline._jpred.PScore -
      -
    -
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    BlastAll - Class in compbio.runner._impl
     
    BlastAll(String) - -Constructor for class compbio.runner._impl.BlastAll -
      -
    BlastParameters - Class in compbio.runner._impl
    Utility class for common Blast parameters
    BlastParser - Class in compbio.pipeline._jpred
     
    BlastParser() - -Constructor for class compbio.pipeline._jpred.BlastParser -
      -
    -
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    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(File, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String, Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(String) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnknownFileFormatException(Throwable) - -Constructor for exception compbio.data.sequence.UnknownFileFormatException -
      -
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeException(Throwable) - -Constructor for exception compbio.metadata.UnsupportedRuntimeException -
      -
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBean() - -Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    Util - Class in compbio.engine.client
     
    Util() - -Constructor for class compbio.engine.client.Util -
      -
    Util - Class in compbio.runner
     
    Util() - -Constructor for class compbio.runner.Util -
      -
    -
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    -
    -
    validate(Validator, String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    validate(PresetManager<T>) - -Method in class compbio.metadata.LimitsManager -
    Validate Limits -
    validate(RunnerConfig<T>) - -Method in class compbio.metadata.PresetManager -
    Checks whether preset option and parameter are defined in RunnerConfig - object. -
    validate() - -Method in class compbio.metadata.RunnerConfig -
    Validate the arguments -
    validateDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validateFastaInput(List<FastaSequence>) - -Static method in class compbio.ws.server.WSUtil -
      -
    validateJobId(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    validatePathNames(List<String>, String) - -Static method in class compbio.engine.client.PathValidator -
      -
    validURL(String) - -Static method in class compbio.ws.client.Jws2Client -
    Attempt to construct the URL object from the string -
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - -Constructor for class compbio.metadata.ValueConstrain -
      -
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.data.sequence.Program -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns the enum constant of this type with the specified name. -
    valueOf(String) - -Static method in enum compbio.engine.cluster.dundee._Queue -
    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.Jws2Client.Services -
    Returns the enum constant of this type with the specified name. -
    values() - -Static method in enum compbio.data._structure.JnetAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data._structure.JpredAnnotation -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.data.sequence.Program -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.client.Executable.ExecProvider -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
    values() - -Static method in enum compbio.engine.cluster.dundee._Queue -
    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.Jws2Client.Services -
    Returns an array containing the constants of this enum type, in -the order they are declared. -
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    waitForFile(long) - -Method in class compbio.engine.FilePuller -
      -
    waitForJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForJob(String, long) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    waitForResult(ClusterSession, String) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    waitForResult() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    waitForResult() - -Method in class compbio.engine.local.LocalRunner -
      -
    waitForResult() - -Method in interface compbio.engine.SyncExecutor -
    Call to this method block for as long as it is required for an executable to finish its job. -
    wasAborted() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    WHITE_SPACE - -Static variable in class compbio.data.sequence.SequenceUtil -
    A whitespace character: [\t\n\x0B\f\r] -
    write(RunConfiguration) - -Static method in class compbio.engine.client.RunConfiguration -
      -
    write(Object, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeAndValidate(Object, String, OutputStream) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    writeClustalAlignment(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 -
    writeFile(String, String, String, boolean) - -Static method in class compbio.engine.client.Util -
      -
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - -Static method in class compbio.runner.Util -
      -
    writeMarker(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    writeStatFile(String, String) - -Static method in class compbio.engine.client.Util -
      -
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object - does not match the actual runnable or then attempting to set the value of - Argument to invalid value.
    WrongParameterException(Option<?>) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterException(String, Throwable) - -Constructor for exception compbio.metadata.WrongParameterException -
      -
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    WrongParameterExceptionBean() - -Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - -Constructor for class compbio.ws.client.WSTester -
      -
    WSUtil - Class in compbio.ws.server
     
    WSUtil() - -Constructor for class compbio.ws.server.WSUtil -
      -
    -
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    _DrmaaExample - Class in compbio.engine.cluster.drmaa
     
    _DrmaaExample() - -Constructor for class compbio.engine.cluster.drmaa._DrmaaExample -
      -
    _JobStatus - Class in compbio.engine.cluster.drmaa
     
    _JobStatus() - -Constructor for class compbio.engine.cluster.drmaa._JobStatus -
      -
    _Jpred - Class in compbio.runner._jpred
     
    _Jpred() - -Constructor for class compbio.runner._jpred._Jpred -
      -
    _Key - Class in compbio.engine.conf
     
    _Key(Class<?>) - -Constructor for class compbio.engine.conf._Key -
      -
    _NativeSpecHelper - Class in compbio.runner
     
    _NativeSpecHelper(int) - -Constructor for class compbio.runner._NativeSpecHelper -
      -
    _NativeSpecHelper(int, int) - -Constructor for class compbio.runner._NativeSpecHelper -
      -
    _Queue - Enum in compbio.engine.cluster.dundee
     
    _QueueConstraints - Class in compbio.engine.cluster.dundee
     
    _SkeletalCommandBuilder - Class in compbio.runner
     
    _SkeletalCommandBuilder() - -Constructor for class compbio.runner._SkeletalCommandBuilder -
      -
    _TrackingExecutor - Class in compbio.engine.local
    This executor extends standard Java ExecutorService by adding the method to - obtain all Runnables which were running and did not complete upon executor - termination.
    _TrackingExecutor(ExecutorService) - -Constructor for class compbio.engine.local._TrackingExecutor -
      -
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    -
    -
    call() - -Method in class compbio.engine.local.ExecutableWrapper -
    It is vital that output and error streams are captured immediately for - this call() to succeed. -
    canAcceptMoreWork() - -Method in class compbio.engine.local.LocalExecutorService -
    If the Executor queue is empty -
    CancelJob - Class in compbio.data.msa.jaxws
     
    CancelJob() - -Constructor for class compbio.data.msa.jaxws.CancelJob -
      -
    cancelJob(String) - -Method in interface compbio.data.msa.MsaWS -
    Stop running job but leave its output untouched -
    cancelJob(String) - -Method in interface compbio.engine.AsyncExecutor -
    Stop running job. -
    cancelJob(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cancelJob(String, ClusterSession) - -Static method in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    cancelJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cancelJob(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cancelJob(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cancelJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    cancelJob() - -Method in interface compbio.engine.SyncExecutor -
    Stops running job. -
    cancelJob(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MafftWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    cancelJob(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    cancelJob(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    CancelJobResponse - Class in compbio.data.msa.jaxws
     
    CancelJobResponse() - -Constructor for class compbio.data.msa.jaxws.CancelJobResponse -
      -
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of string data together with the position in a file from - where corresponding to of the data.
    ChunkHolder(String, long) - -Constructor for class compbio.metadata.ChunkHolder -
      -
    Cleaner - Class in compbio.engine
     
    Cleaner() - -Constructor for class compbio.engine.Cleaner -
      -
    cleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all whitespace chars in the sequence string -
    cleanup(String) - -Method in interface compbio.engine.AsyncExecutor -
    Remove all files and a job directory for a jobid. -
    cleanup(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    cleanup() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    cleanup(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    cleanup(ConfiguredExecutable<?>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    cleanup() - -Method in class compbio.engine.local.LocalRunner -
      -
    cleanup() - -Method in interface compbio.engine.SyncExecutor -
    Clean up after the job -
    close() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - -Constructor for class compbio.data.sequence.ClustalAlignmentUtil -
      -
    ClustalW - Class in compbio.runner.msa
     
    ClustalW() - -Constructor for class compbio.runner.msa.ClustalW -
      -
    ClustalWS - Class in compbio.ws.server
     
    ClustalWS() - -Constructor for class compbio.ws.server.ClustalWS -
      -
    CLUSTER_STAT_IN_SEC - -Static variable in class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    CLUSTER_TASK_ID_PREFIX - -Static variable in class compbio.engine.client.ConfExecutable -
      -
    CLUSTER_WORK_DIRECTORY - -Static variable in class compbio.engine.Configurator -
      -
    ClusterJobId - Class in compbio.engine
     
    ClusterJobId(String) - -Constructor for class compbio.engine.ClusterJobId -
      -
    ClusterNativeSpecExecutable<T> - Interface in compbio.engine.client
     
    ClusterSession - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil() - -Constructor for class compbio.engine.cluster.drmaa.ClusterUtil -
      -
    CommandBuilder<T> - Class in compbio.engine.client
     
    CommandBuilder(String) - -Constructor for class compbio.engine.client.CommandBuilder -
      -
    compareTo(Delayed) - -Method in class compbio.engine.FilePuller -
      -
    compbio.data._structure - package compbio.data._structure
     
    compbio.data.msa - package compbio.data.msa
     
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    compbio.pipeline._jpred - package compbio.pipeline._jpred
     
    compbio.runner._jpred - package compbio.runner._jpred
     
    compbio.runner.psiblast - package compbio.runner.psiblast
     
    compbio.ws.client - package compbio.ws.client
     
    compbio.ws.server - package compbio.ws.server
     
    confDir - -Static variable in class compbio.engine.conf.PropertyHelperManager -
      -
    ConfExecutable<T> - Class in compbio.engine.client
     
    ConfExecutable(Executable<T>, String) - -Constructor for class compbio.engine.client.ConfExecutable -
      -
    Configurator - Class in compbio.engine
     
    Configurator() - -Constructor for class compbio.engine.Configurator -
      -
    ConfiguredExecutable<T> - Interface in compbio.engine.client
     
    configureExecutable(Executable<T>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, List<FastaSequence>) - -Static method in class compbio.engine.Configurator -
      -
    configureExecutable(Executable<T>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    connect(String, Jws2Client.Services) - -Static method in class compbio.ws.client.Jws2Client -
    Connects to a web service by the host and the service name -
    convertToAbsolute(String) - -Static method in class compbio.engine.client.Util -
      -
    copyAndValidateRConfig(RunnerConfig<?>) - -Method in class compbio.metadata.RunnerConfig -
      -
    countMatchesInSequence(String, String) - -Static method in class compbio.data.sequence.FastaSequence -
      -
    CustomAlign - Class in compbio.data.msa.jaxws
     
    CustomAlign() - -Constructor for class compbio.data.msa.jaxws.CustomAlign -
      -
    customAlign(List<FastaSequence>, List<Option<T>>) - -Method in interface compbio.data.msa.MsaWS -
    Align a list of sequences with options. -
    customAlign(List<FastaSequence>, List<Option<ClustalW>>) - -Method in class compbio.ws.server.ClustalWS -
      -
    customAlign(List<FastaSequence>, List<Option<Mafft>>) - -Method in class compbio.ws.server.MafftWS -
      -
    customAlign(List<FastaSequence>, List<Option<Muscle>>) - -Method in class compbio.ws.server.MuscleWS -
      -
    customAlign(List<FastaSequence>, List<Option<Probcons>>) - -Method in class compbio.ws.server.ProbconsWS -
      -
    customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    CustomAlignResponse - Class in compbio.data.msa.jaxws
     
    CustomAlignResponse() - -Constructor for class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    -
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    -
    -
    deepClean() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    deepCleanSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Removes all special characters and digits as well as whitespace chars - from the sequence -
    deleteAllFiles(String) - -Static method in class compbio.engine.Cleaner -
      -
    deleteFiles(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Cleaner -
    This method returns true if all files specified by List files were - successfully removed or there was no files to remove (files list was - empty) -
    DELIM - -Static variable in class compbio.engine.conf._Key -
      -
    DELIM - -Static variable in class compbio.engine.conf.DirectoryManager -
      -
    DIGIT - -Static variable in class compbio.data.sequence.SequenceUtil -
    A digit -
    DirectoryManager - Class in compbio.engine.conf
     
    DirectoryManager() - -Constructor for class compbio.engine.conf.DirectoryManager -
      -
    disconnect() - -Method in class compbio.engine.FilePuller -
      -
    Disembl - Class in compbio.runner._impl
     
    Disembl(String) - -Constructor for class compbio.runner._impl.Disembl -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    -
    -
    Environment - Class in compbio.runner._impl
    This is utility class to encapsulate environmental variables like directory paths
    EnvVariableProcessor - Class in compbio.engine.client
     
    EnvVariableProcessor() - -Constructor for class compbio.engine.client.EnvVariableProcessor -
      -
    equals(Object) - -Method in class compbio.data.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.engine.client.CommandBuilder -
      -
    equals(Object) - -Method in class compbio.engine.client.RunConfiguration -
      -
    equals(Object) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    equals(Object) - -Method in class compbio.engine.ClusterJobId -
      -
    equals(Object) - -Method in class compbio.engine.conf._Key -
      -
    equals(Object) - -Method in class compbio.engine.FilePuller -
      -
    equals(Object) - -Method in class compbio.engine.Job -
      -
    equals(Object) - -Method in class compbio.metadata.ChunkHolder -
      -
    equals(Object) - -Method in class compbio.metadata.Limit -
      -
    equals(Object) - -Method in class compbio.metadata.Option -
      -
    equals(Object) - -Method in class compbio.metadata.Parameter -
      -
    equals(Object) - -Method in class compbio.metadata.Preset -
      -
    equals(Object) - -Method in class compbio.metadata.RunnerConfig -
      -
    equals(Object) - -Method in class compbio.metadata.ValueConstrain -
      -
    equals(Object) - -Method in class compbio.pipeline._jpred.PScore -
      -
    Executable<T> - Interface in compbio.engine.client
    Interface to a native executable.
    Executable.ExecProvider - Enum in compbio.engine.client
     
    ExecutableWrapper - Class in compbio.engine.local
     
    ExecutableWrapper(ConfiguredExecutable<?>, String) - -Constructor for class compbio.engine.local.ExecutableWrapper -
      -
    execute(Runnable) - -Method in class compbio.engine.local._TrackingExecutor -
      -
    executeJob() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    executeJob() - -Method in class compbio.engine.local.LocalRunner -
      -
    executeJob() - -Method in interface compbio.engine.SyncExecutor -
    Execute the job -
    -
    - - - - - - - - - - - - - - - -
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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 -
    FilePuller - Class in compbio.engine
     
    FIRST_MEMORY_LIMIT - -Static variable in class compbio.engine.cluster.dundee._QueueConstraints -
      -
    -
    - - - - - - - - - - - - - - - -
    - - - - - - - - - - - - -
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    - - - - - - - - - - - - - - - -
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    -G

    -
    -
    gapchar - -Static variable in class compbio.data.sequence.ClustalAlignmentUtil -
    Dash char to be used as gap char in the alignments -
    get(String) - -Static method in class compbio.engine.PulledFileCache -
      -
    getActualNumberofSequences() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getActualNumberofSequences() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getAllConstrainedParametersWithBorderValues(boolean) - -Method in class compbio.runner.OptionCombinator -
      -
    getAllConstrainedParametersWithRandomValues() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllOptions() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllParameters() - -Method in class compbio.runner.OptionCombinator -
      -
    getAllStats() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getApproprieteQueue() - -Method in class compbio.runner._NativeSpecHelper -
      -
    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 -
      -
    getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getAsyncEngine(String) - -Static method in class compbio.engine.Configurator -
      -
    getAvgSeqLength() - -Method in class compbio.metadata.Limit -
      -
    getAvgSequenceLength(List<FastaSequence>) - -Static method in class compbio.metadata.Limit -
    Calculates an average sequence length of the dataset -
    getBlastAllRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getBlastBinDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getByJobId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getByTaskId(String, List<Job>) - -Static method in class compbio.engine.Job -
      -
    getCalculationTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCancelledTasks() - -Method in class compbio.engine.local._TrackingExecutor -
      -
    getChunk() - -Method in class compbio.metadata.ChunkHolder -
      -
    getClass(String) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getClusterCpuNum() - -Static method in class compbio.runner.msa.Tcoffee -
      -
    getClusterJobId(String) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getClusterSettings() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCommand(Executable.ExecProvider) - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getCommand(Executable.ExecProvider, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Disembl -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Mcl -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.Ronn -
      -
    getCommand(Executable.ExecProvider) - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCommandName() - -Method in class compbio.runner._impl.Disembl -
      -
    getCommandName() - -Method in class compbio.runner._impl.Mcl -
      -
    getCommandName() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCommandName() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCommandName() - -Method in class compbio.runner._impl.Ronn -
      -
    getCommandName() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getCommands() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getCommands(List<Option<T>>, String) - -Static method in class compbio.ws.server.WSUtil -
      -
    getCommandString() - -Method in class compbio.engine.client.CommandBuilder -
      -
    getConfExecutable() - -Method in class compbio.engine.Job -
      -
    getCPUTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCPUUsageTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getCreatedFiles() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getCreatedFiles() - -Method in interface compbio.engine.client.Executable -
      -
    getCreatedFiles() - -Method in class compbio.engine.client.SkeletalExecutable -
    This method cannot really tell whether the files has actually been - created or not. -
    getCreatedFiles() - -Method in class compbio.runner._impl.BlastAll -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Disembl -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Mcl -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.OB -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.Ronn -
      -
    getCreatedFiles() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.ClustalW -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Muscle -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Probcons -
      -
    getCreatedFiles() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getDataTransfered() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getDefaultLimit() - -Method in class compbio.metadata.LimitsManager -
      -
    getDefaultValue() - -Method in interface compbio.metadata.Argument -
      -
    getDefaultValue() - -Method in class compbio.metadata.Option -
    A default value of the option. -
    getDelay(TimeUnit) - -Method in class compbio.engine.FilePuller -
      -
    getDescription() - -Method in interface compbio.metadata.Argument -
      -
    getDescription() - -Method in class compbio.metadata.Option -
    A long description of the Option -
    getDescription() - -Method in class compbio.metadata.Preset -
      -
    getDisemblRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getEmail() - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getEndTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getEngine(Executable<?>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(Executable<V>, List<FastaSequence>) - -Static method in class compbio.engine.LoadBalancer -
      -
    getEngine(ConfiguredExecutable<?>) - -Static method in class compbio.ws.server.WSUtil -
      -
    getEnvironment() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getEnvironment() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getEnvVariables(String, Class<?>) - -Static method in class compbio.engine.client.EnvVariableProcessor -
      -
    getError() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getError() - -Method in interface compbio.engine.client.Executable -
      -
    getError() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getError() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getError() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getError() - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getExecProperty(String, Executable<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProperty(String, Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getExecProvider() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecProvider() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutable() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getExecutable() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getExecutionStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getExecutor() - -Static method in class compbio.engine.local.LocalExecutorService -
    This method returns the single instance of CachedThreadPoolExecutor which - it cashes internally -
    getExitStatus() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.Align -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getFastaSequences() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getFile() - -Method in class compbio.engine.FilePuller -
      -
    getFormatedSequence(int) - -Method in class compbio.data.sequence.FastaSequence -
    Format sequence per width letter in one string. -
    getFormattedFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getFullPath(String, String) - -Static method in class compbio.engine.client.Util -
      -
    getFurtherDetails() - -Method in interface compbio.metadata.Argument -
      -
    getFurtherDetails() - -Method in class compbio.metadata.Option -
    The URL where further details about the option can be found -
    getGapchar() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    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 -
    getInput() - -Method in class compbio.engine.client.ConfExecutable -
    Not all input paths are relative! Input path could be absolute! -
    getInput() - -Method in interface compbio.engine.client.Executable -
      -
    getInput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getInput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getInput() - -Method in class compbio.runner._impl.BlastAll -
      -
    getInput() - -Method in class compbio.runner._impl.Disembl -
      -
    getInput() - -Method in class compbio.runner._impl.Mcl -
      -
    getInput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getInput() - -Method in class compbio.runner._impl.OB -
      -
    getInput() - -Method in class compbio.runner._impl.PSIBlast -
      -
    getInput() - -Method in class compbio.runner._impl.Ronn -
      -
    getInput() - -Method in class compbio.runner._impl.RPSBlast -
      -
    getInstance(ConfiguredExecutable<?>) - -Static method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getIOWait() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.CancelJob -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetProgress -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.GetResult -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getJobId() - -Method in class compbio.data.msa.jaxws.PullFile -
      -
    getJobId() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getJobId() - -Method in class compbio.engine.ClusterJobId -
      -
    getJobId() - -Method in class compbio.engine.Job -
      -
    getJobInfo() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
    This method will block before the calculation has completed and then - return the object containing a job execution statistics -
    getJobPriority() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - -Constructor for class compbio.data.msa.jaxws.GetJobStatus -
      -
    getJobStatus(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the status of the job. -
    getJobStatus(String) - -Method in interface compbio.engine.AsyncExecutor -
    Query the status of the job -
    getJobStatus(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid - engine cancelled job is the same as failed. -
    getJobStatus(ClusterJobId) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
    Apparently completed jobs cannot be found! If this happened most likely - that the job is not running any more and Most likely it has been - cancelled, finished or failed. -
    getJobStatus(int) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
    Deprecated.  -
    getJobStatus() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getJobStatus(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getJobStatus(Future<ConfiguredExecutable<?>>) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getJobStatus() - -Method in class compbio.engine.local.LocalRunner -
      -
    getJobStatus() - -Method in interface compbio.engine.SyncExecutor -
    Query the status of the job by its id. -
    getJobStatus(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getJobStatus(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getJobStatus(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
     
    GetJobStatusResponse() - -Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    getLength() - -Method in class compbio.data.sequence.FastaSequence -
      -
    GetLimit - Class in compbio.data.msa.jaxws
     
    GetLimit() - -Constructor for class compbio.data.msa.jaxws.GetLimit -
      -
    getLimit(String) - -Method in interface compbio.data.msa.MsaWS -
    Get a Limit for a preset. -
    getLimit(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimit(String) - -Method in interface compbio.engine.client.Executable -
      -
    getLimit(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimit(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getLimit(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    getLimit(String) - -Method in class compbio.runner.msa.Mafft -
      -
    getLimit(String) - -Method in class compbio.runner.msa.Muscle -
      -
    getLimit(String) - -Method in class compbio.runner.msa.Probcons -
      -
    getLimit(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getLimit(String) - -Method in class compbio.runner.psiblast.PsiBlast -
      -
    getLimit(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimit(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    getLimitByName(String) - -Method in class compbio.metadata.LimitsManager -
      -
    GetLimitResponse - Class in compbio.data.msa.jaxws
     
    GetLimitResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitResponse -
      -
    GetLimits - Class in compbio.data.msa.jaxws
     
    GetLimits() - -Constructor for class compbio.data.msa.jaxws.GetLimits -
      -
    getLimits() - -Method in interface compbio.data.msa.MsaWS -
    List Limits supported by a web service. -
    getLimits() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getLimits() - -Method in interface compbio.engine.client.Executable -
      -
    getLimits() - -Method in class compbio.metadata.LimitsManager -
      -
    getLimits() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getLimits() - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getLimits() - -Method in class compbio.runner.msa.ClustalW -
      -
    getLimits() - -Method in class compbio.runner.msa.Mafft -
      -
    getLimits() - -Method in class compbio.runner.msa.Muscle -
      -
    getLimits() - -Method in class compbio.runner.msa.Probcons -
      -
    getLimits() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getLimits() - -Method in class compbio.runner.psiblast.PsiBlast -
      -
    getLimits(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
    For now just assume that all parameters which came in needs setting it - will be a client responsibility to prepare RunnerConfig object then -
    getLimits() - -Method in class compbio.ws.server.ClustalWS -
      -
    getLimits() - -Method in class compbio.ws.server.MafftWS -
      -
    getLimits() - -Method in class compbio.ws.server.MuscleWS -
      -
    getLimits() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getLimits() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetLimitsResponse - Class in compbio.data.msa.jaxws
     
    GetLimitsResponse() - -Constructor for class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getLocalPath() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Method return the absolute path to the project root directory. -
    getMax() - -Method in class compbio.metadata.ValueConstrain -
      -
    getMaxVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMclRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getMemoryLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    return max memory limit in Mb -
    getMemoryStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.JobExecutionExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean -
      -
    getMessage() - -Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean -
      -
    getMetadata() - -Method in class compbio.data.sequence.Alignment -
      -
    getMin() - -Method in class compbio.metadata.ValueConstrain -
      -
    getName() - -Method in interface compbio.metadata.Argument -
      -
    getName() - -Method in class compbio.metadata.Option -
    Human readable name of the option -
    getName() - -Method in class compbio.metadata.Preset -
      -
    getName() - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getNativeSpec() - -Method in class compbio.runner._NativeSpecHelper -
      -
    getNativeSpecs() - -Method in interface compbio.engine.client.ClusterNativeSpecExecutable -
      -
    getNativeSpecs() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getNetNglycRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getNextPosition() - -Method in class compbio.metadata.ChunkHolder -
      -
    getNumberOfSequencesAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getNumberOfSequencesAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getOBRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getOnelineFasta() - -Method in class compbio.data.sequence.FastaSequence -
      -
    getOptionName() - -Method in class compbio.metadata.Parameter -
      -
    getOptionNames() - -Method in class compbio.metadata.Option -
      -
    getOptions() - -Method in class compbio.data.msa.jaxws.CustomAlign -
      -
    getOptions() - -Method in class compbio.metadata.Preset -
      -
    getOptions() - -Method in class compbio.metadata.RunnerConfig -
      -
    getOptionsAtRandom() - -Method in class compbio.runner.OptionCombinator -
      -
    getOutput() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getOutput() - -Method in interface compbio.engine.client.Executable -
      -
    getOutput() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getOutput() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getOutput() - -Method in class compbio.runner._impl.NetNglyc -
      -
    getOutput() - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getParameters() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getParameters() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getParameters(Executable.ExecProvider) - -Method in interface compbio.engine.client.Executable -
      -
    getParameters() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getParameters() - -Method in class compbio.metadata.RunnerConfig -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getParameters(Executable.ExecProvider) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getParamValue(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    getPosition() - -Method in class compbio.data.msa.jaxws.PullExecStatistics -
      -
    getPosition() - -Method in class compbio.data.msa.jaxws.PullFile -
      -
    getPossibleValues() - -Method in interface compbio.metadata.Argument -
      -
    getPossibleValues() - -Method in class compbio.metadata.Option -
    List of possible optionNames -
    getPossibleValues() - -Method in class compbio.metadata.Parameter -
    List is more convenient to work with -
    getPreset() - -Method in class compbio.data.msa.jaxws.PresetAlign -
      -
    getPreset() - -Method in class compbio.metadata.Limit -
      -
    getPresetByName(String) - -Method in class compbio.metadata.PresetManager -
      -
    getPresetName() - -Method in class compbio.data.msa.jaxws.GetLimit -
      -
    GetPresets - Class in compbio.data.msa.jaxws
     
    GetPresets() - -Constructor for class compbio.data.msa.jaxws.GetPresets -
      -
    getPresets() - -Method in interface compbio.data.msa.MsaWS -
    Get presets supported by a web service -
    getPresets() - -Method in class compbio.metadata.PresetManager -
      -
    getPresets(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getPresets() - -Method in class compbio.ws.server.ClustalWS -
      -
    getPresets() - -Method in class compbio.ws.server.MafftWS -
      -
    getPresets() - -Method in class compbio.ws.server.MuscleWS -
      -
    getPresets() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getPresets() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetPresetsResponse - Class in compbio.data.msa.jaxws
     
    GetPresetsResponse() - -Constructor for class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getPrmSeparator() - -Method in class compbio.metadata.RunnerConfig -
      -
    getProgram() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    GetProgress - Class in compbio.data.msa.jaxws
     
    GetProgress() - -Constructor for class compbio.data.msa.jaxws.GetProgress -
      -
    getProgress() - -Method in class compbio.engine.FilePuller -
      -
    getProgress(String) - -Static method in class compbio.engine.ProgressGetter -
      -
    getProgress(String) - -Static method in class compbio.ws.server.WSUtil -
      -
    GetProgressResponse - Class in compbio.data.msa.jaxws
     
    GetProgressResponse() - -Constructor for class compbio.data.msa.jaxws.GetProgressResponse -
      -
    getPropertyHelper() - -Static method in class compbio.engine.conf.PropertyHelperManager -
    Ways to fix path problem: 1) find a path to WEB-INF directory based on - the path to a known class. -
    getPSIBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getQueue(int, int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
      -
    getQueue(String) - -Method in enum compbio.engine.cluster.dundee._Queue -
      -
    getQueue() - -Method in class compbio.runner._NativeSpecHelper -
      -
    getQueueByMemoryRequirements(int) - -Static method in enum compbio.engine.cluster.dundee._Queue -
      -
    getRawUsage() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getRecordedJobStatus(String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getRemoteAddress(WebServiceContext) - -Static method in class compbio.ws.server.WSUtil -
      -
    GetResult - Class in compbio.data.msa.jaxws
     
    GetResult() - -Constructor for class compbio.data.msa.jaxws.GetResult -
      -
    getResult(String) - -Method in interface compbio.data.msa.MsaWS -
    Return the result of the job. -
    getResult(String) - -Method in class compbio.ws.server.ClustalWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MafftWS -
      -
    getResult(String) - -Method in class compbio.ws.server.MuscleWS -
      -
    getResult(String) - -Method in class compbio.ws.server.ProbconsWS -
      -
    getResult(String) - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetResultResponse - Class in compbio.data.msa.jaxws
     
    GetResultResponse() - -Constructor for class compbio.data.msa.jaxws.GetResultResponse -
      -
    getResults(String) - -Method in interface compbio.engine.AsyncExecutor -
    Retrieve the results of the job. -
    getResults() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults(String) - -Method in class compbio.engine.client.ConfExecutable -
      -
    getResults() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getResults(String) - -Method in interface compbio.engine.client.Executable -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getResults(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getResults(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getResults(Future<ConfiguredExecutable<?>>, String) - -Static method in class compbio.engine.local.LocalEngineUtil -
      -
    getResults(String) - -Method in class compbio.runner._impl.NetNglyc -
      -
    getResults(String) - -Method in class compbio.runner._SkeletalCommandBuilder -
      -
    getResults(String) - -Method in class compbio.runner.msa.ClustalW -
      -
    getResults(String) - -Method in class compbio.runner.msa.Mafft -
      -
    getResults(String) - -Method in class compbio.runner.msa.Muscle -
      -
    getResults(String) - -Method in class compbio.runner.msa.Probcons -
      -
    getResults(String) - -Method in class compbio.runner.msa.Tcoffee -
      -
    getResults(String) - -Method in class compbio.runner.psiblast.PsiBlast -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.AlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.CustomAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetJobStatusResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetLimitsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetPresetsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetProgressResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetResultResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PresetAlignResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse -
      -
    getReturn() - -Method in class compbio.data.msa.jaxws.PullFileResponse -
      -
    getRonnRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRPSBlastDatabasesDir() - -Static method in class compbio.runner._impl.Environment -
      -
    getRPSBlastRunnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getRunConfiguration() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerClassName() - -Method in class compbio.engine.client.RunConfiguration -
      -
    getRunnerClassName() - -Method in class compbio.metadata.PresetManager -
      -
    getRunnerClassName() - -Method in class compbio.metadata.RunnerConfig -
      -
    getRunnerLimits(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
    This method should be executed once and result of its execution reused. -
    GetRunnerOptions - Class in compbio.data.msa.jaxws
     
    GetRunnerOptions() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptions -
      -
    getRunnerOptions() - -Method in interface compbio.data.msa.MsaWS -
    Get options supported by a web service -
    getRunnerOptions(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ClustalWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MafftWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.MuscleWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.ProbconsWS -
      -
    getRunnerOptions() - -Method in class compbio.ws.server.TcoffeeWS -
      -
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
     
    GetRunnerOptionsResponse() - -Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse -
      -
    getRunnerPresets(Class<? extends Executable<V>>) - -Static method in class compbio.engine.client.ConfExecutable -
      -
    getSchema(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getSeqNumber() - -Method in class compbio.metadata.Limit -
      -
    getSequence() - -Method in class compbio.data.sequence.FastaSequence -
    Gets the value of sequence -
    getSequenceLenghtActual() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtActual() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequenceLenghtAllowed() - -Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean -
      -
    getSequenceLenghtAllowed() - -Method in exception compbio.metadata.LimitExceededException -
      -
    getSequences() - -Method in class compbio.data.sequence.Alignment -
      -
    getServiceName(String[]) - -Static method in class compbio.ws.client.Jws2Client -
    Extracts service name from the command line -
    getSession() - -Method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getSize() - -Method in class compbio.data.sequence.Alignment -
      -
    getStartTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getStatFile() - -Static method in class compbio.runner.msa.ClustalW -
      -
    getStatFile() - -Static method in class compbio.runner.msa.Muscle -
      -
    getStatistics(JobInfo) - -Static method in class compbio.engine.cluster.drmaa.ClusterSession -
      -
    getSubmissionTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getSupportedOptions(Class<? extends Executable<T>>) - -Static method in class compbio.runner.Util -
      -
    getSupportedRuntimes() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getSupportedRuntimes() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getSupportedRuntimes(Class<?>) - -Static method in class compbio.engine.client.Util -
      -
    getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - -Static method in class compbio.engine.Configurator -
      -
    getSyncEngine(ConfiguredExecutable<?>) - -Static method in class compbio.engine.Configurator -
      -
    getTask(String) - -Static method in class compbio.engine.SubmissionManager -
      -
    getTaskDirectory(Class<?>) - -Static method in class compbio.engine.conf.DirectoryManager -
      -
    getTaskId() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getTaskId() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getTaskId() - -Method in class compbio.engine.Job -
      -
    getTestArgs() - -Static method in class compbio.runner._impl.Disembl -
      -
    getTestArgs() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestArgs() - -Method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Disembl -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.NetNglyc -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.OB -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.Ronn -
      -
    getTestCommand() - -Static method in class compbio.runner._impl.RPSBlast -
      -
    getTestParams() - -Static method in class compbio.runner._impl.Mcl -
      -
    getTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
    0 - unlimited -
    getTimeStat() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getTmhmm2Runnable(String) - -Static method in class compbio.runner._impl.Runners -
      -
    getType() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    getType() - -Method in class compbio.metadata.ValueConstrain -
      -
    getType() - -Method in class compbio.runner.msa.ClustalW -
      -
    getType() - -Method in class compbio.runner.msa.Mafft -
      -
    getType() - -Method in class compbio.runner.msa.Muscle -
      -
    getType() - -Method in class compbio.runner.msa.Probcons -
      -
    getType() - -Method in class compbio.runner.msa.Tcoffee -
      -
    getType() - -Method in class compbio.runner.psiblast.PsiBlast -
      -
    getUsedSysTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getUsedUserTime() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getValidator(String) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidator(Schema) - -Static method in class compbio.engine.conf.RunnerConfigMarshaller -
      -
    getValidValue() - -Method in class compbio.metadata.Parameter -
      -
    getVMem() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    getWorkDirectory(String) - -Method in interface compbio.engine.AsyncExecutor -
      -
    getWorkDirectory() - -Method in class compbio.engine.client.ConfExecutable -
      -
    getWorkDirectory() - -Method in interface compbio.engine.client.ConfiguredExecutable -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.cluster.drmaa.AsyncJobRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.cluster.drmaa.JobRunner -
      -
    getWorkDirectory(String) - -Static method in class compbio.engine.Configurator -
      -
    getWorkDirectory(String) - -Method in class compbio.engine.local.AsyncLocalRunner -
      -
    getWorkDirectory() - -Method in class compbio.engine.local.LocalRunner -
      -
    getWorkDirectory() - -Method in interface compbio.engine.SyncExecutor -
      -
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    hasDump() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasExited() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hashCode() - -Method in class compbio.data.sequence.AlignmentMetadata -
      -
    hashCode() - -Method in class compbio.engine.client.CommandBuilder -
      -
    hashCode() - -Method in class compbio.engine.client.RunConfiguration -
      -
    hashCode() - -Method in class compbio.engine.client.SkeletalExecutable -
      -
    hashCode() - -Method in class compbio.engine.ClusterJobId -
      -
    hashCode() - -Method in class compbio.engine.conf._Key -
      -
    hashCode() - -Method in class compbio.engine.FilePuller -
      -
    hashCode() - -Method in class compbio.engine.Job -
      -
    hashCode() - -Method in class compbio.metadata.ChunkHolder -
      -
    hashCode() - -Method in class compbio.metadata.Limit -
      -
    hashCode() - -Method in class compbio.metadata.Option -
      -
    hashCode() - -Method in class compbio.metadata.Parameter -
      -
    hashCode() - -Method in class compbio.metadata.Preset -
      -
    hashCode() - -Method in class compbio.metadata.ValueConstrain -
      -
    hashCode() - -Method in class compbio.pipeline._jpred.PScore -
      -
    hasMoreData() - -Method in class compbio.engine.FilePuller -
      -
    hasParam(String) - -Method in class compbio.engine.client.CommandBuilder -
      -
    hasSignaled() - -Method in class compbio.engine.cluster.drmaa.StatisticManager -
      -
    hasTimeLimit() - -Method in enum compbio.engine.cluster.dundee._Queue -
      -
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    initPull() - -Method in class compbio.engine.FilePuller -
      -
    IS_CLUSTER_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    IS_LOCAL_ENGINE_ENABLED - -Static variable in class compbio.engine.Configurator -
      -
    isAbsolutePath(String) - -Static method in class compbio.engine.client.PathValidator -
    Whether a certain path is absolute or not is operation system dependent! -
    isAmbiguosProtein(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Check whether the sequence confirms to amboguous protein sequence -
    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 limits the values defined by this Limit -
    isFileCreated() - -Method in class compbio.engine.FilePuller -
      -
    isMarked(String, JobStatus) - -Static method in class compbio.engine.client.Util -
      -
    isNonAmbNucleotideSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one - (!) - B char -
    isNucleotideSequence(FastaSequence) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isProteinSequence(String) - -Static method in class compbio.data.sequence.SequenceUtil -
      -
    isRequired() - -Method in class compbio.metadata.Option -
    Flag that indicated that this option must be specified in the command - line for an executable to run -
    isReturn() - -Method in class compbio.data.msa.jaxws.CancelJobResponse -
      -
    isShutdown() - -Method in class compbio.engine.local._TrackingExecutor -
      -
    isTerminated() - -Method in class compbio.engine.local._TrackingExecutor -
      -
    isValidClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -
      -
    isValidDirectory(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidExecutable(String) - -Static method in class compbio.engine.client.PathValidator -
      -
    isValidJobId(String) - -Static method in class compbio.engine.client.Util -
      -
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    -Packages
    compbio.data._structure 
    compbio.data.msa 
    compbio.data.msa.jaxws 
    compbio.data.sequenceA data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project.
    compbio.engine 
    compbio.engine.clientClasses and interfaces representing an input for engines.
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters.
    compbio.engine.cluster.dundee 
    compbio.engine.confClasses commonly used by both engines.
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer - (the same machine as JVM running these classes).
    compbio.metadataA meta-data model for multiple sequence alignment web services - Classes in this package have no dependencies to other sources in the project.
    compbio.pipeline._jpred 
    compbio.runnerUtilities commonly used by all runners.
    compbio.runner._impl 
    compbio.runner._jpred 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa)
    compbio.runner.psiblast 
    compbio.ws.client 
    compbio.ws.server 
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    Package Hierarchies:
    compbio.data._structure, compbio.data.msa, compbio.data.msa.jaxws, compbio.data.sequence, compbio.engine, compbio.engine.client, compbio.engine.cluster.drmaa, compbio.engine.cluster.dundee, compbio.engine.conf, compbio.engine.local, compbio.metadata, compbio.pipeline._jpred, compbio.runner, compbio.runner._impl, compbio.runner._jpred, compbio.runner.msa, compbio.runner.psiblast, compbio.ws.client, compbio.ws.server
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    -int aSequenceLenghtActual
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    -serialVersionUID: -5475613614578761L - -

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    -Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    - -

    -serialVersionUID: -86624836785110293L - -

    - -

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    -Class compbio.metadata.WrongParameterException extends java.lang.Exception implements Serializable
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