X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-7.html;h=2a53e54773f95e46a0dee049c1d4c18cc78a1ed4;hb=f1bdd8da517901fe1d7957d388ea579ad1fbaa3b;hp=f2382f2ddaf642417d81ff9cf60c26b82ea2db1e;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-7.html b/website/full_javadoc/index-files/index-7.html index f2382f2..2a53e54 100644 --- a/website/full_javadoc/index-files/index-7.html +++ b/website/full_javadoc/index-files/index-7.html @@ -2,12 +2,12 @@ - + G-Index - + @@ -85,9 +85,21 @@ function windowTitle()
gapchar - Static variable in class compbio.data.sequence.ClustalAlignmentUtil
Dash char to be used as gap char in the alignments -
get(String) - +
GAUtils - Class in compbio.ws.server
 
GAUtils() - +Constructor for class compbio.ws.server.GAUtils +
  +
GenericMetadataService<T> - Class in compbio.ws.server
 
get(String) - Static method in class compbio.engine.PulledFileCache
  +
getAbandoned() - +Method in class compbio.stat.servlet.util.Totals +
  +
getAbandonedCount(Timestamp, Timestamp) - +Method in class compbio.stat.collector.StatDB +
  +
getAbandonedJobs() - +Method in class compbio.stat.collector.StatProcessor +
Not collected.
getActualNumberofSequences() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
  @@ -106,15 +118,51 @@ Method in class compbio.runner.getAllParameters() - Method in class compbio.runner.OptionCombinator
  +
getAllStat() - +Method in class compbio.stat.servlet.util.StatCollection +
 
getAllStats() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
GetAnnotation - Class in compbio.data.msa.jaxws
 
GetAnnotation() - +Constructor for class compbio.data.msa.jaxws.GetAnnotation +
  +
getAnnotation(String) - +Method in interface compbio.data.msa.SequenceAnnotation +
Return the result of the job. +
getAnnotation(String) - +Method in class compbio.ws.server.SequenceAnnotationService +
  +
getAnnotation(String, Logger) - +Static method in class compbio.ws.server.WSUtil +
  +
getAnnotationForSequence(String) - +Method in class compbio.data.sequence.ScoreManager +
  +
GetAnnotationResponse - Class in compbio.data.msa.jaxws
 
GetAnnotationResponse() - +Constructor for class compbio.data.msa.jaxws.GetAnnotationResponse +
 
getApproprieteQueue() - Method in class compbio.runner._NativeSpecHelper +
Deprecated.   +
getArg0() - +Method in class compbio.data.msa.jaxws.GetLastTested +
  +
getArg0() - +Method in class compbio.data.msa.jaxws.GetLastTestedOn +
  +
getArg0() - +Method in class compbio.data.msa.jaxws.GetServiceDescription +
  +
getArg0() - +Method in class compbio.data.msa.jaxws.IsOperating +
  +
getArg0() - +Method in class compbio.data.msa.jaxws.TestService
 
getArgument(String) - Method in class compbio.metadata.RunnerConfig -
Returns the argument by its name if found, NULL otherwise +
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 @@ -123,7 +171,8 @@ Method in class compbio.metadata.Converts list of options as String to type Option
getArguments() - Method in class compbio.metadata.RunnerConfig -
  +
Returns list of Parameter and Option supported by current + runner
getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
  @@ -157,8 +206,17 @@ Static method in class compbio.engine.getCalculationTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  -
getCancelledTasks() - -Method in class compbio.engine.local._TrackingExecutor +
getCancelled() - +Method in class compbio.stat.servlet.util.Totals +
  +
getCancelledCount(Timestamp, Timestamp) - +Method in class compbio.stat.collector.StatDB +
  +
getCancelledJobs() - +Method in class compbio.stat.collector.StatProcessor +
  +
getCategories() - +Static method in class compbio.data.msa.Category
 
getChunk() - Method in class compbio.metadata.ChunkHolder @@ -166,15 +224,36 @@ Method in class compbio.metadata.getClass(String) - Static method in class compbio.engine.conf.DirectoryManager
  -
getClusterCpuNum() - -Static method in class compbio.runner.msa.Tcoffee +
getClusterCpuNum(Class<? extends Executable<?>>) - +Static method in class compbio.engine.client.SkeletalExecutable
 
getClusterJobId(String) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
  -
getClusterSettings() - +
getClusterJobId() - +Method in class compbio.stat.collector.JobStat +
  +
getClusterJobs() - +Method in class compbio.stat.collector.StatProcessor +
  +
getClusterJobSettings() - +Method in class compbio.engine.client.ConfExecutable +
  +
getClusterJobSettings() - +Method in interface compbio.engine.client.Executable +
  +
getClusterJobSettings() - Method in class compbio.engine.client.SkeletalExecutable
  +
getClusterJobSettings() - +Method in class compbio.runner._impl.NetNglyc +
  +
getClusterJobSettings() - +Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getClusterStat() - +Method in class compbio.stat.servlet.util.StatCollection +
 
getCommand(Executable.ExecProvider) - Method in class compbio.engine.client.ConfExecutable
  @@ -187,9 +266,6 @@ Static method in class compbio.engine.client.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
  @@ -205,9 +281,6 @@ Method in class compbio.runner._impl.getCommandName() - Method in class compbio.runner._impl.BlastAll
  -
getCommandName() - -Method in class compbio.runner._impl.Disembl -
 
getCommandName() - Method in class compbio.runner._impl.Mcl
  @@ -246,7 +319,7 @@ Method in class compbio.engine.client.getCreatedFiles() - Method in interface compbio.engine.client.Executable -
  +
Deprecated. 
getCreatedFiles() - Method in class compbio.engine.client.SkeletalExecutable
This method cannot really tell whether the files has actually been @@ -254,9 +327,6 @@ Method in class compbio.engine.client.getCreatedFiles() - Method in class compbio.runner._impl.BlastAll
  -
getCreatedFiles() - -Method in class compbio.runner._impl.Disembl -
 
getCreatedFiles() - Method in class compbio.runner._impl.Mcl
  @@ -275,6 +345,12 @@ Method in class compbio.runner._impl.getCreatedFiles() - Method in class compbio.runner._impl.RPSBlast
  +
getCreatedFiles() - +Method in class compbio.runner.conservation.AACon +
  +
getCreatedFiles() - +Method in class compbio.runner.disorder.Jronn +
 
getCreatedFiles() - Method in class compbio.runner.msa.ClustalW
  @@ -311,12 +387,15 @@ Method in class compbio.metadata.getDescription() - Method in class compbio.metadata.Preset
  -
getDisemblRunnable(String) - -Static method in class compbio.runner._impl.Runners +
getDetails() - +Method in class compbio.stat.servlet.ServiceTestResult +
  +
getEarliestRecord() - +Method in class compbio.stat.collector.StatDB
 
getEmail() - Method in class compbio.runner._SkeletalCommandBuilder -
  +
Deprecated.  
getEndTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  @@ -355,6 +434,9 @@ Method in class compbio.runner._impl.getError() - Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getEscJobname() - +Method in class compbio.stat.collector.JobStat
 
getExecProperty(String, Executable<?>) - Static method in class compbio.engine.client.Util @@ -384,18 +466,36 @@ Static method in class compbio.engine.local.getExitStatus() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
getFailed() - +Method in class compbio.stat.servlet.util.Totals +
  +
getFailedJobs() - +Method in class compbio.stat.collector.StatProcessor +
Started & finished but did not produce result
getFastaSequences() - Method in class compbio.data.msa.jaxws.Align
  +
getFastaSequences() - +Method in class compbio.data.msa.jaxws.Analize +
 
getFastaSequences() - Method in class compbio.data.msa.jaxws.CustomAlign
  +
getFastaSequences() - +Method in class compbio.data.msa.jaxws.CustomAnalize +
 
getFastaSequences() - Method in class compbio.data.msa.jaxws.PresetAlign
  +
getFastaSequences() - +Method in class compbio.data.msa.jaxws.PresetAnalize +
 
getFile() - Method in class compbio.engine.FilePuller
  +
getFinish() - +Method in class compbio.stat.collector.JobStat +
 
getFormatedSequence(int) - Method in class compbio.data.sequence.FastaSequence
Format sequence per width letter in one string. @@ -414,12 +514,18 @@ Method in class compbio.metadata.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 +
getIncomplete() - +Method in class compbio.stat.servlet.util.Totals +
  +
getIncompleteCount(Timestamp, Timestamp) - +Method in class compbio.stat.collector.StatDB +
  +
getIncompleteJobs() - +Method in class compbio.stat.collector.StatProcessor +
 
getInput() - Method in class compbio.engine.client.ConfExecutable
Not all input paths are relative! Input path could be absolute! @@ -435,9 +541,6 @@ Method in class compbio.engine.client.getInput() - Method in class compbio.runner._impl.BlastAll
  -
getInput() - -Method in class compbio.runner._impl.Disembl -
 
getInput() - Method in class compbio.runner._impl.Mcl
  @@ -456,30 +559,42 @@ Method in class compbio.runner._impl.getInput() - Method in class compbio.runner._impl.RPSBlast
  +
getInputSize() - +Method in class compbio.stat.collector.JobStat +
 
getInstance(ConfiguredExecutable<?>) - Static method in class compbio.engine.cluster.drmaa.JobRunner
 
getIOWait() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
getIsCancelled() - +Method in class compbio.stat.collector.JobStat +
  +
getIsCollected() - +Method in class compbio.stat.collector.JobStat +
  +
getIsFinished() - +Method in class compbio.stat.collector.JobStat +
  +
getJava() - +Static method in class compbio.engine.client.Util +
Returns the absolute path to the Java executable from JAVA_HOME
getJobId() - Method in class compbio.data.msa.jaxws.CancelJob
  +
getJobId() - +Method in class compbio.data.msa.jaxws.GetAnnotation +
 
getJobId() - Method in class compbio.data.msa.jaxws.GetJobStatus
  -
getJobId() - -Method in class compbio.data.msa.jaxws.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
  @@ -493,14 +608,23 @@ Method in class compbio.engine.JobRunner
This method will block before the calculation has completed and then return the object containing a job execution statistics +
getJobname() - +Method in class compbio.stat.collector.JobStat +
  +
getJobNumber() - +Method in class compbio.stat.collector.StatProcessor +
 
getJobPriority() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
getJobs() - +Method in class compbio.stat.collector.StatProcessor +
 
GetJobStatus - Class in compbio.data.msa.jaxws
 
GetJobStatus() - Constructor for class compbio.data.msa.jaxws.GetJobStatus
  -
getJobStatus(String) - -Method in interface compbio.data.msa.MsaWS +
getJobStatus(String) - +Method in interface compbio.data.msa.JManagement
Return the status of the job.
getJobStatus(String) - Method in interface compbio.engine.AsyncExecutor @@ -532,9 +656,15 @@ Method in class compbio.engine.local.getJobStatus() - Method in interface compbio.engine.SyncExecutor
Query the status of the job by its id. +
getJobStatus(String) - +Method in class compbio.ws.server.ClustalOWS +
 
getJobStatus(String) - Method in class compbio.ws.server.ClustalWS
  +
getJobStatus(String) - +Method in class compbio.ws.server.GenericMetadataService +
 
getJobStatus(String) - Method in class compbio.ws.server.MafftWS
  @@ -553,14 +683,38 @@ Static method in class compbio.ws.server.GetJobStatusResponse - Class in compbio.data.msa.jaxws
 
GetJobStatusResponse() - Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse
  +
GetLastTested - Class in compbio.data.msa.jaxws
 
GetLastTested() - +Constructor for class compbio.data.msa.jaxws.GetLastTested +
  +
getLastTested(Services) - +Method in interface compbio.data.msa.RegistryWS +
Number of seconds since the last test. +
getLastTested(Services) - +Method in class compbio.ws.server.RegistryWS +
  +
GetLastTestedOn - Class in compbio.data.msa.jaxws
 
GetLastTestedOn() - +Constructor for class compbio.data.msa.jaxws.GetLastTestedOn +
  +
getLastTestedOn(Services) - +Method in interface compbio.data.msa.RegistryWS +
The date and time the service has been verified to work last time +
getLastTestedOn(Services) - +Method in class compbio.ws.server.RegistryWS +
Can potentially return null if the service has not been tested yet. +
GetLastTestedOnResponse - Class in compbio.data.msa.jaxws
 
GetLastTestedOnResponse() - +Constructor for class compbio.data.msa.jaxws.GetLastTestedOnResponse +
  +
GetLastTestedResponse - Class in compbio.data.msa.jaxws
 
GetLastTestedResponse() - +Constructor for class compbio.data.msa.jaxws.GetLastTestedResponse +
 
getLength() - Method in class compbio.data.sequence.FastaSequence
 
GetLimit - Class in compbio.data.msa.jaxws
 
GetLimit() - Constructor for class compbio.data.msa.jaxws.GetLimit
  -
getLimit(String) - -Method in interface compbio.data.msa.MsaWS +
getLimit(String) - +Method in interface compbio.data.msa.Metadata
Get a Limit for a preset.
getLimit(String) - Method in class compbio.engine.client.ConfExecutable @@ -568,33 +722,24 @@ Method in class compbio.engine.client.getLimit(String) - Method in interface compbio.engine.client.Executable
  +
getLimit(String) - +Method in class compbio.engine.client.SkeletalExecutable +
 
getLimit(String) - Method in class compbio.runner._impl.NetNglyc
 
getLimit(String) - Method in class compbio.runner._SkeletalCommandBuilder -
  -
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 +
Deprecated.   +
getLimit(String) - +Method in class compbio.ws.server.ClustalOWS
 
getLimit(String) - Method in class compbio.ws.server.ClustalWS
  +
getLimit(String) - +Method in class compbio.ws.server.GenericMetadataService +
 
getLimit(String) - Method in class compbio.ws.server.MafftWS
  @@ -616,8 +761,8 @@ Constructor for class compbio.data.msa.jaxws.GetLimits - Class in compbio.data.msa.jaxws
 
GetLimits() - Constructor for class compbio.data.msa.jaxws.GetLimits
  -
getLimits() - -Method in interface compbio.data.msa.MsaWS +
getLimits() - +Method in interface compbio.data.msa.Metadata
List Limits supported by a web service.
getLimits() - Method in class compbio.engine.client.ConfExecutable @@ -625,6 +770,13 @@ Method in class compbio.engine.client.getLimits() - Method in interface compbio.engine.client.Executable
  +
getLimits() - +Method in class compbio.engine.client.SkeletalExecutable +
  +
getLimits(Class<T>) - +Static method in class compbio.engine.client.Util +
For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
getLimits() - Method in class compbio.metadata.LimitsManager
  @@ -633,32 +785,16 @@ Method in class compbio.runner._impl.getLimits() - Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getLimits() - +Method in class compbio.ws.server.ClustalOWS
  -
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.GenericMetadataService +
 
getLimits() - Method in class compbio.ws.server.MafftWS
  @@ -674,9 +810,15 @@ Method in class compbio.ws.server.GetLimitsResponse - Class in compbio.data.msa.jaxws
 
GetLimitsResponse() - Constructor for class compbio.data.msa.jaxws.GetLimitsResponse
  +
getLocalJobs() - +Method in class compbio.stat.collector.StatProcessor +
 
getLocalPath() - Static method in class compbio.engine.conf.PropertyHelperManager
Method return the absolute path to the project root directory. +
getLocalStat() - +Method in class compbio.stat.servlet.util.StatCollection +
 
getMax() - Method in class compbio.metadata.ValueConstrain
  @@ -688,13 +830,10 @@ Static method in class compbio.runner._impl.getMemoryLimit() - Method in enum compbio.engine.cluster.dundee._Queue -
return max memory limit in Mb +
Deprecated. 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
  @@ -713,6 +852,12 @@ Method in class compbio.data.msa.jaxws.getMetadata() - Method in class compbio.data.sequence.Alignment
  +
getMethod(String) - +Static method in enum compbio.data.sequence.ConservationMethod +
  +
getMethod() - +Method in class compbio.data.sequence.Score +
Returns the ConservationMethod
getMin() - Method in class compbio.metadata.ValueConstrain
  @@ -727,22 +872,22 @@ Method in class compbio.metadata. 
getName() - Method in class compbio.runner._SkeletalCommandBuilder -
  +
Deprecated.  
getNativeSpec() - Method in class compbio.runner._NativeSpecHelper -
  -
getNativeSpecs() - -Method in interface compbio.engine.client.ClusterNativeSpecExecutable -
  -
getNativeSpecs() - -Method in class compbio.runner.msa.Tcoffee -
  +
Deprecated.  
getNetNglycRunnable(String) - Static method in class compbio.runner._impl.Runners
 
getNextPosition() - Method in class compbio.metadata.ChunkHolder
  +
getNumberOfScores() - +Method in class compbio.data.sequence.ScoreManager.ScoreHolder +
  +
getNumberOfSeq() - +Method in class compbio.data.sequence.ScoreManager +
 
getNumberOfSequencesAllowed() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean
  @@ -764,12 +909,15 @@ Method in class compbio.metadata.getOptions() - Method in class compbio.data.msa.jaxws.CustomAlign
  +
getOptions() - +Method in class compbio.data.msa.jaxws.CustomAnalize +
 
getOptions() - Method in class compbio.metadata.Preset
 
getOptions() - Method in class compbio.metadata.RunnerConfig -
  +
Returns the list of the Options supported by the executable of type T
getOptionsAtRandom() - Method in class compbio.runner.OptionCombinator
  @@ -790,6 +938,9 @@ Method in class compbio.runner._impl.getOutput() - Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getOutput() - +Method in class compbio.runner.disorder.IUPred
 
getParameters() - Method in class compbio.engine.client.ConfExecutable @@ -811,12 +962,21 @@ Method in class compbio.engine.client.getParameters() - Method in class compbio.metadata.RunnerConfig -
  +
Returns the list of parameters supported executable of type T.
getParameters(Executable.ExecProvider) - Method in class compbio.runner._impl.NetNglyc
 
getParameters(Executable.ExecProvider) - Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getParameters(Executable.ExecProvider) - +Method in class compbio.runner.conservation.AACon +
  +
getParameters(Executable.ExecProvider) - +Method in class compbio.runner.disorder.Jronn +
  +
getParameters(Executable.ExecProvider) - +Method in class compbio.runner.msa.ClustalO
 
getParameters(Executable.ExecProvider) - Method in class compbio.runner.msa.Tcoffee @@ -827,9 +987,6 @@ Method in class compbio.engine.client.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
  @@ -842,6 +999,9 @@ Method in class compbio.metadata.getPreset() - Method in class compbio.data.msa.jaxws.PresetAlign
  +
getPreset() - +Method in class compbio.data.msa.jaxws.PresetAnalize +
 
getPreset() - Method in class compbio.metadata.Limit
  @@ -854,8 +1014,8 @@ Method in class compbio.data.msa.jaxws.GetPresets - Class in compbio.data.msa.jaxws
 
GetPresets() - Constructor for class compbio.data.msa.jaxws.GetPresets
  -
getPresets() - -Method in interface compbio.data.msa.MsaWS +
getPresets() - +Method in interface compbio.data.msa.Metadata
Get presets supported by a web service
getPresets() - Method in class compbio.metadata.PresetManager @@ -863,9 +1023,15 @@ Method in class compbio.metadata.getPresets(Class<? extends Executable<T>>) - Static method in class compbio.runner.Util
  +
getPresets() - +Method in class compbio.ws.server.ClustalOWS +
 
getPresets() - Method in class compbio.ws.server.ClustalWS
  +
getPresets() - +Method in class compbio.ws.server.GenericMetadataService +
 
getPresets() - Method in class compbio.ws.server.MafftWS
  @@ -887,9 +1053,6 @@ Method in class compbio.metadata.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
  @@ -899,9 +1062,6 @@ Static method in class compbio.engine.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 @@ -911,31 +1071,40 @@ Static method in class compbio.runner._impl.getQueue(int, int) - Static method in enum compbio.engine.cluster.dundee._Queue -
  +
Deprecated.  
getQueue(String) - Method in enum compbio.engine.cluster.dundee._Queue -
  +
Deprecated.  
getQueue() - Method in class compbio.runner._NativeSpecHelper -
  +
Deprecated.  
getQueueByMemoryRequirements(int) - Static method in enum compbio.engine.cluster.dundee._Queue -
  +
Deprecated.   +
getRanges() - +Method in class compbio.data.sequence.Score +
Return Ranges if any Collections.EMPTY_SET otherwise
getRawUsage() - Method in class compbio.engine.cluster.drmaa.StatisticManager
 
getRecordedJobStatus(String) - Static method in class compbio.engine.local.LocalEngineUtil
  -
getRemoteAddress(WebServiceContext) - -Static method in class compbio.ws.server.WSUtil -
  +
getRemoteAddress() - +Method in class compbio.ws.server._WSLogger +
Deprecated.  
GetResult - Class in compbio.data.msa.jaxws
 
GetResult() - Constructor for class compbio.data.msa.jaxws.GetResult
 
getResult(String) - Method in interface compbio.data.msa.MsaWS
Return the result of the job. +
getResult(String) - +Method in class compbio.ws.server._MsaService +
  +
getResult(String) - +Method in class compbio.ws.server.ClustalOWS +
 
getResult(String) - Method in class compbio.ws.server.ClustalWS
  @@ -986,6 +1155,24 @@ Method in class compbio.runner._impl.getResults(String) - Method in class compbio.runner._SkeletalCommandBuilder +
Deprecated.   +
getResults(String) - +Method in class compbio.runner.conservation.AACon +
  +
getResults(String) - +Method in class compbio.runner.disorder.Disembl +
  +
getResults(String) - +Method in class compbio.runner.disorder.GlobPlot +
  +
getResults(String) - +Method in class compbio.runner.disorder.IUPred +
  +
getResults(String) - +Method in class compbio.runner.disorder.Jronn +
  +
getResults(String) - +Method in class compbio.runner.msa.ClustalO
 
getResults(String) - Method in class compbio.runner.msa.ClustalW @@ -1002,18 +1189,33 @@ Method in class compbio.runner.msa.getResults(String) - Method in class compbio.runner.msa.Tcoffee
  -
getResults(String) - -Method in class compbio.runner.psiblast.PsiBlast +
getResultSize() - +Method in class compbio.stat.collector.JobStat
 
getReturn() - Method in class compbio.data.msa.jaxws.AlignResponse
  +
getReturn() - +Method in class compbio.data.msa.jaxws.AnalizeResponse +
 
getReturn() - Method in class compbio.data.msa.jaxws.CustomAlignResponse
  +
getReturn() - +Method in class compbio.data.msa.jaxws.CustomAnalizeResponse +
  +
getReturn() - +Method in class compbio.data.msa.jaxws.GetAnnotationResponse +
 
getReturn() - Method in class compbio.data.msa.jaxws.GetJobStatusResponse
  +
getReturn() - +Method in class compbio.data.msa.jaxws.GetLastTestedOnResponse +
  +
getReturn() - +Method in class compbio.data.msa.jaxws.GetLastTestedResponse +
 
getReturn() - Method in class compbio.data.msa.jaxws.GetLimitResponse
  @@ -1023,23 +1225,35 @@ Method in class compbio.data.msa.jaxws.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.GetServiceCategoriesResponse +
  +
getReturn() - +Method in class compbio.data.msa.jaxws.GetServiceDescriptionResponse +
  +
getReturn() - +Method in class compbio.data.msa.jaxws.GetSupportedServicesResponse +
 
getReturn() - Method in class compbio.data.msa.jaxws.PresetAlignResponse
  +
getReturn() - +Method in class compbio.data.msa.jaxws.PresetAnalizeResponse +
 
getReturn() - Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse
  -
getReturn() - -Method in class compbio.data.msa.jaxws.PullFileResponse +
getReturn() - +Method in class compbio.data.msa.jaxws.TestAllServicesResponse +
  +
getReturn() - +Method in class compbio.data.msa.jaxws.TestServiceResponse
 
getRonnRunnable(String) - Static method in class compbio.runner._impl.Runners @@ -1053,6 +1267,9 @@ Static method in class compbio.runner._impl.getRunConfiguration() - Method in class compbio.engine.client.ConfExecutable
  +
getRunnerByJobDirectory(File) - +Static method in class compbio.ws.client.ServicesUtil +
 
getRunnerClassName() - Method in class compbio.engine.client.RunConfiguration
  @@ -1062,21 +1279,27 @@ Method in class compbio.metadata.getRunnerClassName() - Method in class compbio.metadata.RunnerConfig
  -
getRunnerLimits(Class<? extends Executable<V>>) - +
getRunnerLimits(Class<V>) - Static method in class compbio.engine.client.ConfExecutable
This method should be executed once and result of its execution reused.
GetRunnerOptions - Class in compbio.data.msa.jaxws
 
GetRunnerOptions() - Constructor for class compbio.data.msa.jaxws.GetRunnerOptions
  -
getRunnerOptions() - -Method in interface compbio.data.msa.MsaWS +
getRunnerOptions() - +Method in interface compbio.data.msa.Metadata
Get options supported by a web service
getRunnerOptions(Class<? extends Executable<V>>) - Static method in class compbio.engine.client.ConfExecutable
  +
getRunnerOptions() - +Method in class compbio.ws.server.ClustalOWS +
 
getRunnerOptions() - Method in class compbio.ws.server.ClustalWS
  +
getRunnerOptions() - +Method in class compbio.ws.server.GenericMetadataService +
 
getRunnerOptions() - Method in class compbio.ws.server.MafftWS
  @@ -1095,9 +1318,21 @@ Constructor for class compbio.data.msa.jaxws.getRunnerPresets(Class<? extends Executable<V>>) - Static method in class compbio.engine.client.ConfExecutable
  +
getRuntime() - +Method in class compbio.stat.collector.JobStat +
 
getSchema(String) - Static method in class compbio.engine.conf.RunnerConfigMarshaller
  +
getScoreByMethod(Enum<?>) - +Method in class compbio.data.sequence.ScoreManager.ScoreHolder +
  +
getScoreByMethod(String) - +Method in class compbio.data.sequence.ScoreManager.ScoreHolder +
  +
getScores() - +Method in class compbio.data.sequence.Score +
The column scores for the alignment
getSeqNumber() - Method in class compbio.metadata.Limit
  @@ -1119,18 +1354,81 @@ Method in exception compbio.metadata.getSequences() - Method in class compbio.data.sequence.Alignment
  -
getServiceName(String[]) - +
getService() - +Method in class compbio.stat.servlet.ServiceTestResult +
  +
getService(String) - +Static method in enum compbio.ws.client.Services +
  +
getServiceByJobDirectory(File) - +Static method in class compbio.ws.client.ServicesUtil +
  +
getServiceByRunner(Class<? extends Executable>) - +Static method in class compbio.ws.client.ServicesUtil +
  +
GetServiceCategories - Class in compbio.data.msa.jaxws
 
GetServiceCategories() - +Constructor for class compbio.data.msa.jaxws.GetServiceCategories +
  +
getServiceCategories() - +Method in interface compbio.data.msa.RegistryWS +
Gets the list of services per category. +
getServiceCategories() - +Method in class compbio.ws.server.RegistryWS +
  +
GetServiceCategoriesResponse - Class in compbio.data.msa.jaxws
 
GetServiceCategoriesResponse() - +Constructor for class compbio.data.msa.jaxws.GetServiceCategoriesResponse +
  +
GetServiceDescription - Class in compbio.data.msa.jaxws
 
GetServiceDescription() - +Constructor for class compbio.data.msa.jaxws.GetServiceDescription +
  +
getServiceDescription(Services) - +Method in interface compbio.data.msa.RegistryWS +
Gives the description of the service. +
getServiceDescription(Services) - +Method in class compbio.ws.server.RegistryWS +
  +
GetServiceDescriptionResponse - Class in compbio.data.msa.jaxws
 
GetServiceDescriptionResponse() - +Constructor for class compbio.data.msa.jaxws.GetServiceDescriptionResponse +
  +
getServiceImpl(Services) - +Static method in class compbio.ws.client.ServicesUtil +
  +
getServiceInfo() - +Method in enum compbio.ws.client.Services +
  +
getServices() - +Method in class compbio.data.msa.Category +
  +
getServices(String) - Static method in class compbio.ws.client.Jws2Client -
Extracts service name from the command line +
 
getSession() - Method in class compbio.engine.cluster.drmaa.ClusterSession
  +
getSingleWSStat(Services) - +Method in class compbio.stat.collector.StatProcessor +
 
getSize() - Method in class compbio.data.sequence.Alignment
  +
getSMERFSColumnScore(String) - +Static method in enum compbio.data.sequence.SMERFSConstraints +
  +
getStart() - +Method in class compbio.stat.collector.JobStat +
 
getStartTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
getStatFile() - +Static method in class compbio.runner.conservation.AACon +
  +
getStatFile() - +Static method in class compbio.runner.disorder.Jronn +
  +
getStatFile() - +Static method in class compbio.runner.msa.ClustalO +
 
getStatFile() - Static method in class compbio.runner.msa.ClustalW
  @@ -1140,6 +1438,18 @@ Static method in class compbio.runner.msa.getStatistics(JobInfo) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
  +
getStatLogger(Services, WebServiceContext) - +Static method in class compbio.ws.server._WSLogger +
Deprecated.   +
getStats(int) - +Static method in class compbio.stat.servlet.util.StatCollection +
  +
getStats(Date) - +Static method in class compbio.stat.servlet.util.StatCollection +
  +
getStatus() - +Method in class compbio.stat.servlet.ServiceTestResult +
 
getSubmissionTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  @@ -1155,6 +1465,18 @@ Method in interface compbio.engine.client.getSupportedRuntimes(Class<?>) - Static method in class compbio.engine.client.Util
  +
GetSupportedServices - Class in compbio.data.msa.jaxws
 
GetSupportedServices() - +Constructor for class compbio.data.msa.jaxws.GetSupportedServices +
  +
getSupportedServices() - +Method in interface compbio.data.msa.RegistryWS +
List of services that are functioning on the server. +
getSupportedServices() - +Method in class compbio.ws.server.RegistryWS +
  +
GetSupportedServicesResponse - Class in compbio.data.msa.jaxws
 
GetSupportedServicesResponse() - +Constructor for class compbio.data.msa.jaxws.GetSupportedServicesResponse +
 
getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - Static method in class compbio.engine.Configurator
  @@ -1176,18 +1498,12 @@ Method in interface compbio.engine.client.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
  @@ -1208,19 +1524,46 @@ Static method in class compbio.runner._impl.getTimeLimit() - Method in enum compbio.engine.cluster.dundee._Queue -
0 - unlimited +
Deprecated. 0 - unlimited
getTimeStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager
 
getTmhmm2Runnable(String) - Static method in class compbio.runner._impl.Runners
  +
getTotal() - +Method in class compbio.stat.servlet.util.Totals +
  +
getTotalJobsCount(Timestamp, Timestamp) - +Method in class compbio.stat.collector.StatDB +
  +
getTotalRuntime() - +Method in class compbio.stat.collector.StatProcessor +
 
getType() - Method in class compbio.engine.client.SkeletalExecutable
 
getType() - Method in class compbio.metadata.ValueConstrain
  +
getType() - +Method in class compbio.runner.conservation.AACon +
  +
getType() - +Method in class compbio.runner.disorder.Disembl +
  +
getType() - +Method in class compbio.runner.disorder.GlobPlot +
  +
getType() - +Method in class compbio.runner.disorder.IUPred +
  +
getType() - +Method in class compbio.runner.disorder.Jronn +
  +
getType() - +Method in class compbio.runner.msa.ClustalO +
 
getType() - Method in class compbio.runner.msa.ClustalW
  @@ -1236,9 +1579,6 @@ Method in class compbio.runner.msa.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
  @@ -1257,6 +1597,9 @@ Method in class compbio.metadata.getVMem() - Method in class compbio.engine.cluster.drmaa.StatisticManager
  +
getWebService() - +Method in class compbio.stat.collector.JobStat +
 
getWorkDirectory(String) - Method in interface compbio.engine.AsyncExecutor
  @@ -1284,6 +1627,20 @@ Method in class compbio.engine.local.getWorkDirectory() - Method in interface compbio.engine.SyncExecutor
  +
GlobPlot - Class in compbio.runner.disorder
./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame + + FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file' + Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file' + + Hard-coded values are 10 15 74 4 5.
GlobPlot() - +Constructor for class compbio.runner.disorder.GlobPlot +
  +
GLOBPLOT_INFO - +Static variable in enum compbio.ws.client.Services +
  +
GlobPlotWS - Class in compbio.ws.server
 
GlobPlotWS() - +Constructor for class compbio.ws.server.GlobPlotWS +