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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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