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gapchar
- Static variable in class compbio.data.sequence.
ClustalAlignmentUtil
Dash char to be used as gap char in the alignments
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
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
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
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.
getArgumentByOptionName(String)
- Method in class compbio.metadata.
RunnerConfig
Returns the argument by option name, NULL if the argument is not found
getArguments(RunnerConfig<T>)
- Method in class compbio.metadata.
Preset
Converts list of options as String to type Option
getArguments()
- Method in class compbio.metadata.
RunnerConfig
Returns list of
Parameter
and
Option
supported by current runner
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
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
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
getClass(String)
- Static method in class compbio.engine.conf.
DirectoryManager
getClusterCpuNum(Class<? extends Executable<?>>)
- Static method in class compbio.engine.client.
SkeletalExecutable
getClusterJobId(String)
- Static method in class compbio.engine.cluster.drmaa.
ClusterSession
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
getClusterStat()
- Method in class compbio.stat.servlet.util.
StatCollection
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
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
Deprecated.
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.conservation.
AACon
getCreatedFiles()
- Method in class compbio.runner.disorder.
Jronn
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
getDetails()
- Method in class compbio.stat.servlet.
ServiceTestResult
getEarliestRecord()
- Method in class compbio.stat.collector.
StatDB
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
getEscJobname()
- Method in class compbio.stat.collector.
JobStat
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
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.
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
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!
getInput()
- Method in interface compbio.engine.client.
Executable
getInput()
- Method in class compbio.engine.client.
RunConfiguration
getInput()
- Method in class compbio.engine.client.
SkeletalExecutable
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.
GetResult
getJobId()
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
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
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.
JManagement
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.
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
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
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.
Metadata
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.engine.client.
SkeletalExecutable
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
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.
Metadata
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.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
getLimits()
- Method in class compbio.ws.server.
ClustalOWS
getLimits()
- Method in class compbio.ws.server.
ClustalWS
getLimits()
- Method in class compbio.ws.server.
GenericMetadataService
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
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
getMaxVMem()
- Method in class compbio.engine.cluster.drmaa.
StatisticManager
getMemoryStat()
- Method in class compbio.engine.cluster.drmaa.
StatisticManager
getMessage()
- Method in class compbio.data.msa.jaxws.
JobSubmissionExceptionBean
getMessage()
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
getMessage()
- Method in class compbio.data.msa.jaxws.
ResultNotAvailableExceptionBean
getMessage()
- Method in class compbio.data.msa.jaxws.
UnsupportedRuntimeExceptionBean
getMessage()
- Method in class compbio.data.msa.jaxws.
WrongParameterExceptionBean
getMetadata()
- Method in class compbio.data.sequence.
Alignment
getMethod(String)
- Static method in enum compbio.data.sequence.
ConservationMethod
getMethod()
- Method in class compbio.data.sequence.
Score
Returns the ConservationMethod
getMin()
- Method in class compbio.metadata.
ValueConstrain
getName()
- Method in interface compbio.metadata.
Argument
getName()
- Method in class compbio.metadata.
Option
Human readable name of the option
getName()
- Method in class compbio.metadata.
Preset
getNextPosition()
- Method in class compbio.metadata.
ChunkHolder
getNumberOfScores()
- Method in class compbio.data.sequence.
ScoreManager.ScoreHolder
getNumberOfSeq()
- Method in class compbio.data.sequence.
ScoreManager
getNumberOfSequencesAllowed()
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
getNumberOfSequencesAllowed()
- Method in exception compbio.metadata.
LimitExceededException
getOnelineFasta()
- Method in class compbio.data.sequence.
FastaSequence
getOptionName()
- Method in class compbio.metadata.
Parameter
getOptionNames()
- Method in class compbio.metadata.
Option
getOptions()
- Method in class compbio.data.msa.jaxws.
CustomAlign
getOptions()
- Method in class compbio.data.msa.jaxws.
CustomAnalize
getOptions()
- Method in class compbio.metadata.
Preset
getOptions()
- Method in class compbio.metadata.
RunnerConfig
Returns the list of the Options supported by the executable of type T
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.disorder.
IUPred
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
Returns the list of parameters supported executable of type T.
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
getParamValue(String)
- Method in class compbio.engine.client.
CommandBuilder
getPosition()
- Method in class compbio.data.msa.jaxws.
PullExecStatistics
getPossibleValues()
- Method in interface compbio.metadata.
Argument
getPossibleValues()
- Method in class compbio.metadata.
Option
List of possible optionNames
getPossibleValues()
- Method in class compbio.metadata.
Parameter
List is more convenient to work with
getPreset()
- Method in class compbio.data.msa.jaxws.
PresetAlign
getPreset()
- Method in class compbio.data.msa.jaxws.
PresetAnalize
getPreset()
- Method in class compbio.metadata.
Limit
getPresetByName(String)
- Method in class compbio.metadata.
PresetManager
getPresetName()
- Method in class compbio.data.msa.jaxws.
GetLimit
GetPresets
- Class in
compbio.data.msa.jaxws
GetPresets()
- Constructor for class compbio.data.msa.jaxws.
GetPresets
getPresets()
- Method in interface compbio.data.msa.
Metadata
Get presets supported by a web service
getPresets()
- Method in class compbio.metadata.
PresetManager
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
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()
- 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
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.
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
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.
ClustalOWS
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.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
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
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
getReturn()
- Method in class compbio.data.msa.jaxws.
GetLimitsResponse
getReturn()
- Method in class compbio.data.msa.jaxws.
GetPresetsResponse
getReturn()
- Method in class compbio.data.msa.jaxws.
GetResultResponse
getReturn()
- Method in class compbio.data.msa.jaxws.
GetRunnerOptionsResponse
getReturn()
- Method in class compbio.data.msa.jaxws.
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.
TestAllServicesResponse
getReturn()
- Method in class compbio.data.msa.jaxws.
TestServiceResponse
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
getRunnerClassName()
- Method in class compbio.metadata.
PresetManager
getRunnerClassName()
- Method in class compbio.metadata.
RunnerConfig
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.
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
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
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
getSequence()
- Method in class compbio.data.sequence.
FastaSequence
Gets the value of sequence
getSequenceLenghtActual()
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
getSequenceLenghtActual()
- Method in exception compbio.metadata.
LimitExceededException
getSequenceLenghtAllowed()
- Method in class compbio.data.msa.jaxws.
LimitExceededExceptionBean
getSequenceLenghtAllowed()
- Method in exception compbio.metadata.
LimitExceededException
getSequences()
- Method in class compbio.data.sequence.
Alignment
getService()
- 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
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
getStatFile()
- Static method in class compbio.runner.msa.
Muscle
getStatistics(JobInfo)
- Static method in class compbio.engine.cluster.drmaa.
ClusterSession
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
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
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
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
getTimeStat()
- Method in class compbio.engine.cluster.drmaa.
StatisticManager
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
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
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
getWebService()
- Method in class compbio.stat.collector.
JobStat
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
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
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