A B C D E F G H I J K L M N O P R S T U V W _

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