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

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

getApproprieteQueue() - Method in class compbio.runner._NativeSpecHelper

Deprecated.

getArg0() - Method in class compbio.data.msa.jaxws.GetLastTested

getArg0() - Method in class compbio.data.msa.jaxws.GetLastTestedOn

getArg0() - Method in class compbio.data.msa.jaxws.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

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

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

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

getClusterJobSettings() - Method in class compbio.runner._impl.NetNglyc

getClusterJobSettings() - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

getClusterStat() - Method in class compbio.stat.servlet.util.StatCollection

getCommand(Executable.ExecProvider) - Method in class compbio.engine.client.ConfExecutable

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.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.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

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._impl.BlastAll

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.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

getEarliestRecord() - Method in class compbio.stat.collector.StatDB

getEmail() - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

getEndTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager

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

Deprecated.

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

getInput() - Method in class compbio.runner._impl.BlastAll

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

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.runner._impl.NetNglyc

getLimit(String) - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

getLimit(String) - Method in class compbio.ws.server.ClustalOWS

getLimit(String) - Method in class compbio.ws.server.ClustalWS

getLimit(String) - Method in class compbio.ws.server.GenericMetadataService

getLimit(String) - Method in class compbio.ws.server.MafftWS

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.runner._impl.NetNglyc

getLimits() - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

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

getMclRunnable(String) - Static method in class compbio.runner._impl.Runners

getMemoryLimit() - Method in enum compbio.engine.cluster.dundee._Queue

Deprecated. return max memory limit in Mb

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

getName() - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

getNativeSpec() - Method in class compbio.runner._NativeSpecHelper

Deprecated.

getNetNglycRunnable(String) - Static method in class compbio.runner._impl.Runners

getNextPosition() - Method in class compbio.metadata.ChunkHolder

getNumberOfScores() - Method in class compbio.data.sequence.ScoreManager.ScoreHolder

getNumberOfSeq() - Method in class compbio.data.sequence.ScoreManager

getNumberOfSequencesAllowed() - Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean

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.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._impl.NetNglyc

getOutput() - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

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._impl.NetNglyc

getParameters(Executable.ExecProvider) - Method in class compbio.runner._SkeletalCommandBuilder

Deprecated.

getParameters(Executable.ExecProvider) - Method in class compbio.runner.conservation.AACon

getParameters(Executable.ExecProvider) - Method in class compbio.runner.disorder.Jronn

getParameters(Executable.ExecProvider) - Method in class compbio.runner.msa.ClustalO

getParameters(Executable.ExecProvider) - Method in class compbio.runner.msa.Tcoffee

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.

getPSIBlastRunnable(String) - Static method in class compbio.runner._impl.Runners

getQueue(int, int) - Static method in enum compbio.engine.cluster.dundee._Queue

Deprecated.

getQueue(String) - Method in enum compbio.engine.cluster.dundee._Queue

Deprecated.

getQueue() - Method in class compbio.runner._NativeSpecHelper

Deprecated.

getQueueByMemoryRequirements(int) - Static method in enum compbio.engine.cluster.dundee._Queue

Deprecated.

getRanges() - Method in class compbio.data.sequence.Score

Return Ranges if any Collections.EMPTY_SET otherwise

getRawUsage() - Method in class compbio.engine.cluster.drmaa.StatisticManager

getRecordedJobStatus(String) - Static method in class compbio.engine.local.LocalEngineUtil

getRemoteAddress() - Method in class compbio.ws.server._WSLogger

Deprecated.

GetResult - Class in compbio.data.msa.jaxws

GetResult() - Constructor for class compbio.data.msa.jaxws.GetResult

getResult(String) - Method in interface compbio.data.msa.MsaWS

Return the result of the job.

getResult(String) - Method in class compbio.ws.server._MsaService

getResult(String) - Method in class compbio.ws.server.ClustalOWS

getResult(String) - Method in class compbio.ws.server.ClustalWS

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

Deprecated.

getResults(String) - Method in class compbio.runner.conservation.AACon

getResults(String) - Method in class compbio.runner.disorder.Disembl

getResults(String) - Method in class compbio.runner.disorder.GlobPlot

getResults(String) - Method in class compbio.runner.disorder.IUPred

getResults(String) - Method in class compbio.runner.disorder.Jronn

getResults(String) - Method in class compbio.runner.msa.ClustalO

getResults(String) - Method in class compbio.runner.msa.ClustalW

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.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

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

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(String) - Static method in enum compbio.ws.client.Services

getServiceByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil

getServiceByRunner(Class<Executable<?>>) - Static method in class compbio.ws.client.ServicesUtil

getServiceImpl(Services) - Static method in class compbio.ws.client.ServicesUtil

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

getStatLogger(Services, WebServiceContext) - Static method in class compbio.ws.server._WSLogger

Deprecated.

getStats(int) - Static method in class compbio.stat.servlet.util.StatCollection

getStats(Date) - Static method in class compbio.stat.servlet.util.StatCollection

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

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.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

Deprecated. 0 - unlimited

getTimeStat() - Method in class compbio.engine.cluster.drmaa.StatisticManager

getTmhmm2Runnable(String) - Static method in class compbio.runner._impl.Runners

getTotal() - Method in class compbio.stat.servlet.util.Totals

getTotalJobsCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB

getTotalRuntime() - Method in class compbio.stat.collector.StatProcessor

getType() - Method in class compbio.engine.client.SkeletalExecutable

getType() - Method in class compbio.metadata.ValueConstrain

getType() - Method in class compbio.runner.conservation.AACon

getType() - Method in class compbio.runner.disorder.Disembl

getType() - Method in class compbio.runner.disorder.GlobPlot

getType() - Method in class compbio.runner.disorder.IUPred

getType() - Method in class compbio.runner.disorder.Jronn

getType() - Method in class compbio.runner.msa.ClustalO

getType() - Method in class compbio.runner.msa.ClustalW

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

GlobPlotWS - Class in compbio.ws.server

GlobPlotWS() - Constructor for class compbio.ws.server.GlobPlotWS