- gapchar - Variable in class compbio.data.sequence.AlignmentMetadata
-
- 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
-
- generateSchema(String, String) - Method in class compbio.engine.conf.RunnerConfigMarshaller
-
- GenericMetadataService<T> - Class in compbio.ws.server
-
- GenericMetadataService(SkeletalExecutable<T>, Logger) - Constructor for class compbio.ws.server.GenericMetadataService
-
- 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
-
- getAlignment() - Method in class compbio.data.msa.jaxws.CustomFold
-
- getAlignment() - Method in class compbio.data.msa.jaxws.Fold
-
- getAlignment() - Method in class compbio.data.msa.jaxws.PresetFold
-
- 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(RunnerConfig<T>, String) - Method in class compbio.metadata.PresetManager
-
- 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
- getBasicURL() - Method in class compbio.metadata.Option
-
- getBooleanProperty(String) - Static method in class compbio.engine.conf.PropertyHelperManager
-
- getBooleanProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
-
- 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
-
- getClusterJobDir() - Static method in class compbio.stat.servlet.StatisticCollector
-
- getClusterJobDir() - Static method in class compbio.ws.server.MainManager
-
- getClusterJobId(String) - Static method in class compbio.engine.cluster.drmaa.ClusterSession
-
- getClusterJobID() - Method in class compbio.stat.collector.JobDirectory
-
- 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
-
- getClusterJobTimeOut() - Static method in class compbio.stat.servlet.StatisticCollector
-
- 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.EngineUtil
-
- getCommand(Executable.ExecProvider, Class<?>) - Static method in class compbio.engine.client.Util
-
- getCommandList() - Method in class compbio.engine.client.CommandBuilder
-
- 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.GLprobs
-
- getCreatedFiles() - Method in class compbio.runner.msa.MSAprobs
-
- getCreatedFiles() - Method in class compbio.runner.msa.Muscle
-
- getCreatedFiles() - Method in class compbio.runner.msa.Probcons
-
- getCreatedFiles() - Method in class compbio.runner.msa.Tcoffee
-
- getData() - Method in class compbio.data.sequence.RNAStructScoreManager
-
- getDataTransfered() - Method in class compbio.engine.cluster.drmaa.StatisticManager
-
- getDBConnection() - Static method in class compbio.stat.collector.StatDB
-
- 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
-
- getDelayValue(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
-
- getEndPoints() - Method in class compbio.stat.servlet.ServiceStatus
-
- 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
-
- getEnvVariableList(String) - Static method in class compbio.engine.client.EnvVariableProcessor
-
- getEnvVariableName(String) - Static method in class compbio.engine.client.EnvVariableProcessor
-
- getEnvVariables(String, Class<?>) - Static method in class compbio.engine.client.EnvVariableProcessor
-
- getEnvVariableValue(String) - 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.engine.local.ExecutableWrapper
-
- getEscJobname() - Method in class compbio.stat.collector.JobStat
-
- getExecProperty(String, Executable<?>) - Static method in class compbio.engine.client.EngineUtil
-
- getExecProperty(String, Class<?>) - Static method in class compbio.engine.client.EngineUtil
-
- 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
-
- getExecProvider(ConfiguredExecutable<?>, List<FastaSequence>) - Static method in class compbio.engine.Configurator
-
Depending on the values defined in the properties
(engine.cluster.enable=true and engine.local.enable=true) return either
Cluster job submission engine
#JobRunner
or local job submission
engine
#LocalRunner
If both engines enabled than ask
LoadBalancer
for an engine.
- 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
-
- getFile(String[], String, boolean) - Static method in class compbio.ws.client.IOHelper
-
Checks -i options and return the File if one was provided, null otherwise
- getFinish() - Method in class compbio.stat.collector.JobStat
-
- getFinishedTime() - Method in class compbio.stat.collector.JobDirectory
-
- 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(List<String>) - Method in class compbio.engine.client.ConfExecutable
-
- getFullPath(String, String) - Static method in class compbio.engine.client.EngineUtil
-
- 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
- getFuture() - Method in class compbio.engine.local.LocalRunner
-
- getGapchar() - Method in class compbio.data.sequence.AlignmentMetadata
-
- getGroup() - Method in class compbio.stat.servlet.ServiceTestResult
-
- getHost(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Extracts host name from the command line
- getId() - Method in class compbio.data.sequence.FastaSequence
-
Gets the value of id
- getIncomplete() - Method in class compbio.stat.servlet.util.Totals
-
- getIncompleteCount(Timestamp, Timestamp) - Method in class compbio.stat.collector.StatDB
-
- getIncompleteJobs() - Method in class compbio.stat.collector.StatProcessor
-
- getInput() - Method in class compbio.engine.client.ConfExecutable
-
Not all input paths are relative! Input path could be absolute!
- 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.JobDirectory
-
- getInputSize() - Method in class compbio.stat.collector.JobStat
-
- getInstance(ConfiguredExecutable<?>) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- getInstance() - Static method in class compbio.engine.cluster.drmaa.ClusterSession
-
- getInstance(ConfiguredExecutable<?>) - Static method in class compbio.engine.cluster.drmaa.JobRunner
-
- getInterface(Service) - Method in enum compbio.ws.client.Services
-
- getIntProperty(String) - Static method in class compbio.engine.conf.PropertyHelperManager
-
- getIntProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
-
- getIntResult(Timestamp, Timestamp, String) - Method in class compbio.stat.collector.StatDB
-
- 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
-
- getJabawsVersion() - Method in enum compbio.ws.client.Services
-
- getJava() - Static method in class compbio.engine.client.EngineUtil
-
Returns the absolute path to the Java executable from JAVA_HOME
- getJava() - Static method in class compbio.engine.client.Util
-
Returns the absolute path to the Java executable from JAVA_HOME
- getJobCounts(Date, Date) - Static method in class compbio.stat.servlet.util.StatCollection
-
- 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.ClusterRunner
-
This method will block before the calculation has completed and then
return the object containing a job execution statistics
- 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
-
- getJobReport() - Method in class compbio.stat.collector.JobStat
-
- getJobReportTabulated() - Method in class compbio.stat.collector.JobStat
-
Header Job Started Finished Runtime Input Result
- getJobs() - Method in class compbio.stat.collector.StatProcessor
-
- getJobStat() - Method in class compbio.stat.collector.JobDirectory
-
- 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.AsyncClusterRunner
-
- 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(String) - Static method in class compbio.engine.cluster.drmaa.ClusterRunner
-
This will never return clust.engine.JobStatus.CANCELLED as for sun grid
engine cancelled job is the same as failed.
- getJobStatus() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- 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(String) - Static method in class compbio.engine.cluster.drmaa.JobRunner
-
This will never return clust.engine.JobStatus.CANCELLED as for sun grid
engine cancelled job is the same as failed.
- 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.GLprobsWS
-
- getJobStatus(String) - Method in class compbio.ws.server.MafftWS
-
- getJobStatus(String) - Method in class compbio.ws.server.MSAprobsWS
-
- 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
-
- getJobSubset(boolean) - Method in class compbio.stat.collector.StatProcessor
-
- 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
-
- getLibPath() - Static method in class compbio.runner.conservation.AACon
-
- getLibPath() - Static method in class compbio.runner.disorder.Jronn
-
- 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.GLprobsWS
-
- getLimit(String) - Method in class compbio.ws.server.MafftWS
-
- getLimit(String) - Method in class compbio.ws.server.MSAprobsWS
-
- 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(Class<T>) - Static method in class compbio.engine.client.EngineUtil
-
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 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(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
-
Returns a list of limits supported by web service Each limit correspond
to a particular preset.
- 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.GLprobsWS
-
- getLimits() - Method in class compbio.ws.server.MafftWS
-
- getLimits() - Method in class compbio.ws.server.MSAprobsWS
-
- 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
-
- getLocalJobDir() - Static method in class compbio.stat.servlet.StatisticCollector
-
- getLocalJobDir() - Static method in class compbio.ws.server.MainManager
-
- getLocalJobs() - Method in class compbio.stat.collector.StatProcessor
-
- getLocalJobTimeOut() - Static method in class compbio.stat.servlet.StatisticCollector
-
- 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
-
- getLongestUntestedServiceTime() - Method in class compbio.ws.server.RegistryWS
-
Return time in seconds for the test for the oldest unchecked service
- getLowBorderValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
-
- 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(String) - Method in class compbio.engine.client.CommandBuilder
-
- 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(String) - Method in class compbio.metadata.Preset
-
- getNCore() - Method in class compbio.runner.conservation.AACon
-
- getNCore() - Method in class compbio.runner.disorder.Jronn
-
- getNCore() - Method in class compbio.runner.msa.ClustalO
-
- getNCore() - Method in class compbio.runner.msa.Tcoffee
-
- getNextPosition() - Method in class compbio.metadata.ChunkHolder
-
- GetNonoperatedServices - Class in compbio.data.msa.jaxws
-
- GetNonoperatedServices() - Constructor for class compbio.data.msa.jaxws.GetNonoperatedServices
-
- GetNonoperatedServicesResponse - Class in compbio.data.msa.jaxws
-
- GetNonoperatedServicesResponse() - Constructor for class compbio.data.msa.jaxws.GetNonoperatedServicesResponse
-
- getNonRepeatableNumber() - Static method in class compbio.engine.conf.DirectoryManager
-
- 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
-
- getNumericalFinish() - Method in class compbio.stat.collector.JobStat
-
- getNumericalStart() - Method in class compbio.stat.collector.JobStat
-
- 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.data.msa.jaxws.CustomFold
-
- 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.engine.local.ExecutableWrapper
-
- 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
-
- getParametersList(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
-
Returns a list of options supported by web service
- getParametersList(Metadata<T>, String) - Static method in class compbio.ws.client.MetadataHelper
-
Returns a list of options supported by web service
- getParamName(String) - Static method in class compbio.ws.client.MetadataHelper
-
- getParamValue(String) - Method in class compbio.engine.client.CommandBuilder
-
- getParamValue(String) - Static method in class compbio.ws.client.MetadataHelper
-
- 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.data.msa.jaxws.PresetFold
-
- getPreset() - Method in class compbio.metadata.Limit
-
- getPreset(Metadata<T>, String) - Static method in class compbio.ws.client.MetadataHelper
-
Returns Preset
by its name
- getPresetByName(String) - Method in class compbio.metadata.PresetManager
-
- getPresetList(Metadata<T>) - Static method in class compbio.ws.client.MetadataHelper
-
Returns an objects from which the list of presets supported by web
service can be obtained
- getPresetName() - Method in class compbio.data.msa.jaxws.GetLimit
-
- getPresetName(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Extracts preset name from the command line is any
- 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.RunnerUtil
-
- 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.GLprobsWS
-
- getPresets() - Method in class compbio.ws.server.MafftWS
-
- getPresets() - Method in class compbio.ws.server.MSAprobsWS
-
- 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, long, TimeUnit) - Static method in class compbio.engine.ProgressGetter
-
- 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.
- getRandomValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
-
- 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.cluster.drmaa.ClusterRunner
-
- getRecordedJobStatus(String) - Static method in class compbio.engine.cluster.drmaa.JobRunner
-
- getRecordedJobStatus(String) - Static method in class compbio.engine.local.LocalEngineUtil
-
- getReference() - Method in class compbio.stat.servlet.ServiceTestResult
-
- getReference() - Method in class compbio.ws.client.Services.ServiceInfo
-
- getResourceFromClasspath(String) - Static method in class compbio.engine.conf.PropertyHelperManager
-
- 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.GLprobsWS
-
- getResult(String) - Method in class compbio.ws.server.MafftWS
-
- getResult(String) - Method in class compbio.ws.server.MSAprobsWS
-
- 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.AsyncClusterRunner
-
- 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.GLprobs
-
- getResults(String) - Method in class compbio.runner.msa.Mafft
-
- getResults(String) - Method in class compbio.runner.msa.MSAprobs
-
- 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.structure.RNAalifold
-
- getResultSize() - Method in class compbio.stat.collector.JobDirectory
-
- 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.CustomFoldResponse
-
- getReturn() - Method in class compbio.data.msa.jaxws.FoldResponse
-
- 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.GetNonoperatedServicesResponse
-
- 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.PresetFoldResponse
-
- 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
-
- getRunnerConfiguration(Class<V>, Class<?>, String) - Static method in class compbio.engine.client.ConfExecutable
-
- getRunnerLimits(Class<V>) - Static method in class compbio.engine.client.ConfExecutable
-
This method should be executed once and result of its execution reused.
- getRunnerNameByJobDirectory(File) - Static method in class compbio.ws.client.ServicesUtil
-
- 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.GLprobsWS
-
- getRunnerOptions() - Method in class compbio.ws.server.MafftWS
-
- getRunnerOptions() - Method in class compbio.ws.server.MSAprobsWS
-
- 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
-
- getServerIP() - Static method in class compbio.ws.server.GAUtils
-
- getService() - Method in class compbio.stat.collector.JobDirectory
-
- getService() - Method in class compbio.stat.servlet.ServiceTestResult
-
- getService(String) - Static method in enum compbio.ws.client.Services
-
- getService(URL, String) - 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
-
- getServiceByRunnerName(String) - 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
-
- getServiceGroup() - Method in enum compbio.ws.client.Services
-
- getServiceImpl(Services) - Static method in class compbio.ws.client.ServicesUtil
-
- getServiceInfo() - Method in enum compbio.ws.client.Services
-
- getServiceName(String[]) - Static method in class compbio.ws.client.CmdHelper
-
Extracts service name from the command line
- getServiceNamespace() - Method in enum compbio.ws.client.Services
-
- getServicePath() - Method in class compbio.ws.server.RegistryWS
-
- getServiceReference() - Method in enum compbio.ws.client.Services
-
- getServices() - Method in class compbio.data.msa.Category
-
- getServiceType() - Method in enum compbio.ws.client.Services
-
- getServiceVersion() - Method in enum compbio.ws.client.Services
-
- 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
-
- getSize() - Static method in class compbio.engine.PulledFileCache
-
- 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
-
- getStartTime() - Method in class compbio.stat.collector.JobDirectory
-
- 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() - Method in class compbio.stat.collector.ExecutionStatCollector
-
- 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
-
- getStringProperty(String) - Static method in class compbio.stat.servlet.StatisticCollector
-
- getStructs() - Method in class compbio.data.sequence.RNAStructScoreManager
-
- getSubmissionTime() - Method in class compbio.engine.cluster.drmaa.StatisticManager
-
- getSupportedOptions(Class<? extends Executable<T>>) - Static method in class compbio.runner.RunnerUtil
-
- 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.EngineUtil
-
- 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
-
- getTestDBConnection() - Static method in class compbio.stat.collector.StatDB
-
- 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(File) - Static method in enum compbio.data.sequence.IUPredResult
-
- 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.GLprobs
-
- getType() - Method in class compbio.runner.msa.Mafft
-
- getType() - Method in class compbio.runner.msa.MSAprobs
-
- 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.structure.RNAalifold
-
- getUpperBorderValue(Parameter<?>) - Method in class compbio.runner.OptionCombinator
-
- 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
-
- getValue(String) - Method in class compbio.engine.client.CommandBuilder
-
- getValue() - Method in class compbio.metadata.Parameter
-
- getValue(String) - Method in class compbio.metadata.Preset
-
- getValue(Parameter<?>) - Static method in class compbio.runner.OptionCombinator
-
- getVersion() - Method in class compbio.stat.servlet.ServiceTestResult
-
- getVersion() - Method in class compbio.ws.client.Services.ServiceInfo
-
- 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.AsyncClusterRunner
-
- getWorkDirectory(String) - Method in class compbio.engine.cluster.drmaa.AsyncJobRunner
-
- getWorkDirectory() - Method in class compbio.engine.cluster.drmaa.ClusterRunner
-
- 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
-
- getWriter(File) - Static method in class compbio.ws.client.IOHelper
-
- GLOB_OUTPUT - Static variable in class compbio.runner.disorder.IUPred
-
- 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
-
- GlobProtResult - Enum in compbio.data.sequence
-
- GlobProtResult() - Constructor for enum compbio.data.sequence.GlobProtResult
-
- GLprobs - Class in compbio.runner.msa
-
- GLprobs() - Constructor for class compbio.runner.msa.GLprobs
-
- GLPROBS_INFO - Static variable in enum compbio.ws.client.Services
-
- GLprobsOptions - Static variable in class compbio.ws.server.GLprobsWS
-
- GLprobsWS - Class in compbio.ws.server
-
- GLprobsWS() - Constructor for class compbio.ws.server.GLprobsWS
-
- group - Variable in class compbio.stat.servlet.ServiceTestResult
-