-R-Index -

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-R

Range - Class in compbio.data.sequence
Range(int, int) - -Constructor for class compbio.data.sequence.Range -: -
Range(String[]) - -Constructor for class compbio.data.sequence.Range -: -
rconfigFile - -Static variable in class compbio.engine.client.RunConfiguration -: -
read(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -: -
read(InputStream, Class<V>, Class<?>...) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -: -
readAAConResults(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -: Read AACon result with no alignment files. -
readAndValidate(InputStream, Class<V>) - -Method in class compbio.engine.conf.RunnerConfigMarshaller -: -
readClustalFile(InputStream) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -: Read Clustal formatted alignment. -
readClustalFile(File) - -Static method in class compbio.data.sequence.ClustalAlignmentUtil -: -
readClustalFile(String, String) - -Static method in class compbio.runner.Util -: -
readData(Timestamp, Timestamp, Services, Boolean) - -Method in class compbio.stat.collector.StatDB -: -
readDisembl(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -: > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
readFasta(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -: Reads fasta sequences from inStream into the list of FastaSequence - objects -
readGlobPlot(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -: > Foobar_dundeefriends - - # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343 - - # REM465 355-368 - - # HOTLOOPS 190-204 - - # RESIDUE COILS REM465 HOTLOOPS - - M 0.86010 0.88512 0.37094 - - T 0.79983 0.85864 0.44331 - - >Next Sequence name -
readIUPred(File) - -Static method in class compbio.data.sequence.SequenceUtil -: Read IUPred output -
readJRonn(File) - -Static method in class compbio.data.sequence.SequenceUtil -: -
readJRonn(InputStream) - -Static method in class compbio.data.sequence.SequenceUtil -: Reader for JRonn horizontal file format -
readJronnFile(String, String) - -Static method in class compbio.runner.Util -: -
RegistryWS - Interface in compbio.data.msa: JABAWS services registry
RegistryWS - Class in compbio.ws.server: JABAWS services registry
RegistryWS() - -Constructor for class compbio.ws.server.RegistryWS -: -
REM_EXPECTATION_THRESHOLD - -Variable in class compbio.runner.disorder.Disembl -: -
remove() - -Method in class compbio.data.sequence.FastaReader -: Not implemented -
removeArgument(String) - -Method in class compbio.metadata.RunnerConfig -: Removes the argument Argument if found. -
removeArgumentByOptionName(String) - -Method in class compbio.metadata.RunnerConfig -: Removes the argument which can be a Parameter or an Option instance by - the value in element of the runner configuration - descriptor. -
removeJob(String) - -Method in class compbio.engine.cluster.drmaa.ClusterSession -: -
removeOutput(String) - -Method in class compbio.runner._impl.BlastAll -: -
removeOutput(String) - -Method in class compbio.runner._impl.PSIBlast -: -
removeParam(String) - -Method in class compbio.engine.client.CommandBuilder -: -
removeRecordedJobs(Set<JobStat>) - -Method in class compbio.stat.collector.StatDB -: Removes the job if - - 1) It has already been recorded - - 2) It has not completed and did not timeout - this is to prevent - recording the information on the incomplete jobs. -
removeTask(ConfiguredExecutable<?>) - -Static method in class compbio.engine.SubmissionManager -: -
removeTask(String) - -Static method in class compbio.engine.SubmissionManager -: -
reportStat() - -Method in class compbio.stat.collector.StatProcessor -: -
ResultNotAvailableException - Exception in compbio.metadata: ResultNotAvailableException is thrown wherever the results of the calculation - cannot be obtained.
ResultNotAvailableException(String) - -Constructor for exception compbio.metadata.ResultNotAvailableException -: -
ResultNotAvailableException(Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -: -
ResultNotAvailableException(String, Throwable) - -Constructor for exception compbio.metadata.ResultNotAvailableException -: -
ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws: This class was generated by the JAX-WS RI.
ResultNotAvailableExceptionBean() - -Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean -: -
Ronn - Class in compbio.runner._impl
Ronn(String) - -Constructor for class compbio.runner._impl.Ronn -: -
RPSBlast - Class in compbio.runner._impl
RPSBlast(String) - -Constructor for class compbio.runner._impl.RPSBlast -: -
run() - -Method in class compbio.engine.local.StreamGobbler -: -
run() - -Method in class compbio.stat.collector.ExecutionStatCollector -: -
RunConfiguration - Class in compbio.engine.client: Value class for persisting ConfExecutable instances
RunConfiguration() - -Constructor for class compbio.engine.client.RunConfiguration -: -
RunConfiguration(ConfExecutable<?>) - -Constructor for class compbio.engine.client.RunConfiguration -: -
RunnerConfig<T> - Class in compbio.metadata: The list of Parameters and Options supported by executable.
RunnerConfig() - -Constructor for class compbio.metadata.RunnerConfig -: -
RunnerConfigMarshaller<T> - Class in compbio.engine.conf
RunnerConfigMarshaller(Class<?>) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -: -
RunnerConfigMarshaller(Class<?>, Class<?>...) - -Constructor for class compbio.engine.conf.RunnerConfigMarshaller -: -
Runners - Class in compbio.runner._impl
runPsiBlast() - -Method in class compbio.pipeline._jpred.Jpred4 -: -