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

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