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

R

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

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

readFasta(InputStream) - Static method in class compbio.data.sequence.SequenceUtil

Reads fasta sequences from inStream into the list of FastaSequence objects

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

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

removeTask(ConfiguredExecutable<?>) - Static method in class compbio.engine.SubmissionManager

removeTask(String) - Static method in class compbio.engine.SubmissionManager

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

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