A C D E F G H I J 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

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

Read AACon result with no alignment files.

readClustalFile(InputStream) - Static method in class compbio.data.sequence.ClustalAlignmentUtil

Read Clustal formatted alignment.

readClustalFile(File) - Static method in class compbio.data.sequence.ClustalAlignmentUtil

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

RegistryWS - Interface in compbio.data.msa

JABAWS services registry

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.

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

RunnerConfig<T> - Class in compbio.metadata

The list of Parameters and Options supported by executable.

RunnerConfig() - Constructor for class compbio.metadata.RunnerConfig