- Range - Class in compbio.data.sequence
-
- Range() - Constructor for class compbio.data.sequence.Range
-
- Range(int, int) - Constructor for class compbio.data.sequence.Range
-
- Range(String[]) - Constructor for class compbio.data.sequence.Range
-
- ranges - Variable in class compbio.data.sequence.Score
-
- 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
- readIUPred(InputStream, IUPredResult) - Static method in class compbio.data.sequence.SequenceUtil
-
## Long Disorder
# P53_HUMAN
1 M 0.9943
2 E 0.9917
3 E 0.9879
(every line)
- 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
- readRNAStructStream(InputStream) - Static method in class compbio.data.sequence.RNAStructReader
-
- readRNAStructStream(InputStream, InputStream) - Static method in class compbio.data.sequence.RNAStructReader
-
- regex - Variable in enum compbio.data.sequence.RNAStructReader.AlifoldLine
-
- remove() - Method in class compbio.data.sequence.FastaReader
-
Not implemented
- removeArgument(String) - Method in class compbio.metadata.RunnerConfig
-
- 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
-
- RNAOut() - Constructor for enum compbio.data.sequence.RNAStructReader.RNAOut
-
- RNAStructReader - Class in compbio.data.sequence
-
- RNAStructReader() - Constructor for class compbio.data.sequence.RNAStructReader
-
- RNAStructReader.AlifoldLine - Enum in compbio.data.sequence
-
- RNAStructReader.AlifoldResult - Enum in compbio.data.sequence
-
- RNAStructReader.RNAOut - Enum in compbio.data.sequence
-
- RNAStructScoreManager - Class in compbio.data.sequence
-
- RNAStructScoreManager() - Constructor for class compbio.data.sequence.RNAStructScoreManager
-
- RNAStructScoreManager(List<String>, List<TreeSet<Score>>) - Constructor for class compbio.data.sequence.RNAStructScoreManager
-
- runnerClassName - Variable in class compbio.metadata.LimitsManager
-
- runnerClassName - Variable in class compbio.metadata.PresetManager
-
- runnerClassName - Variable in class compbio.metadata.RunnerConfig
-
The class name of a runnable e.g.
- RunnerConfig<T> - Class in compbio.metadata
-
- RunnerConfig() - Constructor for class compbio.metadata.RunnerConfig
-