Uses of Class
compbio.data.sequence.Score

Packages that use Score

Package	Description
compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.

Uses of Score in compbio.data.sequence

Fields in compbio.data.sequence with type parameters of type Score

Modifier and Type	Field and Description
java.util.TreeSet<Score>	ScoreManager.ScoreHolder.scores

Methods in compbio.data.sequence that return Score

Modifier and Type	Method and Description
Score	ScoreManager.ScoreHolder.getScoreByMethod(java.lang.Enum<?> method)
Score	ScoreManager.ScoreHolder.getScoreByMethod(java.lang.String method)

Methods in compbio.data.sequence that return types with arguments of type Score

Modifier and Type	Method and Description
java.util.Map<java.lang.String,java.util.TreeSet<Score>>	ScoreManager.asMap()
java.util.Set<Score>	ScoreManager.asSet()
java.util.List<java.util.TreeSet<Score>>	RNAStructScoreManager.getData()
static java.util.TreeSet<Score>	RNAStructReader.newEmptyScore(java.lang.Enum<?> res)
private static java.util.TreeSet<Score>	RNAStructReader.newSetScore(java.lang.Enum<?> res, java.util.List<java.lang.Float> scores)
static java.util.HashSet<Score>	SequenceUtil.readAAConResults(java.io.InputStream results) Read AACon result with no alignment files.
static java.util.HashMap<java.lang.String,java.util.Set<Score>>	SequenceUtil.readDisembl(java.io.InputStream input) > 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
static java.util.HashMap<java.lang.String,java.util.Set<Score>>	SequenceUtil.readGlobPlot(java.io.InputStream input) > 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
static java.util.Map<java.lang.String,Score>	SequenceUtil.readIUPred(java.io.File result) Read IUPred output
private static java.util.Map<java.lang.String,Score>	SequenceUtil.readIUPred(java.io.InputStream input, IUPredResult type) ## Long Disorder # P53_HUMAN 1 M 0.9943 2 E 0.9917 3 E 0.9879 (every line)
static java.util.Map<java.lang.String,Score>	SequenceUtil.readJRonn(java.io.File result)
static java.util.Map<java.lang.String,Score>	SequenceUtil.readJRonn(java.io.InputStream inStream) Reader for JRonn horizontal file format

Methods in compbio.data.sequence with parameters of type Score

Modifier and Type	Method and Description
int	Score.compareTo(Score o)

Method parameters in compbio.data.sequence with type arguments of type Score

Modifier and Type	Method and Description
static RNAStructScoreManager	RNAStructScoreManager.newInstance(java.util.List<java.lang.String> structs, java.util.List<java.util.TreeSet<Score>> data)
static ScoreManager	ScoreManager.newInstance(java.util.Map<java.lang.String,java.util.Set<Score>> data)
static ScoreManager	ScoreManager.newInstanceSingleScore(java.util.Map<java.lang.String,Score> seqScoresMap)
static ScoreManager	ScoreManager.newInstanceSingleSequence(java.util.Set<Score> data)
static void	Score.write(java.util.TreeSet<Score> scores, java.io.Writer writer) Outputs the List of Score objects into the Output stream.

Constructor parameters in compbio.data.sequence with type arguments of type Score

Constructor and Description
RNAStructScoreManager(java.util.List<java.lang.String> structs, java.util.List<java.util.TreeSet<Score>> data)
ScoreHolder(java.lang.String id, java.util.Set<Score> scores)
ScoreManager(java.util.Map<java.lang.String,java.util.Set<Score>> data)
ScoreManager(java.lang.String id, java.util.Set<Score> data)