Uses of Class
compbio.data.sequence.Score

Packages that use Score

compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.
compbio.runner	Utilities commonly used by all runners.

Uses of Score in compbio.data.sequence

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

TreeSet<Score>

ScoreManager.ScoreHolder.scores

Methods in compbio.data.sequence that return Score

Score	ScoreManager.ScoreHolder.getScoreByMethod(Enum<?> method)
Score	ScoreManager.ScoreHolder.getScoreByMethod(String method)

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

Map<String,TreeSet<Score>>	ScoreManager.asMap()
Set<Score>	ScoreManager.asSet()
static HashSet<Score>	SequenceUtil.readAAConResults(InputStream results) Read AACon result with no alignment files.
static HashMap<String,Set<Score>>	SequenceUtil.readDisembl(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 HashMap<String,Set<Score>>	SequenceUtil.readGlobPlot(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 Map<String,Score>	SequenceUtil.readIUPred(File result) Read IUPred output
static Map<String,Score>	SequenceUtil.readJRonn(File result)
static Map<String,Score>	SequenceUtil.readJRonn(InputStream inStream) Reader for JRonn horizontal file format

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

int	Score.compareTo(Score o)

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

static ScoreManager	ScoreManager.newInstance(Map<String,Set<Score>> data)
static ScoreManager	ScoreManager.newInstanceSingleScore(Map<String,Score> seqScoresMap)
static ScoreManager	ScoreManager.newInstanceSingleSequence(Set<Score> data)
static void	Score.write(TreeSet<Score> scores, Writer writer) Outputs the List of Score objects into the Output stream.

Uses of Score in compbio.runner

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

static Map<String,Score>

Util.readJronnFile(String workDirectory, String clustFile)