+Uses of Class compbio.data.sequence.Score +

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+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.

+ +

+ + + + + +
+Uses of Score in compbio.data.sequence
+ +

+ + + + + + + + + +
Fields in compbio.data.sequence with type parameters of type Score
+ java.util.TreeSet<Score> ScoreManager.ScoreHolder.scores + +
+
+ +

Fields in compbio.data.sequence with type parameters of type Score
+ `java.util.TreeSet<Score>`	`ScoreManager.ScoreHolder.scores` + + +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Score
+ Score ScoreManager.ScoreHolder.getScoreByMethod(java.lang.Enum<?> method) + +
+
+ Score ScoreManager.ScoreHolder.getScoreByMethod(java.lang.String method) + +
+
+ +

Methods in compbio.data.sequence that return Score
+ `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
+ java.util.Map<java.lang.String,java.util.TreeSet<Score>> ScoreManager.asMap() + +
+
+ java.util.Set<Score> ScoreManager.asSet() + +
+
+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
+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 that return types with arguments of type Score
+ `java.util.Map<java.lang.String,java.util.TreeSet<Score>>`	`ScoreManager.asMap()` + + +
+ `java.util.Set<Score>`	`ScoreManager.asSet()` + + +
+`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
+`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
+ int Score.compareTo(Score o) + +
+
+ +

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(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.
+ +

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