X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FScore.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fclass-use%2FScore.html;h=f502e84b41540f32ba28255e52be29692243442c;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Score.html b/website/full_javadoc/compbio/data/sequence/class-use/Score.html new file mode 100644 index 0000000..f502e84 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/Score.html @@ -0,0 +1,392 @@ + + + +
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+Packages that use Score | +|
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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 | +
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+ +
Fields in compbio.data.sequence with type parameters of type Score | +|
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+ TreeSet<Score> |
+ScoreManager.ScoreHolder.scores
+
++ |
+
+ +
Methods in compbio.data.sequence that return Score | +|
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+ 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 | +|
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+ 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 | +|
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+ int |
+Score.compareTo(Score o)
+
++ |
+
+ +
Method parameters in compbio.data.sequence with type arguments of type Score | +|
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+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 | +
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+ +
Methods in compbio.runner that return types with arguments of type Score | +|
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+static Map<String,Score> |
+Util.readJronnFile(String workDirectory,
+ String clustFile)
+
++ |
+
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