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

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=0000000000000000000000000000000000000000;hb=0bbebf27d045b1345bc042bdf24ef2e6808df251;hp=aecd763d40e88365820697a7efcff9b2a8a4c77e;hpb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;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 deleted file mode 100644 index aecd763..0000000 --- a/website/full_javadoc/compbio/data/sequence/class-use/Score.html +++ /dev/null @@ -1,392 +0,0 @@ - - - - - - -Uses of Class compbio.data.sequence.Score - - - - - - - - - - - - -

- - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

- -

- PREV - NEXT

- FRAMES - NO FRAMES - - - - -

- - - -

- -

-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 - -
-
- -

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 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 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) - -
-
- -

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.
- -

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) - -
-
- -

Methods in compbio.runner that return types with arguments of type Score
-`static Map<String,Score>`	`Util.readJronnFile(String workDirectory, - String clustFile)` - - -