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- -

- -compbio.data.sequence -
-Class Score

-
-java.lang.Object
-  extended by compbio.data.sequence.Score
-
-
-
All Implemented Interfaces:
Comparable<Score>
-
-
-
-
@Immutable
-public class Score
extends Object
implements Comparable<Score>
- - -

-A value class for AACon annotation results storage. The objects of this type - are immutable -

- -

-

-
Author:
-
pvtroshin
-
-
- -

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-Constructor Summary
Score(Enum<?> method, - ArrayList<Float> scores) - -
-          Instantiate the Score
Score(Enum<?> method, - ArrayList<Float> scores, - TreeSet<Range> ranges) - -
-           
Score(Enum<?> method, - float[] scores) - -
-           
Score(Enum<?> method, - TreeSet<Range> ranges) - -
-           
-  - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- intcompareTo(Score o) - -
-           
- booleanequals(Object obj) - -
-           
- StringgetMethod() - -
-          Returns the ConservationMethod
- TreeSet<Range>getRanges() - -
-          Return Ranges if any Collections.EMPTY_SET otherwise
- ArrayList<Float>getScores() - -
-          The column scores for the alignment
- inthashCode() - -
-           
- voidsetRanges(TreeSet<Range> ranges) - -
-           
- StringtoString() - -
-           
-static voidwrite(TreeSet<Score> scores, - Writer writer) - -
-          Outputs the List of Score objects into the Output stream.
-  - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
-  -

- - - - - - - - -
-Constructor Detail
- -

-Score

-
-public Score(Enum<?> method,
-             ArrayList<Float> scores)
-
-
Instantiate the Score -

-

-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             ArrayList<Float> scores,
-             TreeSet<Range> ranges)
-
-
-
Parameters:
method - the ConservationMethod with which scores were - calculated
scores - the actual conservation values for each column of the - alignment
ranges - The set of ranges i.e. parts of the sequence with specific - function, usually can be calculated based on scores
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             TreeSet<Range> ranges)
-
-
-
- -

-Score

-
-public Score(Enum<?> method,
-             float[] scores)
-
-
- - - - - - - - -
-Method Detail
- -

-getMethod

-
-public String getMethod()
-
-
Returns the ConservationMethod -

-

-
-
-
- -
Returns:
the ConservationMethod
-
-
-
- -

-getScores

-
-public ArrayList<Float> getScores()
-
-
The column scores for the alignment -

-

-
-
-
- -
Returns:
the column scores for the alignment
-
-
-
- -

-getRanges

-
-public TreeSet<Range> getRanges()
-
-
Return Ranges if any Collections.EMPTY_SET otherwise -

-

-
-
-
- -
Returns:
ordered set of Range
-
-
-
- -

-setRanges

-
-public void setRanges(TreeSet<Range> ranges)
-
-
-
-
-
-
-
-
-
- -

-toString

-
-public String toString()
-
-
-
Overrides:
toString in class Object
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-
-
-
-
- -

-hashCode

-
-public int hashCode()
-
-
-
Overrides:
hashCode in class Object
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-
-
-
-
-
- -

-equals

-
-public boolean equals(Object obj)
-
-
-
Overrides:
equals in class Object
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-
-
-
-
- -

-write

-
-public static void write(TreeSet<Score> scores,
-                         Writer writer)
-                  throws IOException
-
-
Outputs the List of Score objects into the Output stream. The output - format is as follows: - - 
- #MethodName <space separated list of values>
- 	  
- For example:
- 	 
- #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
- #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
- 
-
- - The maximum precision for values is 3 digits, but can be less. -

-

-
-
-
-
Parameters:
scores - the list of scores to output
writer - -
Throws: -
IOException - if the OutputStream cannot be written into -
NullPointerException - if the output stream is null
-
-
-
- -

-compareTo

-
-public int compareTo(Score o)
-
-
-
Specified by:
compareTo in interface Comparable<Score>
-
-
-
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-
- -
- - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
-		 - -
- PREV CLASS  - NEXT CLASS - FRAMES   - NO FRAMES   -  - - - -
- SUMMARY: NESTED | FIELD | CONSTR | METHOD -DETAIL: FIELD | CONSTR | METHOD
- - - -
- - -