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+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+ + + +
+ +

+ +compbio.data.sequence +
+Class Score

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

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

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + +
+Constructor Summary
Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores) + +
+          Instantiate the Score
Score(java.lang.Enum<?> method, + java.util.ArrayList<java.lang.Float> scores, + java.util.TreeSet<Range> ranges) + +
+           
Score(java.lang.Enum<?> method, + float[] scores) + +
+           
Score(java.lang.Enum<?> method, + java.util.TreeSet<Range> ranges) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ intcompareTo(Score o) + +
+           
+ booleanequals(java.lang.Object obj) + +
+           
+ java.lang.StringgetMethod() + +
+          Returns the ConservationMethod
+ java.util.TreeSet<Range>getRanges() + +
+          Return Ranges if any Collections.EMPTY_SET otherwise
+ java.util.ArrayList<java.lang.Float>getScores() + +
+          The column scores for the alignment
+ inthashCode() + +
+           
+ voidsetRanges(java.util.TreeSet<Range> ranges) + +
+           
+ java.lang.StringtoString() + +
+           
+static voidwrite(java.util.TreeSet<Score> scores, + java.io.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(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.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(java.lang.Enum<?> method,
+             java.util.ArrayList<java.lang.Float> scores,
+             java.util.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(java.lang.Enum<?> method,
+             java.util.TreeSet<Range> ranges)
+
+
+
+ +

+Score

+
+public Score(java.lang.Enum<?> method,
+             float[] scores)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getMethod

+
+public java.lang.String getMethod()
+
+
Returns the ConservationMethod +

+

+
+
+
+ +
Returns:
the ConservationMethod
+
+
+
+ +

+getScores

+
+public java.util.ArrayList<java.lang.Float> getScores()
+
+
The column scores for the alignment +

+

+
+
+
+ +
Returns:
the column scores for the alignment
+
+
+
+ +

+getRanges

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

+

+
+
+
+ +
Returns:
ordered set of Range
+
+
+
+ +

+setRanges

+
+public void setRanges(java.util.TreeSet<Range> ranges)
+
+
+
+
+
+
+
+
+
+ +

+toString

+
+public java.lang.String toString()
+
+
+
Overrides:
toString in class java.lang.Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class java.lang.Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(java.lang.Object obj)
+
+
+
Overrides:
equals in class java.lang.Object
+
+
+
+
+
+
+ +

+write

+
+public static void write(java.util.TreeSet<Score> scores,
+                         java.io.Writer writer)
+                  throws java.io.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: +
java.io.IOException - if the OutputStream cannot be written into +
java.lang.NullPointerException - if the output stream is null
+
+
+
+ +

+compareTo

+
+public int compareTo(Score o)
+
+
+
Specified by:
compareTo in interface java.lang.Comparable<Score>
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
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+ + + +
+ + +