jebl.evolution.align.scores
Class Scores

java.lang.Object
  extended by jebl.evolution.align.scores.Scores
All Implemented Interfaces:
ScoreMatrix
Direct Known Subclasses:
AminoAcidScores, NucleotideScores, SubstScoreMatrix

public abstract class Scores
extends java.lang.Object
implements ScoreMatrix

Base class for all score matrices in the package.

Version:
$Id: Scores.java 916 2008-05-26 03:33:27Z matt_kearse $ Based on code originally by Peter Setsoft. See package.html.
Author:
Alexei Drummond

Field Summary
 float[][] score
           
 
Constructor Summary
Scores()
           
 
Method Summary
static Scores duplicate(Scores scores)
           
static Scores forMatrix(ScoreMatrix scoreMatrix)
           
 java.lang.String getMatrixString()
           
 float getScore(char x, char y)
           
static Scores includeAdditionalCharacters(Scores scores, java.lang.String characters)
          includes additional characters in the score matrix which will all have scored zero when compared to other characters.
static Scores includeGaps(Scores scores, float gapVersusResidueCost, float gapVersusGapCost)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface jebl.evolution.align.scores.ScoreMatrix
getAlphabet, getName
 

Field Detail

score

public float[][] score
Constructor Detail

Scores

public Scores()
Method Detail

getScore

public final float getScore(char x,
                            char y)
Specified by:
getScore in interface ScoreMatrix
Returns:
the score for matching char x with char y

toString

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

forMatrix

public static Scores forMatrix(ScoreMatrix scoreMatrix)
Parameters:
scoreMatrix - A ScoreMatrix with only low ascii characters (< chr(127)) in the alphabet
Returns:
A Scores instance corresponding to scoreMatrix.

duplicate

public static Scores duplicate(Scores scores)

includeGaps

public static Scores includeGaps(Scores scores,
                                 float gapVersusResidueCost,
                                 float gapVersusGapCost)
Parameters:
scores -
gapVersusResidueCost - should be a negative value
gapVersusGapCost - should be a positive value

includeAdditionalCharacters

public static Scores includeAdditionalCharacters(Scores scores,
                                                 java.lang.String characters)
includes additional characters in the score matrix which will all have scored zero when compared to other characters. Current system does not handle special characters well, such as ? Or "R" for NucleotideSequences, which represents a "A" or "G". Currently, we just add all characters to the allowed set of characters, and they are scored as zero cost when comparing to other characters, including themselves. One-day, we should probably introduce better scoring system so that "R" is a positive score compared to "A" or "G", but a negative score compared to "C" or "T". example usage: scores = Scores.includeAdditionalCharacters(scores, "?ABCDEFGHIJKLMNOPQRSTUVWXYZ");

Parameters:
scores -
characters -
Returns:
a new score matrix.

getMatrixString

public java.lang.String getMatrixString()
Returns:
this score matrix as a string.


http://code.google.com/p/jebl2/