jebl.evolution.align.scores
public abstract class Scores extends java.lang.Object implements ScoreMatrix
Modifier and Type | Field and Description |
---|---|
float[][] |
score |
Constructor and Description |
---|
Scores() |
Modifier and Type | Method and Description |
---|---|
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() |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
getAlphabet, getName
public final float getScore(char x, char y)
getScore
in interface ScoreMatrix
public java.lang.String toString()
toString
in class java.lang.Object
public static Scores forMatrix(ScoreMatrix scoreMatrix)
scoreMatrix
- A ScoreMatrix with only low ascii characters (< chr(127)) in the alphabetpublic static Scores includeGaps(Scores scores, float gapVersusResidueCost, float gapVersusGapCost)
scores
- gapVersusResidueCost
- should be a negative valuegapVersusGapCost
- should be a positive valuepublic static Scores includeAdditionalCharacters(Scores scores, java.lang.String characters)
scores
- characters
- public java.lang.String getMatrixString()
http://code.google.com/p/jebl2/