Package jebl.evolution.align.scores
Class Scores
- java.lang.Object
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- jebl.evolution.align.scores.Scores
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- 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
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Field Summary
Fields Modifier and Type Field Description float[][]
score
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Constructor Summary
Constructors Constructor Description Scores()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface jebl.evolution.align.scores.ScoreMatrix
getAlphabet, getName
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Method Detail
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getScore
public final float getScore(char x, char y)
- Specified by:
getScore
in interfaceScoreMatrix
- Returns:
- the score for matching char x with char y
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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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.
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includeGaps
public static Scores includeGaps(Scores scores, float gapVersusResidueCost, float gapVersusGapCost)
- Parameters:
scores
-gapVersusResidueCost
- should be a negative valuegapVersusGapCost
- should be a positive value
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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.
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getMatrixString
public java.lang.String getMatrixString()
- Returns:
- this score matrix as a string.
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