public class GenericEditDistance
extends java.lang.Object
Constructor and Description |
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GenericEditDistance(int encodingLength,
java.util.List<java.lang.String> encodedTraceList,
java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap,
java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
int incrementLikeSubstitutionScore,
float scaleFactor) |
Modifier and Type | Method and Description |
---|---|
float |
getPairWiseGlobalAlignScore(java.lang.String sequence1,
java.lang.String sequence2) |
float |
getPairWiseSemiGlobalAlign(java.lang.String sequence1,
java.lang.String sequence2) |
float[][] |
getSimilarityMatrix() |
void |
incrementLikeSubstitutions(int incrementValue) |
protected void |
printMatrix(int[][] matrix) |
void |
setGapPenalty(int gapPenalty) |
void |
setIndelRightGivenLeftScoreScaleFactor(java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
float indelScaleFactor) |
void |
setLengthRatioThreshold(float lengthRatioThreshold) |
public GenericEditDistance(int encodingLength, java.util.List<java.lang.String> encodedTraceList, java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap, java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, int incrementLikeSubstitutionScore, float scaleFactor)
protected void printMatrix(int[][] matrix)
public void setIndelRightGivenLeftScoreScaleFactor(java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, float indelScaleFactor)
public void incrementLikeSubstitutions(int incrementValue)
public float getPairWiseGlobalAlignScore(java.lang.String sequence1, java.lang.String sequence2)
public float getPairWiseSemiGlobalAlign(java.lang.String sequence1, java.lang.String sequence2)
public void setLengthRatioThreshold(float lengthRatioThreshold)
public void setGapPenalty(int gapPenalty)
public float[][] getSimilarityMatrix()