public class IndelSubstitutionMatrix
extends java.lang.Object
Constructor and Description |
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IndelSubstitutionMatrix(int encodingLength,
java.util.List<java.lang.String> charStreamList) |
Modifier and Type | Method and Description |
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protected void |
computeIndelScores() |
protected void |
computeIndelScores2() |
java.util.Set<java.lang.String> |
get3GramSet() |
java.util.Map<java.lang.String,java.lang.Integer> |
getIndelLeftGivenRightScoreMap() |
java.util.Map<java.lang.String,java.lang.Integer> |
getIndelRightGivenLeftScoreMap() |
java.util.Map<java.lang.String,java.lang.Integer> |
getSubstitutionScoreMap() |
public IndelSubstitutionMatrix(int encodingLength, java.util.List<java.lang.String> charStreamList)
protected void computeIndelScores()
protected void computeIndelScores2()
public java.util.Map<java.lang.String,java.lang.Integer> getSubstitutionScoreMap()
public java.util.Map<java.lang.String,java.lang.Integer> getIndelRightGivenLeftScoreMap()
public java.util.Map<java.lang.String,java.lang.Integer> getIndelLeftGivenRightScoreMap()
public java.util.Set<java.lang.String> get3GramSet()