public class IndelSubstitutionScore
extends java.lang.Object
Constructor and Description |
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IndelSubstitutionScore() |
Modifier and Type | Method and Description |
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void |
decrementIndelScore(int decrementIndelScoreValue) |
void |
deriveScores(int encodingLength,
java.util.Map<java.lang.String,java.lang.String> charActivityMap,
java.util.List<java.lang.String> encodedTraceList) |
void |
generateLikePreferenceScores(int encodingLength,
java.util.Map<java.lang.String,java.lang.String> charActivityMap,
java.util.List<java.lang.String> encodedTraceList) |
void |
generateUnitScores(java.util.Map<java.lang.String,java.lang.String> charActivityMap) |
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() |
void |
incrementLikeSubstitutionScore(int incrementLikeSubstitutionScoreValue) |
void |
loadIndelLeftGivenRightScores(java.lang.String indelLeftGivenRightScoreAbsolutePathName,
java.util.Map<java.lang.String,java.lang.String> activityCharMap) |
void |
loadIndelRightGivenLeftScores(java.lang.String indelRightGivenLeftScoreAbsolutePathName,
java.util.Map<java.lang.String,java.lang.String> activityCharMap) |
void |
loadSubstitutionScores(java.lang.String substitutionScoreAbsolutePathName,
java.util.Map<java.lang.String,java.lang.String> activityCharMap) |
void |
scaleIndelScore(float indelScoreScaleValue) |
public void generateLikePreferenceScores(int encodingLength, java.util.Map<java.lang.String,java.lang.String> charActivityMap, java.util.List<java.lang.String> encodedTraceList)
public void generateUnitScores(java.util.Map<java.lang.String,java.lang.String> charActivityMap)
public void deriveScores(int encodingLength, java.util.Map<java.lang.String,java.lang.String> charActivityMap, java.util.List<java.lang.String> encodedTraceList)
public void loadIndelRightGivenLeftScores(java.lang.String indelRightGivenLeftScoreAbsolutePathName, java.util.Map<java.lang.String,java.lang.String> activityCharMap) throws ActivityNotFoundException
ActivityNotFoundException
public void loadIndelLeftGivenRightScores(java.lang.String indelLeftGivenRightScoreAbsolutePathName, java.util.Map<java.lang.String,java.lang.String> activityCharMap) throws ActivityNotFoundException
ActivityNotFoundException
public void loadSubstitutionScores(java.lang.String substitutionScoreAbsolutePathName, java.util.Map<java.lang.String,java.lang.String> activityCharMap) throws ActivityNotFoundException
ActivityNotFoundException
public void incrementLikeSubstitutionScore(int incrementLikeSubstitutionScoreValue)
public void decrementIndelScore(int decrementIndelScoreValue)
public void scaleIndelScore(float indelScoreScaleValue)
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()