public class SequenceAlignment
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
SequenceAlignment.TraceBack |
Constructor and Description |
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SequenceAlignment(int encodingLength,
java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap,
java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
float scaleFactor) |
Modifier and Type | Method and Description |
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java.lang.String[] |
getPairWiseGlobalAlign(java.lang.String sequence1,
java.lang.String sequence2) |
java.lang.String[] |
getPairWiseSemiGlobalAlign(java.lang.String sequence1,
java.lang.String sequence2) |
java.lang.String[] |
getProfileProfileGlobalAlign(java.lang.String[] profileAlignment1,
java.lang.String[] profileAlignment2) |
java.lang.String[] |
getProfileProfileSemiGlobalAlign(java.lang.String[] profileAlignment1,
java.lang.String[] profileAlignment2) |
java.lang.String[] |
getProfileSequenceGlobalAlign(java.lang.String[] profileAlignment,
java.lang.String sequence) |
void |
incrementLikeSubstitutions(int incrementValue) |
void |
setGapPenalty(int gapPenalty) |
void |
setIndelRightGivenLeftScoreScaleFactor(java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
float indelScaleFactor) |
void |
setLengthRatioThreshold(float lengthRatioThreshold) |
public SequenceAlignment(int encodingLength, java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap, java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, float scaleFactor)
public void setIndelRightGivenLeftScoreScaleFactor(java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, float indelScaleFactor)
public void incrementLikeSubstitutions(int incrementValue)
public java.lang.String[] getPairWiseGlobalAlign(java.lang.String sequence1, java.lang.String sequence2)
public java.lang.String[] getPairWiseSemiGlobalAlign(java.lang.String sequence1, java.lang.String sequence2)
public java.lang.String[] getProfileSequenceGlobalAlign(java.lang.String[] profileAlignment, java.lang.String sequence)
public java.lang.String[] getProfileProfileGlobalAlign(java.lang.String[] profileAlignment1, java.lang.String[] profileAlignment2)
public java.lang.String[] getProfileProfileSemiGlobalAlign(java.lang.String[] profileAlignment1, java.lang.String[] profileAlignment2)
public void setLengthRatioThreshold(float lengthRatioThreshold)
public void setGapPenalty(int gapPenalty)