public class SequenceAlignment
extends java.lang.Object
Constructor and Description |
---|
SequenceAlignment(int encodingLength,
java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap,
java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap,
java.util.Map<java.lang.String,java.lang.Integer> indelLeftGivenRightScoreMap) |
Modifier and Type | Method and Description |
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java.lang.String[] |
getPairWiseGlobalAlignment(java.lang.String[] profileAlignment,
java.lang.String sequence) |
java.lang.String[] |
getPairWiseGlobalAlignment(java.lang.String[] profileAlignment1,
java.lang.String[] profileAlignment2) |
java.lang.String[] |
getPairWiseGlobalAlignment(java.lang.String sequence1,
java.lang.String sequence2) |
java.lang.String[] |
getPairWiseSemiGlobalAlignment(java.lang.String sequence1,
java.lang.String sequence2) |
java.lang.String[] |
getProfileProfileGlobalAlign(java.lang.String[] profileAlignment1,
java.lang.String[] profileAlignment2) |
java.lang.String[] |
getProfileSequenceGlobalAlign(java.lang.String[] profileAlignment,
java.lang.String sequence) |
void |
printFScoreMatrix(java.lang.String[] seq1,
java.lang.String[] seq2,
int[][] M) |
void |
printTraceBack(java.lang.String[] seq1,
java.lang.String[] seq2,
TraceBack[][] T) |
public SequenceAlignment(int encodingLength, java.util.Map<java.lang.String,java.lang.Integer> substitutionScoreMap, java.util.Map<java.lang.String,java.lang.Integer> indelRightGivenLeftScoreMap, java.util.Map<java.lang.String,java.lang.Integer> indelLeftGivenRightScoreMap)
public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String sequence1, java.lang.String sequence2)
public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String[] profileAlignment, java.lang.String sequence)
public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String[] profileAlignment1, java.lang.String[] profileAlignment2)
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[] getPairWiseSemiGlobalAlignment(java.lang.String sequence1, java.lang.String sequence2)
public void printFScoreMatrix(java.lang.String[] seq1, java.lang.String[] seq2, int[][] M)
public void printTraceBack(java.lang.String[] seq1, java.lang.String[] seq2, TraceBack[][] T)