org.processmining.plugins.tracealignmentwithguidetree.msa

Class SequenceAlignmentLeftIndel

java.lang.Object

org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel

public class SequenceAlignmentLeftIndel
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
SequenceAlignmentLeftIndel(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)

Method Summary

Modifier and Type	Method and Description
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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceAlignmentLeftIndel

public SequenceAlignmentLeftIndel(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)

Method Detail

getPairWiseGlobalAlignment

public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String sequence1,
                                                     java.lang.String sequence2)

getPairWiseGlobalAlignment

public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String[] profileAlignment,
                                                     java.lang.String sequence)

getPairWiseGlobalAlignment

public java.lang.String[] getPairWiseGlobalAlignment(java.lang.String[] profileAlignment1,
                                                     java.lang.String[] profileAlignment2)

getProfileSequenceGlobalAlign

public java.lang.String[] getProfileSequenceGlobalAlign(java.lang.String[] profileAlignment,
                                                        java.lang.String sequence)

getProfileProfileGlobalAlign

public java.lang.String[] getProfileProfileGlobalAlign(java.lang.String[] profileAlignment1,
                                                       java.lang.String[] profileAlignment2)

getPairWiseSemiGlobalAlignment

public java.lang.String[] getPairWiseSemiGlobalAlignment(java.lang.String sequence1,
                                                         java.lang.String sequence2)

printFScoreMatrix

public void printFScoreMatrix(java.lang.String[] seq1,
                              java.lang.String[] seq2,
                              int[][] M)

printTraceBack

public void printTraceBack(java.lang.String[] seq1,
                           java.lang.String[] seq2,
                           TraceBack[][] T)