de.jstacs.algorithms.alignment
Class PairwiseStringAlignment

java.lang.Object
  de.jstacs.algorithms.alignment.StringAlignment
      de.jstacs.algorithms.alignment.PairwiseStringAlignment

All Implemented Interfaces:

Comparable<StringAlignment>

public class PairwiseStringAlignment
extends StringAlignment

Class for the representation of an alignment of two Strings. It contains the two Strings that were aligned and expanded by gap-symbols, and the edit-costs according to the employed Costs instance.

Author:

Jan Grau

Constructor Summary

protected

PairwiseStringAlignment(String r1, String r2, double cost, int startPos, int endPos) Creates the instance for the two (extended) Strings and the edit-costs.

Method Summary

int	getEndIndexOfAlignmentForFirst() This method returns the end index of the alignment in the first sequence.
int	getStartIndexOfAlignmentForFirst() This method returns the start index of the alignment in the first sequence.

Methods inherited from class de.jstacs.algorithms.alignment.StringAlignment

compareTo, getAlignedString, getAnnotationResult, getCost, getLength, getNumberOfAlignedSequences, toString, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

PairwiseStringAlignment

protected PairwiseStringAlignment(String r1,
                                  String r2,
                                  double cost,
                                  int startPos,
                                  int endPos)

Creates the instance for the two (extended) Strings and the edit-costs.

Parameters:

r1 - the first String

r2 - the second String

cost - the edit-costs

startPos - the start position of the aligned block in the first String

endPos - the end position of the aligned block in the first String

Method Detail

getStartIndexOfAlignmentForFirst

public int getStartIndexOfAlignmentForFirst()

This method returns the start index of the alignment in the first sequence.

Returns:

the start index of the alignment in the first sequence

getEndIndexOfAlignmentForFirst

public int getEndIndexOfAlignmentForFirst()

This method returns the end index of the alignment in the first sequence.

Returns:

the end index of the alignment in the first sequence