de.jstacs.algorithms.alignment

Class PairwiseStringAlignment

java.lang.Object

de.jstacs.algorithms.alignment.StringAlignment

de.jstacs.algorithms.alignment.PairwiseStringAlignment

All Implemented Interfaces:

Storable, 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

Constructors

Modifier	Constructor and Description
	PairwiseStringAlignment(StringBuffer xml) The standard constructor for the interface Storable.
protected	PairwiseStringAlignment(String r1, String r2, double cost, int startPos, int endPos, int numMatches) Creates the instance for the two (extended) Strings and the edit-costs.

Method Summary

Methods

Modifier and Type	Method and Description
protected void	fromXML(StringBuffer xml) Parses the XML representation.
int	getEndIndexOfAlignmentForFirst() This method returns the end index of the alignment in the first sequence.
int	getNumberOfMatches() Returns the number of matches in this alignment.
int	getStartIndexOfAlignmentForFirst() This method returns the start index of the alignment in the first sequence.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

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,
                       int numMatches)

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

numMatches - the number of matches in the alignment

PairwiseStringAlignment

public PairwiseStringAlignment(StringBuffer xml)
                        throws NonParsableException

The standard constructor for the interface Storable. Creates a new PairwiseStringAlignment out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the PairwiseStringAlignment could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable

Method Detail

getNumberOfMatches

public int getNumberOfMatches()

Returns the number of matches in this alignment.

Returns:

the number of matches

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

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Description copied from class: StringAlignment

Parses the XML representation.

Overrides:

fromXML in class StringAlignment

Parameters:

xml - the XML representation

Throws:

NonParsableException - if XML could not be parsed

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class StringAlignment

Returns:

the XML representation