de.jstacs.algorithms.alignment

Class StringAlignment

java.lang.Object

de.jstacs.algorithms.alignment.StringAlignment

All Implemented Interfaces:

Storable, Comparable<StringAlignment>

Direct Known Subclasses:

PairwiseStringAlignment

public class StringAlignment
extends Object
implements Comparable<StringAlignment>, Storable

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

Author:

Jan Grau, Jens Keilwagen

Constructor Summary

Constructors

Constructor and Description
StringAlignment(double cost, String... strings) This constructor creates an instance storing the aligned Strings and the costs of the alignment.
StringAlignment(double cost, String[] strings, Result res) This constructor creates an instance storing the aligned Strings and the costs of the alignment.
StringAlignment(StringBuffer xml) Restores StringAlignment object from its XML representation.

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(StringAlignment o)
protected void	fromXML(StringBuffer xml) Parses the XML representation.
String	getAlignedString(int index) Returns the aligned String with index index.
Result	getAnnotationResult() Returns the annotation result.
double	getCost() Returns the costs.
int	getLength() This method return the length of the alignment.
int	getNumberOfAlignedSequences() Returns the number of sequences in this alignment.
String	toString()
String	toString(int chunkSize, int simplifyIdx, List<String> annot) This method returns a String representation of the alignment with a given chunk size.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Constructor Detail

StringAlignment

public StringAlignment(StringBuffer xml)
                throws NonParsableException

Restores StringAlignment object from its XML representation.

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the XML could not be parsed

StringAlignment

public StringAlignment(double cost,
               String... strings)

This constructor creates an instance storing the aligned Strings and the costs of the alignment.

Parameters:

cost - the cost of the alignment

strings - the aligned and expanded Strings

StringAlignment

public StringAlignment(double cost,
               String[] strings,
               Result res)

This constructor creates an instance storing the aligned Strings and the costs of the alignment.

Parameters:

cost - the cost of the alignment

strings - the aligned and expanded Strings

res - a result describing the alignment

Method Detail

getAnnotationResult

public Result getAnnotationResult()

Returns the annotation result.

Returns:

the annotation result

getCost

public double getCost()

Returns the costs.

Returns:

the costs

getNumberOfAlignedSequences

public int getNumberOfAlignedSequences()

Returns the number of sequences in this alignment.

Returns:

the number of sequences in this alignment.

getAlignedString

public String getAlignedString(int index)

Returns the aligned String with index index.

Parameters:

index - the index of the String

Returns:

the aligned String with index index

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(int chunkSize,
              int simplifyIdx,
              List<String> annot)

This method returns a String representation of the alignment with a given chunk size. I.e. all aligned sequence will be split each chunkSize symbols.

Parameters:

chunkSize - the size of the chunks

simplifyIdx - if non-negative the alignment is given relative to the sequence with the corresponding index; i.e. match is represented by "." and mismatch by the corresponding symbol

annot - a list of annotations for the aligned Strings, can be null

Returns:

a String representation of the alignment

getLength

public int getLength()

This method return the length of the alignment.

Returns:

the length of the alignment

compareTo

public int compareTo(StringAlignment o)

Specified by:

compareTo in interface Comparable<StringAlignment>

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Parses the XML representation.

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

Returns:

the XML representation