jebl.evolution.alignments

Class ResampledAlignment

java.lang.Object

jebl.evolution.alignments.ResampledAlignment

All Implemented Interfaces:

Alignment, Patterns, Sequences

Direct Known Subclasses:

BootstrappedAlignment, JackknifedAlignment

public class ResampledAlignment
extends java.lang.Object
implements Alignment

Date: 17/01/2006 Time: 08:08:44

Version:

$Id: ResampledAlignment.java 482 2006-10-25 06:30:57Z twobeers $ Provide a re-sampled alignment. This means an alignment constructed by choosing a set of sites from the source alignment and concataneting them. The set may be of any length and may contain duplications (sampling with replacment). Due to Java restrictions on constructors, class is implemented using delegation.

Author:

Joseph Heled

Constructor Summary

Constructors

Constructor and Description
ResampledAlignment()

Method Summary

Methods

Modifier and Type	Method and Description
int	getPatternCount()
int	getPatternLength()
java.util.List<Pattern>	getPatterns() Get a list of all the patterns
Sequence	getSequence(Taxon taxon)
java.util.List<Sequence>	getSequenceList()
java.util.Set<Sequence>	getSequences()
SequenceType	getSequenceType()
int	getSiteCount()
java.util.List<Taxon>	getTaxa()
void	init(Alignment srcAlignment, int[] siteIndices) Setup resampled alignment.

Methods inherited from class java.lang.Object

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

Constructor Detail

ResampledAlignment

public ResampledAlignment()

Method Detail

init

public void init(Alignment srcAlignment,
        int[] siteIndices)

Setup resampled alignment.

Parameters:

srcAlignment - sample sites from this alignment

siteIndices - Use this set to construct the resampled alignment

getSequenceList

public java.util.List<Sequence> getSequenceList()

Specified by:

getSequenceList in interface Alignment

getPatternCount

public int getPatternCount()

Specified by:

getPatternCount in interface Patterns

getPatternLength

public int getPatternLength()

Specified by:

getPatternLength in interface Patterns

getPatterns

public java.util.List<Pattern> getPatterns()

Description copied from interface: Patterns

Get a list of all the patterns

Specified by:

getPatterns in interface Patterns

Returns:

the list

getTaxa

public java.util.List<Taxon> getTaxa()

Specified by:

getTaxa in interface Patterns

Returns:

the list of taxa that the state values correspond to.

getSequenceType

public SequenceType getSequenceType()

Specified by:

getSequenceType in interface Patterns

Returns:

the data type of the states in these site patterns.

getSiteCount

public int getSiteCount()

Specified by:

getSiteCount in interface Alignment

getSequences

public java.util.Set<Sequence> getSequences()

Specified by:

getSequences in interface Sequences

getSequence

public Sequence getSequence(Taxon taxon)

Specified by:

getSequence in interface Sequences