jebl.evolution.alignments
Class BasicAlignment

java.lang.Object
  jebl.evolution.alignments.BasicAlignment

All Implemented Interfaces:

Alignment, Patterns, Sequences

public class BasicAlignment
extends Object
implements Alignment

A basic implementation of the Alignment interface.

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

BasicAlignment()
Constructs a basic alignment with no sequences.

BasicAlignment(Collection<? extends Sequence> sequences)
Constructs a basic alignment from a collection of sequences.

BasicAlignment(Sequence[] sequences)
Constructs a basic alignment from an array of sequences.

Method Summary

void	addSequence(Sequence sequence) Adds a sequence to this alignment
int	getPatternCount()
int	getPatternLength()
List<Pattern>	getPatterns() Get a list of all the patterns
Sequence	getSequence(Taxon taxon)
List<Sequence>	getSequenceList()
Set<Sequence>	getSequences()
SequenceType	getSequenceType()
int	getSiteCount()
List<Taxon>	getTaxa()

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicAlignment

public BasicAlignment()

Constructs a basic alignment with no sequences.

BasicAlignment

public BasicAlignment(Collection<? extends Sequence> sequences)

Constructs a basic alignment from a collection of sequences. The sequence objects are not copied.

Parameters:

sequences -

BasicAlignment

public BasicAlignment(Sequence[] sequences)

Constructs a basic alignment from an array of sequences. The sequence objects are not copied.

Parameters:

sequences -

Method Detail

getSequences

public Set<Sequence> getSequences()

Specified by:

getSequences in interface Sequences

Returns:

a set containing all the sequences in this alignment.

getSequenceList

public List<Sequence> getSequenceList()

Specified by:

getSequenceList in interface Alignment

getSequenceType

public SequenceType getSequenceType()

Specified by:

getSequenceType in interface Patterns

Returns:

the data type of the states in these site patterns.

getSequence

public Sequence getSequence(Taxon taxon)

Specified by:

getSequence in interface Sequences

getSiteCount

public int getSiteCount()

Specified by:

getSiteCount 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 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 List<Taxon> getTaxa()

Specified by:

getTaxa in interface Patterns

Returns:

the list of taxa that the state values correspond to.

addSequence

public void addSequence(Sequence sequence)

Adds a sequence to this alignment

Parameters:

sequence - the new sequence.