jebl.evolution.alignments
Class ConsensusSequence

java.lang.Object
  jebl.evolution.alignments.ConsensusSequence

All Implemented Interfaces:

Comparable, Sequence, Attributable

public abstract class ConsensusSequence
extends Object
implements Sequence

Author:

rambaut, Alexei Drummond

Nested Class Summary

Nested classes/interfaces inherited from interface jebl.util.Attributable

Attributable.Utils

Constructor Summary

ConsensusSequence(Taxon taxon, Alignment source)
Creates a FilteredSequence wrapper to the given source sequence.

Method Summary

int	compareTo(Object o) Sequences are compared by their taxa
static State[]	constructConsensus(Alignment source)
Object	getAttribute(String name)
Set<String>	getAttributeNames()
int	getLength() Returns the length of the sequence
SequenceType	getSequenceType()
State	getState(int site)
byte[]	getStateIndices()
State[]	getStates()
String	getString()
Taxon	getTaxon()
void	setAttribute(String name, Object value) Sets an named attribute for this object.

Methods inherited from class java.lang.Object

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

Methods inherited from interface jebl.util.Attributable

getAttributeMap, removeAttribute

Constructor Detail

ConsensusSequence

public ConsensusSequence(Taxon taxon,
                         Alignment source)

Creates a FilteredSequence wrapper to the given source sequence.

Parameters:

source -

Method Detail

getSequenceType

public SequenceType getSequenceType()

Specified by:

getSequenceType in interface Sequence

Returns:

the type of symbols that this sequence is made up of.

getString

public String getString()

Specified by:

getString in interface Sequence

Returns:

a string representing the sequence of symbols.

getStates

public State[] getStates()

Specified by:

getStates in interface Sequence

Returns:

an array of state objects.

getStateIndices

public byte[] getStateIndices()

Specified by:

getStateIndices in interface Sequence

Returns:

an array of state indices.

getState

public State getState(int site)

Specified by:

getState in interface Sequence

Returns:

the state at site.

getLength

public int getLength()

Returns the length of the sequence

Specified by:

getLength in interface Sequence

Returns:

the length

constructConsensus

public static State[] constructConsensus(Alignment source)

getTaxon

public Taxon getTaxon()

Specified by:

getTaxon in interface Sequence

Returns:

that taxon that this sequence represents (primarily used to match sequences with tree nodes)

compareTo

public int compareTo(Object o)

Sequences are compared by their taxa

Specified by:

compareTo in interface Comparable

Parameters:

o - another sequence

Returns:

an integer

setAttribute

public void setAttribute(String name,
                         Object value)

Description copied from interface: Attributable

Sets an named attribute for this object.

Specified by:

setAttribute in interface Attributable

Parameters:

name - the name of the attribute.

value - the new value of the attribute.

getAttribute

public Object getAttribute(String name)

Specified by:

getAttribute in interface Attributable

Parameters:

name - the name of the attribute of interest.

Returns:

an object representing the named attributed for this object.

getAttributeNames

public Set<String> getAttributeNames()

Specified by:

getAttributeNames in interface Attributable

Returns:

an array of the attributeNames that this object has.