jebl.evolution.alignments

Class ConsensusSequence

java.lang.Object

jebl.evolution.alignments.ConsensusSequence

All Implemented Interfaces:

java.lang.Comparable, Sequence, Attributable

public class ConsensusSequence
extends java.lang.Object
implements Sequence

Version:

$Id: ConsensusSequence.java 365 2006-06-28 07:34:56Z pepster $

Author:

rambaut, Alexei Drummond

Nested Class Summary

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

Attributable.Utils

Constructor Summary

Constructors

Constructor and Description
ConsensusSequence(Taxon taxon, Alignment source) Creates a FilteredSequence wrapper to the given source sequence.
ConsensusSequence(Taxon taxon, Alignment source, boolean includeAmbiguities) Creates a FilteredSequence wrapper to the given source sequence.

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(java.lang.Object o) Sequences are compared by their taxa
static State[]	constructConsensus(Alignment source, boolean includeAmbiguities)
java.lang.Object	getAttribute(java.lang.String name)
java.util.Map<java.lang.String,java.lang.Object>	getAttributeMap() Gets the entire attribute map.
java.util.Set<java.lang.String>	getAttributeNames()
int	getLength() Returns the length of the sequence
SequenceType	getSequenceType()
Alignment	getSource()
State	getState(int site)
byte[]	getStateIndices()
State[]	getStates()
java.lang.String	getString()
Taxon	getTaxon()
void	removeAttribute(java.lang.String name)
void	setAttribute(java.lang.String name, java.lang.Object value) Sets an named attribute for this object.

Methods inherited from class java.lang.Object

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

Constructor Detail

ConsensusSequence

public ConsensusSequence(Taxon taxon,
                 Alignment source)

Creates a FilteredSequence wrapper to the given source sequence.

Parameters:

source -

ConsensusSequence

public ConsensusSequence(Taxon taxon,
                 Alignment source,
                 boolean includeAmbiguities)

Creates a FilteredSequence wrapper to the given source sequence.

Parameters:

source -

Method Detail

getSource

public Alignment getSource()

getSequenceType

public SequenceType getSequenceType()

Specified by:

getSequenceType in interface Sequence

Returns:

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

getString

public java.lang.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,
                         boolean includeAmbiguities)

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(java.lang.Object o)

Sequences are compared by their taxa

Specified by:

compareTo in interface java.lang.Comparable

Parameters:

o - another sequence

Returns:

an integer

setAttribute

public void setAttribute(java.lang.String name,
                java.lang.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 java.lang.Object getAttribute(java.lang.String name)

Specified by:

getAttribute in interface Attributable

Parameters:

name - the name of the attribute of interest, or null if the attribute doesn't exist.

Returns:

an object representing the named attributed for this object.

removeAttribute

public void removeAttribute(java.lang.String name)

Specified by:

removeAttribute in interface Attributable

Parameters:

name - name of attribute to remove

getAttributeNames

public java.util.Set<java.lang.String> getAttributeNames()

Specified by:

getAttributeNames in interface Attributable

Returns:

an array of the attributeNames that this object has.

getAttributeMap

public java.util.Map<java.lang.String,java.lang.Object> getAttributeMap()

Description copied from interface: Attributable

Gets the entire attribute map.

Specified by:

getAttributeMap in interface Attributable

Returns:

an unmodifiable map