jebl.evolution.sequences

Class CanonicalSequence

java.lang.Object

jebl.evolution.sequences.CanonicalSequence

All Implemented Interfaces:

java.lang.Comparable, Sequence, Attributable

public class CanonicalSequence
extends java.lang.Object
implements Sequence

A default implementation of the Sequence interface that converts sequence characters to States such that calling getString() will always return uppercase residues with nucleotide U residues converted to T

Version:

$Id: BasicSequence.java 641 2007-02-16 11:56:21Z rambaut $

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

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

Attributable.Utils

Constructor Summary

Constructors

Constructor and Description
CanonicalSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString) Creates a sequence with a name corresponding to the taxon name.
CanonicalSequence(SequenceType sequenceType, Taxon taxon, State[] states) Creates a sequence with a name corresponding to the taxon name

Method Summary

Methods

Modifier and Type	Method and Description
int	compareTo(java.lang.Object o) Sequences are compared by their taxa
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()
java.lang.String	getCleanString()
int	getLength() Returns the length of the sequence
SequenceType	getSequenceType()
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.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

CanonicalSequence

public CanonicalSequence(SequenceType sequenceType,
                 Taxon taxon,
                 java.lang.CharSequence sequenceString)

Creates a sequence with a name corresponding to the taxon name. Use CharSequence so both a String and a StringBuilder are fine

Parameters:

taxon -

sequenceString -

CanonicalSequence

public CanonicalSequence(SequenceType sequenceType,
                 Taxon taxon,
                 State[] states)

Creates a sequence with a name corresponding to the taxon name

Parameters:

taxon -

sequenceType -

states -

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 java.lang.String getString()

Specified by:

getString in interface Sequence

Returns:

a string representing the sequence of symbols.

getCleanString

public java.lang.String getCleanString()

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

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

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