jebl.evolution.sequences
Class BasicSequence

java.lang.Object
  jebl.evolution.sequences.BasicSequence

All Implemented Interfaces:

Comparable, Sequence, Attributable

public class BasicSequence
extends Object
implements Sequence

A default implementation of the Sequence interface.

Author:

Andrew Rambaut, Alexei Drummond

Nested Class Summary

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

Attributable.Utils

Constructor Summary

BasicSequence(SequenceType sequenceType, Taxon taxon, CharSequence sequenceString)
Creates a sequence with a name corresponding to the taxon name.

BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)
Creates a sequence with a name corresponding to the taxon name

Method Summary

int	compareTo(Object o) Sequences are compared by their taxa
Object	getAttribute(String name)
Map<String,Object>	getAttributeMap() Gets the entire attribute map.
Set<String>	getAttributeNames()
String	getCleanString()
int	getLength() Returns the length of the sequence
SequenceType	getSequenceType()
State	getState(int site)
byte[]	getStateIndices()
State[]	getStates()
String	getString()
Taxon	getTaxon()
void	removeAttribute(String name)
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

Constructor Detail

BasicSequence

public BasicSequence(SequenceType sequenceType,
                     Taxon taxon,
                     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 -

BasicSequence

public BasicSequence(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 String getString()

Specified by:

getString in interface Sequence

Returns:

a string representing the sequence of symbols.

getCleanString

public 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(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.

removeAttribute

public void removeAttribute(String name)

Specified by:

removeAttribute in interface Attributable

Parameters:

name - name of attribute to remove

getAttributeNames

public Set<String> getAttributeNames()

Specified by:

getAttributeNames in interface Attributable

Returns:

an array of the attributeNames that this object has.

getAttributeMap

public Map<String,Object> getAttributeMap()

Description copied from interface: Attributable

Gets the entire attribute map.

Specified by:

getAttributeMap in interface Attributable

Returns:

an unmodifiable map