jebl.evolution.sequences
Class FilteredSequence

java.lang.Object
  jebl.evolution.sequences.FilteredSequence

All Implemented Interfaces:

Comparable, Sequence, Attributable

Direct Known Subclasses:

GaplessSequence, TranslatedSequence

public abstract class FilteredSequence
extends Object
implements Sequence

Author:

rambaut, Alexei Drummond

Nested Class Summary

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

Attributable.Utils

Constructor Summary

FilteredSequence(Sequence source)
Creates a FilteredSequence wrapper to the given source sequence.

Method Summary

int	compareTo(Object o)
protected abstract State[]	filterSequence(Sequence source)
Object	getAttribute(String name)
Map<String,Object>	getAttributeMap() Gets the entire attribute map.
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	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

FilteredSequence

public FilteredSequence(Sequence 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

filterSequence

protected abstract State[] filterSequence(Sequence source)

getTaxon

public Taxon getTaxon()

Specified by:

getTaxon in interface Sequence

Returns:

that taxon that this sequence represents

compareTo

public int compareTo(Object o)

Specified by:

compareTo in interface Comparable

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