org.forester.development

Class AminoAcidSequence

java.lang.Object

org.forester.development.AminoAcidSequence

All Implemented Interfaces:

PhylogenyData

public class AminoAcidSequence
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
AminoAcidSequence(int length)
AminoAcidSequence(java.lang.String name, byte[] sequence)
AminoAcidSequence(java.lang.String name, java.lang.String sequence)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
AminoAcidSequence	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
int	getLength()
java.lang.String	getName()
char	getResidueAt(int position)
java.lang.String	getSequenceAsString()
byte	getStateAt(int position)
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setResidueAt(int position, char residue)
void	setStateAt(int position, byte state)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

AminoAcidSequence

public AminoAcidSequence(int length)

AminoAcidSequence

public AminoAcidSequence(java.lang.String name,
                 byte[] sequence)

AminoAcidSequence

public AminoAcidSequence(java.lang.String name,
                 java.lang.String sequence)

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public AminoAcidSequence copy()

Description copied from interface: PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getLength

public int getLength()

getName

public java.lang.String getName()

getResidueAt

public char getResidueAt(int position)

getSequenceAsString

public java.lang.String getSequenceAsString()

getStateAt

public byte getStateAt(int position)

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

setResidueAt

public void setResidueAt(int position,
                char residue)

setStateAt

public void setStateAt(int position,
              byte state)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object