org.forester.development
Class AminoAcidSequence

java.lang.Object
  extended by org.forester.development.AminoAcidSequence
All Implemented Interfaces:
PhylogenyData

public class AminoAcidSequence
extends Object
implements PhylogenyData


Constructor Summary
AminoAcidSequence(int length)
           
AminoAcidSequence(String name, byte[] sequence)
           
AminoAcidSequence(String name, String sequence)
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 AminoAcidSequence copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 int getLength()
           
 String getName()
           
 char getResidueAt(int position)
           
 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)
           
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 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(String name,
                         byte[] sequence)

AminoAcidSequence

public AminoAcidSequence(String name,
                         String sequence)
Method Detail

asSimpleText

public StringBuffer asSimpleText()
Specified by:
asSimpleText in interface PhylogenyData

asText

public 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 String getName()

getResidueAt

public char getResidueAt(int position)

getSequenceAsString

public 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 StringBuffer toNHX()
Specified by:
toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(Writer writer,
                       int level,
                       String indentation)
                throws IOException
Description copied from interface: PhylogenyData
Writes a phyloXML representation of this phylogeny data.

Specified by:
toPhyloXML in interface PhylogenyData
Throws:
IOException

toString

public String toString()
Overrides:
toString in class Object