org.forester.development
Class AminoAcidSequence
java.lang.Object
org.forester.development.AminoAcidSequence
- All Implemented Interfaces:
- PhylogenyData
public class AminoAcidSequence
- extends Object
- implements PhylogenyData
AminoAcidSequence
public AminoAcidSequence(int length)
AminoAcidSequence
public AminoAcidSequence(String name,
byte[] sequence)
AminoAcidSequence
public AminoAcidSequence(String name,
String sequence)
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