public class AminoAcidSequence extends java.lang.Object implements PhylogenyData
Constructor and Description |
---|
AminoAcidSequence(int length) |
AminoAcidSequence(java.lang.String name,
byte[] sequence) |
AminoAcidSequence(java.lang.String name,
java.lang.String sequence) |
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() |
public AminoAcidSequence(int length)
public AminoAcidSequence(java.lang.String name, byte[] sequence)
public AminoAcidSequence(java.lang.String name, java.lang.String sequence)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public AminoAcidSequence copy()
PhylogenyData
copy
in interface PhylogenyData
public int getLength()
public java.lang.String getName()
public char getResidueAt(int position)
public java.lang.String getSequenceAsString()
public byte getStateAt(int position)
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public void setResidueAt(int position, char residue)
public void setStateAt(int position, byte state)
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object