org.forester.phylogeny.data
public class BinaryCharacters extends java.lang.Object implements PhylogenyData
Modifier and Type | Field and Description |
---|---|
static int |
COUNT_DEFAULT |
Constructor and Description |
---|
BinaryCharacters() |
BinaryCharacters(java.util.SortedSet<java.lang.String> present_characters,
java.util.SortedSet<java.lang.String> gained_characters,
java.util.SortedSet<java.lang.String> lost_characters,
java.lang.String type) |
BinaryCharacters(java.util.SortedSet<java.lang.String> present_characters,
java.util.SortedSet<java.lang.String> gained_characters,
java.util.SortedSet<java.lang.String> lost_characters,
java.lang.String type,
int present_count,
int gained_count,
int lost_count) |
Modifier and Type | Method and Description |
---|---|
void |
addGainedCharacter(java.lang.String binary_character) |
void |
addLostCharacter(java.lang.String binary_character) |
void |
addPresentCharacter(java.lang.String binary_character) |
java.lang.StringBuffer |
asSimpleText() |
java.lang.StringBuffer |
asText() |
PhylogenyData |
copy()
Creates a new PhylogenyData object with identical values as this
PhylogenyData.
|
java.util.SortedSet<java.lang.String> |
getGainedCharacters() |
java.lang.String[] |
getGainedCharactersAsStringArray() |
java.lang.StringBuffer |
getGainedCharactersAsStringBuffer() |
int |
getGainedCount() |
java.util.SortedSet<java.lang.String> |
getLostCharacters() |
java.lang.String[] |
getLostCharactersAsStringArray() |
java.lang.StringBuffer |
getLostCharactersAsStringBuffer() |
int |
getLostCount() |
java.util.SortedSet<java.lang.String> |
getPresentCharacters() |
java.lang.String[] |
getPresentCharactersAsStringArray() |
java.lang.StringBuffer |
getPresentCharactersAsStringBuffer() |
int |
getPresentCount() |
java.lang.String |
getType() |
boolean |
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.
|
void |
setType(java.lang.String type) |
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 static final int COUNT_DEFAULT
public BinaryCharacters()
public BinaryCharacters(java.util.SortedSet<java.lang.String> present_characters, java.util.SortedSet<java.lang.String> gained_characters, java.util.SortedSet<java.lang.String> lost_characters, java.lang.String type)
public BinaryCharacters(java.util.SortedSet<java.lang.String> present_characters, java.util.SortedSet<java.lang.String> gained_characters, java.util.SortedSet<java.lang.String> lost_characters, java.lang.String type, int present_count, int gained_count, int lost_count)
public void addGainedCharacter(java.lang.String binary_character)
public void addLostCharacter(java.lang.String binary_character)
public void addPresentCharacter(java.lang.String binary_character)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
public java.util.SortedSet<java.lang.String> getGainedCharacters()
public java.lang.String[] getGainedCharactersAsStringArray()
public java.lang.StringBuffer getGainedCharactersAsStringBuffer()
public int getGainedCount()
public java.util.SortedSet<java.lang.String> getLostCharacters()
public java.lang.String[] getLostCharactersAsStringArray()
public java.lang.StringBuffer getLostCharactersAsStringBuffer()
public int getLostCount()
public java.util.SortedSet<java.lang.String> getPresentCharacters()
public java.lang.String[] getPresentCharactersAsStringArray()
public java.lang.StringBuffer getPresentCharactersAsStringBuffer()
public int getPresentCount()
public java.lang.String getType()
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public void setType(java.lang.String type)
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