org.forester.phylogeny.data

Class BinaryCharacters

java.lang.Object

org.forester.phylogeny.data.BinaryCharacters

All Implemented Interfaces:

PhylogenyData

public class BinaryCharacters
extends Object
implements PhylogenyData

Field Summary

Fields

Modifier and Type	Field and Description
static int	COUNT_DEFAULT

Constructor Summary

Constructors

Constructor and Description
BinaryCharacters()
BinaryCharacters(SortedSet<String> present_characters, SortedSet<String> gained_characters, SortedSet<String> lost_characters, String type)
BinaryCharacters(SortedSet<String> present_characters, SortedSet<String> gained_characters, SortedSet<String> lost_characters, String type, int present_count, int gained_count, int lost_count)

Method Summary

Modifier and Type	Method and Description
void	addGainedCharacter(String binary_character)
void	addLostCharacter(String binary_character)
void	addPresentCharacter(String binary_character)
StringBuffer	asSimpleText()
StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
SortedSet<String>	getGainedCharacters()
String[]	getGainedCharactersAsStringArray()
StringBuffer	getGainedCharactersAsStringBuffer()
int	getGainedCount()
SortedSet<String>	getLostCharacters()
String[]	getLostCharactersAsStringArray()
StringBuffer	getLostCharactersAsStringBuffer()
int	getLostCount()
SortedSet<String>	getPresentCharacters()
String[]	getPresentCharactersAsStringArray()
StringBuffer	getPresentCharactersAsStringBuffer()
int	getPresentCount()
String	getType()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setType(String type)
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

Field Detail

COUNT_DEFAULT

public static final int COUNT_DEFAULT

See Also:

Constant Field Values

Constructor Detail

BinaryCharacters

public BinaryCharacters()

BinaryCharacters

public BinaryCharacters(SortedSet<String> present_characters,
                        SortedSet<String> gained_characters,
                        SortedSet<String> lost_characters,
                        String type)

BinaryCharacters

public BinaryCharacters(SortedSet<String> present_characters,
                        SortedSet<String> gained_characters,
                        SortedSet<String> lost_characters,
                        String type,
                        int present_count,
                        int gained_count,
                        int lost_count)

Method Detail

addGainedCharacter

public void addGainedCharacter(String binary_character)

addLostCharacter

public void addLostCharacter(String binary_character)

addPresentCharacter

public void addPresentCharacter(String binary_character)

asSimpleText

public StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public StringBuffer asText()

Specified by:

asText in interface PhylogenyData

copy

public PhylogenyData 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

getGainedCharacters

public SortedSet<String> getGainedCharacters()

getGainedCharactersAsStringArray

public String[] getGainedCharactersAsStringArray()

getGainedCharactersAsStringBuffer

public StringBuffer getGainedCharactersAsStringBuffer()

getGainedCount

public int getGainedCount()

getLostCharacters

public SortedSet<String> getLostCharacters()

getLostCharactersAsStringArray

public String[] getLostCharactersAsStringArray()

getLostCharactersAsStringBuffer

public StringBuffer getLostCharactersAsStringBuffer()

getLostCount

public int getLostCount()

getPresentCharacters

public SortedSet<String> getPresentCharacters()

getPresentCharactersAsStringArray

public String[] getPresentCharactersAsStringArray()

getPresentCharactersAsStringBuffer

public StringBuffer getPresentCharactersAsStringBuffer()

getPresentCount

public int getPresentCount()

getType

public String getType()

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

setType

public void setType(String type)

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