org.forester.phylogeny.data

Class BinaryCharacters

java.lang.Object

org.forester.phylogeny.data.BinaryCharacters

All Implemented Interfaces:

PhylogenyData

public class BinaryCharacters
extends java.lang.Object
implements PhylogenyData

Field Summary

Fields

Modifier and Type	Field and Description
static int	COUNT_DEFAULT

Constructor Summary

Constructors

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)

Method Summary

Methods

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()

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(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

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)

Method Detail

addGainedCharacter

public void addGainedCharacter(java.lang.String binary_character)

addLostCharacter

public void addLostCharacter(java.lang.String binary_character)

addPresentCharacter

public void addPresentCharacter(java.lang.String binary_character)

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.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 java.util.SortedSet<java.lang.String> getGainedCharacters()

getGainedCharactersAsStringArray

public java.lang.String[] getGainedCharactersAsStringArray()

getGainedCharactersAsStringBuffer

public java.lang.StringBuffer getGainedCharactersAsStringBuffer()

getGainedCount

public int getGainedCount()

getLostCharacters

public java.util.SortedSet<java.lang.String> getLostCharacters()

getLostCharactersAsStringArray

public java.lang.String[] getLostCharactersAsStringArray()

getLostCharactersAsStringBuffer

public java.lang.StringBuffer getLostCharactersAsStringBuffer()

getLostCount

public int getLostCount()

getPresentCharacters

public java.util.SortedSet<java.lang.String> getPresentCharacters()

getPresentCharactersAsStringArray

public java.lang.String[] getPresentCharactersAsStringArray()

getPresentCharactersAsStringBuffer

public java.lang.StringBuffer getPresentCharactersAsStringBuffer()

getPresentCount

public int getPresentCount()

getType

public java.lang.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(java.lang.String type)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
              int level,
              java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object