Package org.forester.phylogeny.data
Class BinaryCharacters
- java.lang.Object
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- org.forester.phylogeny.data.BinaryCharacters
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- All Implemented Interfaces:
PhylogenyData
public class BinaryCharacters extends java.lang.Object implements PhylogenyData
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Field Summary
Fields Modifier and Type Field Description static int
COUNT_DEFAULT
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Constructor Summary
Constructors Constructor 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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Field Detail
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COUNT_DEFAULT
public static final int COUNT_DEFAULT
- See Also:
- Constant Field Values
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Constructor Detail
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BinaryCharacters
public BinaryCharacters()
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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)
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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)
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Method Detail
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addGainedCharacter
public void addGainedCharacter(java.lang.String binary_character)
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addLostCharacter
public void addLostCharacter(java.lang.String binary_character)
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addPresentCharacter
public void addPresentCharacter(java.lang.String binary_character)
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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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 interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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getGainedCharacters
public java.util.SortedSet<java.lang.String> getGainedCharacters()
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getGainedCharactersAsStringArray
public java.lang.String[] getGainedCharactersAsStringArray()
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getGainedCharactersAsStringBuffer
public java.lang.StringBuffer getGainedCharactersAsStringBuffer()
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getGainedCount
public int getGainedCount()
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getLostCharacters
public java.util.SortedSet<java.lang.String> getLostCharacters()
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getLostCharactersAsStringArray
public java.lang.String[] getLostCharactersAsStringArray()
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getLostCharactersAsStringBuffer
public java.lang.StringBuffer getLostCharactersAsStringBuffer()
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getLostCount
public int getLostCount()
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getPresentCharacters
public java.util.SortedSet<java.lang.String> getPresentCharacters()
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getPresentCharactersAsStringArray
public java.lang.String[] getPresentCharactersAsStringArray()
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getPresentCharactersAsStringBuffer
public java.lang.StringBuffer getPresentCharactersAsStringBuffer()
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getPresentCount
public int getPresentCount()
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getType
public java.lang.String getType()
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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 interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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setType
public void setType(java.lang.String type)
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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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 interfacePhylogenyData
- Throws:
java.io.IOException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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