org.forester.phylogeny.data

Class Reference

java.lang.Object

org.forester.phylogeny.data.Reference

All Implemented Interfaces:

PhylogenyData

public class Reference
extends Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
Reference(String desc)
Reference(String desc, String doi)

Method Summary

Modifier and Type	Method and Description
StringBuffer	asSimpleText()
StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
String	getDescription()
String	getDoi()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setDoi(String doi)
void	setValue(String value)
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

Constructor Detail

Reference

public Reference(String desc)

Reference

public Reference(String desc,
                 String doi)

Method Detail

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

getDoi

public String getDoi()

getDescription

public String getDescription()

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

setDoi

public void setDoi(String doi)
            throws PhyloXmlDataFormatException

Throws:

PhyloXmlDataFormatException

setValue

public void setValue(String value)

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