org.forester.phylogeny.data

Class PropertiesMap

java.lang.Object

org.forester.phylogeny.data.PropertiesMap

All Implemented Interfaces:

PhylogenyData

public class PropertiesMap
extends java.lang.Object
implements PhylogenyData

Constructor Summary

Constructors

Constructor and Description
PropertiesMap()

Method Summary

Methods

Modifier and Type	Method and Description
void	addProperty(Property property)
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
java.util.SortedMap<java.lang.String,Property>	getProperties()
Property[]	getPropertiesArray()
java.util.List<Property>	getPropertiesWithGivenReferencePrefix(java.lang.String ref_prefix)
Property	getProperty(java.lang.String ref)
java.lang.String[]	getPropertyRefs() Returns all property refs of this PhylogenyNode as String array.
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
boolean	refExists(java.lang.String ref)
java.util.List<java.lang.String>	removePropertiesWithGivenReferencePrefix(java.lang.String ref_prefix)
Property	removeProperty(java.lang.String ref)
int	size()
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

Constructor Detail

PropertiesMap

public PropertiesMap()

Method Detail

size

public int size()

addProperty

public void addProperty(Property property)
                 throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

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

getProperties

public java.util.SortedMap<java.lang.String,Property> getProperties()

getPropertiesArray

public Property[] getPropertiesArray()

getPropertiesWithGivenReferencePrefix

public java.util.List<Property> getPropertiesWithGivenReferencePrefix(java.lang.String ref_prefix)
                                                               throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

getProperty

public Property getProperty(java.lang.String ref)
                     throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

getPropertyRefs

public java.lang.String[] getPropertyRefs()

Returns all property refs of this PhylogenyNode as String array.

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

refExists

public boolean refExists(java.lang.String ref)

removeProperty

public Property removeProperty(java.lang.String ref)
                        throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

removePropertiesWithGivenReferencePrefix

public java.util.List<java.lang.String> removePropertiesWithGivenReferencePrefix(java.lang.String ref_prefix)
                                                                          throws java.lang.IllegalArgumentException

Throws:

java.lang.IllegalArgumentException

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