Package org.forester.phylogeny.data
Class PropertiesMap
- java.lang.Object
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- org.forester.phylogeny.data.PropertiesMap
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- All Implemented Interfaces:
PhylogenyData
public class PropertiesMap extends java.lang.Object implements PhylogenyData
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Constructor Summary
Constructors Constructor Description PropertiesMap()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Method Detail
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size
public int size()
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addProperty
public void addProperty(Property property) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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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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getProperties
public java.util.SortedMap<java.lang.String,Property> getProperties()
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getPropertiesArray
public Property[] getPropertiesArray()
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getPropertiesWithGivenReferencePrefix
public java.util.List<Property> getPropertiesWithGivenReferencePrefix(java.lang.String ref_prefix) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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getProperty
public Property getProperty(java.lang.String ref) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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getPropertyRefs
public java.lang.String[] getPropertyRefs()
Returns all property refs of this PhylogenyNode as String array.
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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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refExists
public boolean refExists(java.lang.String ref)
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removeProperty
public Property removeProperty(java.lang.String ref) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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removePropertiesWithGivenReferencePrefix
public java.util.List<java.lang.String> removePropertiesWithGivenReferencePrefix(java.lang.String ref_prefix) throws java.lang.IllegalArgumentException
- Throws:
java.lang.IllegalArgumentException
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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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