Package org.forester.phylogeny.data
Class Annotation
- java.lang.Object
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- org.forester.phylogeny.data.Annotation
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- All Implemented Interfaces:
java.lang.Comparable<Annotation>
,MultipleUris
,PhylogenyData
public class Annotation extends java.lang.Object implements PhylogenyData, MultipleUris, java.lang.Comparable<Annotation>
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Constructor Summary
Constructors Constructor Description Annotation()
Annotation(java.lang.String ref)
Annotation(java.lang.String ref_source, java.lang.String ref_value)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addUri(Uri uri)
java.lang.StringBuffer
asSimpleText()
java.lang.StringBuffer
asText()
int
compareTo(Annotation o)
PhylogenyData
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.boolean
equals(java.lang.Object o)
Confidence
getConfidence()
java.lang.String
getDesc()
java.lang.String
getEvidence()
PropertiesMap
getProperties()
java.lang.String
getRef()
java.lang.String
getRefSource()
java.lang.String
getRefValue()
java.lang.String
getSource()
java.lang.String
getType()
Uri
getUri(int index)
java.util.List<Uri>
getUris()
boolean
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.void
setConfidence(Confidence confidence)
void
setDesc(java.lang.String desc)
void
setEvidence(java.lang.String evidence)
void
setProperties(PropertiesMap property)
void
setSource(java.lang.String source)
void
setType(java.lang.String type)
void
setUris(java.util.List<Uri> uris)
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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addUri
public void addUri(Uri uri)
- Specified by:
addUri
in interfaceMultipleUris
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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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compareTo
public int compareTo(Annotation o)
- Specified by:
compareTo
in interfacejava.lang.Comparable<Annotation>
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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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equals
public boolean equals(java.lang.Object o)
- Overrides:
equals
in classjava.lang.Object
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getConfidence
public Confidence getConfidence()
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getDesc
public java.lang.String getDesc()
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getEvidence
public java.lang.String getEvidence()
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getProperties
public PropertiesMap getProperties()
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getRef
public java.lang.String getRef()
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getRefSource
public final java.lang.String getRefSource()
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getRefValue
public final java.lang.String getRefValue()
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getSource
public java.lang.String getSource()
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getType
public java.lang.String getType()
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getUri
public Uri getUri(int index)
- Specified by:
getUri
in interfaceMultipleUris
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getUris
public java.util.List<Uri> getUris()
- Specified by:
getUris
in interfaceMultipleUris
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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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setConfidence
public void setConfidence(Confidence confidence)
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setDesc
public void setDesc(java.lang.String desc)
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setEvidence
public void setEvidence(java.lang.String evidence)
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setProperties
public void setProperties(PropertiesMap property)
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setSource
public void setSource(java.lang.String source)
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setType
public void setType(java.lang.String type)
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setUris
public void setUris(java.util.List<Uri> uris)
- Specified by:
setUris
in interfaceMultipleUris
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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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