Package org.forester.phylogeny.data
Class BranchData
- java.lang.Object
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- org.forester.phylogeny.data.BranchData
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- All Implemented Interfaces:
PhylogenyData
public class BranchData extends java.lang.Object implements PhylogenyData
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Constructor Summary
Constructors Constructor Description BranchData()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addConfidence(Confidence confidence)
java.lang.StringBuffer
asSimpleText()
java.lang.StringBuffer
asText()
PhylogenyData
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData.BranchColor
getBranchColor()
BranchWidth
getBranchWidth()
Confidence
getConfidence(int index)
java.util.List<Confidence>
getConfidences()
int
getNumberOfConfidences()
boolean
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.boolean
isHasBranchColor()
boolean
isHasBranchWidth()
boolean
isHasConfidences()
void
setBranchColor(BranchColor branch_color)
void
setBranchWidth(BranchWidth branch_width)
java.lang.StringBuffer
toNHX()
void
toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation)
Writes a phyloXML representation of this phylogeny data.
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Method Detail
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addConfidence
public void addConfidence(Confidence confidence)
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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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getBranchColor
public BranchColor getBranchColor()
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getBranchWidth
public BranchWidth getBranchWidth()
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getConfidence
public Confidence getConfidence(int index)
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getConfidences
public java.util.List<Confidence> getConfidences()
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getNumberOfConfidences
public int getNumberOfConfidences()
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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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isHasBranchColor
public boolean isHasBranchColor()
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isHasBranchWidth
public boolean isHasBranchWidth()
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isHasConfidences
public boolean isHasConfidences()
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setBranchColor
public void setBranchColor(BranchColor branch_color)
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setBranchWidth
public void setBranchWidth(BranchWidth branch_width)
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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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