org.forester.phylogeny.data
Class BranchData

java.lang.Object
  extended by org.forester.phylogeny.data.BranchData
All Implemented Interfaces:
PhylogenyData

public class BranchData
extends Object
implements PhylogenyData


Constructor Summary
BranchData()
           
 
Method Summary
 void addConfidence(Confidence confidence)
           
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 BranchColor getBranchColor()
           
 BranchWidth getBranchWidth()
           
 Confidence getConfidence(int index)
           
 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)
           
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BranchData

public BranchData()
Method Detail

addConfidence

public void addConfidence(Confidence confidence)

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

getBranchColor

public BranchColor getBranchColor()

getBranchWidth

public BranchWidth getBranchWidth()

getConfidence

public Confidence getConfidence(int index)

getConfidences

public List<Confidence> getConfidences()

getNumberOfConfidences

public int getNumberOfConfidences()

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

isHasBranchColor

public boolean isHasBranchColor()

isHasBranchWidth

public boolean isHasBranchWidth()

isHasConfidences

public boolean isHasConfidences()

setBranchColor

public void setBranchColor(BranchColor branch_color)

setBranchWidth

public void setBranchWidth(BranchWidth branch_width)

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