org.forester.phylogeny.data
Class BranchData
java.lang.Object
org.forester.phylogeny.data.BranchData
- All Implemented Interfaces:
- PhylogenyData
public class BranchData
- extends Object
- implements PhylogenyData
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BranchData
public BranchData()
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