Package org.forester.phylogeny.data

Class ProteinDomain

java.lang.Object
org.forester.phylogeny.data.ProteinDomain
All Implemented Interfaces:
PhylogenyData
public class ProteinDomain extends Object implements PhylogenyData

  • Field Details

  • Constructor Details

    • ProteinDomain

      public ProteinDomain(String name, int from, int to)

    • ProteinDomain

      public ProteinDomain(String name, int from, int to, double confidence)

    • ProteinDomain

      public ProteinDomain(String name, int from, int to, String id)

    • ProteinDomain

      public ProteinDomain(String name, int from, int to, String id, double confidence)

  • Method Details

    • 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

    • getConfidence

      public double getConfidence()

    • getFrom

      public int getFrom()

    • getId

      public String getId()

    • getLength

      public int getLength()

    • getName

      public String getName()

    • getTo

      public int getTo()

    • isEqual

      public boolean isEqual(PhylogenyData protein_domain)
      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

    • 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

    • toString

      public String toString()
      Overrides:
      toString in class Object