org.forester.phylogeny.data
Class ProteinDomain

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

public class ProteinDomain
extends Object
implements PhylogenyData


Field Summary
static double CONFIDENCE_DEFAULT
           
static String IDENTIFIER_DEFAULT
           
 
Constructor Summary
ProteinDomain(String name, int from, int to)
           
ProteinDomain(String name, int from, int to, double confidence)
           
ProteinDomain(String name, int from, int to, String id)
           
ProteinDomain(String name, int from, int to, String id, double confidence)
           
 
Method Summary
 StringBuffer asSimpleText()
           
 StringBuffer asText()
           
 PhylogenyData copy()
          Creates a new PhylogenyData object with identical values as this PhylogenyData.
 double getConfidence()
           
 int getFrom()
           
 String getId()
           
 int getLength()
           
 String getName()
           
 int getTo()
           
 boolean isEqual(PhylogenyData protein_domain)
          Compares this PhylogenyData to PhylogenyData data.
 StringBuffer toNHX()
           
 void toPhyloXML(Writer writer, int level, String indentation)
          Writes a phyloXML representation of this phylogeny data.
 String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

CONFIDENCE_DEFAULT

public static final double CONFIDENCE_DEFAULT
See Also:
Constant Field Values

IDENTIFIER_DEFAULT

public static final String IDENTIFIER_DEFAULT
See Also:
Constant Field Values
Constructor Detail

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 Detail

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