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
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)
|
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
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)
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