org.forester.phylogeny.data
public class ProteinDomain extends java.lang.Object implements PhylogenyData
Modifier and Type | Field and Description |
---|---|
static double |
CONFIDENCE_DEFAULT |
static java.lang.String |
IDENTIFIER_DEFAULT |
Constructor and Description |
---|
ProteinDomain(java.lang.String name,
int from,
int to) |
ProteinDomain(java.lang.String name,
int from,
int to,
double confidence) |
ProteinDomain(java.lang.String name,
int from,
int to,
java.lang.String id) |
ProteinDomain(java.lang.String name,
int from,
int to,
java.lang.String id,
double confidence) |
Modifier and Type | Method and Description |
---|---|
java.lang.StringBuffer |
asSimpleText() |
java.lang.StringBuffer |
asText() |
PhylogenyData |
copy()
Creates a new PhylogenyData object with identical values as this
PhylogenyData.
|
double |
getConfidence() |
int |
getFrom() |
java.lang.String |
getId() |
int |
getLength() |
java.lang.String |
getName() |
int |
getTo() |
boolean |
isEqual(PhylogenyData protein_domain)
Compares this PhylogenyData to PhylogenyData data.
|
java.lang.StringBuffer |
toNHX() |
void |
toPhyloXML(java.io.Writer writer,
int level,
java.lang.String indentation)
Writes a phyloXML representation of this phylogeny data.
|
java.lang.String |
toString() |
public static final double CONFIDENCE_DEFAULT
public static final java.lang.String IDENTIFIER_DEFAULT
public ProteinDomain(java.lang.String name, int from, int to)
public ProteinDomain(java.lang.String name, int from, int to, double confidence)
public ProteinDomain(java.lang.String name, int from, int to, java.lang.String id)
public ProteinDomain(java.lang.String name, int from, int to, java.lang.String id, double confidence)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
public double getConfidence()
public int getFrom()
public java.lang.String getId()
public int getLength()
public java.lang.String getName()
public int getTo()
public boolean isEqual(PhylogenyData protein_domain)
PhylogenyData
isEqual
in interface PhylogenyData
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
java.io.IOException
public java.lang.String toString()
toString
in class java.lang.Object