Package org.forester.phylogeny.data
Class ProteinDomain
- java.lang.Object
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- org.forester.phylogeny.data.ProteinDomain
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- All Implemented Interfaces:
PhylogenyData
public class ProteinDomain extends java.lang.Object implements PhylogenyData
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Field Summary
Fields Modifier and Type Field Description static double
CONFIDENCE_DEFAULT
static java.lang.String
IDENTIFIER_DEFAULT
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Constructor Summary
Constructors Constructor 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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Field Detail
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CONFIDENCE_DEFAULT
public static final double CONFIDENCE_DEFAULT
- See Also:
- Constant Field Values
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IDENTIFIER_DEFAULT
public static final java.lang.String IDENTIFIER_DEFAULT
- See Also:
- Constant Field Values
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Constructor Detail
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ProteinDomain
public ProteinDomain(java.lang.String name, int from, int to)
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ProteinDomain
public ProteinDomain(java.lang.String name, int from, int to, double confidence)
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ProteinDomain
public ProteinDomain(java.lang.String name, int from, int to, java.lang.String id)
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ProteinDomain
public ProteinDomain(java.lang.String name, int from, int to, java.lang.String id, double confidence)
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Method Detail
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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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 interfacePhylogenyData
- Returns:
- a ~deep~ copy of this PhylogenyData
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getConfidence
public double getConfidence()
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getFrom
public int getFrom()
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getId
public java.lang.String getId()
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getLength
public int getLength()
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getName
public java.lang.String getName()
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getTo
public int getTo()
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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 interfacePhylogenyData
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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toPhyloXML
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
Description copied from interface:PhylogenyData
Writes a phyloXML representation of this phylogeny data.- Specified by:
toPhyloXML
in interfacePhylogenyData
- Throws:
java.io.IOException
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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