Package org.forester.phylogeny.data
Class SequenceRelation
- java.lang.Object
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- org.forester.phylogeny.data.SequenceRelation
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- All Implemented Interfaces:
PhylogenyData
public class SequenceRelation extends java.lang.Object implements PhylogenyData
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SequenceRelation.SEQUENCE_RELATION_TYPE
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
static java.lang.String
SEQUENCE_RELATION_TYPE_ORTHOLOGY
static java.lang.String
SEQUENCE_RELATION_TYPE_OTHER
static java.lang.String
SEQUENCE_RELATION_TYPE_PARALOGY
static java.lang.String
SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
static java.lang.String
SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
static java.lang.String
SEQUENCE_RELATION_TYPE_UNKNOWN
static java.lang.String
SEQUENCE_RELATION_TYPE_XENOLOGY
static java.util.Map<SequenceRelation.SEQUENCE_RELATION_TYPE,java.lang.String>
typesToNames
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Constructor Summary
Constructors Constructor Description SequenceRelation()
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Method Summary
All Methods Static 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.Confidence
getConfidence()
java.lang.Double
getDistance()
static java.lang.String
getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
Sequence
getRef0()
Sequence
getRef1()
SequenceRelation.SEQUENCE_RELATION_TYPE
getType()
boolean
isEqual(PhylogenyData data)
Compares this PhylogenyData to PhylogenyData data.void
setConfidence(Confidence confidence)
void
setDistance(java.lang.Double distance)
void
setRef0(Sequence ref0)
void
setRef1(Sequence ref1)
void
setType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
java.lang.StringBuffer
toNHX()
void
toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation)
Writes a phyloXML representation of this phylogeny data.
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Field Detail
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typesToNames
public static final java.util.Map<SequenceRelation.SEQUENCE_RELATION_TYPE,java.lang.String> typesToNames
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SEQUENCE_RELATION_TYPE_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_ORTHOLOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_PARALOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_PARALOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_XENOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_XENOLOGY
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_UNKNOWN
public static final java.lang.String SEQUENCE_RELATION_TYPE_UNKNOWN
- See Also:
- Constant Field Values
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SEQUENCE_RELATION_TYPE_OTHER
public static final java.lang.String SEQUENCE_RELATION_TYPE_OTHER
- See Also:
- Constant Field Values
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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 Confidence getConfidence()
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getDistance
public java.lang.Double getDistance()
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getRef0
public Sequence getRef0()
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getRef1
public Sequence getRef1()
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getType
public SequenceRelation.SEQUENCE_RELATION_TYPE getType()
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isEqual
public boolean isEqual(PhylogenyData data)
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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setConfidence
public void setConfidence(Confidence confidence)
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setDistance
public void setDistance(java.lang.Double distance)
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setRef0
public void setRef0(Sequence ref0)
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setRef1
public void setRef1(Sequence ref1)
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setType
public void setType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
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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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getPrintableNameByType
public static java.lang.String getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
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