public class SequenceRelation extends java.lang.Object implements PhylogenyData
Modifier and Type | Class and Description |
---|---|
static class |
SequenceRelation.SEQUENCE_RELATION_TYPE |
Modifier and Type | Field and 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 |
Constructor and Description |
---|
SequenceRelation() |
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.
|
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.
|
public static final java.util.Map<SequenceRelation.SEQUENCE_RELATION_TYPE,java.lang.String> typesToNames
public static final java.lang.String SEQUENCE_RELATION_TYPE_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_ONE_TO_ONE_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_SUPER_ORTHOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_PARALOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_ULTRA_PARALOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_XENOLOGY
public static final java.lang.String SEQUENCE_RELATION_TYPE_UNKNOWN
public static final java.lang.String SEQUENCE_RELATION_TYPE_OTHER
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 Confidence getConfidence()
public java.lang.Double getDistance()
public Sequence getRef0()
public Sequence getRef1()
public SequenceRelation.SEQUENCE_RELATION_TYPE getType()
public boolean isEqual(PhylogenyData data)
PhylogenyData
isEqual
in interface PhylogenyData
public void setConfidence(Confidence confidence)
public void setDistance(java.lang.Double distance)
public void setRef0(Sequence ref0)
public void setRef1(Sequence ref1)
public void setType(SequenceRelation.SEQUENCE_RELATION_TYPE type)
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 static java.lang.String getPrintableNameByType(SequenceRelation.SEQUENCE_RELATION_TYPE type)