Package org.forester.phylogeny.data
Class Event
- java.lang.Object
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- org.forester.phylogeny.data.Event
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- All Implemented Interfaces:
PhylogenyData
public class Event extends java.lang.Object implements PhylogenyData
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Event.EventType
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_VALUE
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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.static Event
createSingleDuplicationEvent()
static Event
createSingleSpeciationEvent()
static Event
createSingleSpeciationOrDuplicationEvent()
Confidence
getConfidence()
Event.EventType
getEventType()
int
getNumberOfDuplications()
int
getNumberOfGeneLosses()
int
getNumberOfSpeciations()
boolean
isDuplication()
Returns true if this event contains one or more duplications events onlyboolean
isEqual(PhylogenyData event)
Compares this PhylogenyData to PhylogenyData data.boolean
isFusion()
boolean
isGeneLoss()
Returns true if this event contains one or more gene loss events onlyboolean
isOther()
boolean
isRoot()
boolean
isSpeciation()
Returns true if this event contains one or more speciation events onlyboolean
isSpeciationOrDuplication()
boolean
isTransfer()
boolean
isUnassigned()
void
setConfidence(Confidence confidence)
void
setDuplications(int duplications)
void
setGeneLosses(int gene_losses)
void
setSpeciations(int speciations)
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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DEFAULT_VALUE
public static final int DEFAULT_VALUE
- See Also:
- Constant Field Values
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Constructor Detail
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Event
public Event()
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Event
public Event(Event.EventType type)
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Event
public Event(int duplications, int speciations, int gene_losses)
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Event
public Event(int duplications, int speciations, int gene_losses, java.lang.String type)
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Event
public Event(java.lang.String nhx) throws NHXFormatException
- Throws:
NHXFormatException
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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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getEventType
public Event.EventType getEventType()
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getNumberOfDuplications
public int getNumberOfDuplications()
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getNumberOfGeneLosses
public int getNumberOfGeneLosses()
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getNumberOfSpeciations
public int getNumberOfSpeciations()
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isDuplication
public boolean isDuplication()
Returns true if this event contains one or more duplications events only- Returns:
- true if this event contains one or more duplications events only
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isEqual
public boolean isEqual(PhylogenyData event)
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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isFusion
public boolean isFusion()
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isGeneLoss
public boolean isGeneLoss()
Returns true if this event contains one or more gene loss events only- Returns:
- true if this event contains one or more gene loss events only
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isOther
public boolean isOther()
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isRoot
public boolean isRoot()
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isSpeciation
public boolean isSpeciation()
Returns true if this event contains one or more speciation events only- Returns:
- true if this event contains one or more speciation events only
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isSpeciationOrDuplication
public boolean isSpeciationOrDuplication()
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isTransfer
public boolean isTransfer()
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isUnassigned
public boolean isUnassigned()
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setConfidence
public void setConfidence(Confidence confidence)
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setDuplications
public void setDuplications(int duplications)
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setGeneLosses
public void setGeneLosses(int gene_losses)
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setSpeciations
public void setSpeciations(int speciations)
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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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createSingleDuplicationEvent
public static Event createSingleDuplicationEvent()
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createSingleSpeciationEvent
public static Event createSingleSpeciationEvent()
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createSingleSpeciationOrDuplicationEvent
public static Event createSingleSpeciationOrDuplicationEvent()
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