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java.lang.Objectorg.forester.phylogeny.data.Event
public class Event
Nested Class Summary | |
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static class |
Event.EventType
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Field Summary | |
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static int |
DEFAULT_VALUE
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Constructor Summary | |
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Event()
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Event(Event.EventType type)
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Event(int duplications,
int speciations,
int gene_losses)
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Event(int duplications,
int speciations,
int gene_losses,
String type)
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Event(String nhx)
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Method Summary | |
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StringBuffer |
asSimpleText()
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StringBuffer |
asText()
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PhylogenyData |
copy()
Creates a new PhylogenyData object with identical values as this PhylogenyData. |
static Event |
createSingleDuplicationEvent()
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static Event |
createSingleSpeciationEvent()
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static Event |
createSingleSpeciationOrDuplicationEvent()
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Confidence |
getConfidence()
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Event.EventType |
getEventType()
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int |
getNumberOfDuplications()
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int |
getNumberOfGeneLosses()
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int |
getNumberOfSpeciations()
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boolean |
isDuplication()
Returns true if this event contains one or more duplications events only |
boolean |
isEqual(PhylogenyData event)
Compares this PhylogenyData to PhylogenyData data. |
boolean |
isFusion()
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boolean |
isGeneLoss()
Returns true if this event contains one or more gene loss events only |
boolean |
isOther()
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boolean |
isRoot()
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boolean |
isSpeciation()
Returns true if this event contains one or more speciation events only |
boolean |
isSpeciationOrDuplication()
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boolean |
isTransfer()
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boolean |
isUnassigned()
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void |
setConfidence(Confidence confidence)
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void |
setDuplications(int duplications)
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void |
setGeneLosses(int gene_losses)
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void |
setSpeciations(int speciations)
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StringBuffer |
toNHX()
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void |
toPhyloXML(Writer writer,
int level,
String indentation)
Writes a phyloXML representation of this phylogeny data. |
String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final int DEFAULT_VALUE
Constructor Detail |
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public Event()
public Event(Event.EventType type)
public Event(int duplications, int speciations, int gene_losses)
public Event(int duplications, int speciations, int gene_losses, String type)
public Event(String nhx) throws NHXFormatException
NHXFormatException
Method Detail |
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public StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
public StringBuffer asText()
asText
in interface PhylogenyData
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
public Confidence getConfidence()
public Event.EventType getEventType()
public int getNumberOfDuplications()
public int getNumberOfGeneLosses()
public int getNumberOfSpeciations()
public boolean isDuplication()
public boolean isEqual(PhylogenyData event)
PhylogenyData
isEqual
in interface PhylogenyData
public boolean isFusion()
public boolean isGeneLoss()
public boolean isOther()
public boolean isRoot()
public boolean isSpeciation()
public boolean isSpeciationOrDuplication()
public boolean isTransfer()
public boolean isUnassigned()
public void setConfidence(Confidence confidence)
public void setDuplications(int duplications)
public void setGeneLosses(int gene_losses)
public void setSpeciations(int speciations)
public StringBuffer toNHX()
toNHX
in interface PhylogenyData
public void toPhyloXML(Writer writer, int level, String indentation) throws IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
IOException
public String toString()
toString
in class Object
public static Event createSingleDuplicationEvent()
public static Event createSingleSpeciationEvent()
public static Event createSingleSpeciationOrDuplicationEvent()
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