org.forester.phylogeny.data

Class Event

java.lang.Object

org.forester.phylogeny.data.Event

All Implemented Interfaces:

PhylogenyData

public class Event
extends java.lang.Object
implements PhylogenyData

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Event.EventType

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_VALUE

Constructor Summary

Constructors

Constructor and Description
Event()
Event(Event.EventType type)
Event(int duplications, int speciations, int gene_losses)
Event(int duplications, int speciations, int gene_losses, java.lang.String type)
Event(java.lang.String nhx)

Method Summary

Methods

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.
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 only
boolean	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 only
boolean	isOther()
boolean	isRoot()
boolean	isSpeciation() Returns true if this event contains one or more speciation events only
boolean	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()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT_VALUE

public static final int DEFAULT_VALUE

See Also:

Constant Field Values

Constructor Detail

Event

public Event()

Event

public Event(Event.EventType type)

Event

public Event(int duplications,
     int speciations,
     int gene_losses)

Event

public Event(int duplications,
     int speciations,
     int gene_losses,
     java.lang.String type)

Event

public Event(java.lang.String nhx)
      throws NHXFormatException

Throws:

NHXFormatException

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

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 interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getConfidence

public Confidence getConfidence()

getEventType

public Event.EventType getEventType()

getNumberOfDuplications

public int getNumberOfDuplications()

getNumberOfGeneLosses

public int getNumberOfGeneLosses()

getNumberOfSpeciations

public int getNumberOfSpeciations()

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

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 interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

isFusion

public boolean isFusion()

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

isOther

public boolean isOther()

isRoot

public boolean isRoot()

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

isSpeciationOrDuplication

public boolean isSpeciationOrDuplication()

isTransfer

public boolean isTransfer()

isUnassigned

public boolean isUnassigned()

setConfidence

public void setConfidence(Confidence confidence)

setDuplications

public void setDuplications(int duplications)

setGeneLosses

public void setGeneLosses(int gene_losses)

setSpeciations

public void setSpeciations(int speciations)

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

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 interface PhylogenyData

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

createSingleDuplicationEvent

public static Event createSingleDuplicationEvent()

createSingleSpeciationEvent

public static Event createSingleSpeciationEvent()

createSingleSpeciationOrDuplicationEvent

public static Event createSingleSpeciationOrDuplicationEvent()