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 Description

static class Event.EventType

Field Summary

Fields
Modifier and Type Field Description

static int DEFAULT_VALUE

Constructor Summary

Constructors
Constructor	Description
`Event()`
`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)`
`Event(Event.EventType type)`

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 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()
```

Class Event

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_VALUE

Constructor Detail

Event

Event

Event

Event

Event

Method Detail

asSimpleText

asText

copy

getConfidence

getEventType

getNumberOfDuplications

getNumberOfGeneLosses

getNumberOfSpeciations

isDuplication

isEqual

isFusion

isGeneLoss

isOther

isRoot

isSpeciation

isSpeciationOrDuplication

isTransfer

isUnassigned

setConfidence

setDuplications

setGeneLosses

setSpeciations

toNHX

toPhyloXML

toString

createSingleDuplicationEvent

createSingleSpeciationEvent

createSingleSpeciationOrDuplicationEvent