Annotation

java.lang.Object
- org.forester.phylogeny.data.Annotation

All Implemented Interfaces:: java.lang.Comparable<Annotation>, MultipleUris, PhylogenyData

public class Annotation
extends java.lang.Object
implements PhylogenyData, MultipleUris, java.lang.Comparable<Annotation>

Constructor Summary

Constructors
Constructor and Description

Annotation()

Annotation(java.lang.String ref)

Annotation(java.lang.String ref_source, java.lang.String ref_value)

Constructors
Constructor and Description
`Annotation()`
`Annotation(java.lang.String ref)`
`Annotation(java.lang.String ref_source, java.lang.String ref_value)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addUri(Uri uri)`
`java.lang.StringBuffer`	`asSimpleText()`
`java.lang.StringBuffer`	`asText()`
`int`	`compareTo(Annotation o)`
`PhylogenyData`	`copy()` Creates a new PhylogenyData object with identical values as this PhylogenyData.
`boolean`	`equals(java.lang.Object o)`
`Confidence`	`getConfidence()`
`java.lang.String`	`getDesc()`
`java.lang.String`	`getEvidence()`
`PropertiesMap`	`getProperties()`
`java.lang.String`	`getRef()`
`java.lang.String`	`getRefSource()`
`java.lang.String`	`getRefValue()`
`java.lang.String`	`getSource()`
`java.lang.String`	`getType()`
`Uri`	`getUri(int index)`
`java.util.List<Uri>`	`getUris()`
`boolean`	`isEqual(PhylogenyData data)` Compares this PhylogenyData to PhylogenyData data.
`void`	`setConfidence(Confidence confidence)`
`void`	`setDesc(java.lang.String desc)`
`void`	`setEvidence(java.lang.String evidence)`
`void`	`setProperties(PropertiesMap property)`
`void`	`setSource(java.lang.String source)`
`void`	`setType(java.lang.String type)`
`void`	`setUris(java.util.List<Uri> uris)`
`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, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Annotation
```
public Annotation()
```
  - Annotation
```
public Annotation(java.lang.String ref)
```
  - Annotation
```
public Annotation(java.lang.String ref_source,
                  java.lang.String ref_value)
```
- Method Detail
  - addUri
```
public void addUri(Uri uri)
```
    Specified by:
    
    addUri in interface MultipleUris
  - asSimpleText
```
public java.lang.StringBuffer asSimpleText()
```
    Specified by:
    
    asSimpleText in interface PhylogenyData
  - asText
```
public java.lang.StringBuffer asText()
```
    Specified by:
    
    asText in interface PhylogenyData
  - compareTo
```
public int compareTo(Annotation o)
```
    Specified by:
    
    compareTo in interface java.lang.Comparable<Annotation>
  - 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
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - getConfidence
```
public Confidence getConfidence()
```
  - getDesc
```
public java.lang.String getDesc()
```
  - getEvidence
```
public java.lang.String getEvidence()
```
  - getProperties
```
public PropertiesMap getProperties()
```
  - getRef
```
public java.lang.String getRef()
```
  - getRefSource
```
public final java.lang.String getRefSource()
```
  - getRefValue
```
public final java.lang.String getRefValue()
```
  - getSource
```
public java.lang.String getSource()
```
  - getType
```
public java.lang.String getType()
```
  - getUri
```
public Uri getUri(int index)
```
    Specified by:
    
    getUri in interface MultipleUris
  - getUris
```
public java.util.List<Uri> getUris()
```
    Specified by:
    
    getUris in interface MultipleUris
  - isEqual
```
public boolean isEqual(PhylogenyData data)
```
    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
  - setConfidence
```
public void setConfidence(Confidence confidence)
```
  - setDesc
```
public void setDesc(java.lang.String desc)
```
  - setEvidence
```
public void setEvidence(java.lang.String evidence)
```
  - setProperties
```
public void setProperties(PropertiesMap property)
```
  - setSource
```
public void setSource(java.lang.String source)
```
  - setType
```
public void setType(java.lang.String type)
```
  - setUris
```
public void setUris(java.util.List<Uri> uris)
```
    Specified by:
    
    setUris in interface MultipleUris
  - 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

Class Annotation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Annotation

Annotation

Annotation

Method Detail

addUri

asSimpleText

asText

compareTo

copy

equals

getConfidence

getDesc

getEvidence

getProperties

getRef

getRefSource

getRefValue

getSource

getType

getUri

getUris

isEqual

setConfidence

setDesc

setEvidence

setProperties

setSource

setType

setUris

toNHX

toPhyloXML

toString