BiojavaSequence (managers-biojava 0.0.31 API)

java.lang.Object
- net.bioclipse.core.domain.BioObject
- - net.bioclipse.biojava.domain.BiojavaSequence

All Implemented Interfaces:

net.bioclipse.core.domain.IBioObject, net.bioclipse.core.domain.ISequence, org.eclipse.core.runtime.IAdaptable

Direct Known Subclasses:

BiojavaDNA, BiojavaProtein
```
public class BiojavaSequence
extends net.bioclipse.core.domain.BioObject
implements net.bioclipse.core.domain.ISequence
```
Author:

jonalv, olas

Field Summary
- Fields inherited from class net.bioclipse.core.domain.BioObject
  resource

Constructor Summary

Constructors
Constructor Description

BiojavaSequence()

BiojavaSequence(org.biojava.bio.seq.Sequence sequence)
Create a BiojavaSequence from a Sequence.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Object`	`getAdapter(Class adapter)`
`String`	`getName()`
`Object`	`getParsedResource()`	Returns the RichSequence
`String`	`getPlainSequence()`
`void`	`setRichSequence(org.biojavax.bio.seq.RichSequence richSequence)`
`String`	`toFasta()`	Convert RichSequence to FASTA and return as String.

Methods inherited from class net.bioclipse.core.domain.BioObject
getResource, getUID, setResource

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.bioclipse.core.domain.IBioObject
getResource, getUID, setResource

- Constructor Detail
  - BiojavaSequence
```
public BiojavaSequence(org.biojava.bio.seq.Sequence sequence)
```
    Create a BiojavaSequence from a Sequence.
    
    Parameters:
    
    sequence - sequence to create the object from
  - BiojavaSequence
```
public BiojavaSequence()
```
- Method Detail
  - getPlainSequence
```
public String getPlainSequence()
```
    Specified by:
    
    getPlainSequence in interface net.bioclipse.core.domain.ISequence
  - toFasta
```
public String toFasta()
```
    Convert RichSequence to FASTA and return as String.
    
    Specified by:
    
    toFasta in interface net.bioclipse.core.domain.ISequence
  - getParsedResource
```
public Object getParsedResource()
```
    Returns the RichSequence
    
    Specified by:
    
    getParsedResource in interface net.bioclipse.core.domain.ISequence
  - setRichSequence
```
public void setRichSequence(org.biojavax.bio.seq.RichSequence richSequence)
```
  - getName
```
public String getName()
```
    Specified by:
    
    getName in interface net.bioclipse.core.domain.ISequence
  - getAdapter
```
public Object getAdapter(Class adapter)
```
    Specified by:
    
    getAdapter in interface org.eclipse.core.runtime.IAdaptable
    
    Overrides:
    
    getAdapter in class net.bioclipse.core.domain.BioObject