net.bioclipse.biojava.domain

Class BiojavaSequence

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

Method Summary

Modifier and Type	Method and 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 RichSequence

Parameters:

richSequence -

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

Throws:

IOException

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