Package 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
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Field Summary
Fields inherited from class net.bioclipse.core.domain.BioObject
resource
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Constructor Summary
ConstructorsConstructorDescriptionBiojavaSequence
(org.biojava.bio.seq.Sequence sequence) Create aBiojavaSequence
from aSequence
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Method Summary
Modifier and TypeMethodDescriptiongetAdapter
(Class adapter) getName()
Returns the RichSequencevoid
setRichSequence
(org.biojavax.bio.seq.RichSequence richSequence) 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
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Constructor Details
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BiojavaSequence
public BiojavaSequence(org.biojava.bio.seq.Sequence sequence) Create aBiojavaSequence
from aSequence
.- Parameters:
sequence
- sequence to create the object from
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BiojavaSequence
public BiojavaSequence()
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Method Details
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getPlainSequence
- Specified by:
getPlainSequence
in interfacenet.bioclipse.core.domain.ISequence
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toFasta
Convert RichSequence to FASTA and return as String.- Specified by:
toFasta
in interfacenet.bioclipse.core.domain.ISequence
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getParsedResource
Returns the RichSequence- Specified by:
getParsedResource
in interfacenet.bioclipse.core.domain.ISequence
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setRichSequence
public void setRichSequence(org.biojavax.bio.seq.RichSequence richSequence) -
getName
- Specified by:
getName
in interfacenet.bioclipse.core.domain.ISequence
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getAdapter
- Specified by:
getAdapter
in interfaceorg.eclipse.core.runtime.IAdaptable
- Overrides:
getAdapter
in classnet.bioclipse.core.domain.BioObject
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