uk.ac.ebi.intact.model
Class ProteinImpl

java.lang.Object
  |
  +--uk.ac.ebi.intact.model.IntactObjectImpl
        |
        +--uk.ac.ebi.intact.model.BasicObjectImpl
              |
              +--uk.ac.ebi.intact.model.AnnotatedObjectImpl
                    |
                    +--uk.ac.ebi.intact.model.InteractorImpl
                          |
                          +--uk.ac.ebi.intact.model.ProteinImpl

All Implemented Interfaces:

AnnotatedObject, BasicObject, IntactObject, Interactor, Protein, java.io.Serializable

public class ProteinImpl

extends InteractorImpl

implements Protein

Represents a protein or peptide. The object should only contain the minimum information relevant for IntAct, most information should only be retrieved by the xref.

Version:

$Id: ProteinImpl.java,v 1.1 2004/01/31 11:32:09 skerrien Exp $

Author:

hhe

See Also:

Serialized Form

Field Summary

Fields inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

annotations, curator, curatorAc, fullName, references, shortLabel, xrefs

Fields inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

ac, NEW_LINE

Constructor Summary

ProteinImpl(Institution owner, BioSource source, java.lang.String shortLabel)
Creates a valid Protein instance.

Method Summary

void	addFeature(Feature feature)
void	addModification(Modification modification)
boolean	equals(java.lang.Object o) Equality for Proteins is currently based on equality for Interactors, the sequence and the crc64 checksum.
java.lang.String	getCrc64()
CvProteinForm	getCvProteinForm()
java.lang.String	getCvProteinFormAc()
java.util.Collection	getFeatures()
Protein	getFormOf()
java.lang.String	getFormOfAc()
java.util.Collection	getModifications()
java.lang.String	getSequence()
int	hashCode() Remember that hashCode and equals methods has to be develop in parallel since : if a.equals(b) then a.hoshCode() == b.hashCode() The other way round is NOT true.
void	removeFeature(Feature feature)
void	removeModification(Modification modification)
void	setCrc64(java.lang.String crc64)
void	setCvProteinForm(CvProteinForm cvProteinForm)
void	setCvProteinFormAc(java.lang.String cvProteinFormAc)
void	setFeatures(java.util.Collection someFeature)
void	setFormOf(Protein protein)
void	setFormOfAc(java.lang.String ac)
void	setModifications(java.util.Collection someModification)
void	setSequence(IntactHelper helper, java.lang.String aSequence) If there is existing sequence (and chunks), reuse existing chunk in order to save AC. The update is canceled if the sequence is null or the same.
void	setSequence(IntactHelper helper, java.lang.String aSequence, java.lang.String crc64)

Methods inherited from class uk.ac.ebi.intact.model.InteractorImpl

addActiveInstance, addProduct, getActiveInstances, getBioSource, getBioSourceAc, getProducts, removeActiveInstance, removeProduct, setActiveInstances, setBioSource, setBioSourceAc, setProducts, toString

Methods inherited from class uk.ac.ebi.intact.model.AnnotatedObjectImpl

addAlias, addAnnotation, addReference, addXref, getAliases, getAnnotations, getCurator, getCuratorAc, getFullName, getReferences, getShortLabel, getXrefs, removeAlias, removeAnnotation, removeReference, removeXref, setAliases, setAnnotation, setCurator, setCuratorAc, setFullName, setReferences, setShortLabel, setXrefs, update, updateUniqueAnnotation

Methods inherited from class uk.ac.ebi.intact.model.BasicObjectImpl

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from class uk.ac.ebi.intact.model.IntactObjectImpl

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.ebi.intact.model.Interactor

addActiveInstance, addProduct, getActiveInstances, getBioSource, getBioSourceAc, getProducts, removeActiveInstance, removeProduct, setActiveInstances, setBioSource, setBioSourceAc, setProducts, toString

Methods inherited from interface uk.ac.ebi.intact.model.AnnotatedObject

addAlias, addAnnotation, addReference, addXref, getAliases, getAnnotations, getCurator, getCuratorAc, getFullName, getReferences, getShortLabel, getXrefs, removeAlias, removeAnnotation, removeReference, removeXref, setAliases, setAnnotation, setCurator, setCuratorAc, setFullName, setReferences, setShortLabel, setXrefs, update, updateUniqueAnnotation

Methods inherited from interface uk.ac.ebi.intact.model.BasicObject

addEvidence, getEvidences, getOwner, getOwnerAc, removeEvidence, setEvidences, setOwner, setOwnerAc

Methods inherited from interface uk.ac.ebi.intact.model.IntactObject

getAc, getCreated, getUpdated, setAc, setCreated, setUpdated

Constructor Detail

ProteinImpl

public ProteinImpl(Institution owner,
                   BioSource source,
                   java.lang.String shortLabel)

Creates a valid Protein instance. A valid Protein must have at least an onwer, a short label to refer to it and a biological source specified. A side-effect of this constructor is to set the created and updated fields of the instance to the current time.

Parameters:

owner - The 'owner' of the Protein (what does this mean in real terms??)

source - The biological source of the Protein observation

shortLabel - A memorable label used to refer to the Protein instance

Throws:

java.lang.NullPointerException - thrown if any parameters are null.

Method Detail

getSequence

public java.lang.String getSequence()

Specified by:

getSequence in interface Protein

setSequence

public void setSequence(IntactHelper helper,
                        java.lang.String aSequence,
                        java.lang.String crc64)
                 throws IntactException

Specified by:

setSequence in interface Protein

Parameters:

helper -

aSequence -

crc64 -

Throws:

IntactException

setSequence

public void setSequence(IntactHelper helper,
                        java.lang.String aSequence)
                 throws IntactException

If there is existing sequence (and chunks), reuse existing chunk in order to save AC.
The update is canceled if the sequence is null or the same.

Specified by:

setSequence in interface Protein

Parameters:

helper -

aSequence - the sequence to update in the protein

Throws:

IntactException

getCrc64

public java.lang.String getCrc64()

Specified by:

getCrc64 in interface Protein

setCrc64

public void setCrc64(java.lang.String crc64)

Specified by:

setCrc64 in interface Protein

getFormOf

public Protein getFormOf()

Specified by:

getFormOf in interface Protein

setFormOf

public void setFormOf(Protein protein)

Specified by:

setFormOf in interface Protein

getCvProteinForm

public CvProteinForm getCvProteinForm()

Specified by:

getCvProteinForm in interface Protein

setCvProteinForm

public void setCvProteinForm(CvProteinForm cvProteinForm)

Specified by:

setCvProteinForm in interface Protein

setFeatures

public void setFeatures(java.util.Collection someFeature)

Specified by:

setFeatures in interface Protein

getFeatures

public java.util.Collection getFeatures()

Specified by:

getFeatures in interface Protein

addFeature

public void addFeature(Feature feature)

Specified by:

addFeature in interface Protein

removeFeature

public void removeFeature(Feature feature)

Specified by:

removeFeature in interface Protein

setModifications

public void setModifications(java.util.Collection someModification)

Specified by:

setModifications in interface Protein

getModifications

public java.util.Collection getModifications()

Specified by:

getModifications in interface Protein

addModification

public void addModification(Modification modification)

Specified by:

addModification in interface Protein

removeModification

public void removeModification(Modification modification)

Specified by:

removeModification in interface Protein

getCvProteinFormAc

public java.lang.String getCvProteinFormAc()

Specified by:

getCvProteinFormAc in interface Protein

setCvProteinFormAc

public void setCvProteinFormAc(java.lang.String cvProteinFormAc)

Specified by:

setCvProteinFormAc in interface Protein

getFormOfAc

public java.lang.String getFormOfAc()

Specified by:

getFormOfAc in interface Protein

setFormOfAc

public void setFormOfAc(java.lang.String ac)

Specified by:

setFormOfAc in interface Protein

equals

public boolean equals(java.lang.Object o)

Equality for Proteins is currently based on equality for Interactors, the sequence and the crc64 checksum.

Specified by:

equals in interface Protein

Overrides:

equals in class InteractorImpl

Parameters:

o - The object to check

Returns:

true if the parameter equals this object, false otherwise

See Also:

InteractorImpl

hashCode

public int hashCode()

Remember that hashCode and equals methods has to be develop in parallel since : if a.equals(b) then a.hoshCode() == b.hashCode() The other way round is NOT true. Unless it could break consistancy when storing object in a hash-based collection such as HashMap...

Specified by:

hashCode in interface Protein

Overrides:

hashCode in class InteractorImpl

Returns:

hash code of the object.