edu.mssm.crover.webapps.dimlib.datamodel
Class MutationManager

java.lang.Object
  |
  +--edu.mssm.crover.webapps.dimlib.datamodel.MutationManager

public class MutationManager

extends java.lang.Object

Provides access to the persistent DimLib datamodel.

Author:

Fabien Campagne, luce

Constructor Summary

MutationManager()
Constructs a new mutation manager.

Method Summary

void	abort() Aborts the transaction.
void	addGifXMLtoMP(MutantProtein mp, GifMap xml) Updates the MutantProtein to include the mapping information for the GIF image.
void	addGifXMLtoWTP(WildTypeProtein wtp, GifMap xml) Updates the WildTypeProtein to include the mapping information for the GIF image.
void	begin() Begins a transaction.
void	commit() Commits the transaction.
MutantProtein	createMutantProtein(WildTypeProtein wildtype) Creates a MutantProtein.
WildTypeProtein	createWildTypeProtein(java.lang.String name, java.lang.String family) Creates a WildTypeProtein.
boolean	delete(java.lang.Object object) Deletes a persistent object.
boolean	doesACExist(java.lang.String ac, java.lang.String org) Searches for this accession code in the database.
java.util.Collection	getAllArcadiaAlns() Queries the database for all stored ArcadiaAlignments.
java.util.Collection	getAllFamilies() Returns a Collection of all the families associated with WildTypeProteins in the database.
java.util.Collection	getAllMutantProteins() Returns all MutantProteins in the database.
java.util.Collection	getAllSNPs() Returns all the SNPs in the database.
java.util.Collection	getAllWTProteins() Returns all WildTypeProteins in the database.
ArcadiaAlignment	getArcadiaAlnByID(java.lang.String id) Queries the database for the ArcadiaAlignments with the specific ID.
java.util.Collection	getArcadiaAlnsByKeyword(java.lang.String keyword) Queries the database for ArcadiaAlignments which contain the keyword in either the name or description fields.
java.util.Collection	getArcadiaAlnsByName(java.lang.String name) Queries the database for ArcadiaAlignments whose short_name matches name.
java.util.Collection	getArcadiaAlnsBySeq(java.lang.String keyword) Queries the database for ArcadiaAlignments containing the ArcadiaAlignedSequence seq defined by this keyword.
java.util.Collection	getCorrelatedSNPs() Returns all the SNPs which occur at positions which already have mutations entered for them (for the same protein) in the database.
GenericPosition	getGenericPosition(Mutation mutation, MutantProtein mutant, WildTypeProtein protein) Returns the generic position associated for this mutation.
MutantProtein	getMutantProteinById(java.lang.String id) Queries the database for a MutantProtein by its ID.
java.util.Collection	getMutantProteins(java.lang.String keyword) Queries the database for the presence of a keyword in a MutantProtein.
java.util.Collection	getMutantProteinsByAc(java.lang.String ac) Queries the database for MutantProteins by the accession code of their parent WildTypeProtein.
java.util.Collection	getMutantProteinsByOrg(java.lang.String organism) Queries the database for MutantProteins by the organism of their parent WildTypeProtein.
java.util.Collection	getMutantProteinsByPosition(java.lang.String q) Queries the database for MutantProteins with a mutation at a given position.
java.util.Collection	getMutantProteinsBySubmitter(java.lang.String name) Queries the database for MutantProteins by submitter.
java.util.Collection	getMutantProteinsByWTP(WildTypeProtein w) Queries the database for MutantProteins associated with a WildTypeProtein.
java.util.Collection	getMutantProteinsCriteria()
javax.jdo.PersistenceManager	getPersistenceManager()
java.util.Collection	getProteinsCriteria()
javax.jdo.Transaction	getTrans()
java.util.Collection	getWTPByPosition(java.lang.String q) Queries the database for WildTypeProteins which have MutantProteins with mutations at a given position.
java.util.Collection	getWTPBySubmitter(java.lang.String name) Queries the database for WildTypeProteins submitted by a particular submitter.
WildTypeProtein	getWTProteinByAcOrg(java.lang.String ac, java.lang.String organism) Queries the database for a WildTypeProtein by accession code and organism.
WildTypeProtein	getWTProteinById(java.lang.String id) Queries the database for WildTypeProteins by DiMLib ID.
WildTypeProtein	getWTProteinByMID(java.lang.String id) Queries the database for a WildTypeProtein by mutant id.
WildTypeProtein	getWTProteinByName(java.lang.String name, java.lang.String family, java.lang.String organism) Queries the database for a WildTypeProtein by name and family and organism.
java.util.Collection	getWTProteins(java.lang.String keyword) Queries the database for the presence of a keyword in a WildTypeProtein.
java.util.Collection	getWTProteinsByAc(java.lang.String ac) Queries the database for WildTypeProteins by accession code.
java.util.Collection	getWTProteinsByOrg(java.lang.String organism) Queries the database for a WildTypeProtein by organism.
boolean	isAcInDb(java.lang.String ac, java.lang.String db) Searches for this accession code in the Arcadia database.
boolean	isAutoCommit()
static void	main(java.lang.String[] args)
java.lang.String	mutantExists(WildTypeProtein wtp, MutantProtein mp) Checks if the MutantProtein is already associated with the given WildTypeProtein.
java.util.Collection	selectMutantProteinsByPosition(java.util.Collection c, java.lang.String q)
void	setAutoCommit(boolean autoCommit) Sets auto commit on this manager.
void	setPersistenceManager(javax.jdo.PersistenceManager persistenceManager)
java.lang.String	snpExists(WildTypeProtein wtp, SNP snp) Checks if the SNP is already associated with the given WildTypeProtein.
void	submitAccessionCode(AccessionCode ac) Submits an AccessionCode.
void	submitArcadiaAlignment(ArcadiaAlignment aln)
void	submitMutantProtein(MutantProtein mp) Submits a MutantProtein.
void	submitSNP(SNP snp)
void	submitWildTypeProtein(WildTypeProtein wtp) Submits a WildTypeProtein.
void	updateWildTypeProtein(WildTypeProtein wp, java.util.Collection mp) Updates the MutantProteins associated with a WildTypeProtein.
void	updateWildTypeProtein(WildTypeProtein wp, MutantProtein mp) Updates the MutantProteins associated with a WildTypeProtein.
void	updateWildTypeProtein(WildTypeProtein wp, SNP snp)
void	updateWTPRefs(WildTypeProtein wtp, java.lang.String database, java.lang.String ac) Updates the ExternalReferences associated with a WildTypeProtein.
boolean	wtpExists(WildTypeProtein wtp) Checks if the WildTypeProtein is already in the database.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MutationManager

public MutationManager()

Constructs a new mutation manager. Auto commit is set to true by default.

Method Detail

getGenericPosition

public GenericPosition getGenericPosition(Mutation mutation,
                                          MutantProtein mutant,
                                          WildTypeProtein protein)

Returns the generic position associated for this mutation. The mutation is part of a mutant.

Parameters:

protein - The wild type sequence.

mutant - The mutant which contains the mutation.

mutation - The mutation for which a generic position should be computed.

getAllWTProteins

public java.util.Collection getAllWTProteins()

Returns all WildTypeProteins in the database.

getWTProteins

public java.util.Collection getWTProteins(java.lang.String keyword)

Queries the database for the presence of a keyword in a WildTypeProtein. The keyword can appear in either the the protein name or the protein family.

getWTProteinsByAc

public java.util.Collection getWTProteinsByAc(java.lang.String ac)

Queries the database for WildTypeProteins by accession code.

getWTProteinById

public WildTypeProtein getWTProteinById(java.lang.String id)

Queries the database for WildTypeProteins by DiMLib ID.

getWTProteinByAcOrg

public WildTypeProtein getWTProteinByAcOrg(java.lang.String ac,
                                           java.lang.String organism)

Queries the database for a WildTypeProtein by accession code and organism.

getWTProteinsByOrg

public java.util.Collection getWTProteinsByOrg(java.lang.String organism)

Queries the database for a WildTypeProtein by organism.

getWTProteinByMID

public WildTypeProtein getWTProteinByMID(java.lang.String id)

Queries the database for a WildTypeProtein by mutant id. Searches for a mutant with that id, and returns the WildTypeProtein associated with it.

getWTProteinByName

public WildTypeProtein getWTProteinByName(java.lang.String name,
                                          java.lang.String family,
                                          java.lang.String organism)

Queries the database for a WildTypeProtein by name and family and organism.

getWTPBySubmitter

public java.util.Collection getWTPBySubmitter(java.lang.String name)

Queries the database for WildTypeProteins submitted by a particular submitter.

getWTPByPosition

public java.util.Collection getWTPByPosition(java.lang.String q)

Queries the database for WildTypeProteins which have MutantProteins with mutations at a given position.

getAllMutantProteins

public java.util.Collection getAllMutantProteins()

Returns all MutantProteins in the database.

getProteinsCriteria

public java.util.Collection getProteinsCriteria()

getMutantProteinsCriteria

public java.util.Collection getMutantProteinsCriteria()

getMutantProteins

public java.util.Collection getMutantProteins(java.lang.String keyword)

Queries the database for the presence of a keyword in a MutantProtein. The keyword can appear in the description field (mutant-specific) or in the accession code field, the protein name or the protein family of the WildTypeProtein from which this mutant originates.

getMutantProteinsByAc

public java.util.Collection getMutantProteinsByAc(java.lang.String ac)

Queries the database for MutantProteins by the accession code of their parent WildTypeProtein.

getMutantProteinsByOrg

public java.util.Collection getMutantProteinsByOrg(java.lang.String organism)

Queries the database for MutantProteins by the organism of their parent WildTypeProtein.

getMutantProteinById

public MutantProtein getMutantProteinById(java.lang.String id)

Queries the database for a MutantProtein by its ID.

getMutantProteinsBySubmitter

public java.util.Collection getMutantProteinsBySubmitter(java.lang.String name)

Queries the database for MutantProteins by submitter.

getMutantProteinsByPosition

public java.util.Collection getMutantProteinsByPosition(java.lang.String q)

Queries the database for MutantProteins with a mutation at a given position.

getMutantProteinsByWTP

public java.util.Collection getMutantProteinsByWTP(WildTypeProtein w)

Queries the database for MutantProteins associated with a WildTypeProtein.

getAllArcadiaAlns

public java.util.Collection getAllArcadiaAlns()

Queries the database for all stored ArcadiaAlignments.

getArcadiaAlnByID

public ArcadiaAlignment getArcadiaAlnByID(java.lang.String id)

Queries the database for the ArcadiaAlignments with the specific ID.

getArcadiaAlnsByName

public java.util.Collection getArcadiaAlnsByName(java.lang.String name)

Queries the database for ArcadiaAlignments whose short_name matches name.

getArcadiaAlnsByKeyword

public java.util.Collection getArcadiaAlnsByKeyword(java.lang.String keyword)

Queries the database for ArcadiaAlignments which contain the keyword in either the name or description fields.

getArcadiaAlnsBySeq

public java.util.Collection getArcadiaAlnsBySeq(java.lang.String keyword)

Queries the database for ArcadiaAlignments containing the ArcadiaAlignedSequence seq defined by this keyword. The keyword can be part of the name, family or the accession code.

getAllSNPs

public java.util.Collection getAllSNPs()

Returns all the SNPs in the database.

getCorrelatedSNPs

public java.util.Collection getCorrelatedSNPs()

Returns all the SNPs which occur at positions which already have mutations entered for them (for the same protein) in the database.

getAllFamilies

public java.util.Collection getAllFamilies()

Returns a Collection of all the families associated with WildTypeProteins in the database.

wtpExists

public boolean wtpExists(WildTypeProtein wtp)

Checks if the WildTypeProtein is already in the database. Uses the protein name, family and organism, which are the only fields that are obligatory.

mutantExists

public java.lang.String mutantExists(WildTypeProtein wtp,
                                     MutantProtein mp)

Checks if the MutantProtein is already associated with the given WildTypeProtein. If it is, returns the ID of the mutant which already exists in the database.

doesACExist

public boolean doesACExist(java.lang.String ac,
                           java.lang.String org)

Searches for this accession code in the database. Returns true if this accession code is already associated with this organism.

isAcInDb

public boolean isAcInDb(java.lang.String ac,
                        java.lang.String db)

Searches for this accession code in the Arcadia database. Returns true if this accession code is found in the given database. In this case, the organism field is irrelevant (we can have several organisms with the accession code/database information for the same protein).

snpExists

public java.lang.String snpExists(WildTypeProtein wtp,
                                  SNP snp)

Checks if the SNP is already associated with the given WildTypeProtein. If it is, returns the ID of the mutant which already exists in the database.

submitWildTypeProtein

public void submitWildTypeProtein(WildTypeProtein wtp)

Submits a WildTypeProtein.

Parameters:

wtp - is the instance of the WildTypeProtein that is to be made persistent.

createWildTypeProtein

public WildTypeProtein createWildTypeProtein(java.lang.String name,
                                             java.lang.String family)

Creates a WildTypeProtein.

Parameters:

family - Name of the family to which the new protein will belong.

updateWildTypeProtein

public void updateWildTypeProtein(WildTypeProtein wp,
                                  java.util.Collection mp)

Updates the MutantProteins associated with a WildTypeProtein.

Parameters:

wp - the WildTypeProtein to be updated.

mp - Collection of MutantProteins to be added to the WildTypeProtein.

updateWildTypeProtein

public void updateWildTypeProtein(WildTypeProtein wp,
                                  SNP snp)

updateWTPRefs

public void updateWTPRefs(WildTypeProtein wtp,
                          java.lang.String database,
                          java.lang.String ac)

Updates the ExternalReferences associated with a WildTypeProtein.

Parameters:

database - the database which the new reference refers to.

ac - the accession code which the new reference refers to.

updateWildTypeProtein

public void updateWildTypeProtein(WildTypeProtein wp,
                                  MutantProtein mp)

Updates the MutantProteins associated with a WildTypeProtein.

Parameters:

wp - the WildTypeProtein to be updated.

mp - MutantProtein to be added to the WildTypeProtein.

addGifXMLtoWTP

public void addGifXMLtoWTP(WildTypeProtein wtp,
                           GifMap xml)

Updates the WildTypeProtein to include the mapping information for the GIF image.

submitMutantProtein

public void submitMutantProtein(MutantProtein mp)

Submits a MutantProtein.

Parameters:

mp - - the instance of MutantProtein to be made persistent.

createMutantProtein

public MutantProtein createMutantProtein(WildTypeProtein wildtype)

Creates a MutantProtein.

Parameters:

wildtype - - the WildTypeProtein which is the origin of this MutantProtein.

addGifXMLtoMP

public void addGifXMLtoMP(MutantProtein mp,
                          GifMap xml)

Updates the MutantProtein to include the mapping information for the GIF image.

submitAccessionCode

public void submitAccessionCode(AccessionCode ac)

Submits an AccessionCode.

Parameters:

ac - is the instance of the AccessionCode that is to be made persistent.

submitArcadiaAlignment

public void submitArcadiaAlignment(ArcadiaAlignment aln)

submitSNP

public void submitSNP(SNP snp)

selectMutantProteinsByPosition

public java.util.Collection selectMutantProteinsByPosition(java.util.Collection c,
                                                           java.lang.String q)

delete

public boolean delete(java.lang.Object object)

Deletes a persistent object. The peristent object is no longer persistent when this method succeeds.

Returns:

true when the object has been deleted. false if the object could not be deleted.

getTrans

public javax.jdo.Transaction getTrans()

begin

public void begin()

Begins a transaction.

commit

public void commit()

Commits the transaction. See begin() to start the transaction.

abort

public void abort()

Aborts the transaction. See begin() to start the transaction.

getPersistenceManager

public javax.jdo.PersistenceManager getPersistenceManager()

setPersistenceManager

public void setPersistenceManager(javax.jdo.PersistenceManager persistenceManager)

isAutoCommit

public boolean isAutoCommit()

setAutoCommit

public void setAutoCommit(boolean autoCommit)

Sets auto commit on this manager.

Parameters:

autoCommit - When set to true, the manager will commit a change each time a method succeeds. When false, the client must manage transactions explicitly. Explicit management of transactions can be performed by using the start(), commit() and abort() methods of the manager.

See Also:

begin(), commit(), abort()

main

public static void main(java.lang.String[] args)