org.sigpath.adapter
Class ReactionAdapterImpl

java.lang.Object
  org.sigpath.adapter.ReactionAdapterImpl

All Implemented Interfaces:

ReactionAdapter

public class ReactionAdapterImpl
extends Object
implements ReactionAdapter

Adapter class for creating a new Reaction and storing it to the database.

Version:

1.0

Author:

Manda Wilson

See Also:

Reaction

Constructor Summary

ReactionAdapterImpl(SigPathEntity spe, SPDBManager spdbm, ValidationErrors ve, String substrateSpid, String productSpid)
substrateSpid and productSpid can be null

ReactionAdapterImpl(String spid, SPDBManager spdbm, ValidationErrors ve)

ReactionAdapterImpl(ValidationErrors ve)
Deprecated. Use the DBTask framework instead. Adapters will be dropped form SigPath in the near future.

Method Summary

void	addComplextoRight(String name, String[] spids, boolean isSubstrate, boolean isProduct) Add a new complex to the right-hand side of the reaction.
void	addInteractionSite(String spid, String sites) Adds the interaction sites for the BioPolymer specified via a unique SPID.
void	addLiteratureReference(String pubMedID) Add a new PubMed ID.
void	addLiteratureReferenceNote(String _publicationNote) Add a new Publication Note.
void	addModifiedChemicalToRight(String spid, String name, String type, boolean isSubstrate, boolean isProduct) Add a new modified chemical to the right-hand side of the reaction.
void	addMoleculeToLeft(String spid, String sites, boolean isSubstrate, boolean isProduct) Add a new chemical to the left-hand side of the reaction.
void	addMoleculeToRight(String spid, String sites, boolean isSubstrate, boolean isProduct) Add a new chemical to the right-hand side of the reaction.
void	close() Use this to close the adapter and free resources.
Date	getDateLastModified()
Date	getDateSubmitted()
String	getDescription()
String	getInteractionSite(String spid) Gets the interaction site for the BioPolymer specified via a unique SPID.
Parameter	getKBackward() Get the backward rate of the reaction.
Parameter	getKForward() Get the forward rate of the reaction.
LiteratureReferences	getLiteratureReferences() Get collection of literature references.
Collection	getMoleculesOnLeft() Returns a Collection of MoleculeDisplay objects.
Collection	getMoleculesOnRight() Returns a Collection of MoleculeDisplay objects.
Reaction	getReaction() Returns the reaction.
Reaction	getReaction(EntityManager em) Temporary method to for FO9 testing Returns the reaction.
String	getSpid() Returns the reaction spid.
String	getUser() Gets User
void	removeAllLiteratureReferences() Removes all LiteratureReferences from Reaction.
void	removeInteractionSite(String spid) Removes the interaction site for the BioPolymer specified via a unique SPID.
void	removeKBackward() Remove the backward rate of the reaction.
void	removeKForward() Remove the forward rate of the reaction.
void	removeMoleculeFromLeft(String spid) Remove the chemical specified by the SPID from the left-hand side of the reaction.
void	removeMoleculeFromRight(String spid) Remove the chemical specified by the SPID from the right-hand side of the reaction.
boolean	saveReaction() Saves the reaction to the database.
void	setDbManager(SPDBManager dbm) Set the database manager to use for this adapter.
void	setDescription(String description)
void	setKBackward(double value, String unit) Set the backward rate of the reaction.
void	setKForward(double value, String unit) Set the forward rate of the reaction.
void	setUser(String user_name) Sets User
void	updateReaction() Updates the reaction in the database.
ValidationErrors	validate() Validate the reaction against all known scientific rules.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionAdapterImpl

public ReactionAdapterImpl(ValidationErrors ve)

Deprecated. Use the DBTask framework instead. Adapters will be dropped form SigPath in the near future.

Constructor initializes database manager and reaction. If a database error occurs an error is generated. The errors may be retrieved with the validate method.

See Also:

SPDBManager, Internal Transaction***

ReactionAdapterImpl

public ReactionAdapterImpl(String spid,
                           SPDBManager spdbm,
                           ValidationErrors ve)
                    throws SigPathDatabaseException

Throws:

SigPathDatabaseException

ReactionAdapterImpl

public ReactionAdapterImpl(SigPathEntity spe,
                           SPDBManager spdbm,
                           ValidationErrors ve,
                           String substrateSpid,
                           String productSpid)

substrateSpid and productSpid can be null

Method Detail

setDbManager

public void setDbManager(SPDBManager dbm)

Description copied from interface: ReactionAdapter

Set the database manager to use for this adapter.

Specified by:

setDbManager in interface ReactionAdapter

Parameters:

dbm - Database manager to use for this adapter.

close

public void close()

Use this to close the adapter and free resources.

addMoleculeToLeft

public void addMoleculeToLeft(String spid,
                              String sites,
                              boolean isSubstrate,
                              boolean isProduct)

Add a new chemical to the left-hand side of the reaction. Chemicals are specified via a unique SPID.

Specified by:

addMoleculeToLeft in interface ReactionAdapter

Parameters:

spid - spid of chemical

sites - interaction sites of chemical

isSubstrate - indicates if the molecule is a substrate

isProduct - indicates if the molecule is a product

See Also:

Chemical, ResidueRange, InteractionSites

removeMoleculeFromLeft

public void removeMoleculeFromLeft(String spid)

Remove the chemical specified by the SPID from the left-hand side of the reaction. If the spid has not been added to this side of the reaction an error is created. The errors may be retrieved with the validate method.

Specified by:

removeMoleculeFromLeft in interface ReactionAdapter

Parameters:

spid - spid of chemical

See Also:

Chemical

getMoleculesOnLeft

public Collection getMoleculesOnLeft()

Returns a Collection of MoleculeDisplay objects. There is one MoleculeDisplay object for each Chemical on the left-hand side of the reaction.

Specified by:

getMoleculesOnLeft in interface ReactionAdapter

Returns:

Collection of MoleculeDisplay objects

See Also:

MoleculeDisplay, Chemical

addMoleculeToRight

public void addMoleculeToRight(String spid,
                               String sites,
                               boolean isSubstrate,
                               boolean isProduct)

Add a new chemical to the right-hand side of the reaction. Chemicals are specified via a unique SPID.

Specified by:

addMoleculeToRight in interface ReactionAdapter

Parameters:

spid - spid of chemical

sites - interaction sites of chemical

isSubstrate - indicates if the molecule is a substrate

isProduct - indicates if the molecule is a product

See Also:

Chemical, ResidueRange, InteractionSites

removeMoleculeFromRight

public void removeMoleculeFromRight(String spid)

Remove the chemical specified by the SPID from the right-hand side of the reaction. If the spid has not been added to this side of the reaction an error is created. The errors may be retrieved with the validate method.

Specified by:

removeMoleculeFromRight in interface ReactionAdapter

Parameters:

spid - spid of chemical

See Also:

Chemical

getMoleculesOnRight

public Collection getMoleculesOnRight()

Returns a Collection of MoleculeDisplay objects. There is one MoleculeDisplay object for each Chemical on the right-hand side of the reaction.

Specified by:

getMoleculesOnRight in interface ReactionAdapter

Returns:

Collection of MoleculeDisplay objects

See Also:

MoleculeDisplay, Chemical

addComplextoRight

public void addComplextoRight(String name,
                              String[] spids,
                              boolean isSubstrate,
                              boolean isProduct)

Add a new complex to the right-hand side of the reaction. The complex is made up of the set of molecules specified by the given spids. If there is a database error an error is created. An error is created if a spid does not exist in the database or if the spid does not belong to a Chemical. The errors may be retrieved with the validate method.

Specified by:

addComplextoRight in interface ReactionAdapter

Parameters:

name - name of complex

spids - spids of molecules in complex

isSubstrate - indicates if the molecule is a substrate

isProduct - indicates if the molecule is a product

See Also:

Complex, Internal Transaction***

addModifiedChemicalToRight

public void addModifiedChemicalToRight(String spid,
                                       String name,
                                       String type,
                                       boolean isSubstrate,
                                       boolean isProduct)

Add a new modified chemical to the right-hand side of the reaction. Types of modified chemicals are given in SigPathConstants. If the source SPID does not exist in the database an error is created. If there is a database error an error is created. The errors may be retrieved with the validate method.

Specified by:

addModifiedChemicalToRight in interface ReactionAdapter

Parameters:

spid - spid of source chemical

name - name of modified chemical

type - type of modified chemical

isSubstrate - indicates if the molecule is a substrate

isProduct - indicates if the molecule is a product

See Also:

Chemical, Internal Transaction***

setKForward

public void setKForward(double value,
                        String unit)

Set the forward rate of the reaction.

Specified by:

setKForward in interface ReactionAdapter

Parameters:

value - forward rate of reaction

unit - unit of rate

getKForward

public Parameter getKForward()

Get the forward rate of the reaction.

Specified by:

getKForward in interface ReactionAdapter

Returns:

Parameter

removeKForward

public void removeKForward()

Remove the forward rate of the reaction.

Specified by:

removeKForward in interface ReactionAdapter

setKBackward

public void setKBackward(double value,
                         String unit)

Set the backward rate of the reaction.

Specified by:

setKBackward in interface ReactionAdapter

Parameters:

value - backward rate of reaction

unit - unit of rate

getKBackward

public Parameter getKBackward()

Get the backward rate of the reaction.

Specified by:

getKBackward in interface ReactionAdapter

Returns:

Parameter

removeKBackward

public void removeKBackward()

Remove the backward rate of the reaction.

Specified by:

removeKBackward in interface ReactionAdapter

addLiteratureReference

public void addLiteratureReference(String pubMedID)

Add a new PubMed ID.

Specified by:

addLiteratureReference in interface ReactionAdapter

Parameters:

pubMedID - PubMed ID

addLiteratureReferenceNote

public void addLiteratureReferenceNote(String _publicationNote)

Add a new Publication Note.

Specified by:

addLiteratureReferenceNote in interface ReactionAdapter

Parameters:

_publicationNote - publication note

removeAllLiteratureReferences

public void removeAllLiteratureReferences()

Removes all LiteratureReferences from Reaction.

Specified by:

removeAllLiteratureReferences in interface ReactionAdapter

getLiteratureReferences

public LiteratureReferences getLiteratureReferences()

Get collection of literature references.

Specified by:

getLiteratureReferences in interface ReactionAdapter

Returns:

LiteratureReferences

See Also:

LiteratureReferences

setUser

public void setUser(String user_name)

Description copied from interface: ReactionAdapter

Sets User

Specified by:

setUser in interface ReactionAdapter

getUser

public String getUser()

Description copied from interface: ReactionAdapter

Gets User

Specified by:

getUser in interface ReactionAdapter

getDateSubmitted

public Date getDateSubmitted()

Specified by:

getDateSubmitted in interface ReactionAdapter

getDateLastModified

public Date getDateLastModified()

Specified by:

getDateLastModified in interface ReactionAdapter

setDescription

public void setDescription(String description)

Specified by:

setDescription in interface ReactionAdapter

getDescription

public String getDescription()

Specified by:

getDescription in interface ReactionAdapter

saveReaction

public boolean saveReaction()

Saves the reaction to the database. If a database error occurs an error is created. The errors may be retrieved with the validate method.

Specified by:

saveReaction in interface ReactionAdapter

updateReaction

public void updateReaction()

Updates the reaction in the database. This only updates parameters and pubmed ids. If a database error occurs an error is created. The errors may be retrieved with the validate method.

Specified by:

updateReaction in interface ReactionAdapter

validate

public ValidationErrors validate()

Validate the reaction against all known scientific rules.

Specified by:

validate in interface ReactionAdapter

Returns:

ValidationErrors

See Also:

ValidationErrors

getSpid

public String getSpid()

Returns the reaction spid. Returns null if the reaction has not been created (& saved) yet.

Specified by:

getSpid in interface ReactionAdapter

Returns:

String spid

See Also:

Reaction

getReaction

public Reaction getReaction(EntityManager em)
                     throws SigPathDatabaseException

Temporary method to for FO9 testing Returns the reaction.

Returns:

Reaction

Throws:

SigPathDatabaseException

See Also:

Reaction

getReaction

public Reaction getReaction()
                     throws SigPathDatabaseException

Returns the reaction.

Returns:

Reaction

Throws:

SigPathDatabaseException

See Also:

Reaction

getInteractionSite

public String getInteractionSite(String spid)

Gets the interaction site for the BioPolymer specified via a unique SPID. If there is no interaction site for the BioPolymer an empty string is returned.

Specified by:

getInteractionSite in interface ReactionAdapter

Parameters:

spid - spid of chemical

Returns:

String residue range for the Chemical

See Also:

BioPolymer, ResidueRange, InteractionSites

removeInteractionSite

public void removeInteractionSite(String spid)

Removes the interaction site for the BioPolymer specified via a unique SPID.

Specified by:

removeInteractionSite in interface ReactionAdapter

Parameters:

spid - spid of chemical

See Also:

BioPolymer, ResidueRange, InteractionSites

addInteractionSite

public void addInteractionSite(String spid,
                               String sites)

Adds the interaction sites for the BioPolymer specified via a unique SPID.

Specified by:

addInteractionSite in interface ReactionAdapter

Parameters:

spid - spid of chemical

sites - interaction sites of chemical

See Also:

BioPolymer, ResidueRange, InteractionSites