org.sigpath.adapter
Interface ReactionAdapter

All Known Implementing Classes:

ReactionAdapterImpl

public interface ReactionAdapter

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

Author:

Manda Wilson

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.
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.
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.

Method Detail

setDbManager

void setDbManager(SPDBManager dbm)

Set the database manager to use for this adapter.

Parameters:

dbm - Database manager to use for this adapter.

setDescription

void setDescription(String description)

getDescription

String getDescription()

getInteractionSite

String getInteractionSite(String spid)

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

Parameters:

spid - spid of chemical

Returns:

String residue range for the Chemical

See Also:

BioPolymer, ResidueRange, InteractionSites

removeInteractionSite

void removeInteractionSite(String spid)

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

Parameters:

spid - spid of chemical

See Also:

BioPolymer, ResidueRange, InteractionSites

addInteractionSite

void addInteractionSite(String spid,
                        String sites)

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

Parameters:

spid - spid of chemical

sites - interaction sites of chemical

See Also:

BioPolymer, ResidueRange, InteractionSites

addMoleculeToLeft

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.

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

void removeMoleculeFromLeft(String spid)

Remove the chemical specified by the SPID from the left-hand side of the reaction.

Parameters:

spid - spid of chemical

See Also:

Chemical

getMoleculesOnLeft

Collection getMoleculesOnLeft()

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

Returns:

Collection of MoleculeDisplay objects

See Also:

MoleculeDisplay, Chemical

addMoleculeToRight

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.

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

void removeMoleculeFromRight(String spid)

Remove the chemical specified by the SPID from the right-hand side of the reaction.

Parameters:

spid - spid of chemical

See Also:

Chemical

getMoleculesOnRight

Collection getMoleculesOnRight()

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

Returns:

Collection of MoleculeDisplay objects

See Also:

MoleculeDisplay, Chemical

addComplextoRight

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.

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

addModifiedChemicalToRight

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.

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

setKForward

void setKForward(double value,
                 String unit)
                 throws SigPathDatabaseException

Set the forward rate of the reaction.

Parameters:

value - forward rate of reaction

unit - unit of rate

Throws:

SigPathDatabaseException

getKForward

Parameter getKForward()

Get the forward rate of the reaction.

Returns:

Parameter

removeKForward

void removeKForward()

Remove the forward rate of the reaction.

setKBackward

void setKBackward(double value,
                  String unit)
                  throws SigPathDatabaseException

Set the backward rate of the reaction.

Parameters:

value - backward rate of reaction

unit - unit of rate

Throws:

SigPathDatabaseException

getKBackward

Parameter getKBackward()

Get the backward rate of the reaction.

Returns:

Parameter

removeKBackward

void removeKBackward()

Remove the backward rate of the reaction.

addLiteratureReference

void addLiteratureReference(String pubMedID)

Add a new PubMed ID.

Parameters:

pubMedID - PubMed ID

addLiteratureReferenceNote

void addLiteratureReferenceNote(String _publicationNote)

Add a new Publication Note.

Parameters:

_publicationNote - publication note

getLiteratureReferences

LiteratureReferences getLiteratureReferences()

Get collection of literature references.

Returns:

LiteratureReferences

See Also:

LiteratureReferences

removeAllLiteratureReferences

void removeAllLiteratureReferences()

Removes all LiteratureReferences from Reaction.

getSpid

String getSpid()

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

Returns:

String spid

See Also:

Reaction

saveReaction

boolean saveReaction()

Saves the reaction to the database.

updateReaction

void updateReaction()

Updates the reaction in the database.

validate

ValidationErrors validate()

Validate the reaction against all known scientific rules.

Returns:

ValidationErrors

See Also:

ValidationErrors

setUser

void setUser(String user_name)

Sets User

getUser

String getUser()

Gets User

getDateSubmitted

Date getDateSubmitted()

getDateLastModified

Date getDateLastModified()