org.sigpath.adapter
Interface EnzymaticAdapter

All Known Implementing Classes:

EnzymaticAdapterImpl

public interface EnzymaticAdapter

Interface that provides database functionality regarding EnzymaticReaction objects.

Author:

Benjamin Chiang

See Also:

EnzymaticReaction

Method Summary

Date	getDateLastModified()
Date	getDateSubmitted()
String	getDescription()
EnzymaticReaction	getEnzymaticReaction() get the EnzymaticReaction object associated with this EnzymaticAdapter
MoleculeDisplay	getEnzyme() Get the Enzyme Display object
Parameter	getEnzymeConcentration()
String	getEnzymeConcentrationUnit()
double	getEnzymeConcentrationValue()
Parameter	getKBKP() Deprecated. Use getKBKPValue(), getKBKPUnit(), isKBKPDefined() methods instead.
String	getKbKpUnit()
double	getKbKpValue()
Parameter	getKm() Get the Km of the reaction.
String	getKmUnit()
double	getKmValue()
Parameter	getKp()
String	getKpUnit()
double	getKpValue() Deprecated. Use getKpValue(), getKpUnit, isKpDefined() instead.
ReactionAdapter	getReaction() Get the ReactionAdapter that this EnzymaticAdapter contains
String	getUser()
Parameter	getVMax() Get the VMax of the reaction.
String	getVMaxUnit()
double	getVMaxValue()
boolean	isKbKpDefined()
boolean	isKmDefined() Is the Km parameter defined for this enzymatic reaction?
boolean	isKpDefined()
boolean	isVMaxDefined()
void	removeEnzyme() Remove the Enzyme for the reaction
void	removeKBKP() Remove the ratio of K1 to Kp of the reaction.
void	removeKm() Remove the Km of the reaction.
void	removeKp() Remove the Kp of the reaction.
void	removeVMax() Remove the VMax of the reaction.
boolean	saveReaction() Save the EnzymaticReaction this EnzymaticAdapter contains
void	setDbManager(SPDBManager dbm) Set the database manager to use for this adapter.
void	setDescription(String description)
void	setEnzyme(String spid) Set the Enzyme for the reaction.
void	setKBKP(double v, String u) Set the K1 to Kp Ratio for the reaction.
void	setKm(double v, String u) Set the Km for the reaction.
void	setKp(double v, String u) Set the Kp for the reaction.
void	setReaction(ReactionAdapter reaction) Set the ReactionAdapter representing the Reaction that this EnzymaticAdapter contains
void	setUser(String user_name) Sets User
void	setVMax(double v, String u, double enzymeConcentration, String concentration_unit) Set the VMax for the reaction.
boolean	updateReaction() Update the EnzymaticReaction this EnzymaticAdapter contains
ValidationErrors	validate() Get the ValidationErrors that were produced when this EnzymaticAdapter was setup The EnzymaticAdapter will not save the EnzymaticReaction until no ValidationErrors exist

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.

setEnzyme

void setEnzyme(String spid)

Set the Enzyme for the reaction.

Parameters:

spid - spid of the enzyme to be set in the EnzymaticReaction

removeEnzyme

void removeEnzyme()

Remove the Enzyme for the reaction

getEnzyme

MoleculeDisplay getEnzyme()

Get the Enzyme Display object

Returns:

MoleculeDisplay object representing the enzyme that has been set to this reaction, or null if no enzyme has been set

setDescription

void setDescription(String description)

getDescription

String getDescription()

setKm

void setKm(double v,
           String u)

Set the Km for the reaction.

Parameters:

v - value of the Km Parameter

u - units of the Km Parameter

getKm

Parameter getKm()

Get the Km of the reaction.

Returns:

Parameter object representing the Km value that has been set

getKmValue

double getKmValue()

getKmUnit

String getKmUnit()

removeKm

void removeKm()

Remove the Km of the reaction.

isKmDefined

boolean isKmDefined()

Is the Km parameter defined for this enzymatic reaction?

Returns:

True if Km is defined, False otherwise.

setVMax

void setVMax(double v,
             String u,
             double enzymeConcentration,
             String concentration_unit)

Set the VMax for the reaction.

Parameters:

v - value of the VMax Parameter

u - units of the VMax Parameter

getVMax

Parameter getVMax()

Get the VMax of the reaction.

Returns:

Parameter object representing the VMax value that has been set

getVMaxValue

double getVMaxValue()

getVMaxUnit

String getVMaxUnit()

isVMaxDefined

boolean isVMaxDefined()

getEnzymeConcentration

Parameter getEnzymeConcentration()

getEnzymeConcentrationValue

double getEnzymeConcentrationValue()

getEnzymeConcentrationUnit

String getEnzymeConcentrationUnit()

removeVMax

void removeVMax()

Remove the VMax of the reaction.

setKp

void setKp(double v,
           String u)

Set the Kp for the reaction.

Parameters:

v - value of the Kp Parameter

u - units of the Kp Parameter

getKpValue

double getKpValue()

Deprecated. Use getKpValue(), getKpUnit, isKpDefined() instead.

Get the Kp of the reaction.

Returns:

Parameter object representing the Kp value that has been set

getKpUnit

String getKpUnit()

isKpDefined

boolean isKpDefined()

getKp

Parameter getKp()

removeKp

void removeKp()

Remove the Kp of the reaction.

setKBKP

void setKBKP(double v,
             String u)

Set the K1 to Kp Ratio for the reaction.

Parameters:

v - value of the K1/Kp Parameter

u - units of the K1/Kp Parameter

getKBKP

Parameter getKBKP()

Deprecated. Use getKBKPValue(), getKBKPUnit(), isKBKPDefined() methods instead.

Get the ratio of K1 to Kp.

Returns:

Parameter object representing the K1/Kp value that has been set

getKbKpValue

double getKbKpValue()

getKbKpUnit

String getKbKpUnit()

isKbKpDefined

boolean isKbKpDefined()

removeKBKP

void removeKBKP()

Remove the ratio of K1 to Kp of the reaction.

setReaction

void setReaction(ReactionAdapter reaction)

Set the ReactionAdapter representing the Reaction that this EnzymaticAdapter contains

Parameters:

reaction - ReactionAdapter representing the Reaction that this EnzymaticAdapter contains

getReaction

ReactionAdapter getReaction()

Get the ReactionAdapter that this EnzymaticAdapter contains

Returns:

ReactionAdapter

saveReaction

boolean saveReaction()
                     throws SigPathDatabaseException

Save the EnzymaticReaction this EnzymaticAdapter contains

Returns:

boolean true if reaction successfully saved, otherwise false

Throws:

SigPathDatabaseException

updateReaction

boolean updateReaction()
                       throws SigPathDatabaseException

Update the EnzymaticReaction this EnzymaticAdapter contains

Returns:

boolean true if reaction successfully updated, otherwise false

Throws:

SigPathDatabaseException

validate

ValidationErrors validate()

Get the ValidationErrors that were produced when this EnzymaticAdapter was setup The EnzymaticAdapter will not save the EnzymaticReaction until no ValidationErrors exist

Returns:

ValidationErrors errors that were encountered when setting up this EnzymaticAdapter

getEnzymaticReaction

EnzymaticReaction getEnzymaticReaction()

get the EnzymaticReaction object associated with this EnzymaticAdapter

Returns:

EnzymaticReaction associated with this EnzymaticAdapter

setUser

void setUser(String user_name)

Sets User

getUser

String getUser()

getDateSubmitted

Date getDateSubmitted()

getDateLastModified

Date getDateLastModified()