org.sigpath.tapestry.pages
Class AssembleReaction

java.lang.Object
  org.apache.tapestry.spec.BaseLocatable
      org.apache.tapestry.AbstractComponent
          org.apache.tapestry.BaseComponent
              org.apache.tapestry.AbstractPage
                  org.apache.tapestry.html.BasePage
                      org.sigpath.tapestry.pages.ValidatedPage
                          org.sigpath.tapestry.pages.AssembleReaction

All Implemented Interfaces:

EventListener, PageValidateListener, IComponent, IExternalPage, ILocatable, ILocationHolder, IPage, IRender

public abstract class AssembleReaction
extends ValidatedPage
implements IExternalPage

Field Summary

Fields inherited from class org.sigpath.tapestry.pages.ValidatedPage

_validationDelegate

Constructor Summary

AssembleReaction()

Method Summary

void	activateExternalPage(Object[] parameters, IRequestCycle cycle) Coming into the page from the menu.
void	addPublications(IRequestCycle cycle) opens the addPublications page.
void	addToLeft(IRequestCycle cycle) Add selected Chemicals the the Collection of reactants of the reaction.
void	addToModifiers(IRequestCycle cycle) Add selcted Chemicals the the Collection of modifiers of the reaction.
void	addToRight(IRequestCycle cycle) Add selcted Chemicals the the Collection of products of the reaction.
void	attachKinetic(IRequestCycle cycle) Attaches a kinetic to the Edited KineticInteraction.
void	beginEdit(IRequestCycle cycle, Reaction r) Sets externally the Kinetic property of the page.
Set	getAvailableChemicals()
abstract KineticBindings	getDefaultBinding()
String	getDescription(String bindingName) Bypasses the accessor of the bindingsDescriptions properties.
Reaction	getEditedKineticInteraction() Obtain the castor reaction that this page is assembling.
abstract Kinetic	getKinetic()
abstract String	getKineticName()
Collection	getMolecules(String[] spids) adds a set a reactions to a model from their spids.
IPropertySelectionModel	getUnitListFromExample(String name) Gets the concentratin unit model for a specific parameter.
UserComments	getUserComments()
void	removeFromLeft(IRequestCycle cycle) remove a chemical from the left member of a reaction.
void	removeFromModifiers(IRequestCycle cycle) Removes a chemical from the modifiers member of a reaction.
void	removeFromRight(IRequestCycle cycle) Removes a chemical from the right member of a reaction.
void	saveAndMoveOn(IRequestCycle cycle) Save the kineticInteraction (the reaction) into the database.
abstract void	setDefaultBinding(KineticBindings newval)
abstract void	setKinetic(Kinetic newval)
void	setKinetic(Reaction reaction, String kineticName, Kinetic kinetic) Attach a new kinetic to a reaction.
abstract void	setKineticName(String newName)
void	setUserComments(UserComments comments)

Methods inherited from class org.sigpath.tapestry.pages.ValidatedPage

getModelErrorsList, getValidationDelegate, initialize, moveTo, pageValidate, passErrorsToValidateDelegate, setErrorField

Methods inherited from class org.apache.tapestry.html.BasePage

getResponseWriter

Methods inherited from class org.apache.tapestry.AbstractPage

addPageDetachListener, addPageRenderListener, addPageValidateListener, attach, beginPageRender, beginResponse, detach, endPageRender, firePageBeginRender, firePageDetached, firePageEndRender, firePageValidate, getChangeObserver, getEngine, getExtendedId, getGlobal, getIdPath, getLocale, getNestedComponent, getOutputEncoding, getPageName, getRequestCycle, getVisit, removePageDetachListener, removePageRenderListener, removePageValidateListener, renderPage, setChangeObserver, setLocale, setPageName, setRequestCycle, validate

Methods inherited from class org.apache.tapestry.BaseComponent

addOuter, finishLoad, renderComponent

Methods inherited from class org.apache.tapestry.AbstractComponent

addAsset, addBody, addComponent, cleanupAfterRender, finishLoad, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, fireObservedChange, format, format, format, format, formatString, formatString, formatString, formatString, generateAttributes, getAsset, getAssets, getBeans, getBinding, getBindingNames, getBindings, getBody, getBodyCount, getComponent, getComponents, getContainer, getId, getListeners, getMessage, getMessages, getNamespace, getPage, getProperty, getSpecification, getString, pageEndRender, prepareForRender, render, renderBody, renderInformalParameters, setBinding, setContainer, setId, setNamespace, setPage, setProperty, setSpecification, toString

Methods inherited from class org.apache.tapestry.spec.BaseLocatable

getLocation, setLocation

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.apache.tapestry.IPage

addPageDetachListener, addPageRenderListener, addPageValidateListener, attach, beginPageRender, beginResponse, detach, endPageRender, getChangeObserver, getEngine, getGlobal, getLocale, getNestedComponent, getPageName, getRequestCycle, getResponseWriter, getVisit, removePageDetachListener, removePageRenderListener, removePageValidateListener, renderPage, setChangeObserver, setLocale, setPageName, setRequestCycle, validate

Methods inherited from interface org.apache.tapestry.IComponent

addAsset, addBody, addComponent, finishLoad, getAsset, getAssets, getBinding, getBindingNames, getBindings, getComponent, getComponents, getContainer, getExtendedId, getId, getIdPath, getMessage, getMessages, getNamespace, getPage, getProperty, getSpecification, getString, renderBody, setBinding, setContainer, setId, setNamespace, setPage, setProperty, setSpecification

Methods inherited from interface org.apache.tapestry.IRender

render

Methods inherited from interface org.apache.tapestry.ILocationHolder

setLocation

Methods inherited from interface org.apache.tapestry.ILocatable

getLocation

Constructor Detail

AssembleReaction

public AssembleReaction()

Method Detail

getDefaultBinding

public abstract KineticBindings getDefaultBinding()

setDefaultBinding

public abstract void setDefaultBinding(KineticBindings newval)

getKinetic

public abstract Kinetic getKinetic()

setKinetic

public abstract void setKinetic(Kinetic newval)

activateExternalPage

public void activateExternalPage(Object[] parameters,
                                 IRequestCycle cycle)

Coming into the page from the menu. Clear out any previous work.

Specified by:

activateExternalPage in interface IExternalPage

Parameters:

parameters - incoming parameters. not used

cycle - tapestry cycle

addPublications

public void addPublications(IRequestCycle cycle)

opens the addPublications page.

Parameters:

cycle -

addToLeft

public void addToLeft(IRequestCycle cycle)
               throws SigPathDatabaseException,
                      SigPathKineticException

Add selected Chemicals the the Collection of reactants of the reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

addToModifiers

public void addToModifiers(IRequestCycle cycle)
                    throws SigPathDatabaseException,
                           SigPathKineticException

Add selcted Chemicals the the Collection of modifiers of the reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

addToRight

public void addToRight(IRequestCycle cycle)
                throws SigPathDatabaseException,
                       SigPathKineticException

Add selcted Chemicals the the Collection of products of the reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

getMolecules

public Collection getMolecules(String[] spids)
                        throws SigPathDatabaseException

adds a set a reactions to a model from their spids. Should it be in a task?

Parameters:

spids -

Throws:

SigPathDatabaseException

attachKinetic

public void attachKinetic(IRequestCycle cycle)
                   throws SigPathDatabaseException

Attaches a kinetic to the Edited KineticInteraction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

getKineticName

public abstract String getKineticName()

getEditedKineticInteraction

public Reaction getEditedKineticInteraction()

Obtain the castor reaction that this page is assembling. The Reaction is stored in the Visit.

Returns:

setKinetic

public void setKinetic(Reaction reaction,
                       String kineticName,
                       Kinetic kinetic)
                throws SigPathDatabaseException

Attach a new kinetic to a reaction. Update this page with the symbol bindings that correspond to the new kinetic.

Parameters:

reaction - Reaction the kinetic is associated with.

kineticName - Name of the kinetic to set on reaction.

Throws:

SigPathDatabaseException

setKineticName

public abstract void setKineticName(String newName)

beginEdit

public void beginEdit(IRequestCycle cycle,
                      Reaction r)
               throws IOException,
                      ClassNotFoundException

Sets externally the Kinetic property of the page.

Parameters:

cycle -

r -

Throws:

IOException

ClassNotFoundException

getAvailableChemicals

public Set getAvailableChemicals()

Returns:

Returns the sum of the reactants, the products and the modifiers.

getDescription

public String getDescription(String bindingName)

Bypasses the accessor of the bindingsDescriptions properties.

Parameters:

bindingName -

Returns:

getUserComments

public UserComments getUserComments()

removeFromLeft

public void removeFromLeft(IRequestCycle cycle)
                    throws SigPathDatabaseException,
                           SigPathKineticException

remove a chemical from the left member of a reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

removeFromModifiers

public void removeFromModifiers(IRequestCycle cycle)
                         throws SigPathDatabaseException,
                                SigPathKineticException

Removes a chemical from the modifiers member of a reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

removeFromRight

public void removeFromRight(IRequestCycle cycle)
                     throws SigPathDatabaseException,
                            SigPathKineticException

Removes a chemical from the right member of a reaction.

Parameters:

cycle -

Throws:

SigPathDatabaseException

SigPathKineticException

saveAndMoveOn

public void saveAndMoveOn(IRequestCycle cycle)
                   throws SigPathDatabaseException

Save the kineticInteraction (the reaction) into the database.

Parameters:

cycle -

Throws:

SigPathDatabaseException

setUserComments

public void setUserComments(UserComments comments)

getUnitListFromExample

public IPropertySelectionModel getUnitListFromExample(String name)

Gets the concentratin unit model for a specific parameter. The list changes for each parameter so we aren't caching it.

Parameters:

name - the name of the parameter

Returns:

IPropertySelectionModel the model for the dropdown list