diff --git a/app/assets/javascripts/helpers/mixin.catcher.js.coffee b/app/assets/javascripts/helpers/mixin.catcher.js.coffee index c5ca7e6f..26e23664 100644 --- a/app/assets/javascripts/helpers/mixin.catcher.js.coffee +++ b/app/assets/javascripts/helpers/mixin.catcher.js.coffee @@ -5,9 +5,9 @@ # # @mixin # -class Mixin.Catcher +Mixin.Catcher = - @ClassMethods: + ClassMethods: catchable: ( fns ) -> for name, fn of fns @::[ name ] = ( ) -> @@ -17,13 +17,4 @@ class Mixin.Catcher @_catcher.apply( @, [ @, e ] ) return undefined - @InstanceMethods: {} - - - - - - - - - + InstanceMethods: {} \ No newline at end of file diff --git a/doc/README.md.html b/doc/README.md.html index c40003f7..2dfdfecf 100644 --- a/doc/README.md.html +++ b/doc/README.md.html @@ -2,7 +2,7 @@ - Broyologramming Life API Documentation + CoffeeScript API Documentation @@ -130,21 +130,20 @@

Programming Life: Gigabase

Gigabase: Synthetic Biology Cell Modeling which is modeled by one or more differential equations. The proposed model describes an av- erage cell in a growing population of cells. Ordinary Differential Equations (ODEs) in this model describe the change of molecule concentrations in time.

Installation

Gigabase runs on Rails. You can load this repository onto your hard drive and directly use -it as a rails app. Just run bundle install and rake db: setup and you are good to go. +it as a rails app. Just run bundle install and rake db:setup and you are good to go. For windows users, some gems might not install and display a message such as not native build. Download the Ruby Devkit and run the bundle install command in mysys terminal. All the gems will then perfectly build. Don't forget you might need administrator rights.

Build Status

-

develop

develop

master

master

Pull Requests

We are always open to pull requests. After June 2013 the project will no longer be -fixed in direction, so more freedom on where to go. We do not allow pull requests on master -or release branches. Fork the repository, create a patch/feature/issue branch and -merge to develop.

Your code should be rdoc or codo/coffeedoc commented, assets should be /spec/ tested +

develop

develop

master

master

Pull Requests

After June 2013 the project will no longer have constraints so we could go any direction. +We do not allow pull requests on master or release branches. Fork the repository, create +a patch/feature/issue branch and merge to develop.

Your code should be rdoc or codo/coffeedoc commented, assets should be /spec/ tested and when applied should have /test/functional integration tests. Server side code should also be /test/ unit tested.

-

Broyologramming Life API Documentation

+

CoffeeScript API Documentation

Alphabetic Index

Extra File Listing

@@ -142,12 +142,6 @@

Class Listing A-Z

(Controller) -
  • - Catcher - - (Mixin) - -
  • Cell @@ -187,6 +181,12 @@

    Class Listing A-Z

    (View)
  • +
  • + Catcher + + (Mixin) + +
  • +
    +

    + - (void) onUpdate() +

    +
    +

    Runs when the user comes online

    +
    +
    +
    +
    +
    +

    + - (void) beforeUnload() +

    +
    +

    Runs when the user tries to unload the page

    +
    +
    +
    +
    +
    +

    + - (void) onUnload() +

    +
    +

    Runs when the user has unloaded the page

    +
    +
    +
    +
    +
    +

    + - (void) _catcher(source, e) +

    +
    +

    Catcher for the cell controller errors

    +
    +
    -

    - - (void) onPropertySet(caller, action) +

    + - (void) opPropertyAction(caller, action) (bound)

    @@ -944,25 +1075,6 @@

    Parameters:

    the action invoked -
    -
    -
    -

    - - (Boolean) isLocal() -

    -
    -

    Returns true if local cell

    -
    -
    -

    Returns:

    -
      -
    • - - (Boolean) - — - true if local, false if synced -
    • -
    @@ -1817,7 +1929,7 @@

    Returns:

    - - (self) run(from, to, base_values = [], callback, token, stepsize = 1e-9, iterations = 4000) + - (self) run(from, to, base_values = [], callback, token, options = {})

    Runs this cell

    @@ -1859,6 +1971,25 @@

    Returns:

    chainable instance +
    +
    +
    +

    + - (self) generateWarnings() +

    +
    +

    Generate warnings

    +
    +
    +

    Returns:

    +
      +
    • + + (self) + — + chainable self +
    • +
    @@ -1932,7 +2063,7 @@

    Returns:

    - - (jQuery.Promise) _save_modules() + - (jQuery.Promise) _save_modules(clone = false) (bound)

    @@ -1952,7 +2083,7 @@

    Returns:

    - - (JQuery.Promise) save() + - (JQuery.Promise) save(clone = false)

    Tries to save a module

    @@ -2030,7 +2161,7 @@

    Returns:

    -

    Instance Method Summary

    +

    Class Method Summary

    +

    Instance Method Summary

    + @@ -221,7 +224,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -239,6 +241,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -252,7 +255,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -294,11 +300,63 @@

    #redo, #_createAction

    +

    Class Method Details

    +
    +
    +

    + + (Object) getParameterDefaults(start) +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Parameters:

    +
      +
    • + start + + (Integer) + + — + the start value +
    • +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +
    +

    Constructor Details

    - - (void) constructor(params = {}, start = 1) + - (void) constructor(params = {}, start)

    Constructor for Cell Growth

    @@ -377,62 +435,13 @@

    Parameters:

    the step function -
    -
    -
    -

    - - (Object) _getParameterDefaults(start) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    -

    Instance Method Summary

    +

    Class Method Summary

    +

    Instance Method Summary

    + @@ -219,7 +222,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -237,6 +239,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -250,7 +253,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -292,11 +298,52 @@

    #redo, #_createAction

    +

    Class Method Details

    +
    +
    +

    + + (Object) getParameterDefaults() +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +
    +

    Constructor Details

    - - (void) constructor(params = {}, start = 1, prefix, consume = "p#int") + - (void) constructor(params = {})

    Constructor for DNA

    @@ -312,30 +359,6 @@

    Parameters:

    parameters for this module -
  • - start - - (Integer) - - — - the initial value of dna -
  • -
  • - prefix - - (String) - - — - the prefix name to use -
  • -
  • - consume - - (String) - - — - the metabolite converted to dna -
  • Options Hash: @@ -369,63 +392,11 @@

    -
    -

    Instance Method Details

    -
    -
    -

    - - (Object) _getParameterDefaults(start, prefix, consume) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    -
    -
    -

    Instance Method Summary

    +

    Class Method Summary

    +

    Instance Method Summary

    + @@ -219,7 +222,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -237,6 +239,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -250,7 +253,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -292,11 +298,52 @@

    #redo, #_createAction

    +

    Class Method Details

    +
    +
    +

    + + (Object) getParameterDefaults() +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +
    +

    Constructor Details

    - - (void) constructor(params = {}, start = 1, consume = "s#int") + - (void) constructor(params = {})

    Constructor for lipids

    @@ -312,22 +359,6 @@

    Parameters:

    parameters for this module -
  • - start - - (Integer) - - — - the initial value of lipid, defaults to 1 -
  • -
  • - consume - - (String) - - — - the substrate converted to lipid, defaults to "s#int" -
  • Options Hash: @@ -369,63 +400,11 @@

    -
    -

    Instance Method Details

    -
    -
    -

    - - (Object) _getParameterDefaults(start, consume) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    -
    -
    -

    Instance Method Summary

    +

    Class Method Summary

    +

    Instance Method Summary

    + @@ -255,7 +258,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -273,6 +275,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -286,7 +289,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -328,11 +334,52 @@

    #redo, #_createAction

    +

    Class Method Details

    +
    +
    +

    + + (Object) getParameterDefaults() +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +
    +

    Constructor Details

    - - (void) constructor(params = {}, start = 0, orig = "s#int", dest = "p#int", name = "enzyme") + - (void) constructor(params = {})

    Constructor for Metabolism

    @@ -348,38 +395,6 @@

    Parameters:

    parameters for this module -
  • - orig - - (String) - - — - the substrate to be converted -
  • -
  • - dest - - (String) - - — - the product after conversion -
  • -
  • - start - - (Integer) - - — - the initial value of metabolism, defaults to 0 -
  • -
  • - name - - (String) - - — - the name of the metabolism, defaults to "enzyme" -
  • Options Hash: @@ -445,63 +460,11 @@

    -
    -

    Instance Method Details

    -
    -
    -

    - - (Object) _getParameterDefaults(start, orig, dest, name) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    -
    -

    Class Method Summary

    Inherited Method Summary @@ -253,7 +253,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -271,6 +270,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -284,7 +284,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -328,6 +331,44 @@

    Class Method Details

    +
    +

    + + (Object) getParameterDefaults() +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +

    + (void) sext(params = {}, supply = 1, start = 1, name = "s") @@ -601,7 +642,7 @@

    Constructor Details

    - - (void) constructor(params = {}, start = 1, name, placement = Model.Metabolite.Outside, type = Model.Metabolite.Substrate) + - (void) constructor(params = {}, start, name, placement, type)

    Constructor for Metabolite

    @@ -617,38 +658,6 @@

    Parameters:

    parameters for this module -
  • - start - - (Integer) - - — - the initial value of metabolite, defaults to 1 -
  • -
  • - name - - (String) - - — - the name to use -
  • -
  • - placement - - (Integer) - - — - placement of this metabolite, defaults to Model.Metabolite.Outside -
  • -
  • - type - - (Boolean) - - — - type of this metabolite, defaults to Model.Metabolite.Substrate -
  • Options Hash: @@ -704,62 +713,13 @@

    Parameters:

    The parameters to define -
    -
    -
    -

    - - (Object) _getParameterDefaults(start, placement, type) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -

    - + (void) load(module_id, cell, callback) + + (void) load(module_id, cell, callback, clone = false)

    Loads a module

    @@ -737,25 +740,6 @@

    Parameters:

    the action invoked -
    -
    -
    -

    - - (Boolean) isLocal() -

    -
    -

    Returns true if this is a local instance

    -
    -
    -

    Returns:

    -
      -
    • - - (Boolean) - — - true if local, false if synced instance -
    • -
    @@ -1319,6 +1303,25 @@

    Returns:

    combined instance data +
    +
    +
    +

    + - (Array<String>) getMetaboliteProperties() +

    +
    +

    Gets the properties that have metabolites

    +
    +
    +

    Returns:

    +
      +
    • + + (Array<String>) + — + the properties +
    • +
    @@ -1390,7 +1393,7 @@

    Parameters:

    - - (void) save(cell) + - (void) save(cell, clone = false)

    @@ -1410,7 +1413,7 @@

    Parameters:

    -

    Instance Method Summary

    +

    Class Method Summary

    +

    Instance Method Summary

    + @@ -227,7 +230,6 @@

    #_defineDynamicProperties, #onActionDo, .extractId, - #isLocal, #getCompound, #getMetabolite, #getSubstrate, @@ -245,6 +247,7 @@

    #serialize, #_getModuleTemplate, #_getModuleInstanceData, + #getMetaboliteProperties, #_updateParameters, #_create, #save, @@ -258,7 +261,10 @@

    .extend, .include, - .concern + .concern, + .extractId, + #isLocal, + .parseDate

    Concern Method Summary @@ -300,11 +306,52 @@

    #redo, #_createAction

    +

    Class Method Details

    +
    +
    +

    + + (Object) getParameterDefaults() +

    +
    +

    Get parameter defaults array

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + default values +
    • +
    +
    +
    +
    +

    + + (Object) getParameterMetaData() +

    +
    +

    Get parameter metadata

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + metadata values +
    • +
    +
    +
    +

    Constructor Details

    - - (void) constructor(params = {}, start = 0, consume = "p#int", name = "Protein") + - (void) constructor(params = {})

    Constructor for Protein

    @@ -320,38 +367,6 @@

    Parameters:

    parameters for this module -
  • - consume - - (String, Array<String>) - - — - the metabolite to be converted -
  • -
  • - product - - (String) - - — - the product after conversion -
  • -
  • - start - - (Integer) - - — - the initial value of metabolism, defaults to 0 -
  • -
  • - name - - (String) - - — - the name of the metabolism, defaults to "enzym" -
  • Options Hash: @@ -401,63 +416,11 @@

    -
    -

    Instance Method Details

    -
    -
    -

    - - (Object) _getParameterDefaults(start, name, consume) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    -
    -

    Class Method Summary

    -
    - -
    -

    - - (Object) _getParameterDefaults(start, name, consume, type, direction, transported) -

    -
    -

    Get parameter defaults array

    -
    -
    -

    Parameters:

    -
      -
    • - start - - (Integer) - - — - the start value -
    • -
    -

    Returns:

    -
      -
    • - - (Object) - — - default values -
    • -
    -
    -
    -
    -

    - - (Object) _getParameterMetaData() -

    -
    -

    Get parameter metadata

    -
    -
    -

    Returns:

    -
      -
    • - - (Object) - — - metadata values -
    • -
    @@ -952,7 +955,7 @@

    Returns:

    @@ -514,16 +536,6 @@

    Parameters:

    Kills the cell view by resetting itself and its children

    -
    - -
    -

    - - (void) _createButtons() -

    -
    -

    Creates the interaction buttons

    -
    -
    @@ -601,7 +613,7 @@

    Parameters:

    - - (void) remove(view) + - (void) remove(view, kill = true)

    Removes a view from the container

    @@ -648,6 +660,36 @@

    Returns:

    the view which represents the given module +
    +
    +
    +

    + - (Module.View) getViewByName(name) +

    +
    +

    Get module view by name

    +
    +
    +

    Parameters:

    +
      +
    • + name + + (String) + + — + the module name for which to return the view +
    • +
    +

    Returns:

    +
      +
    • + + (Module.View) + — + the view which represents the given module +
    • +
    @@ -751,8 +793,8 @@

    Returns:

    -

    - - (void) onModuleAdd(cell, module) +

    + - (void) addModule(module) (bound)

    @@ -761,14 +803,6 @@

    Returns:

    Parameters:

      -
    • - cell - - (Model.Cell) - - — - cell added to -
    • module @@ -781,24 +815,16 @@

      Parameters:

    -

    - - (void) onModuleRemove(cell, module) +

    + - (void) removeModule(module) (bound)

    -

    On module removed, removed it from the cell

    +

    On module removed, remove it from the cell

    Parameters:

      -
    • - cell - - (Model.Cell) - - — - cell removed from -
    • module @@ -811,8 +837,8 @@

      Parameters:

    -

    - - (void) onSplineAdd(cell, spline) +

    + - (void) addSpline(spline) (bound)

    @@ -821,14 +847,6 @@

    Parameters:

    Parameters:

      -
    • - cell - - (Model.Cell) - - — - cell added to -
    • spline @@ -841,8 +859,8 @@

      Parameters:

    -

    - - (void) onSplineRemove(cell, spline) +

    + - (void) removeSpline(spline) (bound)

    @@ -851,14 +869,6 @@

    Parameters:

    Parameters:

      -
    • - cell - - (Model.Cell) - - — - cell removed from -
    • spline @@ -911,7 +921,7 @@

      Parameters:

    - - (void) kill() + - (void) kill(reset = false)

    Kills the collection

    +

    Parameters:

    +
      +
    • + reset + + (Boolean) + + — + if true, clears the internal array +
    • +
    @@ -308,13 +343,20 @@

    Parameters:

    Redraws this collection

    +
    +
    +
    +

    + - (void) each(func) +

    +
    -

    - - (void) onModuleCreationAborted(dummy) +

    + - (void) _onModuleCreationStart(dummy, module)

    -

    Gets called when a module creation was aborted

    +

    Gets called when a module creation is begin started

    Parameters:

    @@ -479,21 +547,35 @@

    Parameters:

    (View.DummyModule) — - the dummy for which the module creation was aborted + the dummy for which the module creation is begin started
    -

    - - (void) onModulePropertiesChange(source, key, value) +

    + - (void) _onModuleCreationAborted(dummy)

    -
    +
    +

    Gets called when a module creation was aborted

    +
    +
    +

    Parameters:

    +
      +
    • + dummy + + (View.DummyModule) + + — + the dummy for which the module creation was aborted +
    • +
    -

    - - (void) onModuleAdd(cell, module) +

    + - (void) _onModuleAdd(cell, module)

    On Module Added to the Cell

    @@ -521,8 +603,8 @@

    Parameters:

    -

    - - (void) onModuleRemove(cell, module) +

    + - (void) _onModuleRemove(cell, module)

    On Module Removed from the Cell

    @@ -789,8 +871,8 @@

    Returns:

    -

    - - (void) onModuleSelected(module, selected) +

    + - (void) _onModuleSelected(module, selected)

    Gets called when a module view selected.

    @@ -821,7 +903,7 @@

    Parameters:

    +
    +
    +

    + - (void) _drawEnumeration(id, key, value, params) +

    +
    +
    + TODO: + on clear/kill remove property from option +
    +

    Draws the input for an enumeration

    +
    +
    +

    Parameters:

    +
      +
    • + id + + (String) + + — + the form id +
    • +
    • + key + + (String) + + — + property to set +
    • +
    • + value + + (any) + + — + the current value +
    • +

    - - (void) _getModuleProperties() + - (Object) _getModuleProperties()

    Returns the properties of our module to be

    +

    Returns:

    +
      +
    • + + (Object) + — + the properties +
    • +
    +
    +
    +
    +

    + - (Object) _getModuleDefaults() +

    +
    +

    Returns the defaults of our module to be

    +
    +
    +

    Returns:

    +
      +
    • + + (Object) + — + the defaults +
    • +
    @@ -629,11 +766,44 @@

    Returns:

    -

    - - (void) _bindOnSelectableChange(key, selectable) +

    + - (void) _catcher(source, e) + (bound)

    -

    Binds an on change event to a selectable input that sets the key

    +

    Catcher function for Mixin.Catcher that will notificate any thrown Error on catchable methods

    +
    +
    +

    Parameters:

    +
      +
    • + e + + (Error) + + — + the error to notificate +
    • +
    +
    +
    +
    +

    + - (void) _reset() + (bound) +

    +
    +

    Resets the popover module

    +
    +
    +
    +
    +
    +

    + - (any) _getCurrentValueFor(key) +

    +
    +

    Gets the current value for a key

    Parameters:

    @@ -644,22 +814,52 @@

    Parameters:

    (String) — - property to set + the key to get + +

    Returns:

    +
    • - selectable + + (any) + — + the current value +
    • +
    +
    +
    +
    +

    + - (void) _triggerChange(key, value) +

    +
    +

    Triggers when changed a key

    +
    +
    +

    Parameters:

    +
      +
    • + key - (jQuery.Elem) + (String) + + — + the key of the change +
    • +
    • + value + + (any) — - the selectable to set it on + the new value
    -

    - - (void) onModuleCreationStarted(dummy) +

    + - (void) _onModuleCreationStarted(dummy)

    Will be called when the creation process of a module has started

    @@ -679,8 +879,8 @@

    Parameters:

    -

    - - (void) onModuleCreationAborted(dummy) +

    + - (void) _onModuleCreationAborted(dummy)

    Will be called when the creation process of a module has aborted

    @@ -700,8 +900,8 @@

    Parameters:

    -

    - - (void) onModuleCreationFinished(dummy) +

    + - (void) _onModuleCreationFinished(dummy)

    Will be called when the creation process of a module has finished

    @@ -724,7 +924,7 @@

    Parameters:

    +
    +
    +
    +

    + - (void) _setAction(event) + (bound) +

    +
    @@ -545,7 +568,7 @@

    Returns:

    +
    +
    +
    +

    + - (void) _resetButton() +

    +
    +

    Resets local button

    +
    +
    @@ -306,6 +340,43 @@

    Instance Method Details

    Shows the modal

    +
    + +
    +

    + - (void) _listCells(tbody, cells, origin) +

    +
    +

    Lists the cells from the origin in the tbody

    +
    +
    +

    Parameters:

    +
      +
    • + tbody + + (JQuery) + + — + The tbody +
    • +
    • + cells + + (Array) + + — + The list of cells +
    • +
    • + origin + + (String) + + — + The origin of the cells, either or some other origin +
    • +
    @@ -336,16 +407,39 @@

    Returns:

    - - (void) _prettifyDate(date) + - (String) _prettifyDate(date)

    -
    +
    +

    Prettifies date to say x seconds, minutes, hours ago

    +
    +
    +

    Parameters:

    +
      +
    • + date + + (Date) + + — + the date +
    • +
    +

    Returns:

    +
      +
    • + + (String) + — + pretty formatted string +
    • +
    +
    +

    + - (void) _reset() + (bound) +

    +
    +

    Resets this view

    +
    +
    @@ -1249,6 +1419,28 @@

    Parameters:

    Saves all changed properties to the module.

    +
    + +
    +

    + - (void) _catcher(source, e) + (bound) +

    +
    +

    Catcher function for Mixin.Catcher that will notificate any thrown Error on catchable methods

    +
    +
    +

    Parameters:

    +
      +
    • + e + + (Error) + + — + the error to notificate +
    • +
    @@ -1263,8 +1455,8 @@

    Parameters:

    -

    - - (void) onCompoundsChanged(cell, module) +

    + - (void) _onCompoundsChanged(cell, module)

    Runs when a compound is changed (added/removed)

    @@ -1292,8 +1484,8 @@

    Parameters:

    -

    - - (void) onMetabolitesChanged(cell, module) +

    + - (void) _onMetabolitesChanged(cell, module)

    Runs when a metabolite is changed (added/removed)

    @@ -1321,8 +1513,8 @@

    Parameters:

    -

    - - (void) onModuleDrawn(module) +

    + - (void) _onModuleDrawn(module)

    Gets called when a module view is drawn.

    @@ -1342,8 +1534,8 @@

    Parameters:

    -

    - - (void) onModuleSelected(module, selected) +

    + - (void) _onModuleSelected(module, selected)

    Gets called when a module view selected.

    @@ -1371,8 +1563,8 @@

    Parameters:

    -

    - - (void) onModuleHovered(module, hovered) +

    + - (void) _onModuleHovered(module, hovered)

    Gets called when a module view hovered.

    @@ -1400,8 +1592,8 @@

    Parameters:

    -

    - - (void) onModuleInvalidated(module, action) +

    + - (void) _onModuleInvalidated(module, action)

    Gets called when a module's parameters have changed

    @@ -1421,8 +1613,8 @@

    Parameters:

    -

    - - (void) onModuleCreationStarted() +

    + - (void) _onModuleCreationStarted()

    Gets called when a module creation process has started

    @@ -1434,7 +1626,7 @@

    Parameters:

    @@ -418,7 +422,7 @@

    Returns:

    -

    - - (void) onModuleRemoved(cell, module) +

    + - (void) _onModuleRemoved(cell, module) (bound)

    @@ -481,8 +533,8 @@

    Parameters:

    -

    - - (void) onModuleInvalidated(module) +

    + - (void) _onModuleInvalidated(module) (bound)

    @@ -503,8 +555,8 @@

    Parameters:

    -

    - - (void) onViewMoving(view, dx, dy, dt, ease) +

    + - (void) _onViewMoving(view, dx, dy, dt, ease) (bound)

    @@ -557,8 +609,8 @@

    Parameters:

    -

    - - (void) onViewMoved(module) +

    + - (void) _onViewMoved(module) (bound)

    @@ -579,8 +631,8 @@

    Parameters:

    -

    - - (void) onViewDrawn(module) +

    + - (void) _onViewDrawn(module) (bound)

    @@ -604,7 +656,7 @@

    Parameters: