.. header:: 
   ###Title###

.. footer:: 
   ###Page###


================
The Virtual Leaf
================


Friday 11 June 2010
-------------------

Issues:

 1. Every class that has an association or composition eventually will
    need its own custom view page template, e.g. sed_view. For the moment
    I have set the default view for these classes to dev_view ( a copy of
    base_view ).

 2. An association in UML is cast as a ReferenceField in the resulting
    class schema. Open the association and add the widget:label tag to
    the class that is being associated.

 3. The default description text for a class should be a informative
    description of the class, not the instance, derived from the
    SED-ML manual.

 4. Apply 'searchable' tags to the appropriate class attributes.

 5. I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will
    this work?

 6. What should be added to our implementation of SED-ML to make it
    more than merely a mirror image of the SED-ML XML format? 

     a. The ability to attach files at various points, e.g. parameter files.

     b. Additional output types, e.g. animations.

     c. Custom page templates

     d. Custom search form

     e. Custom catalog indexes

     f. Custom portlet(s)

     g. Custom viewlet(s)


Friday 24 September 2010
------------------------

To Do:
 1. Publish our mercurial repositories (Chris/Martin). This may mesh with deploying Plone.

 2. Create a vleaf mailing list (Henk).

Found an article on SBRML - a markup language for associating systems
biology data with models. At a glance the schema seems bigger than
SED-ML's, but SBRML appears to be SBML specific.



Monday 27 September 2010
------------------------

Spoke with Chris about publishing the Mercurial repositories and
deploying Plone. Both can be accomplished in their own project space
on a server in the DMZ. Chris said he would supply me with login
credentials for both accounts. I will install Plone and Chris (or
Maarten) will help me configure Apache/nginx and Varnish. Chris will
install the required Mercurial packages; after which I can clone the
repositories to their new home.



Tuesday 5 October 20010
-----------------------


tutorial0.pro
+++++++++++++

Added simplugin.h to list of header files. NB: this is the only
tutorial in which simplugin.h appears.


auxingrowthplugin.h
+++++++++++++++++++

Declared, and defined, a virtual function named ``DefaultLeafML()``
which merely returns a QString naming a LeafML filename sans path.



VirtualLeaf.cpp
+++++++++++++++

Moved ``Cell::SetMagnification()`` and ``Cell::SetOffset()`` from
``main()`` to ``MainBase::Init()``.


canvas.h
++++++++

Declare ``exportCellData()``.


canvas.cpp
++++++++++

Add an 'Export cell areas' to the file dropdown menu which invokes - surprise - ``Main::exportCellData()``::

  void Main::exportCellData(void) {
    QFile file("areas.csv");
    if ( file.open( IO_WriteOnly ) ) {
      QTextStream stream( &file );
      mesh.CSVExportCellData(stream);
      mesh.CSVExportMeshData(stream);
      file.close();
    }
  }


mesh.h
++++++

Include ``<QTextStream>``

Set the boundary_poloygon pointer to zero in the class constructor,
and delete it, if it exists, in the class destructor.

Declare ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``::

  double Compactness(double *res_compactness=0, double *res_area=0, double *res_cell_area=0);
  void CSVExportCellData(QTextStream &csv_stream) const;
  void CSVExportMeshData(QTextStream &csv_stream);


mesh.cpp
++++++++

In ``mesh::clear()``, delete the boundary_polygon only if the pointer hasn't been assigned::

 if (boundary_polygon) {
    delete boundary_polygon;
    boundary_polygon=0;
  }

Ditto for ``mesh::clean()``.

Define the code for ``Compactness()``, ``CSVExportCellData()`` and ``CSVExportMeshData()``.



modelcatalogue.cpp
++++++++++++++++++

In ``InstallModel()``, find and load the default LeafML file.

simplugin.h
+++++++++++

Declare ``DefaultLeafML()``::

  // Default LeafML-file to be read after model startup
  virtual QString DefaultLeafML(void);


simplugin.cpp
+++++++++++++

Define ``DefaultLeafML()``. Returns an empty ``QString``::

 QString SimPluginInterface::DefaultLeafML(void) { return QString(); }


xmlwrite.cpp
++++++++++++

In ``Mesh::XMLReadCells()`` - Delete the boundary_ploygon only if its
pointer has been assigned.



Wednesday 6 October 2010
------------------------

Wrote Simon van Mourik about his missing libiconv-2.dll.


Thursday 7 October 2010
-----------------------

Added a Q3FileDialog in ``canvas.cpp:Main::exportCellData(void)`` to
choose where to write the exported cell data.