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+.. 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.