Issues:
++++
+- +
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 ).
+- +
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.
+- +
The default description text for a class should be a informative +description of the class, not the instance, derived from the +SED-ML manual.
+- +
Apply 'searchable' tags to the appropriate class attributes.
+- +
I choose 'isTidyHtmlWithCleanup' as the MathML validator. Will +this work?
+- +
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?
++++
+- The ability to attach files at various points, e.g. parameter files.
+- Additional output types, e.g. animations.
+- Custom page templates
+- Custom search form
+- Custom catalog indexes
+- Custom portlet(s)
+- Custom viewlet(s)
+
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.
+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.
+Added simplugin.h to list of header files. NB: this is the only +tutorial in which simplugin.h appears.
+Declared, and defined, a virtual function named DefaultLeafML() +which merely returns a QString naming a LeafML filename sans path.
+Moved Cell::SetMagnification() and Cell::SetOffset() from +main() to MainBase::Init().
+Declare exportCellData().
+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();
+ }
+}
+
+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); ++
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().
+In InstallModel(), find and load the default LeafML file.
+Declare DefaultLeafML():
++// Default LeafML-file to be read after model startup +virtual QString DefaultLeafML(void); ++
Define DefaultLeafML(). Returns an empty QString:
+
+QString SimPluginInterface::DefaultLeafML(void) { return QString(); }
+
+In Mesh::XMLReadCells() - Delete the boundary_ploygon only if its +pointer has been assigned.
+