The Virtual Leaf

+ +

Friday 11 June 2010

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)
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+
+
+
+

Friday 24 September 2010

To Do:

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