overlayplot legends after unchecking overlay and disabling reset while simulation is running


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3916 d1858a74-f715-0410-99c9-c66fe9cce3d6
new object editor incorporating units for the fields. removed ploting column in the previous


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3917 d1858a74-f715-0410-99c9-c66fe9cce3d6
Moved threading demo inside snippets

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3918 d1858a74-f715-0410-99c9-c66fe9cce3d6
Started a new function in hdfutil to save only a subtree of moose elements.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3919 d1858a74-f715-0410-99c9-c66fe9cce3d6
Enhanced hdfutil to save and load moose subtree starting with arbitrary root node under arbitrary node of hdf5 file.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3920 d1858a74-f715-0410-99c9-c66fe9cce3d6
Further progress on NeuroStencil unit tests.
Implemented ChemMesh::setEntireSize so that the field is now read/write.



git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3921 d1858a74-f715-0410-99c9-c66fe9cce3d6
genesis color-code followed when new molecule added for plot window

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3922 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated the test_tcr code.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3923 d1858a74-f715-0410-99c9-c66fe9cce3d6
Made pymoose element class take care of destFinfo and lookupFinfos as well.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3924 d1858a74-f715-0410-99c9-c66fe9cce3d6
Updated pymoose to allow destField and lookupFields to be accessed
directly on elements (without using to_el). This is inelegant and a
potential source of unwanted surprises for the users because it goes
against the normal concept of flow of information from superclass to
subclass. On the other hand it gives a feeling of virtual classes to
the C++ user.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3925 d1858a74-f715-0410-99c9-c66fe9cce3d6
The python API slightly changed: 

element is a function implemented in C. It can take a path string, an
existing element or an ematrix and return an instance of the
appropriate moose builtin class.

ObjId/element is renamed "melement". This should not be directly
needed by the users. Python code that used element() earlier will
remain valid.

to_el becomes redundant with this change.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3926 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added mulidimensional subscripting support to multidimensional Id.


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3927 d1858a74-f715-0410-99c9-c66fe9cce3d6
added units to the object editor


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3928 d1858a74-f715-0410-99c9-c66fe9cce3d6
alternate colors, units, resizing for objecteditor. Naming convention for the gui


git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3929 d1858a74-f715-0410-99c9-c66fe9cce3d6
duplicate of the same model

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3930 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added olfactory bulb (only cells -- no channels, no synapses/connections) neuroml demo. Updated MorphML.py for a reading bug. Even my smallest model with just cells is too heavy for the GUI. Takes a huge amount of time to rotate/pan/zoom the visualization.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3931 d1858a74-f715-0410-99c9-c66fe9cce3d6
 defaults.py: units for concinit is added,
kineticlayout.py: qGraphicsTextitem are replace with qGraphicsSimpleTextitem to border the text for Colour contrast, 
                  reaction are replaced with reaction arrow.
                  Persisting issue with shifting around compartments is fixed
                  single click on each item (pool,enz,reaction,compartment,cplx) opens object editor
                  Compartment volume can be edited
                  Enz cplx to sumtot line track movement,arrow get updated 
Previous commit 3930: duplicate of same models are  deleted.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3932 d1858a74-f715-0410-99c9-c66fe9cce3d6
added an olfactory bulb network model under Demos/neuroml/OlfactoryBulb that has only approx. 100 cells, for GUI testing purposes.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3933 d1858a74-f715-0410-99c9-c66fe9cce3d6
Added Demos/neuroml/PurkinjeCell - only morphology as the channels are in a deprecated channelml format which will require a completely different and parallel channelmlreader.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3934 d1858a74-f715-0410-99c9-c66fe9cce3d6
Had to make some modifications to MorphML.py for purkinjecell which I did not upload last.

git-svn-id: svn+ssh://svn.code.sf.net/p/moose/code@3935 d1858a74-f715-0410-99c9-c66fe9cce3d6