Dear Chuan Shao,
Thank you for your questions.
Here are our replies inserted below.
> 1, Is there any method about layout?
No there isn't.
You cannot access any method for auto layout via current plugin API.
> 2 and 3.
With the current version,
we don't consider any function to create a new model using plugin API.
You cannot notify a new model containing information on "celldesigner layout
extension", but a pure SBML model using notifySBaseAdded(PluginModel).
After notifySBaseAdded(PluginModel), celldesigner draws the model as pure
SBML on the canvas. Once you create a new model, you can add new species
including type information on the canvas as the following:
//-----
PluginModel model = new PluginModel($B!H(Bmodelname$B!I(B);
CellDesignerPlugin.notifySBaseAdded(PluginModel);
PluginSBase sbase = new PluginSpecies(PluginSpeciesSymbolType.GENE,"gene1");
newModel.addSpecies((PluginSpecies)sbase);
CellDesignerPlugin.notifySBaseAdded(sbase)
//----
4. Tutorial
We are sorry but we do not have any detailed tutorial at hand. We will
prepare it based on feedbacks like yours. If you have any request for
materials for plugin development, please do not hesitate to contact us.
Thank you again for your precious questions/feedback.
Sincerely,
-Yukiko Matsuoka
on behalf of CellDesigner Development Team
======================================================
Dear Yukiko Matsuoka:
Thank you for your reply. Looking forward to the CellDesigner Ver.4.0 .
I have these questions below, wish you can offer me some suggestions:)
1, Is there any method about layout? After I operate
PluginModel.addSpecies(PluginSpecies) many times, is there something like:
PluginModel.layout(...) that can layout the canvas automatically, like in
the
software?
2, seems like those setListOf***() method will not work -- the SBML file may
contain the list information but the canvas will not show the graph; seems
like
only those add***() -- such as addSpecies() can work. I'm following the way
below
now:
//---
PluginModel.addSpecies(PluginSpecies);
...
CellDesignerPlugin.notifySBaseAdded(PluginModel);
//---
which can show the species in another canvas, but the type information is
lost,
all species type turns into protein -- I can guess where is wrong but I
could not
achive the below one:
using CellDesignerPlugin.notifySBaseAdded(PluginModel); -- which can open
model in
another canvas and automatically layout; Meanwhile retain the type
information.
Is it possible to fix that?
3, About the addReaction -- as the question 2 mentioned, if I use
PluginModel.setListOfReactions(PluginListOf ...), it will not work. So I
code like
following:
//----
PluginModel.addReaction(PluginReaction); //====code4reaction===
...
CellDesignerPlugin.notifySBaseAdded(PluginModel);
//----
When i use, my plugin collapse, no new canvas or model or species will show,
nothing happens. If I delete the line above (//===code4reaction===), it's OK
again
-- the species node will show up -- but of course I need the reaction :(
I don't know why this happened and how I can achieve the reaction......
4, Is there some more detailed tutorial(I've read the 9 pages Tutorial^_^)
or
material on the internet? -- because the Document is very simple which
sometimes
makes me confused.
P.S. There is no syntax error on my java code, as the compile work is OK^_^;
I'm
working on Eclipse 3.2.2, Windows XP.
Thank you again for the assistance.
Sincerely
Chuan Shao
=====================================================================
看来CellDesigner开发小组并未将插件开发的功能做的很大——限制因素很多。
继续思索reaction信息表现，同时联系开发小组