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Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 4 19:56:54 2004 UTC (15 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: HEAD, MigrateToNewPackage
Changes since 1.40: +13 -2 lines
Diff to previous 1.40
uses new graph library code to compute total edge multiplicty on a node and
then uses that to decide when to replicate that node in a viz-graph layout.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 8 01:47:39 2004 UTC (15 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-03, forRick-14Jul04-0, forRick-14Jul04-1, mass-spec-01, mass-spec-02, mass-spec-03
Changes since 1.39: +28 -8 lines
Diff to previous 1.39
Redid the pluggin stuff. Now a module that is loaded is expected to have
a function called registerHook.  It takes an argument that is a functin.
You call that function to register INSTANCES of a derivative of KahModule
along with a menu entry name and a help string.

Also, reworked so that we load configuration information and shove it into
the module.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 2 22:08:02 2004 UTC (15 years, 4 months ago) by hwang
Branch: MAIN
Changes since 1.38: +1 -1 lines
Diff to previous 1.38
	To maintain state, self was taken out of local variables

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 23 19:19:10 2004 UTC (15 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: larrys-08jul04
Changes since 1.37: +2 -2 lines
Diff to previous 1.37
migrate import statements to follow move of Recoelem, Reaction, Reactant
from FaST to KahOM

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 23 19:02:51 2004 UTC (15 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.36: +27 -65 lines
Diff to previous 1.36
Migrate data classes to really use FoundryItem.
gut a bunch of old dead code.
merge what used to be separate seed/bss into single.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 15 19:15:57 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.35: +1 -1 lines
Diff to previous 1.35
temporary fixes to get around a problem importing FoundryItemKey:
change all setFoundryId( fid ) to setFoundryItemKey( FoundryItemKey(fid,...))
since we know there's no fik yet.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 9 22:36:10 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-02, forKubal-15Jun04
Changes since 1.34: +121 -44 lines
Diff to previous 1.34
o clean up double foundryId problem in FoundryItems
o change names in CatalogEntry to read() and write()
o write the write() method just mentioned
o get writing to work again, propagate changes into PyGUI
o add plugin capability to modelEditor

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 01:38:25 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.33: +49 -35 lines
Diff to previous 1.33
Lots of work aimed at getting catalog services to work, incorporating
catalog editing into the model editor, and simplifying the api
for going form path to model in hand to work with.

CatalogEntryTop was changed to CatalogEntrBase and made base of CatalogEntry
rather than other way around to break a dependency loop that was causing
python import problems.  CatalogEntry is still the base class to use
for extending to new data factories.

changed open() to return catalogEntry rather than foundryItemKey.  simpler
for the user and more opportunity to encapsulate.

made catalogEntry able to read a recoElem and return it.  all done in
terms of arch abstractions.  this is temorary.  we will add a Navigator
or Manager class and that will be returned from the CatalogEntry rather
than recoElem.  that's becausee Recoelem is just one of many things
that will be present, e.g., conditions data.

PyGui/MainMenuBar.  split out to help stay sane for when that becomes
more complex.

Moved add seed server to menu bar so that right click in catalog panel
coudl be used to pull up catalog editing tools.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 5 23:22:40 2004 UTC (15 years, 6 months ago) by efrank
Branch: MAIN
Changes since 1.32: +1 -2 lines
Diff to previous 1.32
ExcelBasedECTables:
	remove uniqueness constraint (Rxid, MetabShortName) from RxInputs
	and RxOutputs.  Some KEGG/Seed reactions do X + X rather than 2X.

BssDataFactoryWrite.py
BssFactory.py
	Get the writing to work for real.  You can now read from Seed in
	ModelEditor and write to Bss.  The Reaction_py parser now requires
	the + in a reaction to have spaces around it and changes all '
 	in a reaction to '' to escape them for writing to oracle.

	changed doCommit to commit in various placess.  affects name of named arg

RecoElemPanel
	match name change for docommit to commit

SeedDataFactory:
	didn't think i changed it.  hmmmm

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 25 17:08:17 2004 UTC (15 years, 8 months ago) by hwang
Branch: MAIN
Changes since 1.31: +11 -11 lines
Diff to previous 1.31
     Changed all the files so that the past inconsistancies of variable and classes names
 are consistant. I.E. MainLayout import MainLayout.
     In MainLayout, separate functions are made for each panel.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 12 17:38:11 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
Changes since 1.30: +37 -0 lines
Diff to previous 1.30
experimental menu item for writing

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 18 18:54:27 2003 UTC (16 years ago) by efrank
Branch: MAIN
CVS Tags: SC-02
Changes since 1.29: +3 -1 lines
Diff to previous 1.29
fix for node file attrib

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 18 17:44:18 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.28: +22 -8 lines
Diff to previous 1.28
add node file for cytoscape

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 14 20:15:00 2003 UTC (16 years ago) by efrank
Branch: MAIN
CVS Tags: SC-01, sc-14Nov03-linux-01, sc-14Nov03-linux-02
Changes since 1.27: +3 -1 lines
Diff to previous 1.27

Fix bugs for various cases related to cut/pastes happening when
things aren't selected.

Also, extend info in Rx grid so that AUX column shows the Seed RxId.

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 15:23:05 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.26: +5 -1 lines
Diff to previous 1.26

for cytoscape SIF file, special label for inbound irreversible edges

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 01:41:16 2003 UTC (16 years ago) by efrank
Branch: MAIN
CVS Tags: sc-12Nov03-linux-02
Changes since 1.25: +15 -4 lines
Diff to previous 1.25

RecoElemPanel:
	fix a few bugs related to menu commands.  most related to problems
	not detecting special cases like "nothing selected" or "this node
	i9s special because its the root"


CatalogPanel:
	make the Seed part of the tree include a node, "Spontaneous Reactions"
	which olds all the spontaneous reactions in Seed (those without enzymes)

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 22:56:33 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.24: +99 -78 lines
Diff to previous 1.24
Lots of changes to start port to mac.  lots of fiddling with layout because
we are doing something wrong, and it shows up on Mac.

Also alot of work to make enzymes work, including EC.  focus is on seed.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 6 15:24:00 2003 UTC (16 years ago) by efrank
Branch: MAIN
CVS Tags: sc-06Nov03-linuxLeft-01, sc-12Nov03-linux-01
Changes since 1.23: +9 -1 lines
Diff to previous 1.23

Now have both CYTOSCAPE_COMMAND and CYTOSCAPE_HOME to drive execution of
cytoscape

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 6 06:22:07 2003 UTC (16 years ago) by efrank
Branch: MAIN
Changes since 1.22: +45 -9 lines
Diff to previous 1.22
Add ability to export a recoElem branch that has been selected in
SIF format to a temp file.  Then fire off CytoScape to visualize it.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 25 23:48:06 2003 UTC (16 years, 1 month ago) by hwang
Branch: MAIN
CVS Tags: efrank-initialSeed-04Nov03, sc-works-00
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
	Added enzyme buttons/text/grid
	Added exit button to allow user to exit normally

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 23:22:43 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.20: +1 -0 lines
Diff to previous 1.20
fix reco elem paste to actually insert the re into the re hierarchy.  before,
was just messing with the gui display.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 22:38:42 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.19: +13 -11 lines
Diff to previous 1.19
fix reco elem branch cut to actually cut the branch.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 22:29:32 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.18: +19 -21 lines
Diff to previous 1.18
	RecoElempanel.py
	   Parsing of the names error. Use len(recoelem.Reactions) instead to get
	  number

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 21:10:01 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.17: +55 -14 lines
Diff to previous 1.17
	RXpanel.py
	   Default value set as Input
	RecoElempanel.py
	    Text of tree branches works correctly
	    Cut branch implemented

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 18:17:23 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.16: +3 -9 lines
Diff to previous 1.16
	RecoElempanel.py
	   only the treectrl "from rx panel" works to update text
	   has to update others

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 17:53:00 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.15: +3 -4 lines
Diff to previous 1.15
	MainLayout.py
	    changed dimesions of page to a smaller size
	RecoElempanel.py
	    from rx to tree's text branch updatd

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 19 17:37:36 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.14: +27 -1 lines
Diff to previous 1.14
	MainLayout.py
	    Added HelpPanel
	RecoElempanel.py
	    Update text of tree. not yet tested
	main.py
	    Calls the HelpPanel
	HelpPanel.py
	    Loads ModelEditor.html

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 20:08:59 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-01
Changes since 1.13: +63 -13 lines
Diff to previous 1.13
MainLayout:	turn offf multi select for list_box (rx list in receoElem panel)
recoElemPanel:
   rece elem tree branch editing: copy, past, cut.  but cut is impl'd as an error msg.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 19:32:43 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.12: +7 -6 lines
Diff to previous 1.12
	RecoElempanel.py
	   Fixed the position of the popup

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 16:11:02 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.11: +2 -0 lines
Diff to previous 1.11
	-MainLayou.py & RXFromMetPageDialog.py
	   combobox is readonly
	-RXpanel.py
	   grid info is scrollable
	-RecoElempanel.py
	   in the process of getting pt position to line up with popup menu

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 15:55:57 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00
Changes since 1.10: +18 -0 lines
Diff to previous 1.10
Start documenting the code a trifle.  All files have been modified by adding
the list of def'd methods at the top of the class.  Must add description
strings, but this is a start.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 17 23:40:16 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.9: +66 -3 lines
Diff to previous 1.9
RXpanel:
	add getSelectedRx() method.

RecoElempanel:
	add more reaction cut/paste capabilities

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 17 21:39:17 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.8: +51 -43 lines
Diff to previous 1.8
Start working on reaction cut/paste from RecoElem's rx list_box.  This
affects the selected reaction grid since some operations on the list_box
push data there.

also, fixed the clear button for the selecgted reaction grid.   that requied
a name change.  so MainLayout changed.

some rearrangement in RXpanel and additon of methods like addSearchedRx and
addSelectedRx that add rxns into the grids.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Aug 16 20:51:50 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.7: +11 -4 lines
Diff to previous 1.7
Lots of changes here and there to get reaction searching working.
start to work on right-click-in reaction list_box (recoelem page).

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 15 21:34:34 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
Changes since 1.6: +34 -0 lines
Diff to previous 1.6
	RecoElempanel.py
	    Add a popup for the list_box

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 8 22:46:32 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.5: +0 -8 lines
Diff to previous 1.5
MainLayout:
	move a plitter down a bit

RecoElempanel
	comment out prints

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 7 02:39:46 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.4: +3 -4 lines
Diff to previous 1.4
adding to Metabolite panel so that we can search for metabolites.
main.py: move some init stuff out of main.py into associated panel.
mainlayout: clean up and reorg a bit.  lots of renames
rxpanel: commented out to speed up startup.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 5 19:47:32 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.3: +121 -21 lines
Diff to previous 1.3
main, RecoElempanel:
   some restructuring

RecoElempanel:
   add popup menu for editing recoElem nodes:  add subelement, add root node

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 4 16:18:47 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
Changes since 1.2: +16 -4 lines
Diff to previous 1.2
more tweaks for making things work.  no fundamental changes.  oh...except
in RecoElemPanel where we now use wxTreeCtrl EVT_TREE_SEL_CHANGED to figure
out when there's a hit on something.  Before, we were not picking up
selections on the top nodes.  That meant that a recoElem with no kids but
*with* reactions could not have its reactions listed.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 28 17:57:26 2003 UTC (16 years, 3 months ago) by efrank
Branch: MAIN
CVS Tags: efrank-worksBeforeCatalogTree
Changes since 1.1: +2 -2 lines
Diff to previous 1.1
Migrate import statements to package format for FaST.
Need to use along with head of FaST

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 24 21:29:39 2003 UTC (16 years, 3 months ago) by hwang
Branch: MAIN
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