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245 commits

Author SHA1 Message Date
Chris Myers
d0c6471008 Fix issue with user/namespace perferences. 2017-11-23 10:25:01 -07:00
Chris Myers
949a517c87 Updates for L3V2 
Fix for #434
 2017-11-22 14:51:38 -07:00
Chris Myers
6f2a438fef Change SBML to L3V2 
Add new math functions
Remove support for fast reactions
 2017-11-18 09:44:48 -07:00
leandrohw
7612e2ee45 Added option to use jsbml validator. 2017-11-01 22:11:44 -06:00
Chris Myers
88d6a213d5 Don't flatten on errors using libsbml. 2017-10-30 17:46:44 -06:00
Chris Myers
9504181f0a Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2017-10-17 17:59:31 +02:00
Chris Myers
c34694a08b Fixed issues with combine archive extraction order of SBML files. 
Updated reb2sac.mac64
Avoid validation for bad library version with infinite loop
Don't try to update replacements if file fails to load
 2017-10-17 17:59:22 +02:00
Tramy Nguyen
f20486913f Inserted comments for SBML Tech. Map Part 3 2017-10-13 22:25:04 -06:00
Tramy Nguyen
13dfa6fb3a Inserted method contracts for SBML Tech. Map Part 2 2017-10-13 20:53:26 -06:00
Tramy Nguyen
fb8a4feb81 recompiled libSBOLj to run conversion test suite 2017-10-11 16:43:57 -06:00
Tramy Nguyen
69adb1007c tighten check for isSBMLFile() 2017-10-05 10:47:06 -06:00
leandrohw
425f94e49f Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2017-09-27 10:33:18 -06:00
leandrohw
f5cce36573 Fixed some bugs when importing CombineArchieve for DFBA. 2017-09-27 10:33:10 -06:00
Chris Myers
d0a772718f Fixed bug in updating variable during flattening. 
Fixed inf on analysis view
 2017-09-25 20:26:28 -06:00
leandrohw
c7a755dd32 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2017-09-23 22:03:50 -06:00
leandrohw
d765c20d4e Fixed iBioSim headings 2017-09-23 22:03:40 -06:00
Chris Myers
36b7599e0c Do not change id based on SBOL since it can cause id conflicts. 2017-09-23 15:03:49 -06:00
leandrohw
ffd685aeba Updated KISAO for mixed simulator to be more specific since we only 
support the SOA method.
 2017-09-22 08:02:26 -06:00
leandrohw
2885a421ad Using KISAO for DFBA now. 2017-09-22 07:55:48 -06:00
Chris Myers
6f0acc51cb Fix prefences bug 
Update libSBOLj to 2.2.2-SNAPSHOT
 2017-09-19 18:59:54 -06:00
leandrohw
af114395d9 Fixed progress bar for reb2sac 2017-09-12 08:28:04 -06:00
leandrohw
8e0e7933a3 Fixed sbml option in analysis view 2017-09-11 22:07:46 -06:00
leandrohw
4932eaa210 Moved validation to dataModels 2017-09-11 16:11:54 -06:00
Chris Myers
60a806ec70 Preference updates and doc updates 2017-09-11 12:44:42 -06:00
Chris Myers
4c38c2b73c Fixed default preferences 2017-09-10 22:07:27 -06:00
Chris Myers
78f10dfae1 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git 2017-09-10 21:34:47 -06:00
Chris Myers
27f13627aa Updated preferences 2017-09-10 21:34:39 -06:00
leandrohw
ff23b2a4a4 Fixed problem with grid. 2017-09-03 18:07:35 -06:00
leandrohw
aeb7e2734e Merge branch 'master' into refactor_run 
# Conflicts:
#	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java
#	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java
 2017-08-25 11:38:00 -06:00
leandrohw
442f0868f2 Created custom observe pattern implementation. 2017-08-24 13:17:46 -06:00
Chris Myers
b62912218f Updated KISAO term for number of runs 
Changed CombineArchive to use Maven
 2017-08-18 10:49:11 -06:00
Tramy Nguyen
47470946f5 Added SBOL annotations to PromoterPanel. 2017-08-03 18:27:52 -06:00
Tramy Nguyen
7c99662e22 warning dialog for removing associated SBOL 2017-08-02 19:31:08 -06:00
Tramy Nguyen
90d66fd42d revert libSBOLj library from 2.2.2-SNAPSHOT to 2.2.1. 2017-08-02 18:09:38 -06:00
Tramy Nguyen
a6a596f938 removed SBOLAssociationPanel class 2017-07-31 17:48:55 -06:00
Tramy Nguyen
9af737f1de moved SBML utility methods from Converter to SBMLUtilities. 2017-07-31 17:25:29 -06:00
Tramy Nguyen
9c94f4fd67 moved external SBOL path as a function to SBOLUtility. 2017-07-31 16:57:43 -06:00
Tramy Nguyen
39b13f54cf modified uri prefix 2017-07-31 16:41:42 -06:00
Tramy Nguyen
e91d91c879 modified SBOL URI prefix from SBOLUtility. 2017-07-31 14:27:41 -06:00
Tramy Nguyen
cc9dce7b43 refactored read SBOL file to use SBOLUtility read() 2017-07-31 13:42:18 -06:00
Tramy Nguyen
6a40be9ad0 copy SBOL top level objects from source SBOLDocument to target 
SBOLDocument
 2017-07-26 23:20:43 -06:00
Tramy Nguyen
bdff96de92 removed unused methods. 2017-07-24 23:50:12 -06:00
Tramy Nguyen
ab4c533bf5 update libSBOLj version 2017-07-23 23:19:18 -06:00
Chris Myers
cbcaae0fe9 Fixed local parameter bug 2017-07-16 21:11:19 -06:00
Chris Myers
837814f78a Avoid duplicate local parameters. 
Fixed bug in reaction-based abstraction math #346
 2017-07-16 21:04:10 -06:00
Chris Myers
053bd5aa8d Better debugging when having problem on outputing SBML. 2017-07-14 21:14:46 -06:00
Chris Myers
c47c7473f4 Fix a metaId issue. 
Do not create references for implicit nodes.
 2017-07-13 16:55:11 -06:00
leandrohw
8f41520364 Merge remote-tracking branch 'origin/master' into refactor_run 
Conflicts:
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/Nary_Run.java
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/Run.java
 2017-07-11 16:22:28 -06:00
Chris Myers
5810d56b4a Fix windows file separator bug 2017-07-09 19:41:17 -06:00
Chris Myers
71fdaa1109 Change to use File.separator when used in lookup. 2017-07-08 18:14:32 -06:00