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245 commits

Author SHA1 Message Date
Chris Myers
05e8f628be Updated pom file 2018-01-28 15:59:16 -07:00
Tramy Nguyen
58862152b7 sbol tech. map load to GUI 2018-01-27 16:44:45 -05:00
Chris Myers
e7841987a8 Changed System.out to System.err 2018-01-27 09:14:45 -07:00
Tramy Nguyen
be92129081 Merge remote-tracking branch 'origin/master' into sbolTechMap 2018-01-25 23:23:26 -05:00
Chris Myers
515de20b9e Remove libsbmlj.jar dependency 2018-01-23 17:42:22 -07:00
Chris Myers
82ccd186f9 Removed flanagan dependency 
Removed local copy of jlibsedml
 2018-01-20 22:53:35 -07:00
Chris Myers
ef5e4006db Add main method for verification. 
Add jlibsedml snapshot dependency
 2018-01-20 21:29:46 -07:00
leandrohw
54489ea578 Validation report was logged instead of shown in an error dialog. 2018-01-19 11:56:50 -07:00
leandrohw
6f46801b05 Changed how genenet is checked. 0 should be fine. 2018-01-19 01:33:53 -07:00
Tramy Nguyen
3a45e36978 command line for tech. map 2018-01-17 22:46:14 -05:00
Chris Myers
f2da7f64a8 Reduce non-maven jar dependencies. 
Fixed some issues with preferences for analysis.
Save iSSA options in SED-ML.
 2018-01-17 12:14:08 -07:00
Tramy Nguyen
4f4ff739e4 Merge branch 'master' of 
https://github.com/MyersResearchGroup/iBioSim.git into sbolTechMap

Conflicts:
	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java
	synthesis/src/main/java/edu/utah/ece/async/ibiosim/synthesis/SBMLTechMapping/Synthesizer.java
 2018-01-15 19:02:20 -05:00
Leandro Watanabe
46aad27747
Merge pull request #478 from MyersResearchGroup/observer 
Fixed issue with error message display
 2018-01-15 10:20:56 -07:00
Chris Myers
057b53a4cc Fix updates of SED-ML when renaming analysis views. See issue #218 2018-01-14 22:49:14 -07:00
leandrohw
7a7f8271f4 Created two types of error dialog for shorter and longer messages. 2018-01-11 20:45:12 -07:00
leandrohw
938bb21277 Changed how to display warning and error messages in readSBML 2018-01-11 18:55:08 -07:00
leandrohw
4ea8b4bac1 Made error box scrollable when there are big texts. 2018-01-10 23:32:12 -07:00
leandrohw
e79404ae0e Forward message is fixed for the different editors. 2018-01-10 23:22:55 -07:00
leandrohw
c739774cf7 variableInUse notifies observers and observables now. 2018-01-10 22:09:29 -07:00
Tramy Nguyen
0acb2ec9bd attaching SBOL tech map to gui 2018-01-10 23:02:27 -05:00
leandrohw
fcec8f6b69 Ensured that biomodel is observed when needed. 2018-01-10 14:06:53 -07:00
Chris Myers
84de6411f2 Merge branch 'master' of 
https://github.com/MyersResearchGroup/iBioSim.git

Conflicts:
	analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Analysis.java
 2018-01-09 18:10:47 -07:00
Chris Myers
b89383a5ec Added KISAO_LSODA 
Strip path from model source on import
 2018-01-09 18:06:00 -07:00
leandrohw
0a761af0f9 Fixed problem when plotting csv 2018-01-09 11:10:13 -07:00
leandrohw
6f52f94fdc Fixed printing time issue 2018-01-09 11:03:50 -07:00
leandrohw
1ed2fd9271 Merge remote-tracking branch 'origin/master' into learn_standalone 
Conflicts:
	analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
 2018-01-08 09:58:43 -07:00
Chris Myers
fb864e10da Fixed bug in validation preferences 
Fixed issue with analysis from archive
 2018-01-07 19:09:15 -07:00
leandrohw
c415c09993 Some reporting messages to standalone. 2018-01-05 11:48:52 -07:00
Tramy Nguyen
d3da9e434b Merge branch 'nicTechMap' into sbolTechMap 
# Conflicts:
#	synthesis/src/main/java/edu/utah/ece/async/ibiosim/synthesis/SBOLTechMapping/Synthesis.java
#	synthesis/src/test/java/edu/utah/ece/async/ibiosim/synthesis/SBOLTechMap/TempSynthesisRunner.java
 2018-01-05 11:07:26 -07:00
Chris Myers
e033c6b759 Some cleaning up of import of archives 
Clean up of some log messages
Better handling of L3V2 conversion without libsbml
 2018-01-05 08:04:35 -07:00
Chris Myers
77be508a1f If no libsbml, do not try to convert to L3V2. 
Redo perform analysis to not use analysisView
 2018-01-04 19:50:02 -07:00
Chris Myers
318081f921 Updates to address copy/rename of analysis views. 2018-01-02 14:34:00 -07:00
Chris Myers
a76e1a0244 Fixes some warnings and #457 2018-01-02 12:38:30 -07:00
Chris Myers
978e352b8c More refinements to upload 2018-01-02 00:24:03 -07:00
Chris Myers
75f1d1f99a Find executables in path independent of OS. 2017-12-29 21:00:56 -07:00
Tramy Nguyen
fa015a5638 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim into nicTechMap 2017-12-29 12:16:22 -07:00
Chris Myers
520a829fd2 Split graph GUI and graph data into the GUI and datamodels packages. 
Added support for COMBINE archives in and graphs out for the analysis
standalone
 2017-12-29 08:41:21 -07:00
Chris Myers
690de1f441 Fixes #234 2017-12-23 21:57:38 -07:00
Chris Myers
fb29c8e197 Fix a few warnings 
Prevent removal of parameters used in flux bounds
Prevent changing species to promoter using SBOL
 2017-12-23 12:45:29 -07:00
Chris Myers
58dd2df7c3 Fixes #410 2017-12-23 10:40:43 -07:00
Tramy Nguyen
33c4a91e4d Merge branch 'master' into nicTechMap 
# Conflicts:
#	gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java
 2017-12-21 22:21:03 -07:00
leandrohw
03772a23e0 Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim.git into hSSA 2017-12-21 12:50:24 -07:00
leandrohw
abc7ed83c7 Remove unused namespaces on save. 2017-12-21 12:49:16 -07:00
Chris Myers
ff6cd9b86b Use jsbml reader not SBMLutilities.readSBML 2017-12-20 12:38:17 -07:00
Chris Myers
c973aa9564 Restored removeUnusedNamespaces 2017-12-09 14:30:07 -07:00
Chris Myers
d3700d67e0 Restore the L3V2 changes 2017-12-09 14:24:13 -07:00
Chris Myers
178745f3e6 Fixed conflicts maybe 2017-12-09 14:17:00 -07:00
leandrohw
fe0e6090c0 Merge branch 'master' into L3V2 2017-12-08 12:03:10 -07:00
leandrohw
33a520ad2d Check for unused packages and remove namespaces if unused. 2017-12-03 17:34:10 -07:00
leandrohw
28a279e284 Added function to remove unused packages. 2017-11-28 11:14:40 -07:00