Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-10

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All times shown according to UTC.

Time Nick Message
05:48 masak joined #bioclipse
06:30 Gpox joined #bioclipse
06:31 Gpoks joined #bioclipse
06:56 CIA-40 bioclipse: goglepox * r11183 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Added method is2DNew() to check if the editor has generated 2d coordinates
07:05 CIA-40 bioclipse: carl_masak * r11184 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java:
07:05 CIA-40 bioclipse: [ScriptExecution] comment fixes
07:05 CIA-40 bioclipse: Fixed punctuation, spelling, grammar and whitespace issues in some
07:05 CIA-40 bioclipse: comments.
07:07 rojasm joined #bioclipse
07:07 CIA-40 bioclipse: goglepox * r11185 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: Added better error handling to get/createVirtual()
07:38 olass joined #bioclipse
08:08 CIA-40 bioclipse: goglepox * r11186 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java:
08:08 CIA-40 bioclipse: Changed algorithm to find the right alignment
08:08 CIA-40 bioclipse: It now switch on 45,135,225,315 degrees
08:08 CIA-40 bioclipse: not patch in cdk only bioclipse-cdk
08:12 jonalv joined #bioclipse
08:13 jonalv oh hai
08:13 zarah ni hao jonalv
08:43 jonalv @pz jmol view jchempaint
08:43 zarah [1243] JChemPaintView throws exceptio... http://tinyurl.com/mdetso
08:43 zarah Entire list at http://tinyurl.com/kk6vun
08:57 shk3 joined #bioclipse
09:02 CIA-40 bioclipse: carl_masak * r11187 /bioclipse2/trunk/plugins/net.sour​ceforge.jseditor/src/net/sourcefor​ge/jseditor/editors/JSEditor.java: [JSEditor.java] added license information
09:11 shk3 jonalv: I am trying to convet specmol to nwo
09:11 zarah shk3: You have new messages. Write '/msg zarah @messages' to read them.
09:11 shk3 but I get errors
09:11 shk3 Caused by: java.lang.NoClassDefFoundError: org/springframework/aop/SpringProxy
09:11 shk3 does that tell you something?
09:11 jonalv shk3: sounds liek you have not declared all deps
09:12 shk3 which deps where?
09:12 jonalv shk3: for your plugin
09:13 jonalv shk3: look at another business plugin and see what deps it has
09:13 shk3 hm
09:13 shk3 I never had anything to add when converting to nwo
09:13 shk3 I will try to find out
09:13 shk3 thanks anyway
09:16 olass joined #bioclipse
09:18 olass bug 1247 is placeholder for RC2
09:18 olass shk3: RC2 is expected today afternoon
09:19 olass (if things go well)
09:19 shk3 ok
09:22 olass jonalv: what number is your commit that solves 1243 (jmol 2dview thingy)?
09:24 jonalv olass: uhm, maybe I haven't commited that, hang on...
09:24 olass jonalv: please do
09:24 olass else hard to close teh bug
09:25 jonalv olass: I forgot...
09:25 jonalv olass: sorry
09:25 olass no worries :)
09:25 olass I reminded you
09:25 CIA-40 bioclipse: jonalv * r11188 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/views/JmolSelection.java:
09:25 CIA-40 bioclipse: getFristElement should return null if there is no first element.
09:25 CIA-40 bioclipse: fixes bug: #1243
09:25 zarah bug #1243 | http://tinyurl.com/mdetso
09:25 jonalv olass: there it is
09:26 olass gut gut
09:48 shk3 jonalv: the problem is actually when trying to instantiate the JumboSpecmol domain object.
09:48 shk3 is there any particular stuff with respect to domain objects I need to be aware of?
10:09 shk3 ah, found it
10:29 CIA-40 bioclipse: shk3 * r11189 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (15 files in 9 dirs): specmol is nwo (bug #805)
10:29 zarah bug #805 | http://tinyurl.com/c4yf5o
10:30 CIA-40 bioclipse: shk3 * r11190 /bioclipse2/trunk/plugins/net.bioclipse.​nmrshiftdb/src/net/bioclipse/nmrshiftdb/ (6 files in 2 dirs): adopted nmrshiftdb for new specmol
10:31 CIA-40 bioclipse: shk3 * r11191 /bioclipse2/trunk/plugins/net.bioclipse.specmol​.test/src/net/bioclipse/specmol/business/test/ (9 files): specmol is nwo (bug #805)
10:31 zarah bug #805 | http://tinyurl.com/c4yf5o
10:47 CIA-40 bioclipse: carl_masak * r11192 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java:
10:47 CIA-40 bioclipse: [ScriptExecution.java] comment management, renamed variables
10:47 CIA-40 bioclipse: This commit is part of an ongoing rw review of edrin++'s js editor suite
10:47 CIA-40 bioclipse: of classes.
11:08 sneumann Hi shk3,
11:08 sneumann would you agree that it is OK to announce (Beta-level) support for mzML in BC2
11:09 sneumann on the psidev.net web site ? I can send the mail to their list, unless there are objections
11:09 sneumann e.g. because it is too early.
11:11 shk3 well, there is no integration of mzdata to other spectral stuff in bc
11:11 shk3 so depends on you definition of support
11:15 masak always does...
11:15 CIA-40 bioclipse: carl_masak * r11193 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
11:15 CIA-40 bioclipse: [ScriptingConsoleView] \n before tab compl. sugg.
11:15 CIA-40 bioclipse: There was a NEWLINE added after the list of tab completion suggestions, but
11:15 CIA-40 bioclipse: not before. This led to the phenomenon seen in #989. Putting the NEWLINE
11:15 CIA-40 bioclipse: before the list seems to clear up all problems. Fixes #989.
11:15 zarah bug #989 | http://tinyurl.com/nxbe4e
11:22 edrin joined #bioclipse
11:22 shk3 jonalv: did you find a solution for the exception handling in jobs?
11:22 edrin hi
11:22 zarah ni hao edrin
11:22 jonalv shk3: I sure hope so
11:22 jonalv shk3: is it not working?
11:23 shk3 hm no
11:23 jonalv shk3: uhm I mean: A manager method can not throw an exception to the calling code
11:23 jonalv that's the solution :)
11:23 shk3 ah ok
11:23 jonalv for now at least
11:24 shk3 fine for me
11:24 shk3 let's see what egon says
11:24 shk3 :-)
11:24 jonalv I want the behavior of manager methods run as jobs and not run as jobs to be the same
11:24 jonalv bujt I may be wrong...
11:26 jonalv shk3: if you rethrow a BioclipseException the text in that BioclispeException will be in the dialog...
11:26 shk3 ok
11:26 shk3 let me check
11:30 shk3 see private chat
11:32 CIA-40 bioclipse: ospjuth * r11194 /bioclipse2/trunk/features/ne​t.bioclipse.ds.birt_feature/: Initial import.
11:33 CIA-40 bioclipse: ospjuth * r11195 /bioclipse2/trunk/features/ne​t.bioclipse.ds.birt_feature/ (.project build.properties feature.xml): A feature to provide BIRT reporting for Decision Support feature. Requires BIRT to be installed in Eclipse.
11:34 CIA-40 bioclipse: ospjuth * r11196 /bioclipse2/trunk/plugins/net.bioclipse.ds.birt/ (26 files in 10 dirs): Ongoing work to make a BIRT report for Bioclipse-DS.
11:34 CIA-40 bioclipse: ospjuth * r11197 /bioclipse2/trunk/features/net.b​ioclipse.ds_feature/feature.xml: Updated plugins in DS_feature.
11:37 jonalv shk3, olass: Could you guys please stop using SubClipse-- for updating?
11:37 olass jonalv: why?
11:37 * jonalv is tired of updating being sush a problem for you guys
11:37 olass jonalv: what do you mean?
11:37 olass I use what I want for updating, ok?
11:38 jonalv olass: You two ask me questions like: "Which plugin do I have to update?"
11:38 olass yes?
11:38 jonalv olass: and right now shk3 comes complaining about things I have fixed, and says he has updated but that it "perahaps didn't work"
11:38 olass too bad
11:38 CIA-40 bioclipse: goglepox * r11198 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKMolecule.java CDKMoleculeUtils.java): Added clearProperty() and hard coded properties for SMILES, InChI and Fingerprint
11:39 CIA-40 bioclipse: goglepox * r11199 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added manager method for realy calculate SMILES
11:39 CIA-40 bioclipse: goglepox * r11200 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs): Added invalidateProperties() to fireStructureChanged()
11:45 CIA-40 bioclipse: jonalv * r11201 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: help and man for special commands now give some help text. Fixes bug: #1245
11:45 zarah bug #1245 | http://tinyurl.com/mcznwn
11:58 olass Gpox: if 1248 is finished, please close it
12:03 CIA-40 bioclipse: ospjuth * r11202 /bioclipse2/trunk/ (44 files in 44 dirs): Set version to 2.0.0.RC2.
12:03 CIA-40 bioclipse: ospjuth * r11203 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.RC2.
12:03 CIA-40 bioclipse: ospjuth * r11204 /bioclipse2/trunk/plugins/ (12 files in 12 dirs): Set version to 2.0.0.RC2.
12:04 CIA-40 bioclipse: ospjuth * r11205 /bioclipse2/trunk/bioclipse-updatesite/site.xml: Set version to 2.0.0.RC2 and removed hivpred from update site. Solves bug 1223 when uploaded.
12:04 zarah bug #1223 | http://tinyurl.com/n9w9af
12:05 CIA-40 bioclipse: ospjuth * r11206 /bioclipse2/trunk/experime​ntal-updatesite/site.xml: Set version to 2.0.0.RC2.
12:10 CIA-40 bioclipse: ospjuth * r11207 /bioclipse2/trunk/features/ (17 files in 16 dirs): Set version to 2.0.0.RC2 and adapt deps accordingly.
12:11 CIA-40 bioclipse: ospjuth * r11208 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Set version to 2.0.0.RC2.
12:12 CIA-40 bioclipse: ospjuth * r11209 /bioclipse2/trunk/plugins/ne​t.bioclipse.doc.developers/ (9 files in 4 dirs): Set version to 2.0.0.RC2.
12:13 CIA-40 bioclipse: ospjuth * r11210 /bioclipse2/trunk/ (11 files in 11 dirs): Set version to 2.0.0.RC2.
12:13 CIA-40 bioclipse: ospjuth * r11211 /bioclipse2/trunk/experimental-updatesite/ (artifacts.xml content.xml): Removed generated artifacts.
12:14 CIA-40 bioclipse: ospjuth * r11212 /bioclipse2/trunk/features/net.bioc​lipse.platform_feature/feature.xml: Removed ds_frature from platform.
12:15 olass masak: did you note my comment on bug 750?
12:16 olass I reopened that bug...
12:16 masak olass: checking...
12:16 masak @pz 750
12:16 olass with a small request
12:16 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=750
12:16 CIA-40 bioclipse: jonalv * r11213 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: Now presents methods in alphabetical order when doing 'help manager'. Fixes bug: #1246.
12:16 zarah bug #1246 | http://tinyurl.com/le8eub
12:16 masak olass: yes, that's why I asked 'what medium?' earlier today...
12:17 olass ?
12:19 masak olass: workbench/views/vi_jsconsole.html
12:19 masak olass: that one, p'haps?
12:19 olass hmm
12:19 olass no
12:19 masak olass: it's much easier if you write stuff like this in the ticket...
12:19 olass indeed
12:20 masak that way, we don't have to leave our comfy office chairs...
12:21 CIA-40 bioclipse: ospjuth * r11214 /bioclipse2/trunk/features/net.bioclip​se.platform_feature/bioclipse.product: Product now includes platform_feature RC2
12:22 olass masak: net.bioclipse.doc/html/scriptingBioclipse.html
12:22 masak olass: oki.
12:22 * masak adds that to the ticket
12:22 olass sry
12:23 masak olass: s'all right. we're all on a learning curve. :)
12:23 masak the only punishment for vague tickets is slow service. could be worse. :)
12:23 olass right
12:28 shk3 jonalv: i am not using subclipse
12:28 shk3 sorry for trouble
12:28 jonalv shk3: good
12:28 jonalv shk3: do you have something more for me? :)
12:28 jonalv I am out of bugs again...
12:28 * jonalv will start doing bug hunting otherwise...
12:28 shk3 ah, yes, nice message now
12:29 shk3 no idea why my last update did obviously not include everything
12:29 jonalv shk3: what are you using then if you don't mind me sking?
12:30 shk3 svn command line
12:30 jonalv shk3: hm
12:30 jonalv I thought that was bullet proof
12:31 shk3 well, you would think
12:32 masak jonalv: I notice you introduced tab characters into JsConsoleView.java.
12:33 jonalv masak: huh?
12:33 masak jonalv: I notice you introduced tab characters into JsConsoleView.java.
12:33 masak jonalv: please don't do that.
12:33 jonalv masak: I amrunning your xml file I thought it was impossible to generate tabs when doing that...
12:33 masak seems you managed somehow.
12:33 jonalv masak: how?
12:33 masak far as I can see, you don't use 'em for indentation, but for aligning...
12:34 shk3 I thought that was bullet proof
12:34 shk3 ;-)
12:34 masak see, for example, line 271.
12:34 masak jonalv: do you want to clean up after yourself, or shall I?
12:35 CIA-40 bioclipse: goglepox * r11215 /bioclipse2/trunk/plugins/net.bioclipse.​inchi/src/net/bioclipse/inchi/business/ (IInChIManager.java InChIManager.java): Updated inchi.generate() to use generics on BioclipseJob and BioclipseJobUpdateHook
12:35 shk3 jonalv: I would have something to discuss with you, in case you feel bored
12:35 jonalv masak: please explain to me how this can happend
12:35 CIA-40 bioclipse: goglepox * r11216 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Added canceled check to calculateSMILES
12:36 masak jonalv: I don't know how it happened. it never happens to me.
12:36 CIA-40 bioclipse: goglepox * r11217 /bioclipse2/trunk/plugins/net.bioclipse.inchi/src​/net/bioclipse/inchi/business/InChIManager.java: Added canceled check to generate InChI
12:36 CIA-40 bioclipse: goglepox * r11218 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
12:36 CIA-40 bioclipse: Cancel already running calculateInChI/SMILES job before creating a new job
12:36 CIA-40 bioclipse: Fixes bug #1252
12:36 zarah bug #1252 | http://tinyurl.com/l6yovf
12:37 CIA-40 bioclipse: goglepox * r11219 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (3 files in 2 dirs):
12:37 CIA-40 bioclipse: Changed createSDFIndex to return SDFIndexEditorModel
12:37 CIA-40 bioclipse: Also added createSDFIndex(InputStream ...)
12:37 CIA-40 bioclipse: Fixes bug #1251
12:37 zarah bug #1251 | http://tinyurl.com/mgg4dr
12:38 CIA-40 bioclipse: goglepox * r11220 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/ (business/CDKManager.java domain/CDKMolecule.java): Changed setProperty and clearProperty to compare instead of try and create enum
12:40 jonalv olass: who did the InChi stuff for the properties view?
12:40 jonalv olass: I found a problem that I would like to fix but who should I talk to?
12:40 olass egonw and Gpox
12:40 olass talk to Gpox
12:47 CIA-40 bioclipse: goglepox * r11221 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Do not calculate SMILES or InChI for 0 atoms
12:48 CIA-40 bioclipse: carl_masak * r11222 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] whitespace therapy
12:49 CIA-40 bioclipse: carl_masak * r11223 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] replaced a few for-loops with regular expressions
12:50 CIA-40 bioclipse: ospjuth * r11224 /bioclipse2/trunk/features/ne​t.bioclipse.platform_feature/ (bioclipse.product feature.xml): Set version to 2.0.0.RC2 for feature and product.
12:50 CIA-40 bioclipse: goglepox * r11225 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/IMoleculeTableManager.java: Added createSDFIndex with BioclipseJobUpdateHook
13:15 CIA-40 bioclipse: goglepox * r11226 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
13:15 CIA-40 bioclipse: Removed auto regeneration of InChI on strucuture changed
13:15 CIA-40 bioclipse: Fixes bug #1257
13:15 zarah bug #1257 | http://tinyurl.com/md3zse
13:25 CIA-40 bioclipse: shk3 * r11227 /bioclipse2/trunk/plugins/net.bioclipse.sp​ectrum/src/net/bioclipse/spectrum/editor/ (PeakTableViewer.java SpectrumEditor.java): solves bug #1085
13:25 zarah bug #1085 | http://tinyurl.com/mkyk3x
14:09 Gpox joined #bioclipse
14:17 CIA-40 bioclipse: ospjuth * r11228 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Updates to MolTableManager to make use of a returner.
14:35 edrin left #bioclipse
14:44 Gpox joined #bioclipse
14:52 CIA-40 bioclipse: ospjuth * r11229 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Clone CDKMolecule on runTest. Should solve all threading issues.
14:54 CIA-40 bioclipse: ospjuth * r11230 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Made cloning consistent between Test implementations.
14:56 CIA-40 bioclipse: goglepox * r11231 /bioclipse2/trunk/plugins/ (3 files in 2 dirs):
14:56 CIA-40 bioclipse: Changed to createSDFIndex(IFile,updatehook)
14:56 CIA-40 bioclipse: sdf file is now copied to virtual instead of linked
15:02 CIA-40 bioclipse: ospjuth * r11232 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Look up substructure matches in input molecule instead of clone.
15:51 CIA-40 bioclipse: ospjuth * r11233 /bioclipse2/trunk/plugins/​net.bioclipse.ds.dblookup/ (3 files in 2 dirs): Removed try to use Jobs when reading databases from /Virtual since returned 0 molecules.
16:00 Gpox joined #bioclipse
16:30 rojas1 joined #bioclipse
17:47 CIA-40 bioclipse: goglepox * r11234 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java):
17:47 CIA-40 bioclipse: Changed fromm getResourceAsStream to Bundle.getEntry(...).openStream()
17:47 CIA-40 bioclipse: Fixes bug #1263
17:47 zarah bug #1263 | http://tinyurl.com/ne9p6l
18:44 olass joined #bioclipse
18:54 CIA-40 bioclipse: ospjuth * r11235 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (2 files in 2 dirs): Added 'informative' entry in extension point and model class.
18:56 CIA-40 bioclipse: ospjuth * r11236 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (10 files in 3 dirs): Implemented support for informative tests.
18:56 CIA-40 bioclipse: ospjuth * r11237 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Made DBExactMatch an informative test to not affect consensus prediction.
18:57 CIA-40 bioclipse: ospjuth * r11238 /bioclipse2/trunk/plugins/n​et.bioclipse.ds.lipinski/: Initial import of Lipinski Rule of Five test for decision support.
19:00 CIA-40 bioclipse: ospjuth * r11239 /bioclipse2/trunk/plugins/​net.bioclipse.ds.lipinski/ (16 files in 9 dirs): Implemented an informative Lipinski Rule of Five test for Bioclipe Decision Support.
19:18 Gpox joined #bioclipse
19:22 CIA-40 bioclipse: goglepox * r11240 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java:
19:22 CIA-40 bioclipse: Wrapped SMILES calculation in try/catch block
19:22 CIA-40 bioclipse: Catches Exception to avoid errordialog when trying to generate smiles
19:22 CIA-40 bioclipse: goglepox * r11241 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/handlers/ToggleImplicitHydrogens.java:
19:22 CIA-40 bioclipse: Run updateImplicitHydrogensCount() when calling showImplicitHydrogens form popum menu.
19:22 CIA-40 bioclipse: Fixes bug #1250
19:23 zarah bug #1250 | http://tinyurl.com/n4s3hn
19:23 CIA-40 bioclipse: goglepox * r11242 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java:
19:23 CIA-40 bioclipse: Use IFileStore to access file as Virtual may be involved
19:23 CIA-40 bioclipse: Resolves error related to bug #1263
19:23 zarah bug #1263 | http://tinyurl.com/ne9p6l
19:24 CIA-40 bioclipse: goglepox * r11243 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java:
19:24 CIA-40 bioclipse: Commented out updateJCPPage() on selection changed event
19:24 CIA-40 bioclipse: This fixes problem in DSView when clicking substructure match causing fireing of structure changed event
19:31 CIA-40 bioclipse: ospjuth * r11244 /bioclipse2/trunk/ (2 files in 2 dirs): Implemented include/exclude tests.
19:32 CIA-40 bioclipse: ospjuth * r11245 /bioclipse2/trunk/features/net.b​ioclipse.ds_feature/feature.xml: Removed lipinski test from DS feature.
19:43 CIA-40 bioclipse: ospjuth * r11246 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: Store JCPpropertylisteners and try to look them up before adding a new. This makes sure only one listener per jcp part.
19:45 CIA-40 bioclipse: ospjuth * r11247 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: Removed unused imports.
19:47 CIA-40 bioclipse: ospjuth * r11248 /bioclipse2/trunk/plugins/net.bioclipse.ds/​src/net/bioclipse/ds/ui/views/DSView.java: Proper use of Java generics removes all warnings.
20:13 CIA-40 bioclipse: ospjuth * r11249 /bioclipse2/trunk/plugins/net.biocl​ipse.ds/src/net/bioclipse/ds/model/ (TestRun.java TestRunPropertySource.java): Refactored serializing of ITestResult.status from int to String into TestRun.
20:15 CIA-40 bioclipse: ospjuth * r11250 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (6 files in 4 dirs): Moved DBException from model.impl to model.
20:15 CIA-40 bioclipse: ospjuth * r11251 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/META-INF/MANIFEST.MF: Removed ref in manifest to removed model.impl package.
21:10 CIA-40 bioclipse: ospjuth * r11252 /bioclipse2/trunk/plugins/net.bi​oclipse.ds/src/net/bioclipse/ds/ (business/BaseDSPropertyCalculator.java model/TestRun.java):
21:10 CIA-40 bioclipse: * Implemented a BaseDSPropertyCalculator to return a TestRun
21:10 CIA-40 bioclipse: * Updated TestRun.toString() to look better in Moltable cells
21:11 CIA-40 bioclipse: ospjuth * r11253 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): Implemented PropertyCalculators for the active tests
21:12 CIA-40 bioclipse: ospjuth * r11254 /bioclipse2/trunk/plugins/net.bioclips​e.ds.tests/src/net/bioclipse/ds/tests/ (TestBursiSmarts.java TestDBLookup.java TestSignSIc.java): Updated for new API in DSException.
21:20 CIA-40 bioclipse: ospjuth * r11255 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Implemented PropertyCalculators for the active tests.
21:30 CIA-40 bioclipse: ospjuth * r11256 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java): Added check for 0 molecules read and set the different DBLookup to copy different SDFiles to avoid simultaneous reading of same file.
21:33 CIA-40 bioclipse: ospjuth * r11257 /bioclipse2/trunk/features/net.bioclip​se.platform_feature/bioclipse.product: Set version for bioclipse.product to RC2. Must have been forgotten.
23:04 olass good night
23:07 CIA-40 bioclipse: ospjuth * r11258 /bioclipse2/trunk/plugins/net.bioclip​se.ds/src/net/bioclipse/ds/business/ (DSManager.java IDSManager.java): Use java generics, clears all warnings.

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