Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-25

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
07:02 olas joined #bioclipse
07:49 jonalv joined #bioclipse
08:00 thomas_ku joined #bioclipse
08:05 egonw joined #bioclipse
08:06 CIA-44 bioclipse: egonw * r5483 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (11 files in 9 dirs): Template for an editor; time for the 'Eclipse Building Commercial-Quality Plug-ins' book
08:07 CIA-44 bioclipse: egonw * r5484 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/plugin.xml: Added missing plugin.xml
08:13 CIA-44 bioclipse: jonalv * r5485 /bioclipse2/trunk/plugins/net.bioclipse.hsql​db/src/net/bioclipse/hsqldb/HsqldbUtil.java: Removed ugly thread.sleep hack. Each method now waits until the server has reached the desired state before returning.
08:25 olas hi egonw
08:25 olas you need any assistance?
08:26 olas let me know
08:35 egonw olas: yes, I could use some template code in the editor...
08:35 egonw olas: in particular... how to get the two editor tabs, contribute buttons, menus to the main bioclipse window...
08:35 egonw that sort of things...
08:36 egonw any line you could would be helpful
08:36 egonw won't work much on it today, likely not at all...
08:36 egonw daddy-day today
08:44 olas ok
08:44 olas why the naming cdk10.jcp?
08:46 CIA-44 bioclipse: ospjuth * r5486 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (Activator.java BioclipseCache.java QsarProject.java): Added a cache dir for Bioclipse to be used by plugins who want to cache files. Default is "path/to/WorkspaceRoot/tmp".
08:46 egonw because it is the jchempaint based on CDK 1.0.x(2)
08:48 jonalv egonw, so that would be the CDK trunk or?
08:48 egonw no, not CDK trunk
08:49 egonw that's 1.1.x
08:49 egonw or whatevery
08:49 jonalv okey
08:49 egonw and has the new, but unfinished, Java2D-based renderer
08:49 jonalv and the older version used in bc1 what version had it?
08:49 egonw 1.0.0 or so
08:49 olas hmm
08:50 olas are we to base the editor on CDK 1.0?
08:50 egonw yes
08:50 olas is that the same as in Bioclipse1?
08:50 egonw yes
08:50 olas ok
08:50 egonw sorry, but the new one simply is not ready
08:50 olas ok
08:50 olas as long as we get something that works
08:50 olas that's very iomportant
08:50 olas so
08:50 * jonalv was under the impression the new editor was needed because of major changes in cdk. That's not the case then?
08:51 * olas was too
08:51 olas right now I just want something that works
08:51 egonw each editor will have its own file reader
08:51 egonw one format, one editor
08:51 olas JCP from BC1 is enough for now
08:51 egonw so, we'll use CDK1.0 data model for the JCP editors
08:51 olas right
08:52 egonw for other stuff we'll have CDK trunk readers, library
08:52 olas have you added the cdk10 jars to the cdk10.jcp plugin?
08:52 olas yes
08:52 egonw no
08:52 egonw the cdk1.0 libs are in net.bioclipse.cdk10
08:52 olas ok
08:53 olas I'll see to it then to set up a template editor
08:53 olas will start from scratch
08:53 olas or from your plugin
08:53 olas I mean
08:53 egonw there is a pretty scratch in cdk10.jcp
08:53 olas yes
08:53 egonw do with it what you like
08:53 olas will use that
08:53 * olas is checking out now
08:54 egonw not sure if it is suited for the two tab editor
08:54 egonw sounds more like one of the two tabs...
08:54 olas no worries, I'm getting quite familioar with MPEs
08:54 olas but
08:54 olas egonw: how about the SWT widget?
08:54 olas that is equally important
08:55 olas so we can get the structureTable
08:55 egonw we will need to test that too
08:55 egonw right
08:55 egonw we need that for the SDF stuff...
08:55 olas exactly
08:55 egonw how close are you guys with a structure database
08:55 olas so
08:55 egonw with table?
08:55 egonw I could then do the SDF import stuff
08:55 olas jonalv is on that
08:55 olas but you need to finish the widget
08:56 olas how much is left on that?
08:57 jonalv The altest structuredb test that passes creates two databases and saves a folder in each. saving and loading things by name is implemented. I am slmost ready for gui stuff but there is still no fingerprint search...
08:59 olas please make it possible to add/retrieve structures first
09:00 olas then search
09:00 jonalv yea those methods are there
09:00 egonw the widget is finished
09:00 jonalv or rather there is retrieveAll and retrieve by name
09:00 egonw mom, let me look up the details
09:01 jonalv which should be enough...
09:01 egonw http://chem-bla-ics.blogspot.com/2007​/09/swt-view-with-new-jchempaint.html
09:01 egonw screenshot: http://bp2.blogger.com/_5vhaOf2_53I/RvG9qAhjH​AI/AAAAAAAAAHk/nDFobbRt2To/s1600-h/swtJCP.png
09:01 egonw this is the widget with the new renderer
09:01 egonw the widget scales automatically...
09:02 egonw and even changes rendering mode when getting very small
09:02 egonw <200x200 or so
09:02 egonw then it draw atom symbols are boxes
09:02 egonw like on PubChem
09:02 jonalv nice
09:03 egonw now, I'm not sure if this code is already in the bioclipse2/ project
09:03 egonw will need to check that...
09:03 egonw but it's basic SWT code, so easy to port to bioclipse2/plugins/net.bioclipse.cdk
09:03 egonw if not in there already...
09:03 egonw if no one beats me to it today, I'll do that this weekend...
09:04 olas where is it?
09:04 olas I'll put in in right now
09:06 CIA-44 bioclipse: carl_masak * r5487 /bioclipse2/trunk/plugins/net.bioclipse.hsql​db/src/net/bioclipse/hsqldb/HsqldbUtil.java:
09:06 CIA-44 bioclipse: [HsqldbUtil.java]
09:06 CIA-44 bioclipse: * spelling
09:06 CIA-44 bioclipse: * changed type of thrown exception
09:06 CIA-44 bioclipse: * removed unused imports
09:06 olas egonw: is the widget in bc1 trunk?
09:06 egonw mom
09:07 egonw yes, guess so...
09:07 egonw not sure
09:07 * egonw is searching it
09:08 CIA-44 bioclipse: ospjuth * r5488 /bioclipse2/trunk/plugins/net.bioclip​se.biomart/src/net/bioclipse/biomart/ (5 files in 4 dirs): Make use of Biomart caching of config files.
09:08 egonw olas: http://bioclipse.svn.sourceforge.net/viewv​c/bioclipse/bioclipse/trunk/plugins/net.bi​oclipse.cdk.ui/src/net/bioclipse/plugins/s​wt/widgets/JChemPaintView.java?view=markup
09:08 olas hmm
09:08 olas egonw: is it a widget to display structures?
09:09 egonw yes
09:09 olas not to edit?
09:09 egonw no, this is just display
09:09 olas ok, good
09:09 olas thx
09:09 egonw for the table
09:09 egonw editing you would not do in the table anyway
09:09 olas true
09:09 olas about the hack session?
09:09 olas on monday?
09:09 olas any news?
09:09 egonw no, sorry...
09:10 egonw last night Karin and I did not get to discussion holiday schedule...
09:10 olas right
09:11 olas email me as soon as you know
09:14 egonw sure
09:14 egonw ok, /me switches back into a "reading children books to my kids"-mode
10:44 olas joined #bioclipse
11:27 jonalv joined #bioclipse
12:08 egonw joined #bioclipse
12:30 CIA-44 bioclipse: ospjuth * r5489 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (9 files in 5 dirs): Added a template MPE for JCP on first page and Texteditor on second.
12:33 CIA-44 bioclipse: ospjuth * r5490 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/MDLMolfileEditor.java: Template to react on resource changes.
12:38 egonw olas: thanx!
12:38 egonw that sounds like the type of commits to get me started :)
12:39 olas I hope so
12:39 olas Have documented some
12:40 olas there are no actions in toolbar yet
12:40 olas please look at old JCP for that
12:40 * olas is importing the 2Dwidget now
12:40 olas is it based on cdk10?
12:40 olas egonw?
12:40 * olas assumes so
12:41 olas as it was in BC1
12:42 egonw sorry... was adding a last compound to NMRShiftDB...
12:42 egonw 17O NMR data
12:42 egonw no, that SWT widget is trunk based
12:42 egonw so, should go into net.bioclipse.cdk.ui
12:48 olas ok
14:03 CIA-44 bioclipse: ospjuth * r5491 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (4 files in 3 dirs): Added the StructureView from Bioclipse1 based on the new renderer and cdk trunk. To test: Open 2DStructureView in Bioclipse2, add an SDF file to workspace, expand it in navigator, click on any of its children.
14:03 * olas successfully added the 2DStructureView to Bioclipse2
14:03 olas :-)
14:04 olas egonw: Won't there be problems with namespaces if we have both cdk10 and cdk_trunk running at the same time in Bioclipse? For example, I want the Structure2DView open at the same time as JCP
14:05 olas Will there be no problems with that?
14:05 egonw I hope not...
14:05 egonw no idea...
14:05 olas I mean
14:05 egonw but I think the RCP is particularly suited for this...
14:05 olas cdk10 and cdk_trunk share the same namespace...
14:05 egonw I hope
14:05 olas yes, could be
14:05 olas let's hope so
14:06 olas I think it will work out fine on second thoughts
14:06 olas since a plugin clearly imports another plugin as dependency
14:06 egonw one issue might be sharing of resources...
14:06 egonw get a cdk10 IMolecule into a cdk.trunk view
14:06 olas I donät think that will be problematic
14:06 olas hmm
14:06 olas let's wait and see
14:07 olas I think it will work out fine
14:07 egonw might you blog a screenshot in the BC blog?
14:07 olas will do :-)
14:07 olas already started
14:07 egonw oh, and don't forget to link to my blog ? :)
14:08 olas sure thing
14:08 egonw [Fri Apr 25 2008] [11:01:31] <egonw> http://chem-bla-ics.blogspot.com/2007​/09/swt-view-with-new-jchempaint.html
14:08 egonw just to ensure it ends up in the log once more.. hahahaha
14:08 egonw good for my google ranking :)
14:16 CIA-44 bioclipse: ospjuth * r5492 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/ui/editor/JalviewEditor.java: Removed unused editor.
14:17 olas blogging postponed a bit
14:17 olas but will do it soon
14:27 egonw ok
14:27 egonw no rush
14:51 egonw olas: you don't use delicious, do you?
14:55 olas no
14:55 olas gotta run now
14:55 olas have a nice weekend all!
14:55 egonw bye all!
14:55 egonw ummm...
14:56 olas hmm
14:56 egonw bye olas
14:56 olas well
14:56 olas bye egonw
14:56 egonw :)
14:56 olas awaiting my last commit
14:56 olas mom
14:56 egonw hehehe
14:56 egonw SF is rather slow the last weeks
14:56 CIA-44 bioclipse: ospjuth * r5493 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/ (8 files in 3 dirs): Started working on a SDFEditor wit ha StructureTableView on one page.
14:56 egonw olas: anywya... BiB of last week has a paper on BioMoby
14:56 egonw ah, cool!
14:56 olas :-)
14:56 olas just started
14:56 egonw ok, *very nice weekend* then :)
14:56 olas nothing in it yet
14:57 olas see ya
14:57 olas left #bioclipse
14:57 * egonw is leaving too... making dinner
15:53 CIA-44 bioclipse: jonalv * r5494 /bioclipse2/trunk/plugins/net.bioc​lipse.core/src/net/bioclipse/core/​business/BioclipseException.java: added a constructor for giving a cause to a BioclipseException
15:55 CIA-44 bioclipse: jonalv * r5495 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/business/StructuredbManagerTest.java: Wrote test for persisting two structures to a database through the manager and the retrieve them both by name and all at once. For the moment it fails due to CDK trouble though... :(
17:07 rojasm joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary