Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-04

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All times shown according to UTC.

Time Nick Message
06:55 Gpoks joined #bioclipse
07:25 egonw joined #bioclipse
07:27 egonw moin
07:27 zarah oh hai egonw
07:47 CIA-40 bioclipse: egonw * r11009 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Bumped version numbers for changes after beta5
07:47 CIA-40 bioclipse: egonw * r11010 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Method for returning unique substructures
07:48 CIA-40 bioclipse: egonw * r11011 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (3 files in 2 dirs):
07:48 CIA-40 bioclipse: Now properly detects unique matches by giving all atoms unique identifiers and testing if
07:48 CIA-40 bioclipse: a hit is isomorphic with earlier hits, based only on these identifiers, using a new
07:48 CIA-40 bioclipse: dedicated IQueryAtom.
07:48 CIA-40 bioclipse: egonw * r11012 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint.view/META-INF/MANIFEST.MF: Fixed version numbers: we use CDK 1.2.2 or better now
07:49 CIA-40 bioclipse: egonw * r11013 /bioclipse2/trunk/plugins/net.biocli​pse.ui/src/net/bioclipse/ui/dialogs/ (ResourceAndContainerGroup.java SaveAsDialog.java): Copied two classes from Eclipse 3.4.2 (EPL-licensed): SaveAsDialog and ResourceAndContainerGroup.
07:49 CIA-40 bioclipse: egonw * r11014 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs):
07:49 CIA-40 bioclipse: Customized SaveAsDialog to support a drop down box with file types.
07:49 CIA-40 bioclipse: * uses CDK's IResourceFormat for typing
07:49 CIA-40 bioclipse: * checks file extension and updates when appropriate
07:49 CIA-40 bioclipse: egonw * r11015 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Use the new customized SaveAsDialog with CML and MDL molfile as formats
07:50 CIA-40 bioclipse: egonw * r11016 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java:
07:50 CIA-40 bioclipse: Fixed incorrect 'instanceof IMolecule' in saveMolecules (fixes #1148):
07:50 CIA-40 bioclipse: 1. the getAtomContainer() should be tested as IMolecule, not the cdkmol itself
07:50 CIA-40 bioclipse: 2. it should be a CDK IMolecule, not a Bioclipse IMolecule
07:50 zarah bug #1148 | http://tinyurl.com/p3vfcm
07:50 jonalv joined #bioclipse
07:51 jonalv o/
08:11 maclean joined #bioclipse
08:12 shk3 joined #bioclipse
08:12 shk3 hi jonalv
08:27 de__maas joined #bioclipse
08:34 olass joined #bioclipse
08:34 jonalv hi shk3
08:34 shk3 how is nwo going?
08:35 jonalv shk3: there are some threading issues...
08:35 jonalv and a lot of plugins doing strange things...
08:35 jonalv shk3: that save thing seems to be irritating as well...
08:36 shk3 yes
08:36 shk3 i have 2 or 3 cases where it is relevant
08:37 shk3 i will try the bioclipseuijob for this
08:39 jonalv shk3: I think I know the source of that error...
08:39 shk3 ah
08:40 shk3 I thought it's an unwanted consequence of stuff and not an error in that sense?
08:40 shk3 we talk about bug 1111?
08:40 jonalv @pz 1111
08:40 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1111
08:41 jonalv shk3: I am talking about the P/L thing while doing ui.save
08:42 shk3 oh sorry
08:42 shk3 I worked around that by giving file.getPath().getOSString() intead of just file
08:59 CIA-40 bioclipse: ospjuth * r11017 /bioclipse2/trunk/plugins/net.bioclipse.jseditor/ (icons/png/jsfile2.png plugin.xml): Added 'JS' on the javascript icon.
09:01 CIA-40 bioclipse: jonalv * r11018 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: removed scheduling rule stuff when creating a job since it gave trouble with IFiles
09:01 jonalv shk3: next time you find a bug and work around it could you please file it as a bug instead?
09:01 CIA-40 bioclipse: jonalv * r11019 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): removed refresh method on ui manager interface taking a progressmonitor and changed the call in Balloon. A step in the right direction for fixing bug: 1189 and bug: 806.
09:01 zarah bug #1189 | http://tinyurl.com/recf62
09:30 de__maas1 joined #bioclipse
09:30 maclean joined #bioclipse
09:32 de__maas1 left #bioclipse
09:44 CIA-40 bioclipse: ospjuth * r11020 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/BalloonManager.java: Removed comment since bug is fixed.
09:45 CIA-40 bioclipse: ospjuth * r11021 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java: Moved file.exists() into asyncExec call.
09:51 masak joined #bioclipse
09:53 CIA-40 bioclipse: ospjuth * r11022 /bioclipse2/trunk/features/ne​t.bioclipse.platform_feature/ (build.properties feature.xml): Added copyright/license.
09:55 CIA-40 bioclipse: jonalv * r11023 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): refactored ui.revealAndSelect to use the @GuiAction annotation instead.
11:11 CIA-40 bioclipse: goglepox * r11024 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java:
11:11 CIA-40 bioclipse: Dont add column to molTable if the it already exist
11:11 CIA-40 bioclipse: fixes bug #1193
11:11 zarah bug #1193 | http://tinyurl.com/ptz8hb
11:19 jonalv egonw. olass: I wonder about the wizeness of calculating inchis in getInchi method on cdkmolecule. What are the risques of it taking a very long time to do this calculation?
11:19 olass you need to ask egonw about this...
11:20 egonw I prefer them outside the IMolecule
11:20 egonw and you just gave a good argument to back that up! tack!
11:21 jonalv egonw: so I guess you will change this some time then...
11:21 egonw I love to do that for 2.1
11:22 jonalv good
11:22 egonw where we'll have IJmolMolecule too
11:30 CIA-40 bioclipse: jonalv * r11025 /bioclipse2/trunk/plugins/net.bioclipse.inchi/src​/net/bioclipse/inchi/business/InChIManager.java: changed inchi.generate into void and using a returner
11:31 egonw btw, likewise, I am not completely happy with IMolecule.getSMILES() either
11:32 egonw that said... we do need means to convert one IMolecule implementation into another
11:34 CIA-40 bioclipse: goglepox * r11026 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
11:34 CIA-40 bioclipse: Changed bcSelection to object from iterator
11:34 CIA-40 bioclipse: As that is cleary how it should be.
11:34 CIA-40 bioclipse: Fixes bug #1185
11:34 zarah bug #1185 | http://tinyurl.com/p7yxdu
11:37 edrin joined #bioclipse
11:39 edrin hi
11:39 zarah privet edrin
11:39 egonw hi edrin
11:39 edrin hi egonw
11:40 edrin your Re: [WS-XMPP] 2 more webservices -> in theory you can "talk" to the IO data components from google talk... but right now they will not answer i think...
11:41 egonw yes, what about it?
11:41 egonw ah, at the end...
11:41 egonw why?
11:42 egonw not that I care much... at least I was able to mention IO-DATA again
11:42 edrin :)
11:42 egonw would be cool though
11:42 edrin well, talking means "<message/>"...
11:42 edrin the google talk app does not support much more than <message/> and <presence/>
11:43 edrin only a few <iq/> to do roaster management...
11:43 egonw so, everything would be wrapped in <message/>?
11:43 edrin yes
11:43 egonw mmm...
11:43 egonw that makes it hard indeed...
11:43 edrin a chat is wrapped in message
11:43 egonw if you cannot embed anything in <iq/>
11:43 edrin io data usese message to do asyn status notification
11:44 edrin if you run an async job and shutdown bc it will guide the message to your instant messenger as a message in a chat window
11:45 edrin egonw: google talk is just the client. i guess their server would support routing the io data stuff
11:45 edrin just the google talk client is just a chat client and not a "you can do everything"
11:45 egonw do you mean we can have a service inform me via gtalk when it is done already?
11:45 egonw sure, I understand that
11:46 edrin egonw: yes. if you use the same account to run the job and chat no problem
11:46 edrin egonw: you can use the same account even at the same time...
11:47 egonw that's the /home bit?
11:47 edrin yes
11:48 edrin like /bioclipse and /mychatclient
11:48 egonw how would the service know where to sent the 'I'm done message' ?
11:48 edrin if /bioclipse started a job and disconnects the server will route the message to /mychatclient
11:49 edrin or to the next resource that logs in
11:49 egonw ic, nice
11:49 edrin (and sends a <presence/>)
11:50 edrin (but I am not 100% sure if the <presence/> is needed if you login with the same resource the message is directed to...
11:50 edrin )
11:50 edrin could be server implementation dependent
11:51 edrin the presence a client must send to become "online" for people that track him within their contact list/roster
11:51 edrin egonw: this way you can get notifications on your mobile phone using a mobile xmpp client...
11:53 egonw a wiki page on how to set that up would be nice
11:53 edrin hm... what to set up?
11:54 edrin egonw: http://xws4j.svn.sourceforge.net/viewvc​/xws4j/xws4j/trunk/xws4j/src/net/biocli​pse/xws/component/xmpp/modules/MessageD​efault.java?revision=6&amp;view=markup
11:54 zarah edrin's link is also http://tinyurl.com/r3vcw3
11:54 egonw a remote cloud service call, getting message back when done
11:54 egonw on your mobile
11:54 edrin if you have set Config.ECHO.equalsIgnoreCase("true") in the component cfg file the component echos any messages ;)
11:56 edrin egonw: ah, right. the disadvantage of xmpp clients on mobile phones is that it must be "always on"... not good for some mobile phone contracts....
11:56 egonw :)
11:56 olass egonw: is all done for release?
11:56 egonw I'm removing the NewMoleculeWizard duplication
11:57 egonw it's OK, but noticed that the new NewMoleculeWizard pop ups a dialog
11:57 egonw which is annoying...
11:57 egonw it's empty
11:57 egonw because there is nothing to do
11:57 egonw ideas?
11:57 olass what are you talking about?
11:58 olass new MOlecule (2) ?
11:58 egonw @pz 1126
11:58 egonw yes
11:58 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1126
11:58 edrin olass, egonw: for your information http://web.swissjabber.ch/index.php/Aspsms-t
11:58 zarah edrin's link is also http://tinyurl.com/p2s8ve
11:59 olass egonw: is the bug resolved?
12:00 egonw didn't I just ask about ideas?
12:00 olass ideas about what? solutions?
12:00 egonw no, about the problem
12:00 egonw [13:57:13] <egonw> it's OK, but noticed that the new NewMoleculeWizard pop ups a dialog
12:00 egonw [13:57:19] <egonw> which is annoying...
12:00 egonw [13:57:23] <egonw> it's empty
12:01 egonw a solution would be welcome
12:01 egonw but opinions are also fine
12:01 olass does the wizard pop up a second dialog?
12:01 egonw is the above desirable, acceptable?
12:01 olass will test it
12:01 olass (sounds bad)
12:01 egonw thanx
12:01 egonw also
12:01 olass which one?
12:01 egonw the NewFromSMILES wizard should likely also be updated
12:01 olass Molecul or Molecule (2) ?
12:02 egonw to open a JChemPaint editor instead of creating a file
12:02 egonw (2)
12:02 olass I get no dialog for (2)
12:02 egonw e.g. I could ask the user for a name
12:02 egonw olass: funny...
12:02 egonw that's how I though I *had* implemented it...
12:02 olass it seems to work fine
12:03 olass IMHO
12:03 jonalv egonw, olass Well I do get a dialog
12:03 olass ok, coming over to jonalv
12:08 CIA-40 bioclipse: goglepox * r11027 /bioclipse2/trunk/cdk-externals/trunk/o​rg.openscience.cdk.control/src/org/open​science/cdk/controller/MoveModule.java:
12:08 CIA-40 bioclipse: Add call to chemModelRelay.moveAtom() when mouse is released
12:08 CIA-40 bioclipse: This makes sure that a coordinate changed get
12:08 CIA-40 bioclipse: fired but only once for a move.
12:08 CIA-40 bioclipse: Fixes bug #1184
12:08 CIA-40 bioclipse: [jchempaint-primary] r14601
12:08 zarah bug #1184 | http://tinyurl.com/p9ydbh
12:10 olass egonw, jonalv: let me know when you have solved the problem with the wizard
12:15 egonw_ joined #bioclipse
12:15 maclean joined #bioclipse
12:16 egonw_ jonalv: if you like to see this 'git annotate' magic, you have to drop by
12:16 egonw_ I think you will like it
12:16 CIA-40 bioclipse: egonw * r11028 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Removed old NewMolecule*Wizards that created a new file in favor of the new one that does not and opens a JChemPaintEditor instead.
12:16 egonw_ masak likes it too
12:16 * masak does
12:19 Gpox if there shoulb be no dialog any benefits of using a wizard?
12:21 egonw_ I guess I agree
12:21 egonw_ not entirely sure how to convert it into a dialog
12:21 egonw_ and also, I wanted to keep this code around, for the equivalent NewFromSMILESWizard...
12:22 egonw_ which is very much related
12:22 egonw_ and maybe we want to ask for a name of the molecule...
12:22 egonw_ and the bugger simply did not show up in the past...
12:22 egonw_ will try to figure out which commit broke it
12:22 Gpox dialog? a handler is enough
12:23 Gpox cdk.fromSMILES() isn't enough?
12:24 egonw_ huh?
12:24 egonw_ you need an input box not?
12:25 Gpox yes but this one dosen't have that
12:26 egonw_ right
12:40 CIA-40 bioclipse: shk3 * r11029 /bioclipse2/trunk/plugins/net​.bioclipse.data.seneca/data/ (3 files in 3 dirs): added examples for christophs annealing engine
12:41 CIA-40 bioclipse: shk3 * r11030 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (9 files in 6 dirs): the user can now choose between the adaptive annealing engine and christoph's old one
12:41 CIA-40 bioclipse: goglepox * r11031 /bioclipse2/trunk/plugins/net.bioclipse.i​nchi/src/net/bioclipse/inchi/InChI.java:
12:41 CIA-40 bioclipse: Added toString() on InChI
12:41 CIA-40 bioclipse: fixes bug #1194
12:41 zarah bug #1194 | http://tinyurl.com/ouufva
12:41 CIA-40 bioclipse: jonalv * r11032 /bioclipse2/trunk/plugins/net.biocl​ipse.balloon.business/src/net/biocl​ipse/balloon/ui/BalloonDialog.java:
12:41 CIA-40 bioclipse: Make sure the BallonDialog has the default String as actual default integer.
12:41 CIA-40 bioclipse: fixes bug: #1201
12:41 zarah bug #1201 | http://tinyurl.com/paunqq
12:44 olass egonw_: I still get no dialog for New Molecule (2)
12:45 olass after update of all
12:45 egonw_ even after my patch r11028?
12:45 olass mom
12:50 jonalv egonw++ I like the new save as dialog with the cmbo box.
12:50 jonalv egonw_: for 2.1 Could I whish for a little label that contains a little description of the file type as well? :)
12:52 CIA-40 bioclipse: goglepox * r11033 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java:
12:52 CIA-40 bioclipse: Added monitor.isCanceled() check in molTable manager
12:52 CIA-40 bioclipse: Fixes bug #1183
12:52 zarah bug #1183 | http://tinyurl.com/os6396
12:57 CIA-40 bioclipse: ospjuth * r11034 /bioclipse2/trunk/plugins/net.bioclipse.ch​emoinformatics/src/net/bioclipse/chemoinfo​rmatics/ChemoinformaticsPerspective.java: Removed old NewWizardShortcut which pointed to a removed NewCMLFileWizard.
12:59 CIA-40 bioclipse: ospjuth * r11035 /bioclipse2/trunk/plugins/net.bioclipse.ch​emoinformatics/src/net/bioclipse/chemoinfo​rmatics/ChemoinformaticsPerspective.java: Forgot to remove the comment for previously removed code.
13:00 CIA-40 bioclipse: ospjuth * r11036 /bioclipse2/trunk/plugins/net.bioclipse.ch​emoinformatics/src/net/bioclipse/chemoinfo​rmatics/ChemoinformaticsPerspective.java: Removed hardcoded shortcut to Jmol view from Cheminfo perspective. Jmol plugin should contribute this view as a to the perspective.
13:02 egonw_ olass: please file me a bug report about that last one
13:02 olass the contribute shortcut?
13:02 egonw_ yes, for the Jmol view
13:02 CIA-40 bioclipse: goglepox * r11037 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/wizards/NewMoleculeWizard.java: Removed unused code in new molecule wizard.
13:03 olass ok
13:03 egonw_ Gpox: thanx!
13:12 masak egonw_: I don't understand the point about changing the API in your bioclipse-dev email. how is changing the return type of a method, making null a possible return value, _not_ changing the API?
13:12 egonw_ masak: correct... ummm... less-involved
13:13 egonw_ it does change the API
13:13 egonw_ still causing NPEs here and there
13:13 egonw_ but
13:13 egonw_ these NPEs actually indicate a problem in the code
13:13 egonw_ throwing an exception would have helped too
13:13 egonw_ the hasFoo() is interesting
13:13 egonw_ and been suggested in the past
13:14 egonw_ but we postponed such more rigorous API changes until aftern 1.2
13:14 egonw_ which is now
13:14 egonw_ I hope to write some serious API changes for the CDK over the summer
13:14 egonw_ see my email on threading a short while ago on cdk-devel too
13:14 egonw_ in reply to our dicussion this morning
13:15 egonw_ about IMolecule flags
13:15 masak ok.
13:15 masak sounds good.
13:15 masak we're all learning here.
13:15 egonw_ we made quite some mistakes back in september 2000
13:15 masak that's, like, 50 internet years ago.
13:16 egonw_ yes
13:16 egonw_ and about 50 CDK releases too, I'd guess
13:23 * maclean didn't like the look of using flags (and property object-object maps) at all
13:31 olass ok, no more commits?
13:31 * olass will build RC1 then...
13:31 egonw_ no
13:31 egonw_ one more commit
13:31 olass ok
13:31 * olass is updating anyway
13:33 egonw_ fuck
13:35 olass egonw_: what features would you like on experimental? RIght now I have the experimental feature (duh!), qsar, and rdf feature
13:35 olass anything else?
13:35 egonw_ cml
13:35 egonw_ jonalv: structuredb?
13:35 egonw_ xml feature
13:36 olass egonw_: have you confirmed these work in an exported version?
13:36 CIA-40 bioclipse: ospjuth * r11038 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Set version of RDF feature to RC1
13:36 olass structuredb does not work, so not even on experimental
13:36 egonw_ cml and xml, yes
13:36 jonalv egonw_: well no not yet but it shouldn't be too hard to add it when it actually does soemthing right?
13:36 olass egonw_: ok
13:36 olass jonalv: no that is easy
13:36 olass jonalv: no, that is easy
13:36 egonw_ ummm... isn't that the idea of experimental?
13:36 olass egonw_: so add the xml and cml features to experimental?
13:36 egonw_ massspec feature
13:37 egonw_ medea feature
13:37 olass egonw_: we should not put things that we KNOW do not work online
13:37 jonalv olass, egonw_: actually it starts now but it doesn't really do anything for the moment so no real point in adding it.
13:37 egonw_ right
13:37 egonw_ indeed
13:37 olass egonw_: they are hosted by EBI and Halle
13:37 jonalv or ratehr it doesn't do anything graphical yet
13:37 egonw_ I do not KNOW that they are not working
13:37 olass right
13:37 egonw_ olass: OK, good points about medea massspec
13:37 olass ok, so add xml and cml, right?
13:38 egonw_ rdf
13:38 egonw_ you already listed that
13:38 egonw_ so I did not repear
13:38 egonw_ so I did not repeat
13:38 olass yes
13:38 egonw_ it
13:38 egonw_ yes, we can add others later
13:38 olass ok good
13:39 olass egonw_: about your commit?
13:39 olass ETA?
13:39 egonw_ cdk feature and qsar feature are on main update site?
13:39 egonw_ pending...
13:39 olass yes
13:39 olass hmm, qsar is on experimental
13:39 olass cdk on main
13:39 olass is that correct?
13:39 egonw_ yes
13:40 olass did we not rename the cdk feature?
13:40 olass to cdkx or so?
13:40 olass cdk power feature
13:41 olass right now the name and ID is confusing
13:41 egonw_ I think we changed it
13:41 olass hmm
13:41 olass did we?
13:41 olass please confirm
13:42 egonw_ later
13:42 egonw_ want to finish this commit first
13:42 olass ok
13:42 egonw_ that's more important for the RC1
13:42 olass ok
13:44 egonw_ fuck
13:44 egonw_ jonalv: doing anything important for RC1 ?
13:44 jonalv egonw_: nope
13:44 egonw_ if not, can I borrow you and your laptop?
13:44 jonalv egonw_: yes
13:45 olass egonw: cml feature bundles net.bc.cml, net.bc.xom, and org.xmlcml.cmlxom which all are already bundled with the cheminfo feature
13:45 olass I see no reason for the cml feature as it is now
13:45 egonw_ right
13:45 egonw_ and adds a dep on the xml feature
13:45 egonw_ unlike cheminfo
13:45 olass so the purpose of teh feature is to download another feature?
13:45 egonw_ and the xml features pulls in the Web Tools Stack XML editor
13:46 olass the XML feature I am fine with
13:46 egonw_ yes
13:46 olass but I will remove the CML feature
13:46 olass it adds nothing
13:46 olass users can select the XML feature
13:46 egonw_ yes, perhaps
13:46 olass I agree this could be useful in the future
13:46 egonw_ sounds logical now
13:46 olass ack
13:47 egonw_ if your sure about your statements :)
13:47 olass what statement?
13:47 egonw_ nevermind
13:50 CIA-40 bioclipse: ospjuth * r11039 /bioclipse2/trunk/features/net.bi​oclipse.xml_feature/feature.xml: Set version of XML feature to RC1
13:51 CIA-40 bioclipse: ospjuth * r11040 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Set dep for xws4j feature to net.bc.core version RC1
13:52 CIA-40 bioclipse: ospjuth * r11041 /bioclipse2/trunk/features/net.b​ioclipse.sampledata/feature.xml: Set dep for sample data feature to net.bc.core version RC1
13:52 CIA-40 bioclipse: ospjuth * r11042 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Set dep for RDF feature to net.bc.core version RC1
13:53 CIA-40 bioclipse: ospjuth * r11043 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Set version of cheminfo feature to RC1
13:53 masak do fasta files contain AA sequences always, or can they contain DNA/RNA too?
13:54 CIA-40 bioclipse: ospjuth * r11044 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Set dep for QSAR feature to net.bc.core and cheminfo features version RC1
13:55 CIA-40 bioclipse: ospjuth * r11045 /bioclipse2/trunk/features/net.bioc​lipse.platform_feature/feature.xml: Set correct included features for RC1 in platform_feature
13:58 masak ah, Wikipedia says the latter.
14:04 Gpox joined #bioclipse
14:07 CIA-40 bioclipse: ospjuth * r11046 /bioclipse2/trunk/features/net.bi​oclipse.rdf_feature/feature.xml: Removed OWL plugin from RDF feature.
14:13 CIA-40 bioclipse: jonalv * r11047 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (META-INF/MANIFEST.MF plugin.xml): Added perspective extension for the new NewMoleculeWizard.
14:14 CIA-40 bioclipse: jonalv * r11048 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Removed reference to old, removed wizard, now replaced by NewMoleculeWizard.
14:15 CIA-40 bioclipse: ospjuth * r11049 /bioclipse2/trunk/features/net.bio​clipse.pellet_feature/feature.xml: Set version to RC1 for pellet feature, and set dep to RDF feature instead of rdf plugin.
14:29 CIA-40 bioclipse: shk3 * r11050 /bioclipse2/trunk/ (9 files in 7 dirs): updated for speclipse rc1 release
14:33 shk3 can anybody tell me what happened to the NewCMLFileWizard?
14:33 shk3 jonalv, do you have an idea?
14:33 CIA-40 bioclipse: miguelrojasch * r11051 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (13 files in 7 dirs): Added more attributes to the properties panel.
14:35 Gpox I think it was replaced with NewMolecuelWizard
14:37 shk3 ah thanks
14:37 shk3 do you have an idea which plugin this is in?
14:37 Gpox net.bc.cdk.jchempaint
14:38 shk3 thanks
14:42 stain joined #bioclipse
14:59 CIA-40 bioclipse: shk3 * r11052 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (3 files in 3 dirs): update cheat sheet to new newmoleculewizard
15:26 CIA-40 bioclipse: shk3 * r11053 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/wizards/NewMoleculeWizard.java: better exception handling
15:33 edrin joined #bioclipse
15:33 edrin hm
15:33 edrin what is this now?
15:34 edrin did uppsala get disconnected !?
15:34 edrin ws1 is down, too
15:58 CIA-40 bioclipse: shk3 * r11054 /bioclipse2/trunk/net.bioclipse​.speclipse-updatesite/site.xml: updated the update site
16:31 shk3 pele is down too... looks like a major desaster
17:10 shk3 joined #bioclipse
17:18 edrin shk3: not only pele
17:19 edrin ws1 is back online
17:19 edrin cdk services are off
17:19 edrin asdasmd
17:48 edrin left #bioclipse

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