| Time |
S |
Nick |
Message |
| 01:25 |
|
|
rojasm joined #bioclipse |
| 06:29 |
|
|
Gpox joined #bioclipse |
| 07:47 |
|
|
jonalv joined #bioclipse |
| 08:09 |
|
|
shk3 joined #bioclipse |
| 08:16 |
|
|
maclean joined #bioclipse |
| 08:18 |
|
|
egonw joined #bioclipse |
| 08:18 |
|
maclean |
hi egonw |
| 08:22 |
|
egonw |
hi maclean |
| 08:23 |
|
* egonw |
is exhausted from the house move |
| 08:23 |
|
maclean |
but finished? |
| 08:24 |
|
egonw |
Gpox: ping |
| 08:24 |
|
Gpox |
egonw: pong |
| 08:28 |
|
maclean |
maybe he's fallen asleep from exhaustion... |
| 08:30 |
|
egonw |
ubuntu 64 suck big time |
| 08:30 |
|
egonw |
+s |
| 08:30 |
|
egonw |
most unstable ubuntu I ever used |
| 08:30 |
|
egonw |
almost on par with MS products |
| 08:31 |
|
egonw |
(that I used) |
| 08:31 |
|
shk3 |
hi jonalv |
| 08:34 |
|
sneumann |
Can't confirm Ubuntu Problems. |
| 08:34 |
|
sneumann |
WHich problem ? |
| 08:35 |
|
egonw |
64bit... random kernal lock ups (not frequent, some 5-10 so far in a few weeks) |
| 08:35 |
|
egonw |
java just become horribly sluggish |
| 08:35 |
|
sneumann |
Which Ubuntu ? |
| 08:36 |
|
egonw |
no clue what that is about yet |
| 08:36 |
|
egonw |
jaunty |
| 08:36 |
|
sneumann |
Laptop ? |
| 08:36 |
|
egonw |
plasma crashes ones a day |
| 08:36 |
|
egonw |
due to memory misallocation |
| 08:36 |
|
sneumann |
Hm, gnome here |
| 08:36 |
|
egonw |
yes, that latter is a kubuntu bug, strickly speaking |
| 08:37 |
|
egonw |
but the java thingy and kernel lock up not |
| 08:38 |
|
sneumann |
We had sluggish java here as well, |
| 08:38 |
|
sneumann |
IIRC java-15 helped |
| 08:38 |
|
sneumann |
or the other way around ... |
| 08:39 |
|
egonw |
weird thing is... this started only after the weekend... |
| 08:42 |
|
stain |
my Ubuntu 9.04 x64 has been stable |
| 08:42 |
|
stain |
but there's something weird with the mouse pointer - under load it stops moving |
| 08:42 |
|
egonw |
stain: it's very difficult to decide/determine what is the problem... |
| 08:42 |
|
egonw |
maybe my Dell laptop has crappy chips... |
| 08:42 |
|
stain |
I've not seen that since before they started with 'Windows accelerator' display cards in the early 90s |
| 08:42 |
|
stain |
egonw: laptop.. could it be some power save problem? |
| 08:43 |
|
egonw |
perhaps... |
| 08:43 |
|
egonw |
it seems to work generally well... |
| 08:43 |
|
egonw |
and did fine on 32 bit ubuntu earlier |
| 08:43 |
|
stain |
or do you have some weird ndis-wrapper-driver for your network card? |
| 08:43 |
|
egonw |
(expect that 1900x1200 screen resolution is not recognized after a Suspend session |
| 08:43 |
|
|
olass joined #bioclipse |
| 08:43 |
|
stain |
unless you have >3 GB ram I guess you could just go for 32-bit |
| 08:43 |
|
egonw |
no, regular driver there, AFAIK |
| 08:44 |
|
stain |
Linux and hardware.. a constant battle |
| 08:44 |
|
egonw |
that's one of the reasons :) |
| 08:44 |
|
egonw |
I have 4 |
| 08:44 |
|
egonw |
32 actually uses 3.5 of them |
| 08:44 |
|
egonw |
so pretty OK |
| 08:44 |
|
stain |
I'm thinking of ordering some Sony VAIO, but I should check how it is with Linux |
| 08:44 |
|
egonw |
and I can recompile my kernel to have the 32 bit support 4GB |
| 08:44 |
|
egonw |
no clue why that is not default yet |
| 08:45 |
|
shk3 |
do you feel the vibrations through irc? |
| 08:45 |
|
maclean |
:) |
| 08:46 |
|
* maclean |
turns up the music.... |
| 08:46 |
|
egonw |
shk3: no |
| 08:46 |
|
egonw |
earth quake? |
| 08:46 |
|
shk3 |
artifical earthquake, yes |
| 08:47 |
|
maclean |
they're building a car-park next door. |
| 08:47 |
|
* olass |
thought it was the sound of a kernel recompiling |
| 08:48 |
|
olass |
stain: have you considered buying a Mac? |
| 08:48 |
|
stain |
olass: I have one.. a macbook pro |
| 08:48 |
|
olass |
stain: way to go |
| 08:48 |
|
olass |
why switching to something worse? |
| 08:49 |
|
stain |
it's 3 years old.. but now I want something smaller - and it's just a bit disappointing that in 3 years the small laptops like the MacBook Air has worse specs than my 3y old machine |
| 08:49 |
|
stain |
I might go for an iMac instead |
| 08:49 |
|
CIA-40 |
bioclipse: ospjuth * r10909 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (3 files in 2 dirs): Updated decorator for jubs not run. |
| 08:49 |
|
stain |
but I thought it would be more fun with some non-mac-laptop and go back to some linux/windows7 cursing |
| 08:50 |
|
stain |
Apple keeps screwing us up - no Java 6 for my machine for instance |
| 08:51 |
|
maclean |
indeed. no java 6 is annoying. |
| 08:51 |
|
maclean |
"...some linux/windows7 cursing.." : using the curses library, or swearing? |
| 08:52 |
|
egonw |
what library is that? swearing? |
| 08:53 |
|
maclean |
libcurses is an ancient drawing library. I guess he probably wasn't referring to that :) |
| 08:53 |
|
egonw |
yes, I what cursus is... |
| 08:53 |
|
egonw |
but that other one ?!? |
| 08:54 |
|
maclean |
swearing? as in actually cursing. |
| 08:54 |
|
egonw |
ooohhhh :) |
| 08:55 |
|
stain |
cursing, swearing, banning.. kjaert barn har mange navn |
| 08:55 |
|
egonw |
(I thought... let's just play along) |
| 09:00 |
|
CIA-40 |
bioclipse: goglepox * r10910 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs): |
| 09:00 |
|
CIA-40 |
bioclipse: Added method named parse() to IPropertyCalculator |
| 09:00 |
|
CIA-40 |
bioclipse: This method is for parsing SDfile properties to property |
| 09:00 |
|
CIA-40 |
bioclipse: without having to calculate it again. |
| 09:00 |
|
CIA-40 |
bioclipse: goglepox * r10911 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 2 dirs): |
| 09:00 |
|
CIA-40 |
bioclipse: Added method to molTable to parseProperties form |
| 09:00 |
|
CIA-40 |
bioclipse: a file. |
| 09:00 |
|
CIA-40 |
bioclipse: goglepox * r10912 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/editor/MoleculesEditor.java: |
| 09:00 |
|
CIA-40 |
bioclipse: Added parsing of calcuated properties when a file is loaded |
| 09:00 |
|
CIA-40 |
bioclipse: The parsing is run in a separate job |
| 09:24 |
|
maclean |
heh. what are these 'xxxxxxxxxx' on startup of eclipse? |
| 09:24 |
|
maclean |
"xxxxxxxxxxxxxxxxINFO - Bioclipse manager: seneca added to Javascript environment." |
| 09:26 |
|
maclean |
oh, never mind. it's in the predictiontool in seneca. |
| 09:27 |
|
shk3 |
yes |
| 09:27 |
|
shk3 |
will look at these |
| 09:42 |
|
maclean |
olass : hmm. I made a diagram, but its a bit cartoony : http://gilleain.tumblr.com/post/116723953 |
| 09:42 |
|
zarah |
maclean's link is also http://tinyurl.com/kt3hcr |
| 09:42 |
|
olass |
maclean: I like it! |
| 09:42 |
|
maclean |
I'll put it on the wiki, then? |
| 09:42 |
|
olass |
can you add it to the architecture wiki page? |
| 09:42 |
|
olass |
:) |
| 09:43 |
|
olass |
please write a small caption about it as well |
| 09:43 |
|
olass |
to put it in context |
| 09:43 |
|
maclean |
ok, will do. |
| 09:43 |
|
olass |
thanks a lot |
| 09:43 |
|
olass |
that page is now getting quite good |
| 09:44 |
|
olass |
maclean: I like this highlighting: http://gilleain.tumblr.com/post/80100724 |
| 09:44 |
|
zarah |
olass's link is also http://tinyurl.com/mozoqq |
| 09:45 |
|
olass |
is this available in jcp? |
| 09:45 |
|
* olass |
heads for lunch |
| 09:46 |
|
maclean |
not as such, but it was an example of a custom generator, so it could be... |
| 09:46 |
|
maclean |
like the center-of-mass generator. |
| 10:47 |
|
CIA-40 |
bioclipse: jonalv * r10913 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/business/SenecaManager.java: layout changes to 80 cols (I don't like scrolling in two directions...) |
| 10:47 |
|
CIA-40 |
bioclipse: jonalv * r10914 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java: Don't swallow the cause for the BioclipseException but give git it as the casue parmater |
| 10:48 |
|
CIA-40 |
bioclipse: jonalv * r10915 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/business/SenecaManager.java: Rewrote SenecaManager.executeJob to use an IReturner and being void so that it can be run as a job followed by a uiJob |
| 10:50 |
|
|
maclean joined #bioclipse |
| 10:55 |
|
|
masak joined #bioclipse |
| 10:58 |
|
shk3 |
Gpox: does an error message relating to P/Virtual and L/Virtual not matching tell you something? |
| 10:59 |
|
shk3 |
do you know what pathes prefixed with L/ or P/ mean in Eclipse? |
| 11:00 |
|
Gpox |
P=project, L=linked maybe |
| 11:03 |
|
shk3 |
hm, ok |
| 11:06 |
|
CIA-40 |
bioclipse: egonw * r10916 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/ (3 files in 2 dirs): |
| 11:06 |
|
CIA-40 |
bioclipse: Added cdk.newMolecule() (implementes #1138). Also updated CDKMolecule.toString() to deal with molecules |
| 11:06 |
|
CIA-40 |
bioclipse: with zero atoms. |
| 11:07 |
|
CIA-40 |
bioclipse: jonalv * r10917 /bioclipse2/trunk/plugins/net.bioclipse.core/src/net/bioclipse/core/util/LogUtils.java: wrapped pop dialog code in asyncExec so it can be called from any thread |
| 11:10 |
|
CIA-40 |
bioclipse: ospjuth * r10918 /bioclipse2/trunk/plugins/net.bioclipse.ds.dblookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java ExternalMoleculeMatch.java): Partial implementation for DBExactMatch. Still requires calculator for inchi and inchikey. |
| 11:35 |
|
CIA-40 |
bioclipse: egonw * r10919 /bioclipse2/trunk/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java: Fixed spelling and now uses spaces not tabs |
| 11:39 |
|
* egonw |
wonders if we should use myExperiment instead of Gist in some distant future |
| 11:40 |
|
egonw |
since their definition of workflow is pretty fuzzy nowadays (intentionally) |
| 11:41 |
|
egonw |
in a wild strategic move |
| 11:42 |
|
olass |
RC1 will be tomorrow |
| 11:43 |
|
olass |
please have all commits for this done in the early afternoon tomorrow, ~15 swedish time |
| 11:43 |
|
CIA-40 |
bioclipse: ospjuth * r10920 /bioclipse2/trunk/ (37 files in 37 dirs): Set version to 2.0.0.RC1 for release candidate 1. |
| 11:44 |
|
CIA-40 |
bioclipse: ospjuth * r10921 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.RC1 for release candidate 1. |
| 11:44 |
|
egonw |
shk3, rojasm: are you done with cdk10 ? |
| 11:46 |
|
olass |
egonw: do we need to update ID for the CDK plugins? |
| 11:46 |
|
egonw |
for net.bioclipse.cdk yes |
| 11:46 |
|
olass |
yes, done that |
| 11:46 |
|
olass |
but not for the org.opensc.cdk, right? |
| 11:46 |
|
CIA-40 |
bioclipse: ospjuth * r10922 /bioclipse2/trunk/plugins/ (27 files in 19 dirs): Set version to 2.0.0.RC1 for release candidate 1. |
| 11:46 |
|
egonw |
correct |
| 11:46 |
|
olass |
ok |
| 11:47 |
|
egonw |
Gpox: or have you been making commits to .render and .control post beta5? |
| 11:48 |
|
Gpox |
2009-05-29 last commit |
| 11:49 |
|
Gpox |
r14599 |
| 11:49 |
|
egonw |
Gpox: did you update the plugin version number by appending a new data? |
| 11:49 |
|
Gpox |
no |
| 11:49 |
|
egonw |
ok, mom |
| 11:51 |
|
egonw |
olass: there are a few patches since beta5 |
| 11:52 |
|
egonw |
isn't the cheminfo feature not part of the main download? |
| 11:52 |
|
olass |
yes |
| 11:52 |
|
egonw |
so, those two patches don't hurt |
| 11:52 |
|
olass |
oh no |
| 11:52 |
|
olass |
but please increment versions |
| 11:52 |
|
olass |
I had problems before if they weren't touched |
| 11:52 |
|
olass |
but it might work out now anyway |
| 11:53 |
|
|
edrin joined #bioclipse |
| 11:53 |
|
edrin |
olass: your services are down again! |
| 11:53 |
|
olass |
oh no |
| 11:53 |
|
olass |
starting them up |
| 11:53 |
|
olass |
ok, started |
| 11:54 |
|
olass |
edrin: this is not good |
| 11:54 |
|
olass |
why do they go down? |
| 11:54 |
|
olass |
egonw: where was that cron job you set up for autostarting xmpp services? |
| 11:54 |
|
edrin |
olass: it's frequent that tcp/ip connections that last for days break |
| 11:54 |
|
egonw |
in the wiki |
| 11:55 |
|
olass |
xmpp wiki? |
| 11:55 |
|
olass |
ok |
| 11:55 |
|
egonw |
or bioclipse wiki |
| 11:55 |
|
olass |
? |
| 11:55 |
|
olass |
why? |
| 11:55 |
|
egonw |
@pz crontab |
| 11:55 |
|
zarah |
egonw: Zarro boogs found. |
| 11:55 |
|
egonw |
@pz xmpp |
| 11:55 |
|
zarah |
[1017] XMPP commands to list services... http://tinyurl.com/ncqmz7 |
| 11:55 |
|
zarah |
[425] js console throws strange excpe... http://tinyurl.com/deomud |
| 11:55 |
|
zarah |
[842] XMPP service that generates 3D ... http://tinyurl.com/mttfnm |
| 11:55 |
|
zarah |
Entire list at http://tinyurl.com/m48a6q |
| 11:55 |
|
egonw |
olass: as in... I don't remember |
| 11:56 |
|
olass |
egonw: I can't find it on xmpp wiki |
| 11:56 |
|
olass |
it should really be there |
| 11:56 |
|
egonw |
http://wiki.bioclipse.net/inde[…]e=XmppWebServices |
| 11:56 |
|
zarah |
egonw's link is also http://tinyurl.com/5sjy3e |
| 11:56 |
|
egonw |
http://wiki.bioclipse.net/inde[…]o_reboot_services |
| 11:56 |
|
zarah |
egonw's link is also http://tinyurl.com/5sjy3e |
| 11:56 |
|
olass |
egonw: could you please move that info to xmpp wiki? |
| 11:57 |
|
edrin |
olass, egonw: although the components connect via tcp it has a risk to run them from remote. best would be localhost, then such tcp errors wont occur ... |
| 11:57 |
|
egonw |
yes |
| 11:57 |
|
olass |
thanks for the URL |
| 11:57 |
|
edrin |
if not one should run them with a crontab... |
| 11:57 |
|
olass |
edrin: we need to move services to ws1 |
| 11:57 |
|
olass |
lack of time... |
| 11:58 |
|
edrin |
xmpp is good because it can handle such tcp disconnects since the analysis logic is not depending on it in contrast to http soap (without polling) |
| 11:59 |
|
edrin |
but at least we should use the feature of xmpp to reconnect |
| 11:59 |
|
|
maclean joined #bioclipse |
| 11:59 |
|
olass |
ehat do you mean now? |
| 11:59 |
|
egonw |
olass: http://pele.farmbio.uu.se/xmpp[…]index.php/Crontab |
| 11:59 |
|
zarah |
egonw's link is also http://tinyurl.com/ma2n6d |
| 12:01 |
|
olass |
egonw++ |
| 12:03 |
|
maclean |
ugh! I may have mentioned it before, but pages from that wiki look horrible in safari. |
| 12:03 |
|
maclean |
(I know : "don't use safari, then!" :)) |
| 12:03 |
|
masak |
maclean: yes, what were you thinking? :) |
| 12:04 |
|
maclean |
I was thinking "middle-click to open links in a new tab - how convenient!" |
| 12:04 |
|
maclean |
although, since safari-4 beta, I've been thinking "ugh! tabs on the top :(((" |
| 12:11 |
|
egonw |
olass: bumped version number, but will commit later |
| 12:11 |
|
olass |
egonw: ok |
| 12:16 |
|
CIA-40 |
bioclipse: goglepox * r10923 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added support for the use field in choice generator |
| 12:16 |
|
CIA-40 |
bioclipse: goglepox * r10924 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (4 files in 3 dirs): |
| 12:16 |
|
CIA-40 |
bioclipse: Fixed molTable.parseProperties() |
| 12:16 |
|
CIA-40 |
bioclipse: Added toString(value) to IPropertyCalculator interface |
| 12:17 |
|
CIA-40 |
bioclipse: goglepox * r10925 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): |
| 12:17 |
|
CIA-40 |
bioclipse: Added getProperty(String,IMolecule.Property) to ICDKMolecule |
| 12:17 |
|
CIA-40 |
bioclipse: Implemented this method on CDKMolecule |
| 12:17 |
|
CIA-40 |
bioclipse: with a Map<String,Object> |
| 12:17 |
|
CIA-40 |
bioclipse: fixes bug #647 |
| 12:17 |
|
zarah |
bug #647 | http://tinyurl.com/nkg9au |
| 12:25 |
|
CIA-40 |
bioclipse: jonalv * r10926 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): removed IProgressMonitor.unknown from BioclipseJobs and added some stuff that for some reason (don't ask me I have no idea) was neeeded to get progressmonitoring in seneca manager |
| 12:40 |
|
CIA-40 |
bioclipse: ospjuth * r10927 /bioclipse2/trunk/features/ (10 files in 10 dirs): Set version to 2.0.0.RC1 for release candidate 1. |
| 12:52 |
|
CIA-40 |
bioclipse: shk3 * r10928 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/editor/SenecaJobEditor.java: avoids this P/Virtual and L/Virtual not matching problem by giving path as string - not great, but works. |
| 12:53 |
|
egonw |
shk3: under what conditions will it not work? what makes it not great? |
| 12:54 |
|
maclean |
it's 'not great' in the sense of being a hack... |
| 12:54 |
|
egonw |
sure |
| 12:54 |
|
egonw |
what makes it a hack instead of a proper fix? |
| 12:54 |
|
maclean |
is that not obvious? |
| 12:55 |
|
maclean |
well, obviously it is not obvious, but it seems so to me. |
| 12:55 |
|
egonw |
no, it's not obvious to me why using the path as string is suboptimal |
| 12:55 |
|
egonw |
that's why I ask |
| 12:56 |
|
shk3 |
using IFile if we have got it seems better than |
| 12:56 |
|
shk3 |
IFile.getPath().toOSString() |
| 12:56 |
|
shk3 |
I believe |
| 12:56 |
|
egonw |
sounds logical... |
| 12:56 |
|
egonw |
so why is this not great then? |
| 12:57 |
|
maclean |
did you look at the diff? |
| 12:58 |
|
shk3 |
was: |
| 12:58 |
|
shk3 |
.saveSDFile(sdfile, mols); |
| 12:58 |
|
shk3 |
is: |
| 12:58 |
|
shk3 |
.saveSDFile(sdfile.getFullPath().toOSString(), mols); |
| 12:58 |
|
egonw |
maclean: no, not yet... I cannot look at all patches, so scan them first by commit message (which is why they exist, not?) |
| 12:58 |
|
maclean |
uhhh. |
| 12:58 |
|
egonw |
maclean: |
| 12:58 |
|
maclean |
not this again. |
| 12:59 |
|
maclean |
yeesss. |
| 12:59 |
|
egonw |
and no, the diff does not explain me why the new solution is better, but not great |
| 12:59 |
|
maclean |
really? |
| 12:59 |
|
egonw |
please enlighten me |
| 12:59 |
|
egonw |
I seem to be stupid here |
| 12:59 |
|
shk3 |
it's better because it works |
| 13:00 |
|
shk3 |
it's not great because it should not be needed |
| 13:00 |
|
egonw |
ic |
| 13:00 |
|
egonw |
so the underlying problem is that |
| 13:00 |
|
egonw |
saveSDFFile(IFIle) it not working? |
| 13:00 |
|
maclean |
suppose so. |
| 13:00 |
|
shk3 |
in that particular situation, yes |
| 13:00 |
|
egonw |
which makes this hack needed |
| 13:00 |
|
shk3 |
it seems to be related to threading or so |
| 13:01 |
|
egonw |
maclean: it really would have been helpful if the commit would include the reason why this hack was needed |
| 13:01 |
|
egonw |
maclean: yes, that again |
| 13:01 |
|
maclean |
it wasn't my commit! |
| 13:01 |
|
egonw |
maclean: and I wasn't asking you for an explanation |
| 13:02 |
|
shk3 |
ok, my fault |
| 13:02 |
|
egonw |
oh no |
| 13:02 |
|
egonw |
no fault assignments please |
| 13:02 |
|
shk3 |
don't beat each other up, please |
| 13:02 |
|
egonw |
I was just trying to understand the patch |
| 13:02 |
|
CIA-40 |
bioclipse: shk3 * r10929 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/ (3 files in 2 dirs): monitor is now initialised with proper number of steps and is counting them |
| 13:02 |
|
shk3 |
that's as verbose as it gets, I believe |
| 13:24 |
|
CIA-40 |
bioclipse: shk3 * r10930 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/ (3 files in 2 dirs): better handling of steps |
| 13:38 |
|
CIA-40 |
bioclipse: jonalv * r10931 /bioclipse2/trunk/plugins/net.bioclipse.core/src/net/bioclipse/managers/business/AbstractManagerMethodDispatcher.java: pick the returnvalues also from comple returns when runnign JavaScript. |
| 13:39 |
|
CIA-40 |
bioclipse: shk3 * r10932 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/business/SenecaManager.java: removed usage of subprogressmonitor in executejob, since it is not needed and makes things more complicated |
| 13:46 |
|
CIA-40 |
bioclipse: shk3 * r10933 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/editor/SenecaJobEditor.java: empty result (=cancelled) properly handled |
| 13:53 |
|
CIA-40 |
bioclipse: shk3 * r10934 /bioclipse2/trunk/plugins/net.bioclipse.data.seneca/data/hko3/hko3.sjs: proper sjs file for example |
| 14:06 |
|
olass |
shk3: is SaveSDF broken? |
| 14:06 |
|
olass |
if so, is there a bug? |
| 14:06 |
|
shk3 |
for jonalv |
| 14:06 |
|
olass |
good |
| 14:06 |
|
shk3 |
but works for me |
| 14:06 |
|
olass |
hmm |
| 14:06 |
|
olass |
ok |
| 14:07 |
|
shk3 |
I am updating for testing |
| 14:07 |
|
olass |
as long as there is a bug for 2.0 I'm happy |
| 14:07 |
|
* olass |
is trying to make sense for the release |
| 14:07 |
|
olass |
mek sense out of quite some bugs.. |
| 14:07 |
|
olass |
blah |
| 14:07 |
|
* olass |
is relocating to jonalv for some discussions |
| 14:10 |
|
shk3 |
do you do the rc today? |
| 14:11 |
|
CIA-40 |
bioclipse: gilleain * r10935 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/job/StochasticStructureElucidationJob.java: Inner class MonitorWrapper now extends the ProgressMonitorWrapper instead of implementing IProgressMonitor |
| 14:12 |
|
CIA-40 |
bioclipse: shk3 * r10936 /bioclipse2/trunk/plugins/net.bioclipse.bibtex/ (. .settings/): added stuff to svn ignore |
| 14:15 |
|
CIA-40 |
bioclipse: gilleain * r10937 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/anneal/AdaptiveAnnealingEngine.java: Cleaned up if/else construct for code clarity purposes. |
| 14:17 |
|
jonalv |
@pz 816 |
| 14:17 |
|
zarah |
http://pele.farmbio.uu.se/cgi-[…]ow_bug.cgi?id=816 |
| 14:29 |
|
|
masak joined #bioclipse |
| 14:34 |
|
|
Gpox joined #bioclipse |
| 14:38 |
|
|
Gpoks joined #bioclipse |
| 14:46 |
|
CIA-40 |
bioclipse: goglepox * r10938 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Implemented InChI property calculator |
| 14:48 |
|
CIA-40 |
bioclipse: goglepox * r10939 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/business/MoleculeTableManager.java: Only save properties that are cached. |
| 15:16 |
|
CIA-40 |
bioclipse: carl_masak * r10940 /bioclipse2/trunk/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/views/JsConsoleView.java: |
| 15:16 |
|
CIA-40 |
bioclipse: [JsConsoleView] whitespace therapy |
| 15:16 |
|
CIA-40 |
bioclipse: Also fixed one instance of s/"\\n"/NEWLINE/ |
| 15:29 |
|
CIA-40 |
bioclipse: miguelrojasch * r10941 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (12 files in 7 dirs): Added new view-page to visualize reaction and structure from the Reaction editor instance of to have the viewer in the editor. |
| 15:29 |
|
edrin |
hi |
| 15:29 |
|
zarah |
ni hao edrin |
| 15:30 |
|
edrin |
anyone has access to the following article: http://www.ncbi.nlm.nih.gov/pu[…]l.Pubmed_RVDocSum |
| 15:30 |
|
edrin |
PMID: 18374183 |
| 15:30 |
|
zarah |
edrin's link is also http://tinyurl.com/nkkfq4 |
| 15:30 |
|
edrin |
? |
| 15:30 |
|
|
egonw joined #bioclipse |
| 15:31 |
|
olass |
edrin: I'm looking |
| 15:31 |
|
edrin |
cool :) |
| 15:31 |
|
olass |
yes |
| 15:31 |
|
olass |
will send you pdf |
| 15:32 |
|
olass |
edrin: sent |
| 15:34 |
|
edrin |
thank you :) |
| 15:51 |
|
olass |
egonw: please file a bug for Gpox to define datatype in the Calculators extension point using XML schema datatypes |
| 15:51 |
|
olass |
(so you can verify it upon finished) |
| 15:53 |
|
shk3 |
jonalv++ |
| 15:59 |
|
* jonalv |
gives up for today |
| 15:59 |
|
|
Gpox joined #bioclipse |
| 15:59 |
|
|
Gpoks joined #bioclipse |
| 16:03 |
|
CIA-40 |
bioclipse: goglepox * r10942 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdfeditor/ (3 files in 3 dirs): Added InChI calculator to extension |
| 16:04 |
|
CIA-40 |
bioclipse: shk3 * r10943 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/job/StochasticStructureElucidationJob.java: the cancel in java now works |
| 16:04 |
|
|
edrin left #bioclipse |
| 16:06 |
|
CIA-40 |
bioclipse: shk3 * r10944 /bioclipse2/trunk/plugins/net.bioclipse.seneca/src/net/bioclipse/seneca/editor/SenecaJobEditor.java: after a cancel, no sdf editor is opened |
| 16:41 |
|
CIA-40 |
bioclipse: ospjuth * r10945 /bioclipse2/trunk/plugins/ (7 files in 7 dirs): Set version to 2.0.0.RC1 for release candidate 1. |
| 17:37 |
|
|
sneumann_ joined #bioclipse |
| 17:59 |
|
|
sneumann__ joined #bioclipse |
| 18:11 |
|
CIA-40 |
bioclipse: miguelrojasch * r10946 /bioclipse2/trunk/plugins/net.bioclipse.reaction/src/net/bioclipse/reaction/ (2 files in 2 dirs): Added a context menu provider for the boxes |
| 21:29 |
|
CIA-40 |
bioclipse: miguelrojasch * r10947 /bioclipse2/trunk/plugins/net.bioclipse.reaction/src/net/bioclipse/reaction/model/ (CompoundObjectModel.java ReactionObjectModel.java): Initiate a IAtomContainer or IReaction when an AbstractObjectModel is generated |
