Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-09

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All times shown according to UTC.

Time Nick Message
00:36 LaserJock left #cdk
06:31 jbrefort joined #cdk
07:46 neksa joined #cdk
09:20 nielsout morning
09:24 carsten joined #cdk
09:37 nielsout hey carsten
09:37 carsten moin
09:48 edrin joined #cdk
09:48 rojasm joined #cdk
09:52 CIA-31 cdk: nielsout * r8900 /trunk/cdk/src/org/openscience/cdk/controller/ (3 files): dragging working a little bit now
11:00 steinbeck joined #cdk
11:32 * nielsout casts a spell to summon Egon to irc
11:56 egonw joined #cdk
12:01 egonw moin
12:04 nielsout yo edrin
12:04 nielsout my spell worked :)
12:04 nielsout *yo egonw
12:04 egonw hi nielsout
12:06 nielsout egonw did you see my dragging update?
12:06 nielsout i'm using the mouse event to get the 'parent' container to repaint() that container
12:06 nielsout so we don't need to make a listener for that :)
12:06 egonw nielsout: no, not yet
12:06 egonw excellent!
12:06 egonw good job!
12:07 egonw so, that's nicely hidden in the mouseeventrelay ?
12:07 nielsout yeh it's quite nice that it works a bit now
12:07 nielsout yeh
12:07 egonw you added a method in the MouseEventRelay to trigger the repaint() ?
12:07 egonw or do you do a repaint on each mouse event?
12:08 egonw that would be less efficient
12:08 nielsout hm no I changed the drag method to have the mouse event sent to the dumpclosestobject thing
12:08 nielsout so it only repaints when needed
12:08 egonw only a repaint is needed upon a call from one of the controller modules to the controller hub
12:09 egonw how do you propagate the event in the hub to the mouseeventrelay?
12:09 nielsout // Relay the mouse event to the general handlers
12:09 nielsout for (IController2DModule module : generalModules) {
12:09 nielsout module.mouseDrag(worldCoordFrom, worldCoordTo, event);
12:09 nielsout }
12:09 nielsout that's in the controller2d hub
12:09 nielsout so I just changed the interface to have the mouse event in it
12:10 egonw what kind of event is that?
12:10 nielsout public abstract void mouseDrag(int screenCoordXFrom, int screenCoordYFrom, int screenCoordXTo, int screenCoordYTo, MouseEvent event);
12:10 egonw MouseEvent is Swing not?
12:10 nielsout hm think it's general
12:10 nielsout or is it only swing? :O
12:10 egonw make sure SWT uses that same class...
12:10 egonw I think it's Swing specific
12:11 egonw OK, let's do:
12:11 nielsout i'll have a look if swt does the same :)
12:11 egonw rename the IMouseEventRelay to IControllerEventRelay
12:11 egonw and add a method: triggerViewUpdate()
12:11 egonw or updateView()
12:11 egonw so, then only the implementing SwingMouseEventRelay needs to know about MouseEvent
12:13 nielsout swt does have a mouse event.. but it's different :P
12:13 nielsout http://help.eclipse.org/help32/index.jsp?to​pic=/org.eclipse.platform.doc.isv/reference​/api/org/eclipse/swt/events/MouseEvent.html
12:13 egonw right...
12:20 nielsout hm I don't understand exactly where/how you want to call that updateView() as the implementation should be in SwingMouseEventRelay then and DumpClosestObjectToSTDOUTModule doesn't have access to those right?
12:20 egonw nice quote: "Some of you might have read about my analysis about erectile dyscfunction and how the size of the InChI does give a bigger SMILES in general."
12:21 egonw that will fool your SPAM filters :)
12:21 nielsout lol
12:22 egonw umm...
12:22 egonw the module detects something to act on...
12:22 nielsout hmn just figured a way how to make it.. if we should make the 'relay.mouseDrag(dragFromX, dragFromY, event.getX(), event.getY(), event);' return a value and depending on that update or not?
12:22 egonw like a drag event...
12:22 egonw and calls the dragAtom(oldCoord, newCoord, atom) in the hub
12:22 egonw s/dragAtom/moveAtom/
12:23 egonw this moveAtom() will call the updateView() in the IControllerEventRelay that SwingEventRelay implemens... (mind the name change :)
12:23 nielsout hm ok, that makes sense an sich yeah, i'll try to implement it ;)
12:42 CIA-31 jmol: nicove * r8224 /trunk/Jmol-FAH/projects/p3635.xyz.gz: Folding@Home
13:02 nielsout hm that's not 100% correct egonw, as IControllerEventRelay is the interface for what has to happen when a certain mouse move (in Worldcoordinates) happens, so it's independend of swing/swt
13:03 egonw explain
13:04 nielsout so a mouse event enters in SwingMouseEventRelay, and that one calls the relays to handle what has to happen after that mouse
13:04 egonw oh crap...
13:04 nielsout in those relays such as DumpClosestObject it has to call the updateView
13:04 egonw the hub is now the relay, right?
13:05 nielsout which should be implemented in SwingMouseEvent relay prolly
13:05 nielsout hmm yes that's also a relay
13:06 egonw OK, then make a new interface IViewEventRelay
13:06 egonw that can later also hold a method for popups
13:07 egonw and a fourth param in the Controller2DHub, IViewEventRelay
13:07 egonw which would be the Swing adapter
13:10 nielsout ok
13:24 CIA-31 cdk: egonw * r8901 /trunk/cdk/src/org/openscie​nce/cdk/io/PDBWriter.java: Added a statement to say that the current PDBWriter does not write protein structures
13:30 egonw rojasm: around?
13:31 egonw rojasm: what class calculates the pi-gasteiger charges?
13:31 rojasm yes
13:31 egonw GasteigerPEPEPartialCharges, right?
13:31 rojasm yes
13:31 egonw ack..
13:31 rojasm for picharges
13:31 egonw oh: a fifth bug report:
13:32 egonw the JavaDoc cites GM81, which is not found in the database...
13:32 rojasm ups
13:32 egonw see: http://cheminfo.informatics.indiana.edu/~rg​uha/code/java/nightly/api/org/openscience/c​dk/charges/GasteigerPEPEPartialCharges.html
13:34 rojasm I don't have now this paper. I have to look at home
13:34 rojasm where is
13:34 egonw OK, will file a bug report then
13:34 egonw and assign to you
13:34 rojasm perfect
13:35 egonw done
13:39 CIA-31 cdk: nielsout * r8902 /trunk/cdk/src/org/openscience/cdk/ (9 files in 2 dirs): new interface to make updateView() independent so different implementations for swing/swt/etc can be used
13:40 nielsout please check if this is how you'd want it egonw
13:40 nielsout controller2dHub has a IViewEventRelay now
13:41 nielsout and once a IController2DModule is created it will add that same IViewEventRelay to it
13:41 egonw that should not be necessary
13:41 nielsout so each IController2DModule can just call eventRelay.updateView();
13:42 nielsout oh wait, the IChemModelRelay in the IController2DModule already contains the access to that?
13:42 egonw right
13:43 egonw each IChemModelRelay method will call the IViewEventRelay.updateView()
13:45 egonw so, please remove IController2DModule.setEventRelay() again
13:45 nielsout already doing that yeah :)
13:46 egonw btw, I am thinking that the introduction of the IViewEventRelay also makes the rename of IMouseEventRelay to IControllerEventRelay unnecessary...
13:46 nielsout euhm yes, that can be renamed back :)
13:46 nielsout mousedrag at DumpClosestObject shizzle
13:46 nielsout From: -0.11779421242994327/0.00457998212689917 to -0.1304543256262495/0.00457998212689917
13:46 nielsout Dragging atom: Atom(27837671, C, H:3, SP:null, 2D:[(-0.08366706650421182, 0.021820077450104565)], 3D:[null], Fract3D:[null], C:null, FC:-2, AtomType(null, MBO:null, BOS:null, FC:-2, H:null, NC:0, CR:null, VDWR:null, EV:0, Isotope(10, EM:-1.0, AB:-1.0, Element(C, ID:C0, AN:0))))
13:47 nielsout updateView now in Controller2DHub
13:47 nielsout updateView in SwingEventRelay
13:47 nielsout this seems to work now :]
13:47 egonw ack :)
13:47 nielsout IMouseEventRelay is named back now
13:49 CIA-31 cdk: egonw * r8903 /trunk/cdk/src/org/opensci​ence/cdk/math/Primes.java: Applied patch by Bala <bkbsub@gmail.com>: more integers
13:49 CIA-31 cdk: nielsout * r8904 /trunk/cdk/src/org/openscience/cdk/ (7 files in 2 dirs): minor renames and changes
13:50 nielsout so.. next thing to do: when you're dragging an atom, it's repainting the whole object.. instead it should keep the same transformation matrix
13:50 egonw explain
13:50 nielsout if you move one atom atm, the other ones will move aswell because it calculates the atom boundaries again
13:50 nielsout just run it to see what I mean ;)
13:50 nielsout it's very inconvenient to have other atoms moving around when you move one
13:50 egonw I think I understand
13:51 egonw yes, it is...
13:52 egonw sounds like a method: IChemModelRelay.recalculateViewDimensions()
13:52 nielsout hm
13:52 nielsout I think this should be done in the Java2DRenderer
13:52 nielsout just call paintMolecule(IAtomContainer atomCon, Graphics2D graphics) {
13:52 nielsout instead of paintMolecule(IAtomContainer atomCon, Graphics2D graphics, Rectangle2D bounds) {
13:53 egonw ummm... sounds right
13:53 nielsout and then detect somehow if the bounds have to be recalculated
13:53 nielsout i'll rewrite the code in java2dRenderer first
13:54 egonw not sure if you can
13:55 nielsout well was thinking of keeping track of the size of the window in TestEditor, if it doesn't change, just call paintMolecule(IAtomContainer atomCon, Graphics2D graphics)
13:55 steinbeck_ joined #cdk
13:55 CIA-31 jmol: hansonr * r8225 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties Token.java): (log message trimmed)
13:55 CIA-31 jmol: 11.3.17 new feature: Jmol math array element assignment:
13:55 CIA-31 jmol: #
13:55 CIA-31 jmol: # a = "2,3,4,5".split(",")
13:55 CIA-31 jmol: #
13:55 CIA-31 jmol: # a[3] = "now the 4 becomes this phrase"
13:55 CIA-31 jmol: # a[a[2]] = "not any more; now it's this"
14:22 CIA-31 cdk: nielsout * r8905 /trunk/cdk/src/org/openscience/cdk/renderer/progz/ (Java2DRenderer.java TestEditor.java): dragging an atom no longer causes all atoms to move
14:24 nielsout egonw please try the dragging out :)
14:24 egonw mom
14:24 nielsout it has some bugs probably, one of them being while dragging over another atom is starts dragging that atom, but I think I figured out how to fix that ;)
14:25 nielsout time for me to get something to drink, brb
14:35 CIA-31 jmol: hansonr * r8226 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Eval.java Jmol.properties Token.java):
14:35 CIA-31 jmol: 11.3.17 # new feature: Jmol math x = array(a,b,,,,)
14:35 CIA-31 jmol: #
14:35 CIA-31 jmol: # x = array(3,4,5,6)
14:35 CIA-31 jmol: # print x[3]
14:35 CIA-31 jmol: # >> 5
14:35 CIA-31 jmol: #
14:41 CIA-31 cdk: nielsout * r8906 /trunk/cdk/src/org/openscience/cdk/renderer/​progz/DumpClosestObjectToSTDOUTModule.java: minor change to make dragging more pretty
14:43 * nielsout goes doing the dishes
14:46 CIA-31 cdk: egonw * r8907 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Added halogen atom types: neutral and negative
14:46 egonw OK, 3% left
14:47 egonw 7 out of 2212 atom types not perceived... (does not say anything about accuracy though)
15:09 nielsout 2212 atom types? that's a lot :o
15:36 carsten joined #cdk
15:38 egonw 2212 atoms...
15:38 egonw not sure how many atom types...
15:38 egonw not so much, really...
15:39 egonw the list of defined types <30... see cdk.config.data.cdk_atomtypes.xml
15:50 nielsout ah okey :)
15:58 nielsout brb, getting some food :)
16:22 nielsout toasts with salmon and eel were nice :x
16:23 nielsout egonw already found time to check the dragging?
17:09 carsten joined #cdk
17:37 egonw nielsout: looks good
17:58 nielsout thanks :), not everything looks good tho..
17:58 nielsout http://student.science.uva.nl/​~nout/progz/yourImageName.PNG looks somewhat bad :
17:59 egonw that negative charge, you mean?
17:59 nielsout what would the proper location for the '-' sign be? I think it should be at place of the 2, and the H2 some higher
17:59 nielsout yeah
18:30 egonw damn...
18:31 egonw my eclipse crashes all over me...
18:31 nielsout :/
18:31 nielsout ima watch a bit tv, seen too much code today ;)
18:31 egonw nielsout: please blog about dragging atoms...
18:32 egonw and about what you want to do before the 20th
18:32 nielsout ack, will do that after i've had enough of the tv ;)
18:34 egonw ack
18:48 egonw nielsout: got to go
18:48 egonw cu tomorrow...
18:48 egonw I will comment in your blog
20:04 CIA-31 jmol: nicove * r8227 /trunk/Jmol-FAH/projects/p3660.xyz.gz: Folding@Home
20:29 CIA-31 jmol: nicove * r8228 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
21:08 CIA-31 cdk: nielsout * r8908 /trunk/cdk/src/org/openscience/cdk/ (10 files in 2 dirs):
21:08 CIA-31 cdk: -Some files moved from /renderer/progz to /controller
21:08 CIA-31 cdk: -prolly also some fixes ;)
21:08 CIA-31 cdk: -New blog about it at http://progz-jchem.blogspot.com/​2007/09/dragging-bit-around.html
22:07 CIA-31 jmol: hansonr * r8229 /trunk/Jmol/src/org/jmol/util/Escape.java: 11.3.17 -- critical update bug
23:49 CIA-31 jmol: hansonr * r8230 /trunk/Jmol/src/org/ (7 files in 3 dirs): (log message trimmed)
23:49 CIA-31 jmol: version=11.3.18
23:49 CIA-31 jmol: # critical bug fix for 11.3.17 in regard to serialization of arrays
23:49 CIA-31 jmol: # also introduces
23:49 CIA-31 jmol: #
23:49 CIA-31 jmol: # reset ALL # resets all user-created variables
23:49 CIA-31 jmol: #

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