Perl 6 - the future is here, just unevenly distributed

IRC log for #bioclipse, 2014-02-06

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All times shown according to UTC.

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10:40 konditorn Gpox: jag har ett litet problem med att en del atomer  i 2D-vyn blir markerade. Troligen hänger det ihop med SMARTS:en, men jag kan se varför de makeras eller hur jag får bort markeringen… Hur kan man göra för att inga atomer ska bli makerade i 2D-vyn?
10:47 Gpox try JChemPaintView.showExternalGenerators(false)
10:50 konditorn I have done that, but then I get a NPE since the global variable extensionGenerator is null (and from what I can see in the code it's never set any where)
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13:06 Gpox konditorn: row 120 in JChemPaintView
13:07 Gpox konditorn: could it be the canvasView that is null? wither way it should not be null and is the only api to get to turn of the ds highlighting
13:09 konditorn mm, I get the NPE on line 450 in JChemPaintView...
13:11 konditorn and when checking it in debug-mode the extensionGenerator is null...
13:12 Gpox edit row 120 and check that the extensionGenerator gets set there
13:13 konditorn oki.
13:13 Gpox you can separate the extendsonGenerator assingment and the addition to the list
13:21 konditorn I'll try that. After using the debugger I saw that it is assigned there, but it's null when I call that method… mm...
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13:48 konditorn mm… Gpox I put a break on a row below where it's created (131 to be exact). And when passing that line (it have at that point generated it, i.e. executed line 120) the extendsonGenerator is null agin…
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14:06 Gpox the problem is there is a field in JChemPaintWidget named extensionGenerator. change showExternalGeneators to call canvasView.setExtensionGeneators
14:07 Gpox setUseExtensionGenerators
14:16 konditorn now I don't get any NPE, but the highlighted atoms are still highlighted… =(
14:23 Gpox you could check JChemPaintWidget[276] there is a null check there and it could be that it is still null
14:24 Gpox konditorn:  try inverting the boolean
14:24 Gpox no my bad it should not show if it is false
14:26 konditorn didn't work…=(
14:26 Gpox if the highlight comes from the SmartsMatchGenerator that it should be able to turn off with the ChoiseGenerator
14:30 konditorn oki, as (I think) I sad earlier I'm not sure were they are coming from…:/
14:30 Gpox setting the SmartsMatchingConstants.SMARTS_MATCH_PROPERTY property of the molecule to null should also turn off the highlighting. Could be that tis is some unrelated highlighting
14:32 Gpox if you set a break point in OvalElement.accept method you should be able to tell from the call stack from what generator the highgligh is comming from just be sure it is called fromt he JChemPaintView and not the editor
14:33 Gpox scratch that it need to be the constructor on row 85
14:33 Gpox the generator is not involved when accept is called
14:40 konditorn I don't have the source to the OvalElemnt-class…
14:41 Gpox you should, they are in the source bundles of cdk in the target platform
14:42 Gpox or did you mean in package explorer?
14:42 Gpox try shift-cmd-T
14:44 konditorn no, I keen the source cod, I fond it with help of shift-cmd-T
14:46 konditorn and how do I set SmartsMatchingConstants.SMARTS_MATCH_PROPERTY to null, I can't get the class…=(
14:48 Gpox moelcule.setProperty("SMARTS_PROPERTY",null)
14:49 konditorn thats almost to simple...
14:53 Gpox it could have other consequences, but the way I understan it you will not run the smart matching on the smarts themsselfes
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14:57 konditorn it didn't work either… =(
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