Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-17

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All times shown according to UTC.

Time Nick Message
00:06 CIA-16 cdk: egonw * r9451 /branches/egonw/ibondorder/​src/org/openscience/cdk/io/ (MDLReader.java MDLV2000Reader.java): Fixed adding of created bonds
00:07 CIA-16 cdk: egonw * r9452 /branches/egonw/ibondorder/src/org/​openscience/cdk/AtomContainer.java: Fixed the getBondOrderSum() method: don't rely on irdinal()
00:30 CIA-16 cdk: egonw * r9453 /branches/egonw/ibondorder/ (27 files in 20 dirs): Synchronized with trunk rev 9452
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07:35 rojasm moin
07:39 CIA-16 cdk: miguelrojasch * r9454 /branches/miguelrojasch/mf/src/org/open​science/cdk/formula/AdductFormula.java: added constructor without parameters
07:39 egonw hi rojasm
07:40 rojasm hi egonw
07:40 rojasm questions :)
07:40 egonw yes :)
07:40 rojasm the order to put the method should follow a order
07:40 rojasm a
07:40 egonw huh?
07:41 egonw I normally don't pay attention to the order
07:41 rojasm I mean :
07:41 rojasm but may be it is easy then. That all classes follow the same structure
07:42 rojasm first constructors, 2: sets,3 gets, 4 remove
07:42 rojasm or some thing like that
07:42 egonw possible..
07:43 egonw I tend to keep the get and set method together
07:44 rojasm Do you know if others projects follow some rules?
07:44 egonw not that I am aware of...
07:45 rojasm ok, so nothing
07:45 rojasm you commented yesterday about a IEditAduct
07:45 rojasm what was the idea?
07:45 egonw yeah, forget that
07:45 egonw I fixed that in a different way
07:46 egonw by not extending IAdductFormula from IMolecularFormula
07:46 egonw but by copy/pasting the get methods...
07:46 rojasm ok
07:49 rojasm I see that now you call the for size of IMFSet .size() but for IAtomContainerSet.getAtomContainerCount()
07:49 rojasm is there a difference of conept?
07:49 egonw no, but IAtomContainer has many methods that IMF should not have
07:50 egonw which leads to undefined behaviour
07:50 rojasm ok
07:54 rojasm so the idea is to put the minimal name in the method if there is not other methods which confuses
07:56 egonw right
07:56 egonw always
07:56 egonw just like science
07:56 rojasm :)
07:56 egonw do things with the bare minimum you need...
07:56 egonw you otherwise 'overfit'
07:58 rojasm so for removeMolecularFormula is sufficient putting remove, isn't it?
08:00 rojasm and like removeIsotopes in IMolecularFormula because it is the only thing that you can remove
08:06 egonw yes
08:06 egonw but then again...
08:06 egonw you did want addIsotope(IIsotope)
08:07 rojasm I don't know if you say that the essence is to put the minimum now I understand what you put in a first time
08:07 rojasm only add
08:08 rojasm for I think here you have to put addIsotope(Isotope) because you have the other add(IMolecularFormula)
08:09 rojasm in this case I mean you have to distinguish between both
08:09 egonw that's called overloading
08:09 egonw add(IIsotope) can exist next to add(IMolecularFormula)
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08:10 rojasm ok. Than let put only add
08:10 rojasm but a lot of method in cdk have the same rules. I think
08:11 egonw rojasm: yeah... some more consistency there would be nice...
08:13 CIA-16 jmol: hansonr * r8632 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.3.46_dev # bug fix: Jmol math (x[2])[3] indistinguishable from x[2][3]
08:13 * egonw has a new SF project: http://genalg.sf.net/
08:13 egonw and not afraid to advertize it :)
08:20 * rojasm surprising for the new project!
08:20 egonw it's something I worked on 2-3 years ago
08:21 egonw will get some new attention and development time
08:21 rojasm did you ask Ra.... about the compatibility cdk-R
08:21 rojasm ?
08:21 rojasm that is great!
08:21 rojasm that mean I can ask you about R
08:21 egonw :) yeah, sure :)
08:22 egonw no
08:22 egonw have not asked that yet
08:22 egonw will try to work on that next week
08:23 rojasm not problem
08:23 egonw OK, the next step is to try to port your new classes, correct?
08:23 egonw let's put them in cdk.mass ?
08:23 egonw (and move MFAnalyser there too)
08:23 rojasm ok
08:24 rojasm so, for remove we leave them as remove or removeblabla?
08:26 rojasm MFAnalyser should be moved to MolecularFormulaManipulator as I did more o less
08:30 egonw yes, good idea
08:31 egonw rojasm: you decide, your project
08:32 rojasm I understand that but it is not good to have repeated methods
08:33 egonw sounds like you made a decision :)
08:33 rojasm And we think that Manipulator and MFAnalyser is the same
08:33 rojasm should be remove one of both
08:34 egonw yes
08:35 rojasm I created the manipulator because I need other functions that MFAnalyser doesn't have. But I thought It was better the name Manipulator then MFAnalyser
08:36 rojasm according AtomContainer as well
08:37 egonw yes, agreed
08:38 rojasm So you think it is also a good Idea to transfer the method that MFAnalyser contains to Manipulator?
08:38 egonw yes, guess so
08:39 egonw on the other hand... since you ask...
08:39 egonw the Manipulator generally do not calculate things, such as mass
08:39 egonw which requires additional input...
08:39 egonw that is, the manipulators only work with the data passed, and do not add new info or derive new info
08:40 rojasm That is true. But the mass is already contained in the Isotope
08:40 rojasm it has only to read
08:40 egonw only when configured...
08:40 egonw but true...
08:41 rojasm I think ManipulatorAtomContainer is doing the same
08:42 rojasm But may be you mean for getString from the MolecularFormula, right?
08:42 rojasm that is not work of the manipulator!
08:42 egonw right
08:47 egonw rojasm: I am visiting my mother very soon...
08:47 egonw we can chat later
08:48 rojasm ok, not problem
08:48 egonw rojasm: I also would like to start a branch to recode your PhD work code...
08:48 egonw to make use of the new atom types...
08:49 rojasm What you mean. The reaction stoff
08:50 rojasm ok, perfect
08:51 egonw e.g. to have the LPAdder use the new CDK atom types
08:51 rojasm ok, perfect
08:56 egonw rojasm: ok, cu later
09:16 CIA-16 jmol: hansonr * r8633 /trunk/Jmol/src/org/jmol/ (7 files in 4 dirs): version=11.3.46_dev # bug fix: adjustable boundbox in multimodel context not specific to model of selected atoms
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11:08 egonw hi rojasm
11:13 CIA-16 bioclipse: ospjuth * r4258 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (14 files in 5 dirs): Created Bioclipse Navigator based on CNF instead of ProjectExplorer
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17:32 CIA-16 jmol: aherraez * r8634 /trunk/Jmol/src/org/jmol/tr​anslation/JmolApplet/es.po: Spanish
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18:44 CIA-16 cdk: miguelrojasch * r9455 /branches/miguelrojasch/mf/src/org/open​science/cdk/formula/AdductFormula.java: added JavaDoc defining MolecularFormula
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18:46 CIA-16 cdk: miguelrojasch * r9456 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (4 files): added JavaDoc defining MolecularFormula
18:54 CIA-16 cdk: miguelrojasch * r9457 /branches/miguelrojasch/mf/src​/org/openscience/cdk/formula/ (4 files): removed duplicates remove methods
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22:28 CIA-16 jmol: hansonr * r8635 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.3.46_dev # bug fix: isosurface CAP not turned off prior to map sasurface
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23:05 CIA-16 jmol: hansonr * r8636 /trunk/Jmol/src/org/jmol/ (util/Escape.java viewer/Jmol.properties): version=11.3.46_dev # code: refactoring,optimizing Escape.toJSON() and Escape.toReadable()
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