[Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-107-g3966610

28 Jul 2015


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The branch, GUIStates_using_ObservedValue has been created
        at  39666104810fa0b81def8a126ea8445b8f2d6d4c (commit)

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commit 39666104810fa0b81def8a126ea8445b8f2d6d4c
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sat Jul 25 15:06:15 2015 +0200

    Revert "TEMP: Removed QtLogBox for the moment."
    
    This reverts commit 92df042994f7c0a88d2ebb7c6506fd351ed68a39.

commit 8c561c55ba862e01bdef54dafd4cf83c47235b55
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 23:54:14 2015 +0200

    TESTFIX: Marked molecule translation guicheck tests as XFAIL.
    
    - so far, we cannot use a MakroAction as a python function except if not
      arguments are required. Hence, for the moment we mark it as XFAIL.
    - The problem is with the boost::python::def function. We need to fill its
      arguments during compile-time but that would require some weird preprocessor
      magic going through all Actions contained in the MakroAction's sequence.

commit 12dbabd298fcd1338f7e1891a77b04bba9cd14a1
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 22:47:41 2015 +0200

    FIX: GLMoleculeObject_bond had both flipped ids and the side.
    
    - in essence, both do the same thing. We removed all switches that check the
      sides as flipped ids are actually nice and look good in the observerLog.
      We keep the side variable as it might come handy for checking which one we
      are.

commit 38ee22783079a415fc731fb17fdee33cbb575084
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 22:22:53 2015 +0200

    FIX: GLWorldView and QtShapeList do not assert single source in recieveNotification() any more.

commit 2c8c779e85fe26c183ee9f87b0f539a561bef1c5
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 20 11:16:27 2015 +0200

    FIX: Fixing display of shapes in GLWorldView.
    
    - we propagate shape name via S/S system such that we may lookup the name in
      ShapeRegistry and do not have to rely on probably already deallocated
      lastchanged() shape. This affects ShapeAdded() and ShapeRemoved().
    - GLMoleculeObject_shape now copies the shape, ensuring that its present
      while its surface is tesselated.

commit ec4c8a37c36a7bdea2a8f892683cb7fc55f0a3da
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:47:57 2015 +0200

    GLWorldScene lacked assert of Walker in atomClicked().

commit 4c71933b8751e3355f0767fe1db4b5cb3518d4e1
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:47:19 2015 +0200

    Asserted that GLMoleculeObject_molecule::update() is never called.

commit 3bb1aa6e77c7b976d33c3b65bd16e8ff2b52af09
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:46:41 2015 +0200

    AddAtomBonds() now uses just id not ptr as param.

commit 9f49a62ba351fb91b5a72a49774468eb58f66255
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:46:02 2015 +0200

    Avoided use of getId() on molecules and atoms in Qt code where possible.
    
    - it is ok if we are inside O/O functions or functions called from these
      functions.

commit 71f131e47f77bae8ce1504c6acc83988d9dd7432
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:29:37 2015 +0200

    GLMoleculeObject_molecule does not use getAtomCount() anymore.
    
    - this removes any usage of getAtomCount() apart from ObservedValue's.

commit d72ad91b6763f006918053bc544fd3bbea3e2eb4
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 15:25:40 2015 +0200

    GLMoleculeObject_molecule also has ObservedValue for name.
    
    - this removes any (uncached) molecule::getName() from Qt code part.

commit 449a75cd1ecee1ed5d470b813ff060e35901bb1d
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 14:01:14 2015 +0200

    FIX: Setting molecule's name via QtMoleculeList item is again possible.
    
    - this is similar to checkForVisibilityChange(), only now for the name.
    - we required four Actions, i.e. this cannot be undone in a single step but
      needs four. However, right now it is not easily possible to construct
      MakroActions from inside the code at compile-time as we do not have
      access to modify parameters via their tokens.
    - using constructed MakroAction in QtMoleculeList for name change.

commit 926d009fde2bddd25abd80ac9d8c836ce89229be
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 13:35:26 2015 +0200

    Fixed formula usage in Qt part of code.
    
    - formula of a molecule is only access through ObservedValue or directly within
      the World's O/O system.
    - Molecule may disappear before selection event.
    - Atoms may disappear before selection event.

commit 42fa5848022065adc2d06cb88259ce9748bfe172
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 09:08:38 2015 +0200

    QtMainWindow uses QtSelectionChangedAgent.
    
    - QtMoleculeListView and GLWorldView receive its signals. The latter passes it
      on to GLWorldScene.
    - QtMoleculeList has new MoleculeIdToIndex to allow QtMoleculeListView to
      (un)select specific rows on a given index.
    - GLWorldScene passes atom and molecule selection to GLMoleculeObject_molecule.
    - GLMoleculeObject_molecule passes atom selection to respective
      GLMoleculeObject_atom.

commit a6b1ff153a59d5396e615441f550b981712805c6
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 08:36:38 2015 +0200

    Added QtSelectionChangedAgent to transform O/O to S/S system.
    
    - also this will be far more effective, as e.g. not all
      GLMoleculeOBject_molecule will receive SelectionChanged from World if just a
      single molecule has been selected.
    - Atom might not yet have a molecule, i.e. it is not drawn yet. We do nothing
      then.
    - recieveNotification allows for vanished atom (due to removal). We do nothing
      then.

commit 00ed60391ed81d42344d494241a3d714ba0a19dd
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 08:30:51 2015 +0200

    QtMoleculeItem_.. now shout when they receive subjectKilled().
    
    - this way we do not have this double system of both QtMoleculeList (in a lazy
      fashion) and each QtMoleculeList listens for moleculeRemoved (one through the
      Observer channel, the other through subjectKilled()).
    - we simply count the number of QtMoleculeItems that received subjectKilled()
      and if max is reached, the row is removed.
    - to prevent molecule id clash, insertion (of same id) after removal is ok.
      This works cause we first remove and then insert new item. Hence, having the
      same id is possible.

commit 9c55f8c068989047ca8e219489e7749f37e5541b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jul 16 10:29:09 2015 +0200

    FIX: Fixing "pure virtual function called" in QtMoleculeItem.
    
    - as a matter of fact this should not be a problem: Inside QtMoleculeItem's
      dstor body while signing off from the channels, it is no problem to receive
      a notification for a channel we have not signed off yet. The vtable has
      not been touched with respect to QtMoleculeItem.
      I really do not understand this issue. I have tried to reproduce it with
      a few mock classes that have the very same inheritance pattern and used
      locks to force the same case of a virtual function being called while
      inside the dstor's body but it does not reproduce the error.
    - the same holds for the cstor and again the vtable is created before the
      code pointer enters the cstor body, hence it should be no problem ...
    - the solution is to signOn..() and signOff..() on the highest level, i.e.
      on the most derived classes. This causes some code duplication but at
      least it works.

commit d151d9f4db336233533f226f2ce8e33a305f6db5
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jul 16 01:26:09 2015 +0200

    World now first releases id and then destroys the atom/molecule.
    
    - this prevents any access to atoms/molecules in the phase of destruction.

commit 1f87cf2f825c279756c9529dd6d3ec464ec4b374
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jul 16 01:25:22 2015 +0200

    Qt4 instance use new lastChanged..Id() in place of lastChanged().

commit aae4965e5b1ea1ca3c0393f7222712ea13503328
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Jul 16 01:23:30 2015 +0200

    Added lastChanged..Id() to both World and molecule.

commit f3b10dbe5c43e14ebe224a79fa9d9773a3c610e2
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jul 15 17:22:04 2015 +0200

    GLWorldView no longer listens to WorldTime::TimeChanged.
    
    - molecules are re-created when the time changes anyway so the world view is
      informed about the change.
    - removed all commented-out lines.

commit eae257505aca7293f14e3ce7fa082bc103f3a5d8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jul 15 16:01:41 2015 +0200

    GLWorldView does not emit changed() on each general update() from the World and others.

commit d57818b17812190b2314bce6248c969cf31287ec
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jul 15 15:56:58 2015 +0200

    DOCU: Updated documentation on Qt Gui construct.

commit cc970e835c844b58febe62c0f93e724c18630531
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jul 14 15:55:47 2015 +0200

    Fixing QtMoleculeList with list containing only formulas and ids.
    
    - COLUMNTYPE now belongs to QtMoleculeItem not QtMoleculeItemFactory.
    - callback function in QtMoleculeItem signature changed to molid and column.
    - QtMoleculeItem::getType() for obtaining the type to be used as argument in
      the callback.

commit 209ad6b35174e0f5a9e1b1c830879c805c525fe9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Jul 10 12:54:51 2015 +0200

    Using static Observable::..NotificationsChannel() functions.

commit 30842d3369ac305ebdfd515dd9d27ebfd62eac6d
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jul 7 03:10:10 2015 +0200

    QtMoleculeList::informDirtyState() does not need to lock refill_mutex anymore.
    
    - we simply write the QtMoleculeItem to the ToBeMoved list and convert it to
      the very first item in the row in updateItemStates().

commit 1743af8f64dfbe667b6e6d9a91801bbaee471b16
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Jul 7 03:08:58 2015 +0200

    Fixing QtElementList::updateElement().

commit c5c7c71c37cd761f197da27c0aaa1fdea2a36a14
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 20 10:35:41 2015 +0200

    GLWorldScene propagates changed mol id to GLMoleculeObject_molecule.
    
    - GLWorldScene must emit MoleculeRemoved on last subjectKlled().
    - GLWorldScene has internal RemovalMolecule in case moleculeRemoved comes prior
      to moleculeInserted.

commit ba4c71caed50d2eecd35c99adc47613ac0534f59
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:19 2015 +0200

    GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.

commit 5930513559ef8e3ff884ab4fc9eb20b16ea64776
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 06:49:13 2015 +0200

    QtMoleculeItem_... use ObservedValue for internally representing atom's state.
    
    - this affects atomcount, formula, and name. visibility depends on clicked
      state and occurrence is changed elsewhere.

commit ec008cfa3ecb1ca565339d0334ac9f7b14efa729
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 06:46:32 2015 +0200

    GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.

commit 7df9125edabcd62fc91a5c0274168f49cc1eaab4
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:50 2015 +0200

    GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.
    
    - we use internal owner as ref to Observable.

commit 27a26ff8bc8cd9796e1d2b737696a839a8c6a723
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 5 09:55:15 2015 +0200

    Requiring now CodePatterns 1.3.0 due to ObservedValue.
    
    - also we purge the GlobalObservablesInfo in cleanUp().

commit efc3553d8a6c21749d2a3cf049d7e228874464ef
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:57 2015 +0200

    Removed init() and signal WorldSelectionChanged() from GLWorldScene.

commit db3075da45a02e6e71335b33e873d2de5b6371cb
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 18:36:06 2015 +0200

    TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in save-adjacency regression test.
    
    - GuiChecks sees a different (but still valid) ordering in the .adj file in the
      save-adjacency regression test.

commit f7054cab5c6c0b7c73d7b4866501383e989b50da
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 18:13:44 2015 +0200

    TESTFIX: selection molecule by name had escaped ticks.
    
    - also changed GuiCheck tests.

commit 80f678157992ab9328be5ba384216ae6e1548684
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 12:03:43 2015 +0200

    FIX: Added Parameters Value_Elements to correctly set vector of elements from string.
    
    - this fixes that fit-potential action is not correctly called from python
      scripts. There, we require correct setter of a value from a given string.
      As all arguments to a python command must be given as single string,
      even if it is a vector of arguments, we must correctly decode this string
      again.

commit c569220c375bbffdf838cc2cfd11de122bf57a86
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jul 8 12:33:49 2015 +0200

    TESTFIX: regression test DepthFirstSearch had extra linebreak.

commit 024c65bc14cdcf98c86fcf1892e8bc3b3c0c6764
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Jul 8 08:47:52 2015 +0200

    TESTFIX: atom selection regression tests with shapes were very noisy and hence very slow.

commit 7a0456949e5c8efe51fc75d2a5902483c296feec
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 6 15:07:00 2015 +0200

    TESTFIX: regression test SubgraphDissection Redo was broken.
    
    - also changed derived GuiChecks test.

commit 42b40a4b4a9210b1ed60a0be93acd12541dedde9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Jun 19 13:45:49 2015 +0200

    Added TriangleMatcher to safely compare tesselation .dat files.
    
    - is used in tests/regression Tesselations, tests/Tesselations, and has its own
      regression test, too. Also added tests/GuiChecks.
    - added trianglematcher to testsuite dependencies.

commit a82f61a466e15715e16f9470a56c3bdadfcb3895
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 14:39:16 2015 +0200

    Added Action::setOptionValue() which allows setting the option via a string.
    
    - this is preparatory for allowing the creation of MakroActions inside the
      code. We need to set the options without going through dialogs in some
      way or another and without being completely inside the Actions as is the
      case for the COMMAND variants and the python function calls.

commit 143263bb92532b8d3e50535a2c7cfae698a6ab6d
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 08:15:39 2015 +0200

    Added getSelected..Ids() for both atoms and molecules.
    
    - added static function getKey() to _take in Helpers.

commit fe0ddfc870329d8adcaf7269129b4690ddd98db4
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 22:58:57 2015 +0200

    FIX: atom_atominfo lacked some notifies or had them wrong.
    
    - ElementChanged only when element actually changes it not helpful
      (QtElementList has then no chance of detecting new atoms with default
      element of hydrogen).
    - TrajectoryChanged was signalled only when current timestep was added or
      removed, rather we signal always and assert that we do not remove or append
      the current time step.

commit f5452477d87da2369a118585276d5b6793a46480
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 15:34:40 2015 +0200

    FIX: Molecule has new signal IndexChanged.
    
    - this has been overlooked so far, index may be changed similarly as for atoms.

commit c6719db9d555d7c3f1b43c5cd90b1ccc2a8df1c8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jun 21 06:45:30 2015 +0200

    FIX: atom_bondedparticle signatures changed to more const versions.
    
    - added getBond() for obtaining bond in const manner.

commit df3f2f34f6c9dbddae6f42d32b7a644c3b756eb8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 20:29:39 2015 +0200

    Group item with atom count of 0 is confusing in QtMoleculeList, creating with empty string.

commit a963cf91fe5fac81f5a6c9c3e2c5d8100868fea3
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Jul 19 12:03:05 2015 +0200

    executePythonScriptFile() calls executePythonScript() now.

commit 883ea068fbdbd4af0bcd8dfb11919f5f24ecb781
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Jul 20 00:21:57 2015 +0200

    FIX: QTUIFactory's test-single was not working right.

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[Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue created. v1.4.11-107-g3966610

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