[SCM] branch GLWorldScene_stores_objects created. v1.5.1-176-g900613b

19 Apr 2016


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The branch, GLWorldScene_stores_objects has been created
        at  900613bdeac8339019bbb702193d7701d33e9fb7 (commit)

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commit 900613bdeac8339019bbb702193d7701d33e9fb7
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Apr 18 22:57:47 2016 +0200

    Protecting access to atom and bond functions in GLWorldScene with mutexes.
    
    - mutex are now for general access to internal maps, not just NodesInSceneMap.

commit 2601f676523a6afb69fee0b7be0fa2a9dcfe0fe9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Apr 18 22:53:43 2016 +0200

    FIX: Exchanged boolean for real mutex in QtMoleculeListView, QtFragmentList, QtHomologyList, QtShapeList.

commit 4ed5d1af4a5592cf81f75c7f09ce62115fc7e915
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Apr 17 23:27:36 2016 +0200

    Revert "GLWorldScene checks that on dstor all internal containers are empty."
    
    This reverts commit b8b7cf664617761e7d4fb3bd97ca0eba8596b029.

commit c34cc982bd74e9a17e8e9b0f7cc348db61dad997
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Sun Apr 17 23:26:58 2016 +0200

    GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.

commit 1d92a2c7e6fa9f33825129f67fd49add5f63a174
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Apr 15 13:05:44 2016 +0200

    GLWorldScene checks that on dstor all internal containers are empty.

commit ba93668168af26f09867bc157b221e2a505eaacd
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Apr 15 09:38:55 2016 +0200

    GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
    
    - this is to ensure that lifetime of the observed value instance is as long as
      required.

commit 7f9e1141c00d489c45032dcabc026c7d72823022
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 14 09:55:41 2016 +0200

    GLWorldScene needs to store observed values to ensure duration of their lifetime.

commit 82a0cecfab903645af724686ca4f3190a3e9cb4f
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 14 10:08:36 2016 +0200

    FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.

commit 8402d7878c8760f716708a337f48655883946d5b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 14 10:01:31 2016 +0200

    QtObservedBond returns ::ptr instead of ptr from left and right atom.
    
    - FIX: GLWorldScene crashed on resolving sender() of a reparent..() signal
      because the object got destroyed in the meantime.

commit 6d5324de098712f778115f1c698241a5c10d5276
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 14 09:47:20 2016 +0200

    QtObserved... signals indexChanged does not transmit ids anymore.
    
    - since the change to ObservedValue_Index_t, the id is not used anymore. Only
      in the GUI for the objectid.

commit 9bc8f12d79aa27b27b866f5f19ae4ec866029f2a
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 13 16:10:40 2016 +0200

    Added checks abd verbosity to reparenting in GLWorldScene.

commit a275213219e4fe9704c9dddc8c476c7ef92d42e9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 13 15:43:20 2016 +0200

    FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
    
    - the atom, bond, or molecule may be removed before and reinstantiated at the
      same address. Hence, it is not a good unique index. The only sensible index
      is the memory address of the QtObserved... instance itself.

commit 50b3ff921aa5f0e3c450362baf79ffcdada99776
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 21:55:27 2016 +0200

    FIX: Empty row in QtMoleculeList was not deleted.

commit d4cfdb38ab11676404a3dfca7bf6288936a22bbe
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 21:21:00 2016 +0200

    FIX: MoleculeList crashed when selected molecule changed its place.

commit 8789e2699574085630badc8849aa083b507dc5d6
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:37:31 2016 +0200

    GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
    
    - parent maps are now bimaps.

commit fbe3cb26795156b8823d895077b14876e3b2c3f8
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:19:47 2016 +0200

    GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
    
    - this will allow to change them into a bimap and then browse through them with
      the index of a newly instantiated GLMoleculeObject_molecule in order to
      assign them a proper parent.

commit 7251f314288937f6d4693d437b15665ddbe2c23e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:17:46 2016 +0200

    FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
    
    - this function is only meant to be used in interaction with the user, i.e.
      while the GUI does not change.

commit 9816ce7ab26dd31df4cdf96835a492a6b30dbd63
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:30 2016 +0200

    QtObservedMolecule uses fixed index which it returns.

commit 6541968e65c5fe753173f8f218048ec0c9e6698e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:22 2016 +0200

    QtObservedBond uses fixed index which it returns.

commit f04cbbbae853cced53a3b9a8e5c2c782944ce0aa
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 20:16:13 2016 +0200

    QtObservedAtom uses fixed index which it returns.

commit 9d4a2c5bd762f7bed73d0f6bde661c95ab2036c9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 16:32:13 2016 +0200

    FIX: made disconnect() check for NULL pointers.

commit e7a56576618201aeb9c2d4e831eea508ba18fa53
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 16:24:10 2016 +0200

    FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.

commit 490b8ae07ea57c0aa7ef5ad6881f7a454b1d6126
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 14:02:45 2016 +0200

    GLWorldScene now properly reassigns parents of GLMoleculeObjects.
    
    - this is important for atoms and bonds such that they disappear when their
      associated molecule is visualized as a tesselated surface.

commit fd1dd8ad308cb638f6194021321292e5784b2f82
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 13:29:56 2016 +0200

    QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
    
    - the molecule index is not part of the atom's state, hence cannot be directly
      observed. The only thing we observe is the association to the molecule. For
      this a O/O-signal is available and we may actively change the ref when
      getting this signal without breaking anything as it occurs in the same
      thread, hence the board can be safely accessed.
    - QtObservedBond now needs to access mol index through the molecule ref.
    - QtInfoBox may now conveniently access atom'smol ref directly.
    - FIX: Removed static QtObservedBond::getMolecule().

commit b968a860444fb3652e997e8343d0335d584f58c3
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 13:19:05 2016 +0200

    QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
    
    - leftatom and rightatom are const throughout the lifetime of the bond. Hence,
      there is no need to update them and we simply store the refs directly. This
      will be different for the atom, where the molecule ref may change over the
      lifetime!

commit f608b3e93700e05b3ba2b5bddb9584af2f2da597
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 10:51:06 2016 +0200

    Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.

commit 160a886ca6f16ae2d51cf41b4dbd8cfcdef4fc64
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Apr 7 18:14:04 2016 +0200

    FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
    
    - changed QtInfoBox and QtObservedBond::getMoleculeIndex() which used it.

commit 0987c41bb19346d573e028c97685061807335325
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Apr 6 19:04:01 2016 +0200

    QtObservedBond now simply gets both QtObservedAtoms on construction.
    
    - they must exist as QtObservedInstanceBoard is in the current update() loop.
    - and we don't need to take care of them and may throw them away when the bonf
      itself is removed. We don't need to care for anything else.

commit 04c45ddbd3bdbbe381f189c797d32b061b662a5b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 29 20:47:16 2016 +0200

    getObserved...() checks whether id is still present.

commit f68ecbcbf10193a7166999a527a1ed8787b9f405
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 23 11:02:43 2016 +0100

    Removed partial specialization of ObservedValue_wCallback for index.
    
    - we don't need this anymore as ObservedValues now have a unique and permanent
      index, which we can bind right from the start.
    - adapted QtObservedAtom and QtObservedMolecule's initObservedValues().

commit 20a7cda8f82b208fbf128febd45f98ac91b216aa
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Mar 24 14:26:51 2016 +0100

    Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
    
    - GLWorldScene transmits bondInserted/bondRemoved similarly to those for the
      atoms to the molecule if aLready present and otherwise into the
      MissedStateMap.

commit af593bd3bc9e44ea0b113055d09b2e8506ea0183
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 15 11:10:54 2016 +0100

    Added QtObservedBond, managed by QtObservedInstanceBoard.
    
    - QtObservedBond is special because it observes not only a bond, but also two
      atoms and a molecule in total.
    - but the general idea is to rather have information duplicate, i.e. the left
      atom's position is also available via the QtObservedAtom. But in this way
      QtObservedBond does not depend on the QtObservedAtom being still or already
      present.

commit 9dafcd80a67ad8c8777de34fae935aaa89ede55e
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Thu Mar 24 14:13:31 2016 +0100

    FIX: Removed GLMoleculeObject_molecule's molref.

commit 2bfb97a5e35a695b5b35463b22b68133414da618
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 23 10:56:51 2016 +0100

    QtObservedMolecule also uses new index internally.

commit 4de3573335967314e96416c284ba3e35359f4462
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 22 12:58:35 2016 +0100

    QtObservedAtom uses new index internally.
    
    - thus we don't have to jump through the loops with constructing prior an
      IndexGetter in initObservedValues().

commit 6dfe0960939bf4c37bc57267d6672d3f02f86a48
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 23 10:58:26 2016 +0100

    FIX: QtObservedMolecule::initObservedValues was still static.

commit 9a9a92cb72926a3e4c818017c9a478c1333fa95b
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Wed Mar 23 11:06:23 2016 +0100

    Removed unneeded specialization ObservedValue_UpdateAtoms.

commit a2fa3a6d5e9791e5a5dfe63ae43abdde9c300d18
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 22 00:38:09 2016 +0100

    Changed atomRemoved slot of GLMoleculeObject_molecule.
    
    - this required AtomsInSceneMap to use new Index.

commit 15dac91b9762acbbeb2b64d6924e4ebc4a756e81
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 22 00:32:47 2016 +0100

    Removed GLMoleculeObject_molecule::getPresentAtoms().

commit 037f27579e88833f5a762818716c3265a293d12a
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 22 00:12:07 2016 +0100

    FIX: Removed some unnecessary observer code from GLWorldView.

commit cf2bd632ed1b18798095d54cf453f4412752be65
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 23:36:39 2016 +0100

    Changed slots of GLWorldScene and GLWorldView.

commit 31fedf84e71e028fd6f4265aea62af210c4fa69d
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Mar 29 16:56:56 2016 +0200

    MoleculeList discerns between internal and external name change.

commit 76ea826df7e55bea3fd8193fc9b51824625791cb
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 23:02:31 2016 +0100

    Changed slots of QtElementList, QtMoleculeList, and QtMoleculeListView.
    
    - this is not all of them, but they now all used ObservedValue_Index_t.

commit 5b370456f75d78a273af10a14d5c775aaccc2665
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 22:13:43 2016 +0100

    QtObserved...Observed now get index on ...Removed() signal.

commit 9b7ac059fd9058736a876f0c035e058c8723bf9d
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 22:42:14 2016 +0100

    Added convenience function to return current id for given index.
    
    - this is mainly for printing in asserts and logs.
    - required to convert IdtoIndex to bimap.
    - ...Observed wire through getIdtoIndex() function.

commit c7c6d21a861eb2aa5200c32485360da0d4b0de81
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 21:42:05 2016 +0100

    Introduced unique and permanent ObservedValue_Index_t.
    
    - this is currently the address of the observable which is not perfectly
      secure but might work for the moment.
    - QtObservedInstanceBoard uses the index internally and only has an additional
      map to serve instances on request for the their atomId_t, moleculeId_t, ....
      However, this id should nowhere else be used because it may change during
      the lifetime of the object.
    - this should prevent the hazzle with the possibly changing atomId_t,
      moleculeId_t, ... in all classes that work with QtObserved... instances.

commit bff202c6e3d0515447a54bacfa6e9ed5ffca83cf
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Tue Apr 12 15:19:44 2016 +0200

    FIX: QtMoleculeList's FormulaVisibilityCountMap was not inserted into on new group item.

commit 743eabedffa61ec5ac67780d49badf443f6daef9
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 20:56:27 2016 +0100

    Added missing updateState() to QtMoleculeList.
    
    - As QtMoleculeItem no longer recieve notifications, QtMoleculeList must
      update each item itself.

commit b6587939d0431dec255b436d437b2c3d64d32c2c
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 20:44:17 2016 +0100

    QtMoleculeItems do not store ObservedMolecule::ptr any longer.
    
    - it is given as parameter in updateState().
    - in the cstor they only get it to initiate the item text properly.

commit 55443e28a0241b365a47745e7933c4c58a27e0d2
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 20:43:25 2016 +0100

    FIX: QtMoleculeList::moveItem() does not need to search for groupitem.

commit ea26633a5a6e22128ba0fcc52a60bb13aed31710
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Mon Mar 21 11:27:58 2016 +0100

    QtMoleculeItemFactory is pure static.
    
    - QtMoleculeItemFactory was never needed as singleton as it has now state,
      contains now purely static variables and functions.

commit 5771e66594e586dad5518921119581034d3235d2
Author: Frederik Heber <heber@ins.uni-bonn.de>
Date:   Fri Mar 18 11:17:01 2016 +0100

    Removed all mutexes and updateDirtyStates() in QtMoleculeList, replaced by simpler slots.
    
    - thanks to events we don't need this humonguous system of lists, update
      timers, and mutexes. We simply need to take action whenever an event comes
      in.

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