[Molecuilder-devel] [SCM] branch AddingConstDescriptors created. v1.4.10-100-g3a7fbdb

Fri Jun 26 08:39:42 CEST 2015

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The branch, AddingConstDescriptors has been created
        at  3a7fbdb3980327cf8c58023011fc82e04ec2ff45 (commit)

- Log -----------------------------------------------------------------
commit 3a7fbdb3980327cf8c58023011fc82e04ec2ff45
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:01:13 2015 +0200

    FIX: GLWorldView was signed in to atomInserted and atomRemoved without any need.

commit f1c63ec75e47d1e82ae5d1db0cac02d0e0a2f11b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:00:55 2015 +0200

    FIX: GLWorldScene did not initialize SelectionMode properly.

commit b179c135029db35a9e15df1791cd1160b710e864
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:59:19 2015 +0200

    Extracted signing on to molecule into activateObserver.

    - is called by GLWorldScene after all "missed" signals have been emitted.

commit be6513482eb74c2dde3e9dbd0461d7b9eb30e55a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:58:32 2015 +0200

    FIX: QDebugStream is now thread-safe.

    - also Fix to QTextCursor not registered.

commit 8736f13edcd47abe8c5d87ce2f6361f3ffbd1592
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 16 20:37:07 2015 +0200

    QtInfoBox updates information on update signal.

commit e4ec8026ad3934cd3adb61a89d304a69cc3d1924
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 15 23:01:19 2015 +0200

    FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted.

commit 3c920eeba50450f2ae3476350c0809d8573eb987
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:24:00 2015 +0200

    FIX: GLWorldView must not listen to moleculeRemoved but to its subjectKilled.

    - atoms of a molecule a removed after moleculeRemoved which only gives a prior
      note about the removal. Then, we are flooded with atomRemoved for each of
      its atom which go into MoleculeMissedStateMap and pop up when a same-id
      molecule is instantiated, causing assert failures.

commit 74d36b1dbb907e876588c25c11fd198d51a7ea2b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 11 09:33:58 2015 +0200

    FIX: GLWorldScene/View capture all missed signals for each GLMoleculeObject_molecule.

    - Taking note of subscribed molecules to sign Off on GLWorldView's destruct.
    - GLWorldView::recieveNotification() is checking for whether molecule actually
      exists still.

commit 3a4735d39a576bc0bb81d21306d90a87559e0c5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 8 19:05:01 2015 +0200

    Removed GLMoleculeObject_molecule's init() and reinit().

    - also removed InitAtomMap and associated code.
    - removed changeAtomId slot/signal in GLWorldScene.

commit a672755cf76afcecb7ca097241ec3b1273e2c490
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 8 18:26:34 2015 +0200

    UIs are now initialized before any action takes place.

    - UIFactory::doneInitializing() is set after mainwindow is instantiated.
    - QTUIFactory::testrun() waits till UI is done initializing.

commit 97e87d558f6a0b45ee829d6068438f649516681b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:11:15 2015 +0200

    Removed lots of code in GLWorldScene that now resides in GLMoleculeObject_molecule.

    - atoms and their bonds are now controlled by the latter.

commit 1c4609d547fded5e9eee0944ce926a33c1ba9ae8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:10:49 2015 +0200

    FIX: GLMoleculeObject_molecule was not informed of atom index change.

commit 6812deb27fdef9db7a23dc18847bd9149b7702ce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:45:20 2015 +0200

    FIX: QtElementList does not have a changed() signal.

commit 8cbf1b0a1050788344dc0d2e933e0f159e7190d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 13:23:35 2015 +0200

    FIX: QtInfoBox now works mostly on ids.

    - slots are requested as ..Id_t and not as ptrs anymore for some time.

commit f22820cccd1a8019685e2e2f40bb8f9fbea5b37a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 12:43:49 2015 +0200

    FIX: molecule's Formula is not changed when atom changes element.

commit bb1c7216c5ef03cac53c597b14822990226f3f22
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 12:41:40 2015 +0200

    FIX: GLMoleculeObject_molecule() may overlap with atomInserted() signal.

    - this is because GLMoleculeObject_molecule takes some time till init() is
      called and its runs in a separate thread (hence, further atoms may be
      loaded into the just created atoms). As we first signOn() and then call
      init(), we may end up initializing atoms whose atomInserted signal then
      also comes in but lateron. This causes the AtomsInSceneMap to have
      double entries and the assertion to fail.
      We now keep book of all atomic ids inserted during init() and these
      are ok to appear doubly and their signal is skipped.

commit 158d6c807e21323f2ed6c3f8cd3dbccc1b072e63
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 10:52:11 2015 +0200

    Converted FormatParser::save() to using vector of const atom ptrs.

    - required to change all save() functions in all parsers.

commit c9c8159bbca13346b7c615018241f8ace718a074
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 10:32:10 2015 +0200

    Replaced all World::getSelected...() to const version where possible.

    - also added const version of World::getSelectedAtoms().

commit 46a369dda68b9d4bc339e2f7fa590c5b836057e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:13:27 2015 +0200

    tempcommit: World::getSelectedMolecules() changes hiccup.

    - why did this actually change?

commit 94434acb82e8a7ac6bef4e8ae761d93e2474edad
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:31 2015 +0200

    tempcommit: Change associated to TremoloParser.

commit d838ee9ac135c75bc165f55aea6f69725601cf12
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:08 2015 +0200

    tempcommit: More ConstAtomComposite hiccup.

commit f865f634f4b1d2af973ed2621ba5a902ccbdd4bd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:36 2015 +0200

    tempcommit: PdbParser change hiccup.

commit 3d83556b0f87597c7aaeb49fd94a4b8ffa52334a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:23 2015 +0200

    tempcommit: Value_atom changes hiccups.

commit 54bea0a5f25cc3f5f136999ff8574d9f4e22b7ad
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:07 2015 +0200

    tempcommit: ConstAtomComposite change hiccups.

commit dc5328c10cae4577cd63ebeab5f5922e94aadbf9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:16:02 2015 +0200

    Replaced World::getAllAtoms() by const version where possible.

commit 678a40dab0cc3801ac1889ee6053217e2bb6b1cc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:14:10 2015 +0200

    tempcommit: AtomIdSet changes hiccup.

commit 30ea04207ba67e8611ca7092d91e082a1c4493ea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:53:40 2015 +0200

    tempcommit: molecule::const_iterator problems (due to FromIdToConstAtom).

commit 813ce8e00593ab48abe527a859517e9ff0ac6beb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 10:20:24 2015 +0200

    tempcommit: Changes due to molecule::const_iterator (FromAtomToId).

commit 7d15687a2875543bdc832a4c26049186004165b5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 18:57:36 2015 +0200

    Replaced World::getAtom() wherever possible by const version.

    - some AtomSet member functions now have const atom ptr instead of atom ptr.
    - molecule can return const and non-const AtomSet.
    - added FromIdToConstAtom to allow iterate through atoms in molecule (which
      are stored by id, not by ptr) in const fashion.
    - in molecule::isInMolecule() is now const, ::CopyMolecule..() is non-const
      (because copying involves father atom who is stored non-const).

commit 132fdc19f787e27e726dcc13d9e9074acc2cd2c9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:56:36 2015 +0200

    Replaced World::getAllMolecules() wherever possible by const version.

commit 593fda06ac31d55e34af79c3d078c517d995a009
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 10:20:59 2015 +0200

    tempcommit: Changes due to const atom::getMolecule().

commit 5e2b9c88352638ee8452214c1a3b30cb25188f4f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:48:35 2015 +0200

    Replaced getMolecule() by const access version where possible.

    - so far this is done done via const_casting the World.

commit 6606392ebe28e7de140ce98a390c29fc637f24ba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 10:30:56 2015 +0200

    World::getAtoms() now has const versions as well.

    - this in turn required to adapt all AtomDescriptors and some fixes, e.g.
      predicate is now const member and works on const atom ptr.

commit 2052d0d1329d6393d8d11a01db8d243eb98d6102
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:42:00 2015 +0200

    World::getMolecules..() now has const versions as well.

    - this required to adapt all MoleculeDescriptors accordingly.

commit fcb8cce47856ef5981a301c9925c1dbe2b90bf95
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:22:29 2015 +0200

    atom::getMolecule() now returns ptr to const molecule.

    - changed some places where getMolecule() was used. Most of them required only
      const access anyway. World is allowed to const'cast the constness away as
      it commands over molecules anyway.

commit d33c172900f537fed258f467d3e916dd16f6bb05
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:42:19 2015 +0200

    DOCU: Corrected userguide.

    - this still needs some more work, e.g. w.r.t to code snippets indentation.

commit 1b18c5a348b3cd8c86e1d55f69a3788f31ad6a74
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:44 2015 +0200

    FIX: createGuiChecks can handle multi-lines.

    - also we reduce verbosity by default.
    - redid all GuiCheck test scripts.

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