From git at ins.uni-bonn.de  Fri Jun 12 15:48:47 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 12 Jun 2015 15:48:47 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.11 created.
	v1.4.10-45-g8a83d57
Message-ID: <20150612134847.8DF645FD6E@saturn.ins.uni-bonn.de>

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The branch, Candidate_v1.4.11 has been created
        at  8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f (commit)

- Log -----------------------------------------------------------------
commit 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 21:23:35 2015 +0200

    Set version to 1.4.11.
    
    - MoleCuilder library is now 14:3:1.
    - Codename "Soccer" (It is one for all and all for one football).

commit 3fa16b482f696edb18618700ef768e366d06813c
Merge: 08d042d 19dfdf7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 12 15:27:22 2015 +0200

    Merge branch 'GUI_niceties' into Candidate_v1.4.11

commit 08d042d999587b9169fbb5763d93a65241a1cf4f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 09:34:31 2015 +0200

    Added "--testsingle" switch for line-by-line execution.
    
    - QTUIFactory checks for additional "single" and activates then a special
      mode which uses the newly split executePythonScript.

commit 37a67f216a1ec48288bc1b314c99cfb0d6cb6963
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 15:50:53 2015 +0200

    Replaced Query.. class and query..() function declarations in Dialog.. by boost preprocessor magic.
    
    - this removes a lot of copy&paste code.

commit 0435989b70a2b793f218705f1cf498471af2bdd2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 06:24:19 2015 +0200

    Replaced all std::string by ParameterPair where used as ("key = value;") tuples.
    
    - this fixes an issue with vectors of key-value-pairs converted into a single
      string for use in a python command.

commit 33e80133683ce15eb991faac6abc6d540afee182
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 06:22:43 2015 +0200

    Added ParameterPair (i.e. "key = value;") to allow other string output.
    
    - this will solve the problem of vectors of key-value-pairs not properly
      converted into a single string because of missing semicolon.
    - FIX: toCLIString used functions toPythonString if possible.

commit dd6c07d2c5d563c8e46c0a4b01a0de11563eb584
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 15 10:22:40 2015 +0200

    Added all new guichecks regression tests generated from createGuiChecks.sh script.

commit fae462dafc0b0506501581e2bccedaef6813450d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 15 10:03:03 2015 +0200

    Added script file to generate guichecks testsuite from regression tests.
    
    - options-no-elements.db and options-empty-configs works with faulty arguments.
      This cannot be replicated with molecuildergui.
    - all load- and store-sessions removed due to (then) multiply occurrences of
      said action (we need store-session to create the script for molecuildergui).
    - dry-run will not cause errors, hence error code of script creation call must
      always be 0.
    - refreshes TESTSCRIPTS variable in Makefile.am.

commit f3db6059ff3cc60a56408536bc8c419fc809da01
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 15 09:12:44 2015 +0200

    Added DryRun and NoDryRun actions.
    
    - actions (un)set a flag inside ActionQueue to which only those permitted by an
      advocate pattern have access.
    - added testsuite tests for both dry-run, no-dry-run, and storing sessions.
    - explained use of action in userguide.

commit 0907ad2590d5fe8b17e1ee653a60c21f3b4e11d0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 13 22:24:48 2015 +0200

    Added GuiCheck "AddAtoms".

commit 0f0407ad8f57ba8adda5a1059fe7125b8aaa5b92
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 13 21:49:52 2015 +0200

    Added testsuite "GuiChecks" with extra target guicheck.
    
    - this allows starting the testsuite on the graphical interface.
    - checks for working testlauncher inside molecuildergui with single and
      multiple scripts.

commit 15e1978cca9c4568b8ac921a0fee1cac72517d81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 13 20:20:52 2015 +0200

    Command-line arguments are passed to QApplication inside QtUIFactory.

commit 3054689a58736f5438fa03886a4337356078607b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 13 20:17:55 2015 +0200

    Added "--test"-mode to UI switch in builder_init.
    
    - this will allow to launch molecuildergui with a set of scripts to execute.

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From git at ins.uni-bonn.de  Fri Jun 12 15:49:27 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 12 Jun 2015 15:49:27 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch MolecuilderGuiTestSuite deleted.
	v1.4.10-39-g80b555f
Message-ID: <20150612134927.0455F5FD6E@saturn.ins.uni-bonn.de>

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The branch, MolecuilderGuiTestSuite has been deleted
       was  80b555f2762e4c07533b77c414b36bce168fb47e

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80b555f2762e4c07533b77c414b36bce168fb47e Added "--testsingle" switch for line-by-line execution.
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From git at ins.uni-bonn.de  Fri Jun 12 15:49:31 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 12 Jun 2015 15:49:31 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch MolecuilderGuiTestSuite created.
	v1.4.10-39-g08d042d
Message-ID: <20150612134931.953735FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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From git at ins.uni-bonn.de  Thu Jun 18 04:07:57 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Thu, 18 Jun 2015 04:07:57 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads created.
	v1.4.10-151-g0312e23
Message-ID: <20150618020757.BC5D65FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "".

The branch, SeparatingOutQtThreads has been created
        at  0312e2354381e345b8509d9898560703d82ee90a (commit)

- Log -----------------------------------------------------------------
commit 0312e2354381e345b8509d9898560703d82ee90a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:58:12 2015 +0200

    tempcommit: Fixes to ActionQueue. Merge with 85d6396e

commit 9c9df11556737d29a82e1a1277f89b90b17db9fb
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.

commit 81e16f2e4caa917357195e371372440b06cda3ce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:26 2015 +0200

    tempcommit: Trying to fix MakroAction's outputAsPython().

commit 70a5d45f6149e0e84a6c006a2fb596ecf38ee02c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:32:03 2015 +0200

    FIX: QtMoleculeListView caused Command to be executed when selection changed internally.
    
    - we check via selecting but change is propagated via emit. Now we use
      DirectConnection.

commit 9b45d73a2d2248ad6809d20dd26fc517d8958b36
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 16e19e268e1ad1704eddd2bdda78ed2495a76d9d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:23:10 2015 +0200

    tempcommit: Fixes to GLWorldScene/View w.r.t. MoleculeMissedStateMap.

commit 85d6396e8fcb865db8682c30f6f784751c40112b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:56:26 2015 +0200

    FIX: ActionQueue::isIdle() states whether actions are executed or not.
    
    - QtUIFactory uses this to wait till test running next action.

commit a986e0aade340029e655abfb95199d2d855562e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:43:15 2015 +0200

    tempcommit: QtTimeLine needs DirectConnection.

commit 1e1ca86824b1a12b7e16bb8dbb2a5de3dc24e543
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:42:44 2015 +0200

    FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account.

commit ef2088a6433ebb723bdda9b3ccf6cc88be54def3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:42:13 2015 +0200

    FIX: QtTimeLine would cause another WorldSetTime action.
    
    - we did not catch where setValue() was called from, from an obtained
      Observable update() or from changing the slider.

commit f39bd7b352b67634c1bd5e2dc6e9bb808cfb7156
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:41:07 2015 +0200

    FIX: QtElementList now uses new updateElement().
    
    - old refill() polls complete list of atoms of specific type in the moment
      an atom is destroyed ... now we only get informed about newly created
      atoms (safe) and changing elements (also safe).

commit 1a5c53c499d6fa4717a6efe302e3a3e283bd2342
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:40:40 2015 +0200

    tempcommit: THREAD_BOUNCER change

commit da26034e22ef024e4f92421bcfc79d8a5b5c86b6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:40:23 2015 +0200

    tempcommit: Changes to QDebugStream, to no avail.

commit a19377e652d285ebcfd83e10a501c470a7907af5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:40:06 2015 +0200

    tempcommit: Changes to QtMoleculeList mutex usage.

commit 88c7eb48d0c3d1517234b97cafd7cb1e773e295d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:39:28 2015 +0200

    TEMP: Removed QtLogBox for the moment.
    
    - ever and again causes SEGFAULT at QDebugStream::61 (QTextEdit::append()).

commit b812fcf938a98a6c8e66717f9bb58b3709dcfc7b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:45 2015 +0200

    cleanUp() overwrites threadid as there we trigger lots of Observables.

commit 2f860f8500be2daab4a5d3695b0f2a7ccdaf96a8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:25 2015 +0200

    tempcommit: QtHomologyList::needsRefill() uses QueuedConnection.

commit eec6fd48ce5a64813dca05f78029bbc4accd800a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:10 2015 +0200

    Added QMutex to QtElementList for refill().

commit 5950531d074e0a39394fddbe9343df656c012159
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:08:27 2015 +0200

    tempcommit: GLWorldScene and View use DirectConnection for acting on inserted molecules.
    
    - this should let this signal pass through right away with little delay.

commit 6b62ab6eae7b3bb0833c4e36d0e2bd169a3023ca
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:07:56 2015 +0200

    tempcommit: QTUIFactory::testrun() waits till UI is done initializing.

commit 6c8da4f23ba9d5622fdb91c093248e581fda7201
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:07:40 2015 +0200

    tempcommit: Fix to THREAD_BOUNCEr.

commit 69cec0aea0fa1a1116386518fadb77df2e820b32
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:06:29 2015 +0200

    tempcommit: Fixes to QtMoleculeItem.
    
    - all QtMoleculeItems signOn to molecule::AboutToBeRemoved.
    - getMolecule() may return NULL, is caught at two places.
    - getMoleculeId() for allowing QtMoleculeList to acess molid.

commit 3343be024125ac82ba567222c3e68a1237e90ced
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 23:35:20 2015 +0200

    FIX: QtMoleculeItem did not access getMolecule() from World as const.
    
    - this triggered an update in the World.

commit 64dcb92dab022c3a8678f0b235a487ccfd65b7f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 23:35:04 2015 +0200

    tempcommit: Deactivated THREAD_BOUNDER, only .._VIP active.

commit 7efd69375a557e74b040101627716da68741e4f7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 23:34:46 2015 +0200

    tempcommit: Further THREAD_BOUNcER fixes.

commit 45736c64442252050628d0e5bb5fa61273c56694
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 23:33:30 2015 +0200

    tempcommit: FIX: QDebugStream is now thread-safe. Merge with <QTextCursor registering>
    
    - also Fix to QTextCursor not registered.

commit 2cda9e5eccd4912ab2e57624bbee9188526eb183
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 23:21:42 2015 +0200

    tempcommit: Fixing ObservedMolecules complaining about missing molecule. Merge with ...
    
    - we get one subjectKilled per channel!

commit 3f3feb76057456c7372a4bf14a5494cebfdbd00d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 20:32:37 2015 +0200

    DROPME: Added THREAD_BOUNDER and .._VIP everywhere.

commit 4ce6318731c8aebedd419f362437b0c3e9ae19ea
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 20:10:59 2015 +0200

    tempcommit: Merge with f2129a4

commit 6e278aa9d97103a742a70671dbd9c3b4167cc661
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:27:25 2015 +0200

    Added ThreadGuard include in every Qt module.

commit f2129a4044e7428a570f6dcb83de4a72fde459f3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:15:04 2015 +0200

    Storing the id of the main thread in static global variable.
    
    - this is preparatory for thread guard to be used in the context of Qt.

commit 0708ac1c1694fdb01b4060dd01c069080333c0f5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:02:27 2015 +0200

    FIX: GLWorldView::recieveNotification() is checking for whether molecule actually exists still.

commit 20173d899dfe873ab99c679f30a5aedf403d945b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:01:51 2015 +0200

    DROPME: Making sense out of why subjectKilled goes to wrong observer.

commit ab3323811e53c46d541bf31b43d63aeb735eee64
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 61f6eb3f850e9ee1e78df1896f5a67246e98860b
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 497876e9730b36a0844b68e26cfd0eb342e55171
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 634622679668fadca2d997160aaf00da82e9f754
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:58:32 2015 +0200

    tempcommit: Attempt at fixing QTextCursor not registered error.

commit c1a3fdc492d04cde685082208acb969a0e3a0dcc
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 fb3ff0d970b1edbf90b1ad9e3c3d4681040ce519
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 15 23:01:44 2015 +0200

    tempcommit: Taking note of subscribed molecules to sign Off on GLWorldView's destruct.

commit 750e6bfb879681b62fe1c092d7bf7fde04f28c54
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 15 23:01:19 2015 +0200

    tempcommit: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted.

commit 00a4670cf6c8929ac6da73af4ceb29aea78aa41f
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.

commit 78d5dad6dfbcae9f1f8be551956919aad589597e
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 f6efee1791b105055db281150be732dcaff08464
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 8 18:27:25 2015 +0200

    tempcommit: Merge with 9e859c19

commit 04a74e50838356c9bbdb18c94de78610452c7442
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.

commit 6eabab62aaeb92f03ecf56bc34206e2fd3a30462
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:19:49 2015 +0200

    Revert "tempcommit: Attempt on fixing the asynchronous handling of signal/slot and observer/observable systems in GLMoleculeObject_molecule."
    
    This reverts commit 5888dcffe918e3788a2e25fe116597943cff6cec.

commit 5888dcffe918e3788a2e25fe116597943cff6cec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 19:11:51 2015 +0200

    tempcommit: Attempt on fixing the asynchronous handling of signal/slot and observer/observable systems in GLMoleculeObject_molecule.

commit df9b6859b1d0b312539d3fae9d5402640d31bb14
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 16006dbeb16f74c42c8d29d8ba6497af7bfc1282
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 f302731d0890e3dee562d9972a71a32f3470cedb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:54:00 2015 +0200

    Revert "FIX: GLMoleculeObject_molecule::init() is now a slot."
    
    This reverts commit 11313115aa28c8de65d26aa5cba377547126f6b5.

commit b4bfa7037399a6e7be88c8c983b57873c23fadb5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:53:38 2015 +0200

    tempcommit: Merge with 8acec5c6

commit f1162b71de76b98015a439aa6a92db7774a52580
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:45:20 2015 +0200

    tempcommit: QtElementList does not have a changed() signal. Merge with ...

commit 11313115aa28c8de65d26aa5cba377547126f6b5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 14:44:22 2015 +0200

    FIX: GLMoleculeObject_molecule::init() is now a slot.
    
    - this should fix non-causality of signal/slot with observer-related signals,
      i.e. atomRemoved may get in before the atom has been instantiated within
      init().

commit d2a3e6168da7375b33b28c6c9d1cc1e4a700ac32
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 3a852aefbeca35371e57a6c1bcd4c569e01d7adf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 13:23:24 2015 +0200

    tempcommit: Merge with 8acec5c6

commit 95e7efa17499e5c2fd508f0052e35890112385dc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Jun 2 12:43:49 2015 +0200

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

commit 8acec5c66a90d043870fea994a212285bf1153af
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 f82b1b9c5919a6428a0ada2e891e5a3220cc77f5
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 6308b5c267220cd45e610b5d5f98a8c3c727bae1
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 e425c3f8e807861c3ff09b9bde415c9ad6deab81
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:14:10 2015 +0200

    tempcommit: AtomIdSet changes hiccup.

commit 4517da28262baee58762721a801aa598498e4884
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 e973bf4445d3cfe90893f0191eb601beb39b1fae
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:13:04 2015 +0200

    tempcommit: ParserXyZUnitTest hiccup.

commit 04cd84a317a6a256f270906b4e3eb423a14e9444
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:53 2015 +0200

    tempcommit: MoleculeDescriptorUnitTest hiccup.

commit a1777369e1ab75c4d5c05e128dbd722a80d20e72
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:31 2015 +0200

    tempcommit: Change associated to TremoloParser.

commit 310a571cdd564f17170ff98a6667b8f723b460e7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:08 2015 +0200

    tempcommit: More ConstAtomComposite hiccup.

commit 6357a7781590d2a371a8e839caf53da98a880056
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:55:38 2015 +0200

    tempcommit: Forgot Makefile.am change in AtomNameDescriptor adding.

commit be9f02462ecccd27bc5ae8a5143c1d23eb63e029
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:36 2015 +0200

    tempcommit: PdbParser change hiccup.

commit 8d69856c8f974617deef515ad8b0dcdbc80dd458
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:23 2015 +0200

    tempcommit: Value_atom changes hiccups.

commit ffdc50797acf2e252d63930d6c79568d3369b423
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:07 2015 +0200

    tempcommit: ConstAtomComposite change hiccups.

commit 6221a31dc4c1159fa8263a27cfe8e537d0b5287d
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 6a3ca760b4092aa67b57ffe88f745eff843fd5db
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:23:21 2015 +0200

    tempcommit: Probably due to changes to get..Molecule..()

commit 111c4b44ee95848dfcca88188fcbfbf19c4894a6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:16:32 2015 +0200

    tempcommit: Merge possibly with 20f88fee

commit ed3a55ff2e70dc044ae10fb3c9954620430b5d6f
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 30e530076bcc6a5a2f000648b93d15970c7ba78d
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 20f88fee951e0f0975e03dab347bb29f38bb8832
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 565777c816ad145911eda994458c07fa9adb3ea3
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 f73a348113c0d657d8f53d1d478e30555dfaf4cc
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 c8320fe241f4c1c68f30b7b1fbcc521bee3060d6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 09:42:19 2015 +0200

    tempcommit: DOCU: Corrected userguide.
    
    - this still needs some more work, e.g. w.r.t to code snippets indentation.

commit 5dabe20d14db77a7f638c6fce075e81d038cc2aa
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 daadba6cd9e872a5628db5a17075fd72a6960fe0
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 0c326f15463110db89fdf2110b2aaafc868e5faa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:01:34 2015 +0200

    Molecule has new channel FormulaChanged used by specific QtMoleculeItem.

commit 2054e6b36d8608258d6d67b0a929c6ab2aaf41e8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:00:52 2015 +0200

    tempcommit: Attempt to replace QtElementList::refill() by faster system.
    
    - this is not finished or tested as it is incompatible right now right refill().

commit 200da30b5cbf895becc7c8b64685706c7a729fbf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:59:56 2015 +0200

    FIX: Neither World nor MoleculeListClass do not sign on to molecule changes.

commit 4fee79b8c5ecdb10388059db8ed19fe83f2a5ba7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:09:31 2015 +0200

    QtElementList now listens to AtomObserver and not MoleculeListClass anymore.

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From git at ins.uni-bonn.de  Tue Jun 23 08:08:12 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue, 23 Jun 2015 08:08:12 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.11 deleted.
	v1.4.10-45-g8a83d57
Message-ID: <20150623060812.BDD605FD6E@saturn.ins.uni-bonn.de>

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The branch, Candidate_v1.4.11 has been deleted
       was  8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f

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8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f Set version to 1.4.11.
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From git at ins.uni-bonn.de  Tue Jun 23 08:08:21 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Tue, 23 Jun 2015 08:08:21 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Candidate_v1.4.11 created.
	v1.4.10-47-g2fc697b
Message-ID: <20150623060821.57A9B5FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.11 has been created
        at  2fc697b743f39b710d3866f7ce2c17542470e39f (commit)

- Log -----------------------------------------------------------------
commit 2fc697b743f39b710d3866f7ce2c17542470e39f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 21:23:35 2015 +0200

    Set version to 1.4.11.
    
    - MoleCuilder library is now 14:3:1.
    - Codename "Soccer" (It is one for all and all for one football).

commit d8255bbda7b87bfebfa457e976bada1578123c45
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 18:48:29 2015 +0200

    FIX: ActionQueue would not set LastActionOk to false on general exception.

commit dbfb03a85551f15ae02eedfa06c4440bc0aea8ef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 15 19:05:37 2015 +0200

    FIX: QtUIFactory used executePythonScript without HAVE_PYTHON brackets.

commit 3fa16b482f696edb18618700ef768e366d06813c
Merge: 08d042d 19dfdf7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 12 15:27:22 2015 +0200

    Merge branch 'GUI_niceties' into Candidate_v1.4.11

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From git at ins.uni-bonn.de  Wed Jun 24 07:47:49 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed, 24 Jun 2015 07:47:49 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	created. v1.4.10-132-g75364b6
Message-ID: <20150624054749.4246C5FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, GUIStates_using_ObservedValue has been created
        at  75364b686379f02ac5e498e654e0795023f18760 (commit)

- Log -----------------------------------------------------------------
commit 75364b686379f02ac5e498e654e0795023f18760
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 16:22:02 2015 +0200

    tempcommit: Fix to _molecule.

commit 2410be1fa9782611b278ab9942ee59a2b1ce2873
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:37:56 2015 +0200

    tempcommit: Fix to GLWorldView, forget to remove connect statement.

commit 5cfa4ab44f1d295de9828752fc068b3eb150a81e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:37 2015 +0200

    GLMoleculeObject_molecule also allows for changing molecule's index.
    
    - GLWorldScene has new slot changeMoleculeId(), similarly to
      GLMoleculeObject_molecule's changeAtomId().

commit 9dd7471d60d45f92ddeeeec69ed6b9438a6f6ba0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:03 2015 +0200

    tempcommit: Fixes to _bond.

commit e9df649b4dc60c66eff7926f013d60662886f58f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:35:39 2015 +0200

    tempcommit: Fixes to _atom.

commit 501c783fd89f5449a215c563e3ecad374635c344
Author: Frederik Heber <heber at 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 e40bc0b3ef2de970bd77a644850e0ab75ee40f26
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:57 2015 +0200

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

commit 3398eeaea723e5f23b899d49c8f38b7c25920484
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:19 2015 +0200

    GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.

commit 87bf4b017499c8fb4b4dae5d5850d61c5ecae85c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:56 2015 +0200

    tempcommit: Changes to _bond.

commit 5a226170ae06409be3dfb3f676fdc81c7072c3d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:44 2015 +0200

    tempcommit: Changes to _atom

commit ceb7eaf8398ff03223b7d31cfeedd36625a79bee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:21 2015 +0200

    tempcommit: Changes to QtMoleculeItem.

commit 15116102d2a378e82c6953aa5dbd354ebaf6dac0
Author: Frederik Heber <heber at 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 32786c5d94ac8ebaa0c1343df23406b0a1d41ef7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:46:32 2015 +0200

    GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.

commit 3e35890170299753563813b8ece39731d08bc9ad
Author: Frederik Heber <heber at 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 14124a72c8f2dde5a0b6f11a8e7846e64d8dd06e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jun 20 02:40:43 2015 +0200

    tempcommit: Fixe to trianglematcherin in GuiChecks. Merge with ...

commit 177cd5d8acc620f79ea4ee15c566597679b3613a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:50 2015 +0200

    GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.

commit 2236c48da4587d6a348761a17505bc7aa817e990
Author: Frederik Heber <heber at 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 623bcb1f9132d9ba0eb2455152954b5fe13b5333
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:05 2015 +0200

    tempcommit: trianglematcher also used in GuiChecks. Merge with ...

commit 808f306013fb312d950ed58d870d4ca2d13486fc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:35:50 2015 +0200

    FIX: tests/regression FragmentationAutomation had a white space after line break.

commit c68bd8c4827d4380ef9dabd63c840a2baadabd11
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 13:51:08 2015 +0200

    tempcommit: Added molecuilderguitest to testsuite dependencies.

commit 336814126baeb79fb92853d81a593c0008feb935
Author: Frederik Heber <heber at 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.
    - added trianglematcher to testsuite dependencies.

commit be7af04f282e3df004fb1dcf84edfcfe0cca851b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 11:32:31 2015 +0200

    tempcommit: QtElementList fixes.

commit ebf349fcecd354b4743ee6afbde824fb61439c93
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:26 2015 +0200

    tempcommit: Trying to fix MakroAction's outputAsPython().

commit 7b9cb7c6ef0864811496d7556cdbd5bfe29c2d34
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:32:03 2015 +0200

    FIX: QtMoleculeListView caused Command to be executed when selection changed internally.
    
    - we check via selecting but change is propagated via emit. Now we use
      DirectConnection.

commit 82f55be7db82e14ea5003cd699aae3efd0fbecef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:56:26 2015 +0200

    FIX: ActionQueue::isIdle() states whether actions are executed or not.
    
    - QtUIFactory uses this to wait till test running next action.

commit e69c446f97c5f2264235dbcb04a0ed8ff90c681e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:42:44 2015 +0200

    FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account.

commit d8817de17af7bdeec6d29b050755e82c16d062b9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:42:13 2015 +0200

    FIX: QtTimeLine would cause another WorldSetTime action.
    
    - we did not catch where setValue() was called from, from an obtained
      Observable update() or from changing the slider.
    - QtTimeLine needs DirectConnection for valueChanged.

commit 2ea6398a0c7e0f824bccb50acfd6c469e7c6cb8b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:41:07 2015 +0200

    FIX: QtElementList now uses new updateElement().
    
    - old refill() polls complete list of atoms of specific type in the moment
      an atom is destroyed ... now we only get informed about newly created
      atoms (safe) and changing elements (also safe).

commit 42ca24539427a0df1e16f3d9056bbe0e371766c3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:39:28 2015 +0200

    TEMP: Removed QtLogBox for the moment.
    
    - ever and again causes SEGFAULT at QDebugStream::61 (QTextEdit::append()).

commit 5acaee28c74e200aaa11bce984b3a58892019c2d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:10 2015 +0200

    Added QMutex to QtElementList for refill().

commit e6f9daaf049ccc62152eee423dbb2fe39ab07c15
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:06:29 2015 +0200

    FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed.
    
    - all QtMoleculeItems signOn to molecule::AboutToBeRemoved.
    - getMolecule() may return NULL, is caught at two places.
    - getMoleculeId() for allowing QtMoleculeList to acess molid.

commit 55897f55f9c8eb402aa2cad4748a214a1be92e03
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 10:50:48 2015 +0200

    FIX: QtHomologyList::refill() is now called via signal/slot.

commit d750f9ca2d9d9d8dd90fc8712f62a9fad9e47421
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:15:04 2015 +0200

    Storing the id of the main thread in static global variable.
    
    - this is preparatory for thread guard to be used in the context of Qt.

commit a9aaa9fa45883d2588e2eb520aafa5b4d093baa9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:23:10 2015 +0200

    tempcommit: Fixes to GLWorldScene/View w.r.t. MoleculeMissedStateMap.

commit c6c3d202875b7b91e9846cb5bb142f8474e83a2c
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 d1241a84f58c89a92d65ec372692a9d1ebfd5ecb
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 eb87a44364f1c58010634d4325a07c9c25dd68cd
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 988c787c883c5184f305c9fd492347c6d75ca166
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 1009de2c02cb28ccc60406f38e59f3228fa83cfb
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 938d2741d92c9aa35323d4376311541b94610a4f
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 50baad1ef1a40b8e3f40807920ad2e8ce27e5ed5
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 5397d9e586abce51a4da3f4072fe07a8380f587f
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 95d39ebf0ff53b32fee0f09c3a5a9216020ba38e
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 568df3abb720d6fd5586317005e8e8ff702424fd
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 f5f2cbbc2a3e492cc8e276ce80c146cc218be402
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 ef24213beb39fec4c3093ecc8c8f90d18837615d
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 ee6636f10f556951bce74fd93be9816d5ab02b70
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 d619fb42140095bd77e8922aa48840a4dfeb3d7a
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 004956992457b92f9eb2138bb0c261c8252c614d
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 09b198f8c3961b48c7e2da012539d5e375caf448
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 be07501b238c0001b883faad00e456c984bc8dfe
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 bfab8cdbdebae3e1f19201c7cf006ec77d9c8ff8
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 4df3e041dd475cf188ebfe959de58ae1cf339c24
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 2d452371d4c6ea7e9f173b633aecd0f7dea79f09
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:31 2015 +0200

    tempcommit: Change associated to TremoloParser.

commit ff227812c319df2a68cebff77ca3a30c91006edd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:01:08 2015 +0200

    tempcommit: More ConstAtomComposite hiccup.

commit dc3c74999aa6d536deec0801950487af6406ef58
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:36 2015 +0200

    tempcommit: PdbParser change hiccup.

commit d4f2d600952480ea78371e6cb70c002f2ebbd188
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:23 2015 +0200

    tempcommit: Value_atom changes hiccups.

commit 743123116d5f96ab5d765f8236e8b4a0815df178
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 21:54:07 2015 +0200

    tempcommit: ConstAtomComposite change hiccups.

commit 8794eb8147db17c46f1166768e8c5b9531ffea7e
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 6d62faac63cc9c12fbfb945eae60933d6eece2cb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jun 1 22:14:10 2015 +0200

    tempcommit: AtomIdSet changes hiccup.

commit c1d27ffc8b4ddf42e5a64df590ad9973d1dc7ab5
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 c63553f8ee6372f6a110ea8bc29cf3869982f043
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 3246e73829c6d7b1cd8be824094bd6672e31e5c9
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 02aa4691c99cd62a240d4894f577781015bcfbf4
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 28f4dfb5c9024f2a3636ecdd0fb36beaedaaf355
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 2902cb44427b977cd9c13f1e63db5c781159b7d8
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 75ed1736c4851cda5e1cc76a20b76dd448f59684
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 a98e8851aa93546be7523c3f809b0a4961758152
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 5b5759db0e40c1195bf4edbd4e6785e016cbdf44
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 52fe9b5dc5e6d61b562fef9173d0f36f3508c733
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 888aeaf77fc02915e74e3a5d7b4665dc41ff9080
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.

commit fe380db1f83b7f01c50f99bb11e26ad655e287e7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:00:52 2015 +0200

    tempcommit: Attempt to replace QtElementList::refill() by faster system.
    
    - this is not finished or tested as it is incompatible right now right refill().

commit 5d329da8ae726a361331d42676201803ec25f7fc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:01:34 2015 +0200

    Molecule has new channel FormulaChanged used by specific QtMoleculeItem.

commit a15f778c88c4281ef19809961831866b52082ac4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:59:56 2015 +0200

    FIX: Neither World nor MoleculeListClass do not sign on to molecule changes.

commit 88a5527c3477146c7d6484481e3f9e0686ddcd85
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:09:31 2015 +0200

    QtElementList now listens to AtomObserver and not MoleculeListClass anymore.

commit 3aebefb0c61597eb24f2d9ebd90cdfd2eda6c4be
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 23:14:50 2015 +0200

    QtMoleculeItem now uses moleculeId_t instead molecule*.

commit b7a98838af4c0d95a103210f033ae0e8e39be431
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 22:18:58 2015 +0200

    Changed hoverChanged() from mol* to moleculeId_t.
    
    - also changed signatures for atom.

commit e090e83b073ff14293ffb5b5087ebe39c1ef52c9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:56 2015 +0200

    FIX: World does not to heed updates from internal MoleculeListClass.
    
    - there is not even an World::update() nor ::recieveNotifications().

commit 9496f81208bac10da06f74cc8b30276fc05d4d69
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:40 2015 +0200

    Fixed ObserverLog message in GLWorldView.

commit 7e8ffd3ec3cd5fb1839cc8d05eae6e1db33acf11
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:57:49 2015 +0200

    FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid.
    
    - also fixed assertion message in GLMoleculeObject_molecule::atomInserted().

commit 95b53d67ef9d958641335a62e364c8f8da6225d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:05:31 2015 +0200

    FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem.

commit 17556af46363f62fe2726d83e74807532897dd68
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:04:49 2015 +0200

    GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap.

commit decc6255d96b42a91c81a215640178ca41fe0400
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 19:37:52 2015 +0200

    GLWorldScene::moleculeInserted() gets moleculeId_t as param.
    
    - we must not use pointers to instances outside the Qt world as parameters.
    - we add NULL into MoleculesInSceneMap for moleculeRemoved to remove the entry.

commit 4a67f0f5ce8cc9ecd55a6f1a00a4c816fc007ddf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue May 19 07:28:36 2015 +0200

    Gui is returning error code of 5 (in test mode) if (last) action failed.
    
    - this allows to take over return code checks in testsuite.

commit 4af30a01bc258772ee450427210b23449468a224
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 14:30:06 2015 +0200

    FIX: print on CommandHelp("help") not required in python regression test.
    
    - also fixed double disclaimer.

commit abcddcc256bdfacce2d562ae00d49371764e3b58
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:58:20 2015 +0200

    FIX: parser-parameters in regression tests basis and maxiter contained white spaces.

commit 509feca10513e95acde1f09e84666eae6ab9fbc4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 10:04:04 2015 +0200

    FIX: Regression test set-parameters-mpqc undo compared against wrong file.
    
    - functionality is actually working and removed XFAIL_IF.
    - regression test set-parameters-mpqc had too many white spaces in
      parser-parameters.

commit 8a83d57ddb0c534c7541b6e6ca36f69fbdb6257f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat May 23 21:23:35 2015 +0200

    Set version to 1.4.11.
    
    - MoleCuilder library is now 14:3:1.
    - Codename "Soccer" (It is one for all and all for one football).

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Jun 24 18:38:17 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Wed, 24 Jun 2015 18:38:17 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch Fixing_MolecuilderGui created.
	v1.4.10-63-g8cd4341
Message-ID: <20150624163817.58E665FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Fixing_MolecuilderGui has been created
        at  8cd434159764699e9aa7b69302b9835339eee8f4 (commit)

- Log -----------------------------------------------------------------
commit 8cd434159764699e9aa7b69302b9835339eee8f4
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:00:52 2015 +0200

    tempcommit: Attempt to replace QtElementList::refill() by faster system.
    
    - this is not finished or tested as it is incompatible right now right refill().

commit 64c10c32beb00befda40da4e9d54a623bb5bb90f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 18:01:34 2015 +0200

    Molecule has new channel FormulaChanged used by specific QtMoleculeItem.

commit 76d35758983956624b2c1a3db3ccf0eaa43bb2c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:59:56 2015 +0200

    FIX: Neither World nor MoleculeListClass do not sign on to molecule changes.

commit 6b474e1aa04d153d6d0b68b8cf8de9ed806ef258
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 31 17:09:31 2015 +0200

    QtElementList now listens to AtomObserver and not MoleculeListClass anymore.

commit 69b434b1d1a5180a87c3d669024542593104c8e0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 23:14:50 2015 +0200

    QtMoleculeItem now uses moleculeId_t instead molecule*.

commit 704d59ccf5f2559ab48b197552d1bea827b92ad2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri May 22 22:18:58 2015 +0200

    Changed hoverChanged() from mol* to moleculeId_t.
    
    - also changed signatures for atom.

commit 34641b910ee6b9ce05b01bd6c5aa2e558ef54466
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:56 2015 +0200

    FIX: World does not to heed updates from internal MoleculeListClass.
    
    - there is not even an World::update() nor ::recieveNotifications().

commit eac542d5b19b04687918ad9252e1d9cb4adfc4cd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 22:56:40 2015 +0200

    Fixed ObserverLog message in GLWorldView.

commit 2520ccbe1eb2cf5456bd770eedc0656bcef7846f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:57:49 2015 +0200

    FIX: GLWorldScene::changeAtomId() reinserted with oldid instead of newid.
    
    - also fixed assertion message in GLMoleculeObject_molecule::atomInserted().

commit ec6abc5fcbede9d754e9e8267ef3dc93f92ab49a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:05:31 2015 +0200

    FIX: QtMoleculeListView::moleculeSelected() did not check for presence of molitem.

commit 4669341c36fbec6d4f4114ed868a2c6ca3c34085
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:04:49 2015 +0200

    GLWorldScene::atomInserted() also adds NULL object to ..inSceneMap.

commit ef3013cd854f882cf600cfb78dc0c9cd4f78897b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 19:37:52 2015 +0200

    GLWorldScene::moleculeInserted() gets moleculeId_t as param.
    
    - we must not use pointers to instances outside the Qt world as parameters.
    - we add NULL into MoleculesInSceneMap for moleculeRemoved to remove the entry.

commit c13b913f78b416eebfc6ff8ac0031329a4944e78
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue May 19 07:28:36 2015 +0200

    Gui is returning error code of 5 (in test mode) if (last) action failed.
    
    - this allows to take over return code checks in testsuite.

commit 068a852341119fad16f4f312d9ab6289fe0edd65
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 14:30:06 2015 +0200

    FIX: print on CommandHelp("help") not required in python regression test.
    
    - also fixed double disclaimer.

commit 7774f7e70f2ae517967d41e9125f5dba0adf1dbe
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed May 20 20:58:20 2015 +0200

    FIX: parser-parameters in regression tests basis and maxiter contained white spaces.

commit 23110a4092c457be30e89f88181ea2df46c504e5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun May 17 10:04:04 2015 +0200

    FIX: Regression test set-parameters-mpqc undo compared against wrong file.
    
    - functionality is actually working and removed XFAIL_IF.
    - regression test set-parameters-mpqc had too many white spaces in
      parser-parameters.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Jun 26 08:38:31 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:38:31 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	deleted. v1.4.10-132-g75364b6
Message-ID: <20150626063831.6CB935FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
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The branch, GUIStates_using_ObservedValue has been deleted
       was  75364b686379f02ac5e498e654e0795023f18760

- Log -----------------------------------------------------------------
75364b686379f02ac5e498e654e0795023f18760 tempcommit: Fix to _molecule.
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From git at ins.uni-bonn.de  Fri Jun 26 08:39:42 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:39:42 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch AddingConstDescriptors created.
	v1.4.10-100-g3a7fbdb
Message-ID: <20150626063942.2178F5FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
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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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From git at ins.uni-bonn.de  Fri Jun 26 08:39:52 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:39:52 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads deleted.
	v1.4.10-151-g0312e23
Message-ID: <20150626063952.2DBCF5FD6E@saturn.ins.uni-bonn.de>

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The branch, SeparatingOutQtThreads has been deleted
       was  0312e2354381e345b8509d9898560703d82ee90a

- Log -----------------------------------------------------------------
0312e2354381e345b8509d9898560703d82ee90a tempcommit: Fixes to ActionQueue. Merge with 85d6396e
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From git at ins.uni-bonn.de  Fri Jun 26 08:39:56 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:39:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch SeparatingOutQtThreads created.
	v1.4.10-117-g935c985
Message-ID: <20150626063956.51A7C5FD6E@saturn.ins.uni-bonn.de>

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The branch, SeparatingOutQtThreads has been created
        at  935c9855a319b377fe6bcf247e2c9430fc26b545 (commit)

- Log -----------------------------------------------------------------
commit 935c9855a319b377fe6bcf247e2c9430fc26b545
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:05 2015 +0200

    tempcommit: trianglematcher also used in GuiChecks. Merge with ...

commit 203087ea983e3a7f91ceac4ed3cc933064b1e99d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:35:50 2015 +0200

    FIX: tests/regression FragmentationAutomation had a white space after line break.

commit 9c091218924f29e321b092def7157f246905469a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 13:51:08 2015 +0200

    tempcommit: Added molecuilderguitest to testsuite dependencies.

commit 20a208006acad8888c84aa157782fc6ba108d95b
Author: Frederik Heber <heber at 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.
    - added trianglematcher to testsuite dependencies.

commit 62487341d36923bded258ac308dfadb6ad2d4b18
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 11:32:31 2015 +0200

    tempcommit: QtElementList fixes.

commit 14e81c54774a77168b919f56da2c212a0d1eb34c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:53:26 2015 +0200

    tempcommit: Trying to fix MakroAction's outputAsPython().

commit b99a609e3caf322f8b3003fa82a2cd1c6a055d0f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:32:03 2015 +0200

    FIX: QtMoleculeListView caused Command to be executed when selection changed internally.
    
    - we check via selecting but change is propagated via emit. Now we use
      DirectConnection.

commit 02caa913ec97598b7f8dfc8a4de0683032d36a0a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:56:26 2015 +0200

    FIX: ActionQueue::isIdle() states whether actions are executed or not.
    
    - QtUIFactory uses this to wait till test running next action.

commit b737f3b236707a8f2fe947f59c9e71d3d1bcb5fb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 02:42:44 2015 +0200

    FIX: Cuboid_impl::getNormal() did not take numerical imprecision into account.

commit 670e9a0a0c176c8b29536ec141f7bec28ce8a3f7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:42:13 2015 +0200

    FIX: QtTimeLine would cause another WorldSetTime action.
    
    - we did not catch where setValue() was called from, from an obtained
      Observable update() or from changing the slider.
    - QtTimeLine needs DirectConnection for valueChanged.

commit 80219d3d499f0017023ba55ded9eaaf74eb8780d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:41:07 2015 +0200

    FIX: QtElementList now uses new updateElement().
    
    - old refill() polls complete list of atoms of specific type in the moment
      an atom is destroyed ... now we only get informed about newly created
      atoms (safe) and changing elements (also safe).

commit 8785566de18c713ecca9290309d55dacc803ebdd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 01:39:28 2015 +0200

    TEMP: Removed QtLogBox for the moment.
    
    - ever and again causes SEGFAULT at QDebugStream::61 (QTextEdit::append()).

commit 241e80f361c7c674d786cc6e59ca96f84c0835fb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:09:10 2015 +0200

    Added QMutex to QtElementList for refill().

commit 59704e782aea97f14a3988edbe81b06dd22d3f33
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 00:06:29 2015 +0200

    FIX: QtMoleculeItem would not correctly signOff prior to molecule being destroyed.
    
    - all QtMoleculeItems signOn to molecule::AboutToBeRemoved.
    - getMolecule() may return NULL, is caught at two places.
    - getMoleculeId() for allowing QtMoleculeList to acess molid.

commit 9ca8c1d77b2865cca26fd259914687db3e13a0bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 10:50:48 2015 +0200

    FIX: QtHomologyList::refill() is now called via signal/slot.

commit b4918a3090ef0a090c4723509a1c2fda173d8e61
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 17 19:15:04 2015 +0200

    Storing the id of the main thread in static global variable.
    
    - this is preparatory for thread guard to be used in the context of Qt.

commit 21347227f6f1698d786a6b03cb86911147ddc537
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Jun 18 03:23:10 2015 +0200

    tempcommit: Fixes to GLWorldScene/View w.r.t. MoleculeMissedStateMap.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Jun 26 08:40:02 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:40:02 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	created. v1.4.10-135-g6f86d56
Message-ID: <20150626064002.68AB25FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "".

The branch, GUIStates_using_ObservedValue has been created
        at  6f86d564e844880acbb0998455b21f43c03c6490 (commit)

- Log -----------------------------------------------------------------
commit 6f86d564e844880acbb0998455b21f43c03c6490
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jun 24 14:29:03 2015 +0200

    tempcommit: Fixing trianglematcher.in chmodding in GuiChecks. Merge with 14124a72

commit a75d3ddfc57ca7ca6d484091c1022984f966a1be
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 16:22:02 2015 +0200

    tempcommit: Fix to _molecule.

commit 9194b2027e603bdff9a684abb5a9c206060b8e50
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:37:56 2015 +0200

    tempcommit: Fix to GLWorldView, forget to remove connect statement.

commit af177306e813db1d0a17dd736d25861d357c1b26
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:37 2015 +0200

    GLMoleculeObject_molecule also allows for changing molecule's index.
    
    - GLWorldScene has new slot changeMoleculeId(), similarly to
      GLMoleculeObject_molecule's changeAtomId().

commit af1c0ef9aedaa7c54abf430a1aca5ed9799bc56e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:03 2015 +0200

    tempcommit: Fixes to _bond.

commit 49cdf099cad53a20f0486fc074697a9229dc239e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:35:39 2015 +0200

    tempcommit: Fixes to _atom.

commit a3c18df27007d9d51c19a9d42863c6483ac27202
Author: Frederik Heber <heber at 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 501a7083685dcf6178a1ea86ddc51147f6843996
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:57 2015 +0200

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

commit 33cbf452ff771b55e011ed54743779946ff13e1c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:19 2015 +0200

    GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.

commit 8956498927343ed006ae8cc49b68ad294e089974
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:56 2015 +0200

    tempcommit: Changes to _bond.

commit fc71a1758dfe5194d017859bb419f9d19694c802
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:44 2015 +0200

    tempcommit: Changes to _atom

commit de245b649d45c1dcee62c4b8e958a02c269cd4f9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:21 2015 +0200

    tempcommit: Changes to QtMoleculeItem.

commit 4940eb583608c7a6c8ef3490162b19b6c066ecc9
Author: Frederik Heber <heber at 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 6e93169c0dc6b457fd46cc140fd17263bb29bdcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:46:32 2015 +0200

    GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.

commit cf3782c0920dea06b62c981ba99b8bea6413b7b0
Author: Frederik Heber <heber at 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 169d4c0e7e5c7d684b29be37605c07912facd017
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jun 20 02:40:43 2015 +0200

    tempcommit: Fixe to trianglematcherin in GuiChecks. Merge with ...

commit f9e7f2cd8a5e0deade81d97b22dd4a0a4bda87e7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:50 2015 +0200

    GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.

commit 28bc7bb0c30470321562d29fef637e9ec685db95
Author: Frederik Heber <heber at 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.

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From git at ins.uni-bonn.de  Fri Jun 26 08:41:34 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:41:34 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	deleted. v1.4.10-135-g6f86d56
Message-ID: <20150626064134.8A6055FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, GUIStates_using_ObservedValue has been deleted
       was  6f86d564e844880acbb0998455b21f43c03c6490

- Log -----------------------------------------------------------------
6f86d564e844880acbb0998455b21f43c03c6490 tempcommit: Fixing trianglematcher.in chmodding in GuiChecks. Merge with 14124a72
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From git at ins.uni-bonn.de  Fri Jun 26 08:41:39 2015
From: git at ins.uni-bonn.de (git at ins.uni-bonn.de)
Date: Fri, 26 Jun 2015 08:41:39 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] branch GUIStates_using_ObservedValue
	created. v1.4.10-134-ga8e27aa
Message-ID: <20150626064139.3439A5FD6E@saturn.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "".

The branch, GUIStates_using_ObservedValue has been created
        at  a8e27aa65ba2fcf21bb580942f710348a3472e86 (commit)

- Log -----------------------------------------------------------------
commit a8e27aa65ba2fcf21bb580942f710348a3472e86
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 16:22:02 2015 +0200

    tempcommit: Fix to _molecule.

commit b3d4f3e83da991700af2ea100273a8b2f564198d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:37:56 2015 +0200

    tempcommit: Fix to GLWorldView, forget to remove connect statement.

commit e20994a5ba2a31da4a55106c300ab08f49193506
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:37 2015 +0200

    GLMoleculeObject_molecule also allows for changing molecule's index.
    
    - GLWorldScene has new slot changeMoleculeId(), similarly to
      GLMoleculeObject_molecule's changeAtomId().

commit 4c0c2d09ddfed0453877f72436a9b9ffedd81c4f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:36:03 2015 +0200

    tempcommit: Fixes to _bond.

commit 45be03354887f3af2b3e1326b04c5ec45ee06be6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 15:35:39 2015 +0200

    tempcommit: Fixes to _atom.

commit 7e2842b79e6024e8adcff96b6e9b05dd460045f8
Author: Frederik Heber <heber at 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 c932a5dccacdff7fc0450a81662cfa5b003af7a5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:57 2015 +0200

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

commit 2d8091bff6023a03c2bd48edb9eb7a5b1db1d5ba
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:16:19 2015 +0200

    GLMoleculeObject_molecule uses ObservedValue for internally representing atom's state.

commit 0359df1a7b5981b4123363ac848f60a3cc694b04
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:56 2015 +0200

    tempcommit: Changes to _bond.

commit 4bdb3209570ae392ca927e8b9aacf8ce9e662e48
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:44 2015 +0200

    tempcommit: Changes to _atom

commit 216da4130b79d394f024345d0362be66747c7704
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 14:15:21 2015 +0200

    tempcommit: Changes to QtMoleculeItem.

commit 694cb3dee613604e9475d28b474dbbe01088814d
Author: Frederik Heber <heber at 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 3fe4dbfb032ea6bbcaa3bfde1cb9c7fcc839cc8d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jun 21 06:46:32 2015 +0200

    GLMoleculeObject_bond uses ObservedValue for internally representing atom's state.

commit 41e624570e038330c120ec352e8b46868f9045d4
Author: Frederik Heber <heber at 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 4bacf86e5b84083631a32f7370acd26db82d9cb2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Jun 20 02:40:43 2015 +0200

    tempcommit: Fixe to trianglematcherin in GuiChecks. Merge with ...

commit f9e7f2cd8a5e0deade81d97b22dd4a0a4bda87e7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jun 19 19:37:50 2015 +0200

    GLMoleculeObject_atom uses ObservedValue for internally representing atom's state.

commit 28bc7bb0c30470321562d29fef637e9ec685db95
Author: Frederik Heber <heber at 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.

-----------------------------------------------------------------------


hooks/post-receive
--