[Molecuilder-devel] [SCM] MoleCuilder branch SeveralGUIFixes created. v1.4.9-65-ge83aca7

Mon Jan 26 21:09:13 CET 2015

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The branch, SeveralGUIFixes has been created
        at  e83aca7ab965d17d3fe72ff5ab7e657327061bda (commit)

- Log -----------------------------------------------------------------
commit e83aca7ab965d17d3fe72ff5ab7e657327061bda
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 12:07:22 2015 +0100

    tempcommit: Looking for bug to wrongly scaled bond length after width change.

    - this seems to be a bug in Qt3D ... we should check this on Ubuntu 14.04

commit e5a4de9d12b3462673384b90ec21994a00901104
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 22:19:53 2015 +0100

    FIX: QDebugStream is now protected against multiple writes to log window.

    - writes bracketed with bool.
    - we had multiple, seemingly random segfaults in QDebugStream when inserting
      new text.

commit 66316d0cad6f435e2f0143d8e573ffd37bc989ed
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 18:37:49 2015 +0100

    FIX: MPQCCommandFragmentController failed to add jobs due to false return value type.

    - bool is now an unsigned int.
    - kudos to Ralph Thesen und Sambasiva Rao Chinnamsetty for stumbling over the
      bug.

commit 66821020c7999d6f6e2762a441294d20d960afaf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 16:51:25 2015 +0100

    FIX: FragmentationAutomationAction checks FragmentControllers' exitflags.

    - this way we can tell when the connection to the server fails and we need to
      interrupt the Action and return failure.

commit d915f7956e372b428d5f1e29dac552785a15c3a9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 16:50:27 2015 +0100

    FIX: ActionSequence now checks whether an Action in the sequence fails.

    - otherwise if we are to repeat the sequence for 200 steps and one of the
      Actions fails on the first step, we still go through all of the
      remaining steps.

commit c5b67886320da2341ee9debe98857c3dcd310784
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 14:31:53 2015 +0100

    Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect.

    - this fixes the bug where the molecular dynamics actions would flip the double
      bonds in an aromatic ring during the simulation steps because the bond
      degrees are reset even though the bond graph is present and should be
      re-used.

commit 7614bbdf5ab794816579d338583dbffc805fc41d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 14:30:48 2015 +0100

    Added correct-bonddegree to MolDyn and StructOpt Actions.

    - this is not really necessary as FragmentationAction will correct bond degrees
      but it is nonetheless cleaner this way.

commit b5642b098bdc8ce4d30e084a5d2196d90d1d5eb5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 13:57:10 2015 +0100

    FIX: MakroAction had ref to ActionSequence, hence removing actions would do so permanently.

    - this fixes the segfault when calling a MakroAction such as MolecularDynamics
      and unchecking output-every-step, causing the OutputAction to be removed
      from the sequence, and when re-performing Action with again unchecked option,
      the action cannot be removed any longer.
    - now each MakroAction has its own copy of the sequence, it is copied on clone
      and may be freely manipulated.

commit 3dca11658d0c26ca4ec03795f113bfed5a5e2530
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 13:37:44 2015 +0100

    Undoing atom/molecule removal will also recreate bonds.

commit f82008d985e0e63d38c3d296f1aa9c6add203c4c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 13:34:57 2015 +0100

    Renamed Bond::Contains to Bond::ContainsNr() and added ::ContainsId().

    - I just stumbled over this, trying to recreate bonds from removed atoms and
      Contains looks for the Nr not the Id ...

commit e7cf5be9f4cc5f16f898a6c7e5b427d97835c088
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jan 23 20:43:55 2015 +0100

    FIX: Action..::outputAsPython now accesses parameters via getUnvalidated().

    - added Value::getUnvalidated() and Parameter::getUnvalidated() for access at store-session.
    - this fixes a bug when OutputAsAction had been used whose filename would no
      longer be valid as the file now exists. This would cause an assertion and the
      whole OutputAsAction would fail.

commit dc0642fc1a4eb53147c23a507d5ddfa9d0ef06a7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 13:44:56 2015 +0100

    tempcommit: Commented-out all debugging messages in QtMoleculeList rewrite. Merge with ...

commit 9d622f6f69e19a9b2cb08476a77f6dc0cdc14c86
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 25 12:15:08 2015 +0100

    tempcommit: Fixes to QtMoleculeList. Merge with ...

    - using vector of molecule pointers and set operations to fulfil validity of
      updates.

commit 08915c9d88c94f542b0b8ffa782b7b109cb8302c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jan 23 19:25:38 2015 +0100

    tempcommit: MoleculeRemoved channels just makes mol inserted into toBeRemoved. Merge with ...

    - this is safer than removing the entry in MoleculeBiMap right away as thread
      in GUI and Action thread do not access in an orderly fashion.

commit ee617a5ea465afe71546de922fe6a67f130150f7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Jan 23 00:05:47 2015 +0100

    Visibility checkstate is working for molecule and group item.

    - signals are emitted and states are correctly changed, tested on amylose
      molecule in a box filled with ~3000 water molecules.

commit 0da9b3193f1851d475315d6686aff09b53ab09bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jan 19 19:18:52 2015 +0100

    DROPME: qDebug on selectionChanged() in view.

commit 5a9c977ffe22ccf75bfe553b851830db9036052a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jan 19 19:16:54 2015 +0100

    tempcommit: Fixing updateItemStates() such that different updates don't interfere with one another.

    - i.e. moving a row and removing the row entirely does not mix. Updating it and
      then removing it is ill-spent time.
    - split off removing a group item from setting its occurrence.
    - emitDirtyState() only uses the first column item despite for the dirty items
      set. Otherwise we have multiple moves of the same row.

commit 6fac57fc6f8d6a0a1d77838b1a6d4e7be8ddbf73
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Jan 19 19:16:13 2015 +0100

    tempcommit: FIxing accesses to already deleted molecules due to their row becoming unselected before destruction.

commit 08f25e3aed02e5896599ac806543bcbcd6769c8b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 23:56:51 2015 +0100

    tempcommit: Added selecting braces to select() calls in QtMoleculeListView. Required? Useful?

commit ae0310fb681c73af0d74798d4dd9bf91fc5f4e7f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 23:55:30 2015 +0100

    DROPME: In case you need to see when selectionChanged() is triggered in QtMoleculeListView.

    - uncomment me!

commit 0371cb1fc2a6163b8df394f5db19a615e8922eaa
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 23:54:30 2015 +0100

    tempcommit: QtMoleculeList removes group items after setOccurrence().

    - setOccurrence() gives index of row back if it should be romoved.

commit b63a112570a1c4f216f02010c05a882c467882e3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 21:07:11 2015 +0100

    tempcommit: Removed emitDataChanged() and updateSteps() is just void.

commit d77afe108713a7a8d5b245b5fd77bf10eda67de6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 21:01:55 2015 +0100

    Moved rowsSelected() over to QtMoleculeListView.

commit 7a53bcd163402f54a72241cbe2bfd3e54c389c84
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 20:00:01 2015 +0100

    tempcommit: Fix to factory for visitem selectable. Merge with ...

commit dbcbcc2de2fdfdbc0eb120616ac11017d973cd01
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 18:56:25 2015 +0100

    tempcommit: Fixes to list. Merge with ...

commit c91d016d3a652cb44adb74e54c6c4722925cab6e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 18:55:45 2015 +0100

    tempcommit: Fixes to specific items. Merge with ...

commit b3b5fe4d571cbd6546f3df2b7130b435bf574121
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 17:08:42 2015 +0100

    tempcommit: Fixes to list. Merge with ...

commit 674ab4de68b797f20f8a397aacec35896d421c39
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 17:08:27 2015 +0100

    tempcommit: Fixes to items. Merge with ...

commit 3f2f38368024d5a70d6b54c4b6a98ff6a5917fef
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 15:04:26 2015 +0100

    Modified QtMoleculeList to use QtMoleculeItemFactory.

commit e2c12d9350e39dd6772f70233c1cf65fecc4b078
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 14:33:42 2015 +0100

    Added a slew of specific QtMoleculeItem for each of the COLUMNs.

    - all are produced solely by the factory and are very specific.

commit aac20a7748ce394b1787cbb85c01c694317adf35
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 13:26:55 2015 +0100

    Added basic QtMoleculeItem and ...Factory.

commit 11fca39b215de52d5b248e0ab1b949afa6bdba16
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Jan 18 13:22:39 2015 +0100

    Moved QtMoleculeList files into own subfolder.

    - added QtMoleculeListView.
    - we are going to need a lot of classes for this to work properly.

commit c122211ef5fbd30855d6bbca7f4182fe7c0b04d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jan 14 23:33:09 2015 +0100

    Header row is correct again in QtMoleculeList.

    - had to overwrite headerData().

commit 3d9f245199267605d22fec011bd1e71a555a8fed
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Jan 14 23:32:34 2015 +0100

    First change to convert QtMoleculeList into QStandardItemModel.

    - this will keep the QtMoleculeList up-to-date automatically.

commit 11aa68b4eb0deeac242bb25cc1651efab67025c2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 21:05:41 2014 +0100

    tempcommit: New update scheme for QtMoleculeList requires changing flag to prevent VisibilityChanged() trigger.

commit 95f44cfa70e7c8ce7126ed5b5a4098812a3bd357
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Dec 12 20:43:05 2014 +0100

    tempcommit: Extracted add/removeItem in QtMoleculeList, no more complete refilling on update.

    - this is unfinished as we can't find the item to a molecule that is about to
      be removed.

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