[Molecuilder-devel] [SCM] branch Candidate_v1.5.3 created. v1.5.1-181-ga95f5d3
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Mon Apr 25 09:18:15 CEST 2016
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The branch, Candidate_v1.5.3 has been created
at a95f5d33525f59abab6d0c6c038124f19f3dce8f (commit)
- Log -----------------------------------------------------------------
commit a95f5d33525f59abab6d0c6c038124f19f3dce8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Apr 25 09:11:24 2016 +0200
Set version to 1.5.3.
- MoleCuilder library is now 16:0:0.
- Codename "" ().
commit 9d1a7852dfe99a1cb296f633da73d5db75927b7d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 24 16:19:38 2016 +0200
FIX: GLWorldScene used iterator also in NDEBUG, connect still outside mutex.
commit abb1154e536baa00480c16bd3f03a86d8c3b1827
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 24 16:16:40 2016 +0200
FIX: QtMoleculeListView::rowsSelected() checks for illegal id from get..ToIndex().
- also check was faulty before and we still tried getting the mol from the
world before.
commit 097da78c5ee5df3259577e1b98ad9c5dfba1f859
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 24 16:15:37 2016 +0200
FIX: QtMoleculeList has flag to tell when nameChanged came from outside.
- this causes irregular calls to getMoleculeIdToIndex() which could crash the
code due to the present assertion.
commit 006f6a88499dfff7622fae1a1ebbbebf94c10e25
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 24 16:15:11 2016 +0200
QtObservedInstanceBoard::get..ToIndex() now serve -1 as illegal id when index not found
commit ffa69c3a5430f43a2fcff8f8332be2d5df161bcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 24 16:14:09 2016 +0200
FIX: PdbParser scanned through all present atoms once per ATOM line.
- this was the cause of a O(N^2) scaling issue.
commit 30b134008ab63ad98ce7dfb5bee4983ddc68169d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Fri Apr 22 10:50:56 2016 +0200
FIX: GLWorldScene::removeBond() needs to check whether molecule changed already.
- there are two possibilities for bonds to be removed: Either the molecule is
removed (with its atoms) and this one we got so far. Or the bond is simply
removed (because auf adjacency recreation) and this we did not check so far.
- If the simply the bond is removed, then we receive removeBond() but no
moleculeChanged() signals. Hence, the QtObservedBond is never removed.
We need to check in removeBonds() whether the associated molecules are
not NULL and then reset the parent entries ourselves.
commit 67c4ea8af8af5680e462a6c86512e875859b1852
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Fri Apr 22 10:29:28 2016 +0200
FIX: molecule returned BondCount twice as large.
commit 0bddd1ed82f44fe38f41c7b31c9a974b63b4a862
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Fri Apr 22 09:30:12 2016 +0200
Made GLWorldScene::resetParent() safe for multiple threads.
commit ea79260c69a50c8b23e40674182e6bd828d52ff6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 20 07:45:11 2016 +0200
Split ObservedValueIndexLookup such that it is protected under atom or bond mutex.
commit 1eba7cfbf78368fcfda41c0aafd0173295c50739
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Apr 18 22:57:47 2016 +0200
Protecting access to atom and bond functions in GLWorldScene with mutexes.
- mutex are now for general access to internal maps, not just NodesInSceneMap.
commit efeeb77d0498bbfe882b8473da74a31a8d40277f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Sun Apr 17 23:26:58 2016 +0200
GLWorldScene now holds onto atoms and bonds until ..Removed() signal and parent(s) is reset.
commit 649f59a7ea5ca2db2837dd54e016436f34564ec3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Fri Apr 15 09:38:55 2016 +0200
GLWorldScene removes stored observed values only after both parent is NULL and atomRemoved() came in.
- this is to ensure that lifetime of the observed value instance is as long as
required.
commit 13684213eddb4d1e92250a7618e5af0715cd87e9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 14 09:55:41 2016 +0200
GLWorldScene needs to store observed values to ensure duration of their lifetime.
commit d16a06ce12b228789f8b4bbb0b922c6d57fd9d2a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 14 10:08:36 2016 +0200
FIX: GLMoleculeObject_atom did not use QtObservedAtom for selected.
commit 507f3ce7e91faebcd1012d9752b9561db91064ff
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 14 10:01:31 2016 +0200
QtObservedBond returns ::ptr instead of ptr from left and right atom.
- FIX: GLWorldScene crashed on resolving sender() of a reparent..() signal
because the object got destroyed in the meantime.
commit 522c456e53a0b038cad5c4e43564052c0e06d8c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 14 09:47:20 2016 +0200
QtObserved... signals indexChanged does not transmit ids anymore.
- since the change to ObservedValue_Index_t, the id is not used anymore. Only
in the GUI for the objectid.
commit 6c4b69d116a458152c8f6d55ce5f08afa7882f7a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 13 16:10:40 2016 +0200
Added checks abd verbosity to reparenting in GLWorldScene.
commit 08a7eccd3406971777d82560ee81d569921045ec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 13 15:43:20 2016 +0200
FIX: ObservedValue_Index_t is now the memory address of the Observer instance.
- the atom, bond, or molecule may be removed before and reinstantiated at the
same address. Hence, it is not a good unique index. The only sensible index
is the memory address of the QtObserved... instance itself.
commit 375bc3f1ea4847031faded1937b326d122ce6ce3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 21:55:27 2016 +0200
FIX: Empty row in QtMoleculeList was not deleted.
commit b2eeafa325f99ae34f45cf7e6aff1c93efa6eaa9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 21:21:00 2016 +0200
FIX: MoleculeList crashed when selected molecule changed its place.
commit a13f2bb2167e2b7f751acdd3c12df751bb03a105
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:37:31 2016 +0200
GLWorldScene can now reparent atoms and bonds whose molecule is instantiated later.
- parent maps are now bimaps.
commit 5026148ed739f29b2229d07be76ad31aca20fe30
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:19:47 2016 +0200
GLWorldScene's parent maps now store the parent as ObservedValue_Index_t.
- this will allow to change them into a bimap and then browse through them with
the index of a newly instantiated GLMoleculeObject_molecule in order to
assign them a proper parent.
commit 6e1628b7373c59c6545f88f455af8d047506193e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:17:46 2016 +0200
FIX: QtMoleculeList should not use getIdtoIndex unnecessarily.
- this function is only meant to be used in interaction with the user, i.e.
while the GUI does not change.
commit 2560f1b24789baa35df95165f384b1b4741ed2d5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:16:30 2016 +0200
QtObservedMolecule uses fixed index which it returns.
commit 20538962d2829639cd69cee58b8ff49473984aec
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:16:22 2016 +0200
QtObservedBond uses fixed index which it returns.
commit 498c678babf7da7e93da5832726a8c44043533d3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 20:16:13 2016 +0200
QtObservedAtom uses fixed index which it returns.
commit 50246c63f842a77b7c479453a59b17092c472339
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 16:32:13 2016 +0200
FIX: made disconnect() check for NULL pointers.
commit 691533f57d4b19acfb8ebfa5dd9096e4754f42c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 16:24:10 2016 +0200
FIX: GLMoleculeObject_molecule only updates tesselation hull when necessary.
commit bd676856deb95da62852a3d3d0a1bfdd7e404f1b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 14:02:45 2016 +0200
GLWorldScene now properly reassigns parents of GLMoleculeObjects.
- this is important for atoms and bonds such that they disappear when their
associated molecule is visualized as a tesselated surface.
commit 273c8a207d79d5a69b073ffc4c58dd18220aa90b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 13:29:56 2016 +0200
QtObservedAtom only offers direct access to associated const QtObservedMolecule ref.
- the molecule index is not part of the atom's state, hence cannot be directly
observed. The only thing we observe is the association to the molecule. For
this a O/O-signal is available and we may actively change the ref when
getting this signal without breaking anything as it occurs in the same
thread, hence the board can be safely accessed.
- QtObservedBond now needs to access mol index through the molecule ref.
- QtInfoBox may now conveniently access atom'smol ref directly.
- FIX: Removed static QtObservedBond::getMolecule().
commit 7f185f928e77138d9f68a9af929ddf86c7ed5bf1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 13:19:05 2016 +0200
QtObservedBond also offers direct access to stored QtObservedAtoms as const refs.
- leftatom and rightatom are const throughout the lifetime of the bond. Hence,
there is no need to update them and we simply store the refs directly. This
will be different for the atom, where the molecule ref may change over the
lifetime!
commit f1b5ca904ef2ca5bf64048122b7d6dc1ed4716e3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Apr 12 10:51:06 2016 +0200
Only GLWorldScene creates stuff, GLMoleculeObject_.. are just visual reps.
commit 785d89098de752b05e69ab46e0145f0a07a87128
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Apr 7 18:14:04 2016 +0200
FIX: QtObservedAtom: getAtomMolecule() -> getMoleculeIndex().
- changed QtInfoBox and QtObservedBond::getMoleculeIndex() which used it.
commit 411269194c0e399da21c636ada2ea31c72975d31
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Apr 6 19:04:01 2016 +0200
QtObservedBond now simply gets both QtObservedAtoms on construction.
- they must exist as QtObservedInstanceBoard is in the current update() loop.
- and we don't need to take care of them and may throw them away when the bonf
itself is removed. We don't need to care for anything else.
commit e4b13a04aa3b6fa93fd0438be7cb89dd9ad312cc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 29 20:47:16 2016 +0200
getObserved...() checks whether id is still present.
commit d48a1666332f282b0853f2214a842d9d2da6b67c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 23 11:02:43 2016 +0100
Removed partial specialization of ObservedValue_wCallback for index.
- we don't need this anymore as ObservedValues now have a unique and permanent
index, which we can bind right from the start.
- adapted QtObservedAtom and QtObservedMolecule's initObservedValues().
commit 96f14ae4f021b1976486ad5658a68c30645c7467
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Mar 24 14:26:51 2016 +0100
Modified all GLMoleculeObjects and GLWorldScene to the new QtObservedBond.
- GLWorldScene transmits bondInserted/bondRemoved similarly to those for the
atoms to the molecule if aLready present and otherwise into the
MissedStateMap.
commit b4bd0ec170830621ec3bcc64a4a1a99403399bd9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 15 11:10:54 2016 +0100
Added QtObservedBond, managed by QtObservedInstanceBoard.
- QtObservedBond is special because it observes not only a bond, but also two
atoms and a molecule in total.
- but the general idea is to rather have information duplicate, i.e. the left
atom's position is also available via the QtObservedAtom. But in this way
QtObservedBond does not depend on the QtObservedAtom being still or already
present.
commit 6af6a62fa039882142c48e7ac4a0e1d2c5364715
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Thu Mar 24 14:13:31 2016 +0100
FIX: Removed GLMoleculeObject_molecule's molref.
commit bf6245259c76b4be2e6085db24148e21e1844c8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 23 10:56:51 2016 +0100
QtObservedMolecule also uses new index internally.
commit ee3fb8349db0a97b7274dd3ae8a157fc0387a363
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 22 12:58:35 2016 +0100
QtObservedAtom uses new index internally.
- thus we don't have to jump through the loops with constructing prior an
IndexGetter in initObservedValues().
commit 62a127cb29522511523a9fc2274cd27e608670b2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 23 10:58:26 2016 +0100
FIX: QtObservedMolecule::initObservedValues was still static.
commit 4690a7201ee4bd9d43ddb96d1a3d9c79f986b917
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Wed Mar 23 11:06:23 2016 +0100
Removed unneeded specialization ObservedValue_UpdateAtoms.
commit 76c238dfdd440371633103e91a848b5dcc8838ee
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 22 00:32:47 2016 +0100
Removed GLMoleculeObject_molecule::getPresentAtoms() and changed atomRemoved slot of GLMoleculeObject_molecule.
- this required AtomsInSceneMap to use new Index.
commit 1d9b6dd666010d66bb843c17134d6df49aa030df
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 22 00:12:07 2016 +0100
FIX: Removed some unnecessary observer code from GLWorldView.
commit f91ef6007a43260154696025a6213300e1067126
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Mar 21 23:36:39 2016 +0100
Changed slots of GLWorldScene and GLWorldView.
commit 0a558d693706673fef514adf5851afe6aed5661e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Tue Mar 29 16:56:56 2016 +0200
MoleculeList discerns between internal and external name change.
commit 3054f4a837e9cb89d591549c873572989e548c33
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Mar 21 22:13:43 2016 +0100
QtObserved...Observed now get index on ...Removed() signal.
- Changed slots of QtElementList, QtMoleculeList, and QtMoleculeListView. This
is not all of them, but they now all used ObservedValue_Index_t.
commit 1a58ce8105d4937e5093f614ba56c6d4688852bc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Mar 21 22:42:14 2016 +0100
Added convenience function to return current id for given index.
- this is mainly for printing in asserts and logs.
- required to convert IdtoIndex to bimap.
- ...Observed wire through getIdtoIndex() function.
commit 59eabc83f7f01a0f2797b83aea97182aa3c14b71
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date: Mon Mar 21 21:42:05 2016 +0100
Introduced unique and permanent ObservedValue_Index_t.
- this is currently the address of the observable which is not perfectly
secure but might work for the moment.
- QtObservedInstanceBoard uses the index internally and only has an additional
map to serve instances on request for the their atomId_t, moleculeId_t, ....
However, this id should nowhere else be used because it may change during
the lifetime of the object.
- this should prevent the hazzle with the possibly changing atomId_t,
moleculeId_t, ... in all classes that work with QtObserved... instances.
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