alignment_manager.cpp

ncbi源码

            if (*a == single) {
                BlockAligner::AlignmentList::const_iterator n, ne = newAlignments.end();
                for (n=newAlignments.begin(); n!=ne; ++n)
                    replacedList.push_back(*n);
                foundSingle = true;
            } else
                replacedList.push_back((*a)->Clone());
        }
        if (!foundSingle) ERRORMSG(
            "AlignmentManager::ThreadUpdate() - threaded alignment not found in update viewer!");
        updateViewer->ReplaceAlignments(replacedList);

        // tell the sequenceViewer that rows have been merged into the multiple
        if (nRowsAddedToMultiple > 0)
            sequenceViewer->GetCurrentDisplay()->
                RowsAdded(nRowsAddedToMultiple, currentMultiple);
    }
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: alignment_manager.cpp,v $
* Revision 1000.2  2004/06/01 18:27:33  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.94
*
* Revision 1.94  2004/05/21 21:41:38  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.93  2004/05/20 18:49:21  thiessen
* don't do structure realignment if < 3 coords present
*
* Revision 1.92  2004/03/15 17:17:56  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.91  2004/02/19 17:04:38  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.90  2003/10/13 14:16:31  thiessen
* add -n option to not show alignment window
*
* Revision 1.89  2003/10/13 13:23:31  thiessen
* add -i option to show import window
*
* Revision 1.88  2003/09/22 17:33:12  thiessen
* add AlignmentChanged flag; flush message file; check row order of repeats
*
* Revision 1.87  2003/09/22 16:17:29  thiessen
* fix typo
*
* Revision 1.86  2003/09/22 16:15:28  thiessen
* better diagnostic messages for change checks
*
* Revision 1.85  2003/07/17 16:52:34  thiessen
* add FileSaved message with edit typing
*
* Revision 1.84  2003/07/14 18:37:07  thiessen
* change GetUngappedAlignedBlocks() param types; other syntax changes
*
* Revision 1.83  2003/02/03 19:19:59  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.82  2003/01/29 01:41:05  thiessen
* add merge neighbor instead of merge near highlight
*
* Revision 1.81  2003/01/28 21:07:56  thiessen
* add block fit coloring algorithm; tweak row dragging; fix style bug
*
* Revision 1.80  2002/11/10 20:32:04  thiessen
* show/hide optimizations, esp. show domains with highlights
*
* Revision 1.79  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.78  2002/10/13 22:58:07  thiessen
* add redo ability to editor
*
* Revision 1.77  2002/10/08 12:35:42  thiessen
* use delete[] for arrays
*
* Revision 1.76  2002/09/30 17:13:02  thiessen
* change structure import to do sequences as well; change cache to hold mimes; change block aligner vocabulary; fix block aligner dialog bugs
*
* Revision 1.75  2002/09/19 12:51:08  thiessen
* fix block aligner / update bug; add distance select for other molecules only
*
* Revision 1.74  2002/09/16 21:24:58  thiessen
* add block freezing to block aligner
*
* Revision 1.73  2002/07/26 15:28:43  thiessen
* add Alejandro's block alignment algorithm
*
* Revision 1.72  2002/07/01 15:30:20  thiessen
* fix for container type switch in Dense-seg
*
* Revision 1.71  2002/03/07 19:16:04  thiessen
* don't auto-show sequence windows
*
* Revision 1.70  2002/02/19 14:59:38  thiessen
* add CDD reject and purge sequence
*
* Revision 1.69  2002/02/12 17:19:20  thiessen
* first working structure import
*
* Revision 1.68  2001/12/06 23:13:43  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.67  2001/11/30 14:02:04  thiessen
* progress on sequence imports to single structures
*
* Revision 1.66  2001/11/27 16:26:05  thiessen
* major update to data management system
*
* Revision 1.65  2001/09/27 15:37:57  thiessen
* decouple sequence import and BLAST
*
* Revision 1.64  2001/06/21 02:02:33  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.63  2001/06/07 19:05:37  thiessen
* functional (although incomplete) render settings panel ; highlight title - not sequence - upon mouse click
*
* Revision 1.62  2001/06/05 13:21:08  thiessen
* fix structure alignment list problems
*
* Revision 1.61  2001/06/02 17:22:45  thiessen
* fixes for GCC
*
* Revision 1.60  2001/05/31 18:47:05  thiessen
* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks
*
* Revision 1.59  2001/05/24 13:32:15  thiessen
* fix merge status reporting bug
*
* Revision 1.58  2001/05/15 23:48:35  thiessen
* minor adjustments to compile under Solaris/wxGTK
*
* Revision 1.57  2001/05/11 02:10:41  thiessen
* add better merge fail indicators; tweaks to windowing/taskbar
*
* Revision 1.56  2001/05/03 14:39:14  thiessen
* put ViewableAlignment in its own (non-wx) header
*
* Revision 1.55  2001/05/02 13:46:26  thiessen
* major revision of stuff relating to saving of updates; allow stored null-alignments
*
* Revision 1.54  2001/04/20 18:02:57  thiessen
* don't open update viewer right away
*
* Revision 1.53  2001/04/19 12:58:32  thiessen
* allow merge and delete of individual updates
*
* Revision 1.52  2001/04/17 20:15:38  thiessen
* load 'pending' Cdd alignments into update window
*
* Revision 1.51  2001/04/05 22:55:34  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.50  2001/04/04 00:27:13  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.49  2001/03/30 03:07:33  thiessen
* add threader score calculation & sorting
*
* Revision 1.48  2001/03/22 18:14:49  thiessen
* fix null-pointer error in alignment retrieval
*
* Revision 1.47  2001/03/22 00:33:16  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.46  2001/03/17 14:06:48  thiessen
* more workarounds for namespace/#define conflicts
*
* Revision 1.45  2001/03/13 01:25:05  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.44  2001/03/10 22:23:02  thiessen
* damn wx/string problem again
*
* Revision 1.43  2001/03/09 15:49:03  thiessen
* major changes to add initial update viewer
*
* Revision 1.42  2001/03/06 20:20:50  thiessen
* progress towards >1 alignment in a SequenceDisplay ; misc minor fixes
*
* Revision 1.41  2001/03/02 15:32:52  thiessen
* minor fixes to save & show/hide dialogs, wx string headers
*
* Revision 1.40  2001/03/01 20:15:50  thiessen
* major rearrangement of sequence viewer code into base and derived classes
*
* Revision 1.39  2001/02/16 00:40:01  thiessen
* remove unused sequences from asn data
*
* Revision 1.38  2001/02/13 01:03:55  thiessen
* backward-compatible domain ID's in output; add ability to delete rows
*
* Revision 1.37  2001/02/09 20:17:32  thiessen
* ignore atoms w/o alpha when doing structure realignment
*
* Revision 1.36  2001/02/08 23:01:48  thiessen
* hook up C-toolkit stuff for threading; working PSSM calculation
*
* Revision 1.35  2001/02/02 20:17:33  thiessen
* can read in CDD with multi-structure but no struct. alignments
*
* Revision 1.34  2001/01/30 20:51:18  thiessen
* minor fixes
*
* Revision 1.33  2001/01/18 19:37:28  thiessen
* save structure (re)alignments to asn output
*
* Revision 1.32  2000/12/29 19:23:38  thiessen
* save row order
*
* Revision 1.31  2000/12/26 16:47:36  thiessen
* preserve block boundaries
*
* Revision 1.30  2000/12/19 16:39:08  thiessen
* tweaks to show/hide
*
* Revision 1.29  2000/12/15 15:51:46  thiessen
* show/hide system installed
*
* Revision 1.28  2000/11/30 15:49:34  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.27  2000/11/17 19:48:13  thiessen
* working show/hide alignment row
*
* Revision 1.26  2000/11/13 18:06:52  thiessen
* working structure re-superpositioning
*
* Revision 1.25  2000/11/12 04:02:59  thiessen
* working file save including alignment edits
*
* Revision 1.24  2000/11/11 21:15:53  thiessen
* create Seq-annot from BlockMultipleAlignment
*
* Revision 1.23  2000/11/09 18:14:40  vasilche
* Fixed nonstandard behaviour of 'for' statement on MS VC.
*
* Revision 1.22  2000/11/03 01:12:44  thiessen
* fix memory problem with alignment cloning
*
* Revision 1.21  2000/11/02 16:56:00  thiessen
* working editor undo; dynamic slave transforms
*
* Revision 1.20  2000/10/17 14:35:06  thiessen
* added row shift - editor basically complete
*
* Revision 1.19  2000/10/16 20:03:06  thiessen
* working block creation
*
* Revision 1.18  2000/10/16 14:25:47  thiessen
* working alignment fit coloring
*
* Revision 1.17  2000/10/12 19:20:45  thiessen
* working block deletion
*
* Revision 1.16  2000/10/12 16:22:45  thiessen
* working block split
*
* Revision 1.15  2000/10/12 02:14:56  thiessen
* working block boundary editing
*
* Revision 1.14  2000/10/05 18:34:43  thiessen
* first working editing operation
*
* Revision 1.13  2000/10/04 17:41:29  thiessen
* change highlight color (cell background) handling
*
* Revision 1.12  2000/10/02 23:25:19  thiessen
* working sequence identifier window in sequence viewer
*
* Revision 1.11  2000/09/20 22:22:26  thiessen
* working conservation coloring; split and center unaligned justification
*
* Revision 1.10  2000/09/15 19:24:22  thiessen
* allow repeated structures w/o different local id
*
* Revision 1.9  2000/09/12 01:47:38  thiessen
* fix minor but obscure bug
*
* Revision 1.8  2000/09/11 22:57:31  thiessen
* working highlighting
*
* Revision 1.7  2000/09/11 14:06:28  thiessen
* working alignment coloring
*
* Revision 1.6  2000/09/11 01:46:13  thiessen
* working messenger for sequence<->structure window communication
*
* Revision 1.5  2000/09/08 20:16:55  thiessen
* working dynamic alignment views
*
* Revision 1.4  2000/09/03 18:46:47  thiessen
* working generalized sequence viewer
*
* Revision 1.3  2000/08/30 23:46:26  thiessen
* working alignment display
*
* Revision 1.2  2000/08/30 19:48:41  thiessen
* working sequence window
*
* Revision 1.1  2000/08/29 04:34:35  thiessen
* working alignment manager, IBM
*
*/