update_viewer.cpp

ncbi源码

    // find alignment, to replace it with BLAST result
    AlignmentList::iterator a, ae = GetCurrentAlignments().end();
    for (a=GetCurrentAlignments().begin(); a!=ae; ++a)
        if (*a == update) break;
    if (a == GetCurrentAlignments().end()) return;

    // set up BLAST-2-sequences between update slave and each sequence from the multiple
    BLASTer::AlignmentList toRealign;
    for (int row=0; row<multiple->NRows(); ++row) {
        BlockMultipleAlignment::SequenceList *seqs = new BlockMultipleAlignment::SequenceList(2);
        (*seqs)[0] = multiple->GetSequenceOfRow(row);
        (*seqs)[1] = updateSeq;
        BlockMultipleAlignment *newAlignment =
            new BlockMultipleAlignment(seqs, updateSeq->parentSet->alignmentManager);
        if (newAlignment->AddUnalignedBlocks() && newAlignment->UpdateBlockMapAndColors(false))
        {
            int excess = 0;
            if (!RegistryGetInteger(REG_ADVANCED_SECTION, REG_FOOTPRINT_RES, &excess))
                WARNINGMSG("Can't get footprint excess residues from registry");
            newAlignment->alignMasterFrom = uaBlocks.front()->GetRangeOfRow(row)->from - excess;
            if (newAlignment->alignMasterFrom < 0)
                newAlignment->alignMasterFrom = 0;
            newAlignment->alignMasterTo = uaBlocks.back()->GetRangeOfRow(row)->to + excess;
            if (newAlignment->alignMasterTo >= (*seqs)[0]->Length())
                newAlignment->alignMasterTo = (*seqs)[0]->Length() - 1;
            newAlignment->alignSlaveFrom = update->alignSlaveFrom;
            newAlignment->alignSlaveTo = update->alignSlaveTo;
            toRealign.push_back(newAlignment);
        } else {
            ERRORMSG("error finalizing alignment");
            delete newAlignment;
        }
    }

    // actually do BLAST alignments
    BLASTer::AlignmentList newAlignments;
    SetDiagPostLevel(eDiag_Error); // ignore all but Errors while reading data
    alignmentManager->blaster->
        CreateNewPairwiseAlignmentsByBlast(NULL, toRealign, &newAlignments, false);
    SetDiagPostLevel(eDiag_Info);
    DELETE_ALL_AND_CLEAR(toRealign, BLASTer::AlignmentList);
    if (newAlignments.size() != multiple->NRows()) {
        ERRORMSG("UpdateViewer::BlastUpdate() - CreateNewPairwiseAlignmentsByBlast() failed");
        return;
    }

    // replace alignment with result
    BlockMultipleAlignment *alignmentByNeighbor = GetAlignmentByBestNeighbor(multiple, newAlignments);
    DELETE_ALL_AND_CLEAR(newAlignments, BLASTer::AlignmentList);
    if (!alignmentByNeighbor) {
        WARNINGMSG("alignment unchanged");
        return;
    }
    TRACEMSG("BLAST Neighbor succeeded - replacing alignment");
    delete update;
    *a = alignmentByNeighbor;

    // recreate alignment display with new alignment
    AlignmentList copy = GetCurrentAlignments();
    GetCurrentAlignments().clear();
    GetCurrentDisplay()->Empty();
    AddAlignments(copy);
//    (*viewerWindow)->ScrollToColumn(GetCurrentDisplay()->GetStartingColumn());
}

// comparison function: if CompareRows(a, b) == true, then row a moves up
typedef bool (*CompareUpdates)(BlockMultipleAlignment *a, BlockMultipleAlignment *b);

static bool CompareUpdatesByIdentifier(BlockMultipleAlignment *a, BlockMultipleAlignment *b)
{
    return MoleculeIdentifier::CompareIdentifiers(
        a->GetSequenceOfRow(1)->identifier, // sort by first slave row
        b->GetSequenceOfRow(1)->identifier);
}

static CompareUpdates updateComparisonFunction = NULL;

void UpdateViewer::SortByIdentifier(void)
{
    TRACEMSG("sorting updates by identifier");
    updateComparisonFunction = CompareUpdatesByIdentifier;
    SortUpdates();
}

void UpdateViewer::SortUpdates(void)
{
    if (!updateComparisonFunction) {
        ERRORMSG("UpdateViewer::SortUpdates() - must first set comparison function");
        return;
    }

    // make vector of alignments
    AlignmentList& currentAlignments = GetCurrentAlignments();
    if (currentAlignments.size() < 2) return;
    vector < BlockMultipleAlignment * > sortedVector(currentAlignments.size());
    AlignmentList::const_iterator a, ae = currentAlignments.end();
    int i = 0;
    for (a=currentAlignments.begin(); a!=ae; ++a) sortedVector[i++] = *a;

    // sort them
    stable_sort(sortedVector.begin(), sortedVector.end(), updateComparisonFunction);
    updateComparisonFunction = NULL;

    // replace window contents with sorted list
    currentAlignments.clear();
    GetCurrentDisplay()->Empty();

    AlignmentList sortedList;
    for (i=0; i<sortedVector.size(); ++i) sortedList.push_back(sortedVector[i]);
    AddAlignments(sortedList);
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: update_viewer.cpp,v $
* Revision 1000.3  2004/06/01 18:29:49  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.73
*
* Revision 1.73  2004/05/21 21:41:40  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.72  2004/05/21 17:29:51  thiessen
* allow conversion of mime to cdd data
*
* Revision 1.71  2004/03/15 18:38:52  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.70  2004/02/19 17:05:20  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.69  2004/01/17 00:17:32  thiessen
* add Biostruc and network structure load
*
* Revision 1.68  2004/01/05 17:09:16  thiessen
* abort import and warn if same accession different gi
*
* Revision 1.67  2003/11/06 18:52:32  thiessen
* make geometry violations shown on/off; allow multiple pmid entry in ref dialog
*
* Revision 1.66  2003/09/25 14:11:43  thiessen
* don't assume gi Seq-id's for imported structure's sequences
*
* Revision 1.65  2003/08/21 18:27:40  thiessen
* change header order for Mac compilation
*
* Revision 1.64  2003/07/14 18:37:08  thiessen
* change GetUngappedAlignedBlocks() param types; other syntax changes
*
* Revision 1.63  2003/04/04 14:02:22  thiessen
* more informative error messages on structure import
*
* Revision 1.62  2003/04/02 18:03:16  thiessen
* fix wxString/string confusion
*
* Revision 1.61  2003/04/02 17:49:18  thiessen
* allow pdb id's in structure import dialog
*
* Revision 1.60  2003/03/14 19:57:07  thiessen
* adjust wxStringTokenizer mode
*
* Revision 1.59  2003/03/14 19:48:51  thiessen
* allow multiple gi's in network sequence import dialog
*
* Revision 1.58  2003/03/13 18:55:17  thiessen
* tweak file load error reporting
*
* Revision 1.57  2003/02/03 19:20:08  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.56  2003/01/31 17:18:58  thiessen
* many small additions and changes...
*
* Revision 1.55  2003/01/23 20:03:05  thiessen
* add BLAST Neighbor algorithm
*
* Revision 1.54  2002/11/19 21:19:44  thiessen
* more const changes for objects; fix user vs default style bug
*
* Revision 1.53  2002/11/06 00:18:10  thiessen
* fixes for new CRef/const rules in objects
*
* Revision 1.52  2002/10/27 22:23:51  thiessen
* save structure alignments from vastalign.cgi imports
*
* Revision 1.51  2002/10/25 19:00:02  thiessen
* retrieve VAST alignment from vastalign.cgi on structure import
*
* Revision 1.50  2002/10/15 22:04:09  thiessen
* fix geom vltns bug
*
* Revision 1.49  2002/10/13 22:58:08  thiessen
* add redo ability to editor
*
* Revision 1.48  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 1.47  2002/09/26 18:31:24  thiessen
* allow simultaneous import of multiple chains from single PDB
*
* Revision 1.46  2002/09/16 21:24:58  thiessen
* add block freezing to block aligner
*
* Revision 1.45  2002/09/09 13:38:23  thiessen
* separate save and save-as
*
* Revision 1.44  2002/08/15 22:13:18  thiessen
* update for wx2.3.2+ only; add structure pick dialog; fix MultitextDialog bug
*
* Revision 1.43  2002/08/13 20:46:37  thiessen
* add global block aligner
*
* Revision 1.42  2002/07/27 12:29:52  thiessen
* fix block aligner crash
*
* Revision 1.41  2002/07/26 15:28:48  thiessen
* add Alejandro's block alignment algorithm
*
* Revision 1.40  2002/07/26 13:07:01  thiessen
* fix const object problem
*
* Revision 1.39  2002/07/01 23:17:04  thiessen
* skip warning if master choice canceled
*
* Revision 1.38  2002/06/06 01:30:02  thiessen
* fixes for linux/gcc
*
* Revision 1.37  2002/06/05 14:28:41  thiessen
* reorganize handling of window titles
*
* Revision 1.36  2002/06/04 12:48:56  thiessen
* tweaks for release ; fill out help menu
*
* Revision 1.35  2002/05/22 17:17:09  thiessen
* progress on BLAST interface ; change custom spin ctrl implementation
*
* Revision 1.34  2002/05/17 19:10:27  thiessen
* preliminary range restriction for BLAST/PSSM
*
* Revision 1.33  2002/04/26 19:01:00  thiessen
* fix display delete bug
*
* Revision 1.32  2002/03/28 14:06:02  thiessen
* preliminary BLAST/PSSM ; new CD startup style
*
* Revision 1.31  2002/03/07 19:16:04  thiessen
* don't auto-show sequence windows
*
* Revision 1.30  2002/03/04 15:52:15  thiessen
* hide sequence windows instead of destroying ; add perspective/orthographic projection choice
*
* Revision 1.29  2002/02/27 16:29:42  thiessen
* add model type flag to general mime type
*
* Revision 1.28  2002/02/22 14:24:01  thiessen
* sort sequences in reject dialog ; general identifier comparison
*
* Revision 1.27  2002/02/13 14:53:30  thiessen
* add update sort
*
* Revision 1.26  2002/02/12 17:19:22  thiessen
* first working structure import
*
* Revision 1.25  2002/02/01 00:41:21  thiessen
* tweaks
*
* Revision 1.24  2002/01/24 20:07:57  thiessen
* read multiple FAST sequences
*
* Revision 1.23  2002/01/02 02:08:29  thiessen
* go back to viewer.cgi to test http/301 forwarding
*
* Revision 1.22  2001/12/15 03:15:59  thiessen
* adjustments for slightly changed object loader Set...() API
*
* Revision 1.21  2001/12/12 14:58:10  thiessen
* change URL to viewer.fcgi
*
* Revision 1.20  2001/12/06 23:13:47  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.19  2001/11/30 14:02:05  thiessen
* progress on sequence imports to single structures
*
* Revision 1.18  2001/11/27 16:26:10  thiessen
* major update to data management system
*
* Revision 1.17  2001/10/01 16:04:25  thiessen
* make CDD annotation window non-modal; add SetWindowTitle to viewers
*
* Revision 1.16  2001/09/27 15:38:00  thiessen
* decouple sequence import and BLAST
*
* Revision 1.15  2001/09/20 19:31:30  thiessen
* fixes for SGI and wxWin 2.3.2
*
* Revision 1.14  2001/09/19 22:55:39  thiessen
* add preliminary net import and BLAST
*
* Revision 1.13  2001/09/18 03:10:46  thiessen
* add preliminary sequence import pipeline
*
* Revision 1.12  2001/06/02 17:22:46  thiessen
* fixes for GCC
*
* Revision 1.11  2001/05/17 18:34:26  thiessen
* spelling fixes; change dialogs to inherit from wxDialog
*
* Revision 1.10  2001/05/02 13:46:28  thiessen
* major revision of stuff relating to saving of updates; allow stored null-alignments
*
* Revision 1.9  2001/04/20 18:02:41  thiessen
* don't open update viewer right away
*
* Revision 1.8  2001/04/19 12:58:32  thiessen
* allow merge and delete of individual updates
*
* Revision 1.7  2001/04/05 22:55:36  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.6  2001/04/04 00:27:15  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.5  2001/03/30 03:07:34  thiessen
* add threader score calculation & sorting
*
* Revision 1.4  2001/03/22 00:33:17  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.3  2001/03/17 14:06:49  thiessen
* more workarounds for namespace/#define conflicts
*
* Revision 1.2  2001/03/13 01:25:06  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.1  2001/03/09 15:49:06  thiessen
* major changes to add initial update viewer
*
*/