sequence_viewer_window.cpp

ncbi源码

    int i;
    for (i=1; i<sequences.size(); ++i)  // assuming master is first sequence
        titleStrs[i - 1] = sequences[i]->identifier->ToString().c_str();

    vector < bool > selectedSlaves(sequences.size() - 1, false);

    wxString title = "Realign Slaves of ";
    title.Append(alignment->GetMaster()->identifier->ToString().c_str());
    ShowHideDialog dialog(
        titleStrs, &selectedSlaves,
        NULL,   // no "apply" button or callback
        true, this, -1, title, wxPoint(200, 100));
    dialog.ShowModal();

    // make list of slave rows to be realigned
    vector < int > rowOrder, realignSlaves;
    sequenceViewer->GetCurrentDisplay()->GetRowOrder(alignment, &rowOrder);
    for (i=0; i<selectedSlaves.size(); ++i)
        if (selectedSlaves[i])
            realignSlaves.push_back(rowOrder[i + 1]);

    // do the realignment
    if (realignSlaves.size() >= 0)
        sequenceViewer->alignmentManager->RealignSlaveSequences(alignment, realignSlaves);
}

#define MASTER_HAS_STRUCTURE \
    (sequenceViewer->alignmentManager != NULL && \
     sequenceViewer->alignmentManager->GetCurrentMultipleAlignment() != NULL && \
     sequenceViewer->alignmentManager->GetCurrentMultipleAlignment()->GetSequenceOfRow(0)->molecule != NULL)

void SequenceViewerWindow::OnSort(wxCommandEvent& event)
{
    switch (event.GetId()) {
        case MID_SORT_IDENT:
            if (DoProximitySort()) ProximitySortOff();
            sequenceViewer->GetCurrentDisplay()->SortRowsByIdentifier();
            break;
        case MID_SORT_THREADER:
        {
            if (DoProximitySort()) ProximitySortOff();
            GetFloatingPointDialog fpDialog(NULL,
                "Weighting of PSSM/Contact score? ([0..1], 1 = PSSM only)", "Enter PSSM Weight",
                0.0, 1.0, 0.05, (MASTER_HAS_STRUCTURE ?
                    ((prevPSSMWeight >= 0.0) ? prevPSSMWeight : 0.5) : 1.0));
            if (fpDialog.ShowModal() == wxOK) {
                double weightPSSM = prevPSSMWeight = fpDialog.GetValue();
                SetCursor(*wxHOURGLASS_CURSOR);
                sequenceViewer->GetCurrentDisplay()->SortRowsByThreadingScore(weightPSSM);
                SetCursor(wxNullCursor);
            }
            break;
        }
        case MID_FLOAT_HIGHLIGHTS:
            if (DoProximitySort()) ProximitySortOff();
            sequenceViewer->GetCurrentDisplay()->FloatHighlightsToTop();
            break;
        case MID_FLOAT_PDBS:
            if (DoProximitySort()) ProximitySortOff();
            sequenceViewer->GetCurrentDisplay()->FloatPDBRowsToTop();
            break;
        case MID_FLOAT_G_V:
            if (DoProximitySort()) ProximitySortOff();
            sequenceViewer->GetCurrentDisplay()->FloatGVToTop();
            break;
        case MID_SORT_SELF_HIT:
            if (DoProximitySort()) ProximitySortOff();
            sequenceViewer->GetCurrentDisplay()->SortRowsBySelfHit();
            break;
        case MID_PROXIMITY_SORT:
            CancelAllSpecialModesExcept(MID_PROXIMITY_SORT);
            if (DoProximitySort())
                SetCursor(*wxCROSS_CURSOR);
            else
                ProximitySortOff();
            break;
    }
}

void SequenceViewerWindow::OnScoreThreader(wxCommandEvent& event)
{
    GetFloatingPointDialog fpDialog(NULL,
        "Weighting of PSSM/Contact score? ([0..1], 1 = PSSM only)", "Enter PSSM Weight",
        0.0, 1.0, 0.05, (MASTER_HAS_STRUCTURE ?
            ((prevPSSMWeight >= 0.0) ? prevPSSMWeight : 0.5) : 1.0));
    if (fpDialog.ShowModal() == wxOK) {
        double weightPSSM = prevPSSMWeight = fpDialog.GetValue();
        SetCursor(*wxHOURGLASS_CURSOR);
        if (sequenceViewer->GetCurrentDisplay()->IsEditable())
            sequenceViewer->GetCurrentDisplay()->CalculateRowScoresWithThreader(weightPSSM);
        SetCursor(wxNullCursor);
    }
}

void SequenceViewerWindow::OnMarkBlock(wxCommandEvent& event)
{
    switch (event.GetId()) {
        case MID_MARK_BLOCK:
            CancelAllSpecialModesExcept(MID_MARK_BLOCK);
            if (DoMarkBlock())
                SetCursor(*wxCROSS_CURSOR);
            else
                MarkBlockOff();
            break;
        case MID_CLEAR_MARKS:
            if (sequenceViewer->GetCurrentAlignments().size() > 0 &&
                    sequenceViewer->GetCurrentAlignments().front()->ClearMarks())
                GlobalMessenger()->PostRedrawSequenceViewer(sequenceViewer);
            break;
    }
}

void SequenceViewerWindow::TurnOnEditor(void)
{
    if (!menuBar->IsChecked(MID_ENABLE_EDIT))
        Command(SequenceViewerWindow::MID_ENABLE_EDIT);
}

void SequenceViewerWindow::OnExport(wxCommandEvent& event)
{
    SequenceViewer::eExportType type;
    if (event.GetId() == MID_EXPORT_FASTA) type = SequenceViewer::asFASTA;
    else if (event.GetId() == MID_EXPORT_A2M) type = SequenceViewer::asFASTAa2m;
    else if (event.GetId() == MID_EXPORT_TEXT) type = SequenceViewer::asText;
    else if (event.GetId() == MID_EXPORT_HTML) type = SequenceViewer::asHTML;
    sequenceViewer->ExportAlignment(type);
}

void SequenceViewerWindow::OnSelfHit(wxCommandEvent& event)
{
    if (sequenceViewer->GetCurrentAlignments().size() > 0) {
        const BlockMultipleAlignment *multiple = sequenceViewer->GetCurrentAlignments().front();
        sequenceViewer->alignmentManager->blaster->CalculateSelfHitScores(multiple);
    }
}

void SequenceViewerWindow::OnTaxonomy(wxCommandEvent& event)
{
    if (!taxonomyTree) taxonomyTree = new TaxonomyTree();
    if (sequenceViewer->GetCurrentAlignments().size() > 0)
        taxonomyTree->ShowTreeForAlignment(this, sequenceViewer->GetCurrentAlignments().front(),
            (event.GetId() == MID_TAXONOMY_ABBR));
}

void SequenceViewerWindow::OnHighlightBlocks(wxCommandEvent& event)
{
    if (sequenceViewer->GetCurrentAlignments().size() == 0) return;
    GlobalMessenger()->RemoveAllHighlights(true);

    const BlockMultipleAlignment *multiple = sequenceViewer->GetCurrentAlignments().front();
    BlockMultipleAlignment::UngappedAlignedBlockList blocks;
    multiple->GetUngappedAlignedBlocks(&blocks);
    if (blocks.size() == 0) return;

    BlockMultipleAlignment::UngappedAlignedBlockList::const_iterator b, be = blocks.end();
    const Sequence *seq;
    const Block::Range *range;
    for (int row=0; row<multiple->NRows(); ++row) {
        seq = multiple->GetSequenceOfRow(row);
        for (b = blocks.begin(); b!=be; ++b) {
            range = (*b)->GetRangeOfRow(row);
            GlobalMessenger()->AddHighlights(seq, range->from, range->to);
        }
    }
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: sequence_viewer_window.cpp,v $
* Revision 1000.2  2004/06/01 18:29:17  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.54
*
* Revision 1.54  2004/05/21 21:41:40  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.53  2004/03/15 18:32:03  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.52  2004/02/19 17:05:10  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.51  2003/10/20 13:17:15  thiessen
* add float geometry violations sorting
*
* Revision 1.50  2003/08/23 22:42:17  thiessen
* add highlight blocks command
*
* Revision 1.49  2003/03/06 19:23:56  thiessen
* fix for compilation problem (seqfeat macros)
*
* Revision 1.48  2003/02/03 19:20:06  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.47  2003/01/14 14:15:07  thiessen
* default PSSM score = 1.0 when no structure
*
* Revision 1.46  2002/12/19 14:15:37  thiessen
* mac fixes to menus, add icon
*
* Revision 1.45  2002/12/06 17:07:15  thiessen
* remove seqrow export format; add choice of repeat handling for FASTA export; export rows in display order
*
* Revision 1.44  2002/12/02 13:37:09  thiessen
* add seqrow format export
*
* Revision 1.43  2002/10/13 22:58:08  thiessen
* add redo ability to editor
*
* Revision 1.42  2002/10/07 18:51:53  thiessen
* add abbreviated taxonomy tree
*
* Revision 1.41  2002/10/04 18:45:28  thiessen
* updates to taxonomy viewer
*
* Revision 1.40  2002/09/09 22:51:19  thiessen
* add basic taxonomy tree viewer
*
* Revision 1.39  2002/09/09 13:38:23  thiessen
* separate save and save-as
*
* Revision 1.38  2002/09/06 13:06:31  thiessen
* fix menu accelerator conflicts
*
* Revision 1.37  2002/09/05 18:38:57  thiessen
* add sort by highlights
*
* Revision 1.36  2002/09/03 13:15:58  thiessen
* add A2M export
*
* Revision 1.35  2002/08/15 22:13:17  thiessen
* update for wx2.3.2+ only; add structure pick dialog; fix MultitextDialog bug
*
* Revision 1.34  2002/06/13 14:54:07  thiessen
* add sort by self-hit
*
* Revision 1.33  2002/06/13 13:32:39  thiessen
* add self-hit calculation
*
* Revision 1.32  2002/06/05 17:25:47  thiessen
* change 'update' to 'import' in GUI
*
* Revision 1.31  2002/06/05 14:28:40  thiessen
* reorganize handling of window titles
*
* Revision 1.30  2002/05/17 19:10:27  thiessen
* preliminary range restriction for BLAST/PSSM
*
* Revision 1.29  2002/04/22 14:27:29  thiessen
* add alignment export
*
* Revision 1.28  2002/03/19 18:48:00  thiessen
* small bug fixes; remember PSSM weight
*
* Revision 1.27  2002/03/04 15:52:14  thiessen
* hide sequence windows instead of destroying ; add perspective/orthographic projection choice
*
* Revision 1.26  2002/02/13 14:53:30  thiessen
* add update sort
*
* Revision 1.25  2001/12/06 23:13:45  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.24  2001/10/20 20:16:32  thiessen
* don't use wxDefaultPosition for dialogs (win2000 problem)
*
* Revision 1.23  2001/10/08 14:18:33  thiessen
* fix show/hide dialog under wxGTK
*
* Revision 1.22  2001/10/01 16:04:24  thiessen
* make CDD annotation window non-modal; add SetWindowTitle to viewers
*
* Revision 1.21  2001/09/06 13:10:10  thiessen
* tweak show hide dialog layout
*
* Revision 1.20  2001/08/24 18:53:43  thiessen
* add filename to sequence viewer window titles
*
* Revision 1.19  2001/06/21 02:02:34  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.18  2001/06/04 14:58:00  thiessen
* add proximity sort; highlight sequence on browser launch
*
* Revision 1.17  2001/06/01 14:05:13  thiessen
* add float PDB sort
*
* Revision 1.16  2001/05/17 18:34:26  thiessen
* spelling fixes; change dialogs to inherit from wxDialog
*
* Revision 1.15  2001/05/15 23:48:37  thiessen
* minor adjustments to compile under Solaris/wxGTK
*
* Revision 1.14  2001/05/11 02:10:42  thiessen
* add better merge fail indicators; tweaks to windowing/taskbar
*
* Revision 1.13  2001/05/09 17:15:07  thiessen
* add automatic block removal upon demotion
*
* Revision 1.12  2001/05/08 21:15:44  thiessen
* add PSSM weight dialog for sorting
*
* Revision 1.11  2001/04/04 00:27:15  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.10  2001/03/30 14:43:41  thiessen
* show threader scores in status line; misc UI tweaks
*
* Revision 1.9  2001/03/30 03:07:34  thiessen
* add threader score calculation & sorting
*
* Revision 1.8  2001/03/19 15:50:40  thiessen
* add sort rows by identifier
*
* Revision 1.7  2001/03/17 14:06:49  thiessen
* more workarounds for namespace/#define conflicts
*
* Revision 1.6  2001/03/13 01:25:06  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.5  2001/03/09 15:49:05  thiessen
* major changes to add initial update viewer
*
* Revision 1.4  2001/03/06 20:20:51  thiessen
* progress towards >1 alignment in a SequenceDisplay ; misc minor fixes
*
* Revision 1.3  2001/03/02 15:32:52  thiessen
* minor fixes to save & show/hide dialogs, wx string headers
*
* Revision 1.2  2001/03/02 03:26:59  thiessen
* fix dangling pointer upon app close
*
* Revision 1.1  2001/03/01 20:15:51  thiessen
* major rearrangement of sequence viewer code into base and derived classes
*
*/