sequence_display.cpp

ncbi源码

        if (j > 0) ++i;
        if (N > 0 && N < arrangedByProximity.size())
            arrangedByProximity[N] = sortedByScore[R++];
    }

    // recreate the row list with new order
    RowVector newRows(rows.size());
    int nNewRows = 0;
    for (row=0; row<rows.size(); ++row) {
        DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(rows[row]);
        if (alnRow)
            newRows[row] = arrangedByProximity[nNewRows++];   // put arranged rows in place
        else
            newRows[row] = rows[row];           // leave other rows in original order
    }
    if (nNewRows == arrangedByProximity.size())   // sanity check
        rows = newRows;
    else
        ERRORMSG("SequenceDisplay::ProximitySort() - internal inconsistency");

    // finally, highlight the key row and scroll approximately there
    GlobalMessenger()->RemoveAllHighlights(true);
    GlobalMessenger()->AddHighlights(seq1, 0, seq1->Length() - 1);
    (*viewerWindow)->ScrollToRow((M - 3) > 0 ? (M - 3) : 0);
    (*viewerWindow)->viewer->Save();   // make this an undoable operation
	(*viewerWindow)->UpdateDisplay(this);
    return true;
}

bool SequenceDisplay::CalculateRowScoresWithThreader(double weightPSSM)
{
    if (isEditable) {
        SequenceViewer *seqViewer = dynamic_cast<SequenceViewer*>((*viewerWindow)->viewer);
        if (seqViewer) {
            seqViewer->alignmentManager->CalculateRowScoresWithThreader(weightPSSM);
            TRACEMSG("calculated row scores");
            return true;
        }
    }
    return false;
}

void SequenceDisplay::RowsAdded(int nRowsAddedToMultiple, BlockMultipleAlignment *multiple, int alnWhere)
{
    if (nRowsAddedToMultiple <= 0) return;

    // find the last row that's from this multiple
    int r, nRows = 0, lastAlnRowIndex, displayWhere = -1;
    DisplayRowFromAlignment *lastAlnRow = NULL;
    for (r=0; r<rows.size(); ++r) {
        DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(rows[r]);
        if (alnRow && alnRow->alignment == multiple) {
            lastAlnRow = alnRow;
            lastAlnRowIndex = r;
            ++nRows;
            if (alnWhere >= 0 && alnRow->row == alnWhere)
                displayWhere = r;  // convert 'where' from alignment row to display row
        }
    }
    if (!lastAlnRow || multiple->NRows() != nRows + nRowsAddedToMultiple) {
        ERRORMSG("SequenceDisplay::RowsAdded() - inconsistent parameters");
        return;
    }
    int rowToMergeAfter = (displayWhere >= 0) ? displayWhere : lastAlnRowIndex;
    INFOMSG("adding new row after display row #" << (rowToMergeAfter+1));

    // move higher rows up to leave space for new rows
    int nRowsToMove = rows.size() - 1 - rowToMergeAfter;
    rows.resize(rows.size() + nRowsAddedToMultiple);
    for (r=0; r<nRowsToMove; ++r)
        rows[rows.size() - 1 - r] = rows[rows.size() - 1 - r - nRowsAddedToMultiple];

    // add new rows, assuming new rows to add to the display are from the last rows of the multiple
    for (r=0; r<nRowsAddedToMultiple; ++r)
        rows[rowToMergeAfter + 1 + r] = new DisplayRowFromAlignment(
            multiple->NRows() + r - nRowsAddedToMultiple, multiple);

    UpdateAfterEdit(multiple);
}

void SequenceDisplay::RowsRemoved(const vector < int >& rowsRemoved,
    const BlockMultipleAlignment *multiple)
{
    if (rowsRemoved.size() == 0) return;

    // first, construct a map of old alignment row numbers -> new row numbers; also do sanity checks
    int i;
    vector < int > alnRowNumbers(multiple->NRows() + rowsRemoved.size());
    vector < bool > removedAlnRows(alnRowNumbers.size(), false);
    for (i=0; i<alnRowNumbers.size(); ++i) alnRowNumbers[i] = i;
    for (i=0; i<rowsRemoved.size(); ++i) {
        if (rowsRemoved[i] < 1 || rowsRemoved[i] >= alnRowNumbers.size()) {
            ERRORMSG("SequenceDisplay::RowsRemoved() - can't remove row " << removedAlnRows[i]);
            return;
        } else
            removedAlnRows[rowsRemoved[i]] = true;
    }
    VectorRemoveElements(alnRowNumbers, removedAlnRows, rowsRemoved.size());
    map < int, int > oldRowToNewRow;
    for (i=0; i<alnRowNumbers.size(); ++i) oldRowToNewRow[alnRowNumbers[i]] = i;

    // then tag rows to remove from display, and update row numbers for rows not removed
    vector < bool > removeDisplayRows(rows.size(), false);
    for (i=0; i<rows.size(); ++i) {
        DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(rows[i]);
        if (alnRow && alnRow->alignment == multiple) {
            if (removedAlnRows[alnRow->row]) {
                delete rows[i];
                removeDisplayRows[i] = true;
            } else
                alnRow->row = oldRowToNewRow[alnRow->row];
        }
    }
    VectorRemoveElements(rows, removeDisplayRows, rowsRemoved.size());

    UpdateAfterEdit(multiple);
}

bool SequenceDisplay::GetDisplayCoordinates(const Molecule *molecule, int seqIndex,
    BlockMultipleAlignment::eUnalignedJustification justification, int *column, int *row)
{
    if (!molecule || seqIndex < 0) return false;

    int displayRow;
    const Sequence *seq;

    // search by Molecule*
    for (displayRow=0; displayRow<NRows(); ++displayRow) {
        seq = rows[displayRow]->GetSequence();
        if (seq && seq->molecule == molecule) {
            *row = displayRow;

            const DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(rows[displayRow]);
            if (alnRow) {
                *column = alnRow->alignment->GetAlignmentIndex(alnRow->row, seqIndex, justification);
                return (*column >= 0);
            }

            const DisplayRowFromSequence *seqRow = dynamic_cast<DisplayRowFromSequence*>(rows[displayRow]);
            if (seqRow && seqIndex >= seqRow->fromIndex && seqIndex <= seqRow->toIndex) {
                *column = seqIndex - seqRow->fromIndex;
                return true;
            }
        }
    }
    return false;
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: sequence_display.cpp,v $
* Revision 1000.3  2004/06/01 18:29:04  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.73
*
* Revision 1.73  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.72  2004/03/15 17:55:06  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.71  2004/02/19 17:05:05  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.70  2003/11/06 19:07:19  thiessen
* leave show gv's on if on already
*
* Revision 1.69  2003/10/20 13:17:15  thiessen
* add float geometry violations sorting
*
* Revision 1.68  2003/07/14 18:37:07  thiessen
* change GetUngappedAlignedBlocks() param types; other syntax changes
*
* Revision 1.67  2003/02/03 19:20:05  thiessen
* format changes: move CVS Log to bottom of file, remove std:: from .cpp files, and use new diagnostic macros
*
* Revision 1.66  2003/01/31 17:18:58  thiessen
* many small additions and changes...
*
* Revision 1.65  2003/01/29 01:41:05  thiessen
* add merge neighbor instead of merge near highlight
*
* Revision 1.64  2003/01/28 21:07:56  thiessen
* add block fit coloring algorithm; tweak row dragging; fix style bug
*
* Revision 1.63  2003/01/27 16:42:24  thiessen
* remove debugging messages
*
* Revision 1.62  2003/01/27 15:52:22  thiessen
* merge after highlighted row; show rejects; trim rejects from new reject list
*
* Revision 1.61  2003/01/23 20:03:05  thiessen
* add BLAST Neighbor algorithm
*
* Revision 1.60  2002/10/13 22:58:08  thiessen
* add redo ability to editor
*
* Revision 1.59  2002/09/16 21:24:58  thiessen
* add block freezing to block aligner
*
* Revision 1.58  2002/09/05 18:38:57  thiessen
* add sort by highlights
*
* Revision 1.57  2002/08/28 20:30:33  thiessen
* fix proximity sort bug
*
* Revision 1.56  2002/08/15 22:13:16  thiessen
* update for wx2.3.2+ only; add structure pick dialog; fix MultitextDialog bug
*
* Revision 1.55  2002/08/15 12:57:07  thiessen
* fix highlight redraw bug
*
* Revision 1.54  2002/08/13 20:46:37  thiessen
* add global block aligner
*
* Revision 1.53  2002/07/26 15:28:48  thiessen
* add Alejandro's block alignment algorithm
*
* Revision 1.52  2002/07/23 15:46:50  thiessen
* print out more BLAST info; tweak save file name
*
* Revision 1.51  2002/06/13 14:54:07  thiessen
* add sort by self-hit
*
* Revision 1.50  2002/05/17 19:10:27  thiessen
* preliminary range restriction for BLAST/PSSM
*
* Revision 1.49  2002/05/07 20:22:47  thiessen
* fix for BLAST/PSSM
*
* Revision 1.48  2002/05/02 18:40:25  thiessen
* do BLAST/PSSM for debug builds only, for testing
*
* Revision 1.47  2002/04/26 19:01:00  thiessen
* fix display delete bug
*
* Revision 1.46  2002/04/26 13:46:36  thiessen
* comment out all blast/pssm methods
*
* Revision 1.45  2002/03/28 14:06:02  thiessen
* preliminary BLAST/PSSM ; new CD startup style
*
* Revision 1.44  2002/02/28 19:11:52  thiessen
* wrap sequences in single-structure mode
*
* Revision 1.43  2002/02/22 14:24:01  thiessen
* sort sequences in reject dialog ; general identifier comparison
*
* Revision 1.42  2002/02/21 12:26:30  thiessen
* fix row delete bug ; remember threader options
*
* Revision 1.41  2002/02/19 14:59:39  thiessen
* add CDD reject and purge sequence
*
* Revision 1.40  2002/02/15 15:27:12  thiessen
* on Mac, use meta for MouseDown events
*
* Revision 1.39  2002/02/15 01:02:17  thiessen
* ctrl+click keeps edit modes
*
* Revision 1.38  2002/02/05 18:53:25  thiessen
* scroll to residue in sequence windows when selected in structure window
*
* Revision 1.37  2001/12/05 17:16:56  thiessen
* fix row insert bug
*
* Revision 1.36  2001/11/30 14:02:05  thiessen
* progress on sequence imports to single structures
*
* Revision 1.35  2001/11/27 16:26:08  thiessen
* major update to data management system
*
* Revision 1.34  2001/10/08 00:00:09  thiessen
* estimate threader N random starts; edit CDD name
*
* Revision 1.33  2001/09/27 15:37:59  thiessen
* decouple sequence import and BLAST
*
* Revision 1.32  2001/09/19 22:55:39  thiessen
* add preliminary net import and BLAST
*
* Revision 1.31  2001/08/24 14:54:50  thiessen
* make status row # order-independent :)
*
* Revision 1.30  2001/08/24 14:32:51  thiessen
* add row # to status line
*
* Revision 1.29  2001/08/08 02:25:27  thiessen
* add <memory>
*
* Revision 1.28  2001/07/10 16:39:55  thiessen
* change selection control keys; add CDD name/notes dialogs
*
* Revision 1.27  2001/06/21 02:02:34  thiessen
* major update to molecule identification and highlighting ; add toggle highlight (via alt)
*
* Revision 1.26  2001/06/07 19:05:38  thiessen
* functional (although incomplete) render settings panel ; highlight title - not sequence - upon mouse click
*
* Revision 1.25  2001/06/05 13:21:08  thiessen
* fix structure alignment list problems
*
* Revision 1.24  2001/06/04 14:58:00  thiessen
* add proximity sort; highlight sequence on browser launch
*
* Revision 1.23  2001/06/01 18:07:27  thiessen
* fix display clone bug
*
* Revision 1.22  2001/06/01 14:05:12  thiessen
* add float PDB sort
*
* Revision 1.21  2001/06/01 13:35:58  thiessen
* add aligned block number to status line
*
* Revision 1.20  2001/05/31 18:47:08  thiessen
* add preliminary style dialog; remove LIST_TYPE; add thread single and delete all; misc tweaks
*
* Revision 1.19  2001/05/22 19:09:31  thiessen
* many minor fixes to compile/run on Solaris/GTK
*
* Revision 1.18  2001/05/14 16:04:31  thiessen
* fix minor row reordering bug
*
* Revision 1.17  2001/05/11 02:10:42  thiessen
* add better merge fail indicators; tweaks to windowing/taskbar
*
* Revision 1.16  2001/05/09 17:15:06  thiessen
* add automatic block removal upon demotion
*
* Revision 1.15  2001/05/02 16:35:15  thiessen
* launch entrez web page on sequence identifier
*
* Revision 1.14  2001/04/19 12:58:32  thiessen
* allow merge and delete of individual updates
*
* Revision 1.13  2001/04/18 15:46:53  thiessen
* show description, length, and PDB numbering in status line
*
* Revision 1.12  2001/04/05 22:55:35  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.11  2001/04/04 00:27:14  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  2001/03/22 00:33:17  thiessen
* initial threading working (PSSM only); free color storage in undo stack
*
* Revision 1.7  2001/03/19 15:50:39  thiessen
* add sort rows by identifier
*
* Revision 1.6  2001/03/13 01:25:05  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.5  2001/03/09 15:49:04  thiessen
* major changes to add initial update viewer
*
* Revision 1.4  2001/03/06 20:49:14  thiessen
* fix row->alignment bug
*
* Revision 1.3  2001/03/06 20:20:50  thiessen
* progress towards >1 alignment in a SequenceDisplay ; misc minor fixes
*
* Revision 1.2  2001/03/02 15:32:52  thiessen
* minor fixes to save & show/hide dialogs, wx string headers
*
* Revision 1.1  2001/03/01 20:15:51  thiessen
* major rearrangement of sequence viewer code into base and derived classes
*
*/