sequence_viewer.cpp

ncbi源码

                    width = 10;
                os << RIGHT_JUSTIFY << setw(width) << (paragraphStart+i+1);
                ++nMarkers;
            }
        }
        if (doHTML) os << "</font>";
        os << '\n';
        if (doHTML) os << "<font color=" << rulerColor << '>';
        for (i=0; i<leftMargin; ++i) os << ' ';
        for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) {
            if ((paragraphStart+i+1)%10 == 0)
                os << '|';
            else if ((paragraphStart+i+1)%5 == 0)
                os << '*';
            else
                os << '.';
        }
        if (doHTML) os << "</font>";
        os << '\n';

        int nDisplayedResidues;

        // output each alignment row
        for (alnRow=0; alnRow<alignment->NRows(); ++alnRow) {
            row = rowOrder[alnRow]; // translate display row -> data row
            const Sequence *sequence = alignment->GetSequenceOfRow(row);

            // actual sequence characters and colors; count how many non-gaps in each row
            nDisplayedResidues = 0;
            string rowChars;
            vector < string > rowColors;
            for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) {
                if (!alignment->GetCharacterTraitsAt(firstCol+paragraphStart+i, row, justification,
                        &ch, &color, &highlighted, &drawBG, &bgCol))
                    ch = '?';
                rowChars += ch;
                wxString colorStr;
                colorStr.Printf("#%02x%02x%02x",
                    (int) (color[0]*255), (int) (color[1]*255), (int) (color[2]*255));
                rowColors.push_back(colorStr.c_str());
                if (ch != '~') ++nDisplayedResidues;
            }

            // title
            if (doHTML && uids[row].size() > 0) {
                os << "<a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
                    << "?cmd=Search&doptcmdl=GenPept&db=Protein&term="
                    << uids[row] << "\" onMouseOut=\"window.status=''\"\n"
                    << "onMouseOver=\"window.status='"
                    << ((sequence->description.size() > 0) ? sequence->description : titles[row])
                    << "';return true\">"
                    << setw(0) << titles[row] << "</a>";
            } else {
                os << setw(0) << titles[row];
            }
            os << setw(maxTitleLength+1-titles[row].size()) << ' ';

            // left start pos (output 1-numbered for humans...)
            if (doHTML) os << "<font color=" << numColor << '>';
            if (nDisplayedResidues > 0)
                os << RIGHT_JUSTIFY << setw(maxSeqLocStrLength) << (lastShownSeqLocs[row]+2) << ' ';
            else
                os << RIGHT_JUSTIFY << setw(maxSeqLocStrLength) << ' ' << ' ';

            // dump sequence, applying color changes only when necessary
            if (doHTML) {
                string prevColor;
                for (i=0; i<rowChars.size(); ++i) {
                    if (rowColors[i] != prevColor) {
                        os << "</font><font color=" << rowColors[i] << '>';
                        prevColor = rowColors[i];
                    }
                    os << rowChars[i];
                }
                os << "</font>";
            } else
                os << rowChars;

            // right end pos
            if (nDisplayedResidues > 0) {
                os << ' ';
                if (doHTML) os << "<font color=" << numColor << '>';
                os << LEFT_JUSTIFY << setw(0) << (lastShownSeqLocs[row]+nDisplayedResidues+1);
                if (doHTML) os << "</font>";
            }
            os << '\n';

            // setup to begin next parag
            lastShownSeqLocs[row] += nDisplayedResidues;
        }

        // end table row
        if (doHTML) os << "</pre></td></tr>\n";
    }

    if (doHTML)
        os << "</TABLE>\n"
            << "</BODY></HTML>\n";

    // additional sanity check on seqloc markers
    if (firstCol == 0 && lastCol == alignment->AlignmentWidth()-1) {
        for (alnRow=0; alnRow<alignment->NRows(); ++alnRow) {
            row = rowOrder[alnRow]; // translate display row -> data row
            if (lastShownSeqLocs[row] !=
                    alignment->GetSequenceOfRow(row)->Length()-1) {
                ERRORMSG("DumpText: full display - seqloc markers don't add up for row " << row);
                break;
            }
        }
        if (alnRow != alignment->NRows())
            ERRORMSG("DumpText: full display - seqloc markers don't add up correctly");
    }
}

void SequenceViewer::ExportAlignment(eExportType type)
{
    // get filename
    wxString extension, wildcard;
    if (type == asFASTA) { extension = ".fsa"; wildcard = "FASTA Files (*.fsa)|*.fsa"; }
    else if (type == asFASTAa2m) { extension = ".a2m"; wildcard = "A2M FASTA (*.a2m)|*.a2m"; }
    else if (type == asText) { extension = ".txt"; wildcard = "Text Files (*.txt)|*.txt"; }
    else if (type == asHTML) { extension = ".html"; wildcard = "HTML Files (*.html)|*.html"; }

    wxString outputFolder = wxString(GetUserDir().c_str(), GetUserDir().size() - 1); // remove trailing /
    wxString baseName, outputFile;
    wxSplitPath(GetWorkingFilename().c_str(), NULL, &baseName, NULL);
    wxFileDialog dialog(sequenceWindow, "Choose a file for alignment export:", outputFolder,
#ifdef __WXGTK__
        baseName + extension,
#else
        baseName,
#endif
        wildcard, wxSAVE | wxOVERWRITE_PROMPT);
    dialog.SetFilterIndex(0);
    if (dialog.ShowModal() == wxID_OK)
        outputFile = dialog.GetPath();

    if (outputFile.size() > 0) {

        // create output stream
        auto_ptr<CNcbiOfstream> ofs(new CNcbiOfstream(outputFile.c_str(), IOS_BASE::out));
        if (!(*ofs)) {
            ERRORMSG("Unable to open output file " << outputFile.c_str());
            return;
        }

        // map display row order to rows in BlockMultipleAlignment
        vector < int > rowOrder;
        const SequenceDisplay *display = GetCurrentDisplay();
        for (int i=0; i<display->rows.size(); ++i) {
            DisplayRowFromAlignment *alnRow = dynamic_cast<DisplayRowFromAlignment*>(display->rows[i]);
            if (alnRow) rowOrder.push_back(alnRow->row);
        }

        // actually write the alignment
        if (type == asFASTA || type == asFASTAa2m) {
            INFOMSG("exporting" << (type == asFASTAa2m ? " A2M " : " ") << "FASTA to " << outputFile.c_str());
            DumpFASTA((type == asFASTAa2m), alignmentManager->GetCurrentMultipleAlignment(),
                rowOrder, sequenceWindow->GetCurrentJustification(), *ofs);
        } else if (type == asText || type == asHTML) {
            INFOMSG("exporting " << (type == asText ? "text" : "HTML") << " to " << outputFile.c_str());
            DumpText((type == asHTML), alignmentManager->GetCurrentMultipleAlignment(),
                rowOrder, sequenceWindow->GetCurrentJustification(), *ofs);
        }
    }
}

END_SCOPE(Cn3D)


/*
* ---------------------------------------------------------------------------
* $Log: sequence_viewer.cpp,v $
* Revision 1000.4  2004/06/01 18:29:12  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.67
*
* Revision 1.67  2004/05/21 21:41:39  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.66  2004/03/15 18:32:03  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* Revision 1.65  2004/02/19 17:05:07  thiessen
* remove cn3d/ from include paths; add pragma to disable annoying msvc warning
*
* Revision 1.64  2003/11/26 20:37:54  thiessen
* prefer gi for URLs
*
* Revision 1.63  2003/11/20 22:08:50  thiessen
* update Entrez url
*
* Revision 1.62  2003/10/13 14:16:31  thiessen
* add -n option to not show alignment window
*
* Revision 1.61  2003/02/05 14:55:22  thiessen
* always load single structure even if structureLimit == 0
*
* Revision 1.60  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 1.59  2002/12/09 16:25:04  thiessen
* allow negative score threshholds
*
* Revision 1.58  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 1.57  2002/12/02 13:37:08  thiessen
* add seqrow format export
*
* Revision 1.56  2002/10/13 22:58:08  thiessen
* add redo ability to editor
*
* Revision 1.55  2002/09/09 13:38:23  thiessen
* separate save and save-as
*
* Revision 1.54  2002/09/03 13:15:58  thiessen
* add A2M export
*
* Revision 1.53  2002/08/15 22:13:16  thiessen
* update for wx2.3.2+ only; add structure pick dialog; fix MultitextDialog bug
*
* Revision 1.52  2002/06/06 01:30:02  thiessen
* fixes for linux/gcc
*
* Revision 1.51  2002/06/05 14:28:40  thiessen
* reorganize handling of window titles
*
* Revision 1.50  2002/04/22 18:01:55  thiessen
* add default extension for alignment export
*
* Revision 1.49  2002/04/22 14:27:28  thiessen
* add alignment export
*
* Revision 1.48  2002/03/07 19:16:04  thiessen
* don't auto-show sequence windows
*
* Revision 1.47  2002/03/04 15:52:14  thiessen
* hide sequence windows instead of destroying ; add perspective/orthographic projection choice
*
* Revision 1.46  2002/03/01 15:48:05  thiessen
* revert to single line per sequence
*
* Revision 1.45  2002/02/28 19:11:52  thiessen
* wrap sequences in single-structure mode
*
* Revision 1.44  2001/12/06 23:13:45  thiessen
* finish import/align new sequences into single-structure data; many small tweaks
*
* Revision 1.43  2001/11/30 14:02:05  thiessen
* progress on sequence imports to single structures
*
* Revision 1.42  2001/10/01 16:04:24  thiessen
* make CDD annotation window non-modal; add SetWindowTitle to viewers
*
* Revision 1.41  2001/04/05 22:55:36  thiessen
* change bg color handling ; show geometry violations
*
* Revision 1.40  2001/04/04 00:27:14  thiessen
* major update - add merging, threader GUI controls
*
* Revision 1.39  2001/03/30 03:07:34  thiessen
* add threader score calculation & sorting
*
* Revision 1.38  2001/03/13 01:25:06  thiessen
* working undo system for >1 alignment (e.g., update window)
*
* Revision 1.37  2001/03/09 15:49:04  thiessen
* major changes to add initial update viewer
*
* Revision 1.36  2001/03/02 15:32:52  thiessen
* minor fixes to save & show/hide dialogs, wx string headers
*
* Revision 1.35  2001/03/01 20:15:51  thiessen
* major rearrangement of sequence viewer code into base and derived classes
*
* Revision 1.34  2001/02/13 01:03:57  thiessen
* backward-compatible domain ID's in output; add ability to delete rows
*
* Revision 1.33  2001/02/08 23:01:51  thiessen
* hook up C-toolkit stuff for threading; working PSSM calculation
*
* Revision 1.32  2001/01/26 19:29:59  thiessen
* limit undo stack size ; fix memory leak
*
* Revision 1.31  2000/12/29 19:23:39  thiessen
* save row order
*
* Revision 1.30  2000/12/21 23:42:16  thiessen
* load structures from cdd's
*
* Revision 1.29  2000/12/15 15:51:47  thiessen
* show/hide system installed
*
* Revision 1.28  2000/11/30 15:49:39  thiessen
* add show/hide rows; unpack sec. struc. and domain features
*
* Revision 1.27  2000/11/17 19:48:14  thiessen
* working show/hide alignment row
*
* Revision 1.26  2000/11/12 04:02:59  thiessen
* working file save including alignment edits
*
* Revision 1.25  2000/11/11 21:15:54  thiessen
* create Seq-annot from BlockMultipleAlignment
*
* Revision 1.24  2000/11/03 01:12:44  thiessen
* fix memory problem with alignment cloning
*
* Revision 1.23  2000/11/02 16:56:02  thiessen
* working editor undo; dynamic slave transforms
*
* Revision 1.22  2000/10/19 12:40:54  thiessen
* avoid multiple sequence redraws with scroll set
*
* Revision 1.21  2000/10/17 14:35:06  thiessen
* added row shift - editor basically complete
*
* Revision 1.20  2000/10/16 20:03:07  thiessen
* working block creation
*
* Revision 1.19  2000/10/12 19:20:45  thiessen
* working block deletion
*
* Revision 1.18  2000/10/12 16:22:45  thiessen
* working block split
*
* Revision 1.17  2000/10/12 02:14:56  thiessen
* working block boundary editing
*
* Revision 1.16  2000/10/05 18:34:43  thiessen
* first working editing operation
*
* Revision 1.15  2000/10/04 17:41:30  thiessen
* change highlight color (cell background) handling
*
* Revision 1.14  2000/10/03 18:59:23  thiessen
* added row/column selection
*
* Revision 1.13  2000/10/02 23:25:22  thiessen
* working sequence identifier window in sequence viewer
*
* Revision 1.12  2000/09/20 22:22:27  thiessen
* working conservation coloring; split and center unaligned justification
*
* Revision 1.11  2000/09/15 19:24:22  thiessen
* allow repeated structures w/o different local id
*
* Revision 1.10  2000/09/14 14:55:34  thiessen
* add row reordering; misc fixes
*
* Revision 1.9  2000/09/12 01:47:38  thiessen
* fix minor but obscure bug
*
* Revision 1.8  2000/09/11 22:57:33  thiessen
* working highlighting
*
* Revision 1.7  2000/09/11 14:06:29  thiessen
* working alignment coloring
*
* Revision 1.6  2000/09/11 01:46:16  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  2000/09/07 17:37:35  thiessen
* minor fixes
*
* Revision 1.3  2000/09/03 18:46:49  thiessen
* working generalized sequence viewer
*
* Revision 1.2  2000/08/30 23:46:28  thiessen
* working alignment display
*
* Revision 1.1  2000/08/30 19:48:42  thiessen
* working sequence window
*
*/