cav_alndisplay.cpp

来自「ncbi源码」· C++ 代码 · 共 1,340 行 · 第 1/4 页

                        if (color != prevColor) {
                            os << "</font><font color=" << color << '>';
                            prevColor = color;
                        }
                        condensedColumns[paragraphStart+i]->DumpRow(os, row);
                    }
                    os << "</font>";
                } else {
                    for (i=0; i<nCondensedColumns; ++i) {
                        condensedColumns[paragraphStart+i]->DumpRow(os, row);
                    }
                }

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

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

            // print alignment annotation characters
            else {
                // skip number
                os << RIGHT_JUSTIFY << setw(maxSeqLocStrLength) << ' ' << ' ';

                // do characters
                for (i=0; i<nCondensedColumns; ++i)
                    condensedColumns[paragraphStart+i]->DumpRow(os, row);

                os << (doHTML ? "</font>\n" : "\n");
            }
        }

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

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

    // add feature legend
    if (nFeatures > 0) {
        os << (doHTML ? "<BR>\n" : "\n");
        for (featIndex=0; featIndex<nFeatures; ++featIndex)
            if (alnFeatures[featIndex].description)
                os << alnFeatures[featIndex].shortName << ": " << alnFeatures[featIndex].description
                   << (doHTML ? "<BR>\n" : "\n");
    }

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

    // additional sanity check on seqloc markers
    if (firstCol == 0 && lastCol == GetWidth()-1) {
        for (alnRow=0; alnRow<GetNRows(); ++alnRow) {
            if (lastShownSeqLocs[alnRow] !=
                    indexAlnLocToSeqLocRows[alnRow]->sequence->sequenceString.size()-1) {
                ERR_POST(Error << "full display - seqloc markers don't add up");
                break;
            }
        }
        if (alnRow == GetNRows())
            ERR_POST(Info << "full display - seqloc markers add up correctly");
    }

    return CAV_SUCCESS;
}

int AlignmentDisplay::DumpText(CNcbiOstream& os, unsigned int options,
    int firstCol, int lastCol, int nColumns, double conservationThreshhold,
    const char *titleHTML, int nFeatures, const AlignmentFeature *alnFeatures) const
{
    bool doHTML = ((options & CAV_HTML) > 0), doHTMLHeader = ((options & CAV_HTML_HEADER) > 0);

    if (firstCol < 0 || lastCol >= GetWidth() || firstCol > lastCol || nColumns < 1) {
        ERR_POST(Error << "AlignmentDisplay::DumpText() - nonsensical display region parameters");
        return CAV_ERROR_BAD_PARAMS;
    }

    // how many rows in the display, including annotations?
    int nDisplayRows = GetNRows();
    if (!alnFeatures) nFeatures = 0;
    if (nFeatures > 0) nDisplayRows += nFeatures;

    // set up the titles and uids, figure out how much space any seqLoc string will take
    vector < string > titles(nDisplayRows), uids(doHTML ? GetNRows() : 0);
    int row, featIndex, alnRow, maxTitleLength = 0, maxSeqLocStrLength = 0, leftMargin, decimalLength;
    bool isAlnRow;
    for (row=0; row<nDisplayRows; ++row) {
        if (options & CAV_ANNOT_BOTTOM) {
            alnRow = row;
            featIndex = row - GetNRows();
        } else {
            featIndex = row;
            alnRow = row - nFeatures;
        }
        isAlnRow = (alnRow >= 0 && alnRow < GetNRows());

        // title
        titles[row] = isAlnRow ?
            indexAlnLocToSeqLocRows[alnRow]->sequence->GetTitle() :
            string(alnFeatures[featIndex].shortName);
        if (titles[row].size() > maxTitleLength) maxTitleLength = titles[row].size();
        if (isAlnRow) {
            decimalLength = ((int) log10((double)
                indexAlnLocToSeqLocRows[alnRow]->sequence->sequenceString.size())) + 1;
            if (decimalLength > maxSeqLocStrLength) maxSeqLocStrLength = decimalLength;
        }

        // uid for link to entrez
        if (doHTML && isAlnRow) {
            if (indexAlnLocToSeqLocRows[alnRow]->sequence->pdbID.size() > 0) {
                if (indexAlnLocToSeqLocRows[alnRow]->sequence->pdbID != "query" &&
                    indexAlnLocToSeqLocRows[alnRow]->sequence->pdbID != "consensus") {
                    uids[alnRow] = indexAlnLocToSeqLocRows[alnRow]->sequence->pdbID;
                    if (indexAlnLocToSeqLocRows[alnRow]->sequence->pdbChain != ' ')
                        uids[alnRow] += (char) indexAlnLocToSeqLocRows[alnRow]->sequence->pdbChain;
                }
            } else if (indexAlnLocToSeqLocRows[alnRow]->sequence->gi != Sequence::NOT_SET) {
                CNcbiOstrstream uidoss;
                uidoss << indexAlnLocToSeqLocRows[alnRow]->sequence->gi << '\0';
                uids[alnRow] = uidoss.str();
                delete uidoss.str();
            } else if (indexAlnLocToSeqLocRows[alnRow]->sequence->accession.size() > 0) {
                uids[alnRow] = indexAlnLocToSeqLocRows[alnRow]->sequence->accession;
            }
        }
    }
    leftMargin = maxTitleLength + maxSeqLocStrLength + 2;

    // need to keep track of first, last seqLocs for each row in each paragraph;
    // find seqLoc of first residue >= firstCol
    vector < int > lastShownSeqLocs(GetNRows());
    int alnLoc;
    for (alnRow=0; alnRow<GetNRows(); ++alnRow) {
        lastShownSeqLocs[alnRow] = -1;
        for (alnLoc=0; alnLoc<firstCol; ++alnLoc)
            if (!IsGap(textRows[alnRow]->GetCharAt(alnLoc))) lastShownSeqLocs[alnRow]++;
    }

    // header
    if (doHTML && doHTMLHeader)
        os << "<HTML><TITLE>" << (titleHTML ? titleHTML : "CDDAlignView HTML Display") <<
            "</TITLE><BODY BGCOLOR=" << bgColor << ">\n";;

    // do make look-up location index for each feature
    vector < vector < bool > > annotLocsByIndex;
    int i, masterIndex;
    if (nFeatures > 0) {
        annotLocsByIndex.resize(nFeatures);
        for (featIndex=0; featIndex<nFeatures; ++featIndex) {
            annotLocsByIndex[featIndex].resize(indexAlnLocToSeqLocRows[0]->sequence->Length(), false);
            for (i=0; i<alnFeatures[featIndex].nLocations; ++i) {
                masterIndex = alnFeatures[featIndex].locations[i];
                if (masterIndex >= 0 && masterIndex < indexAlnLocToSeqLocRows[0]->sequence->Length())
                    annotLocsByIndex[featIndex][masterIndex] = true;
            }
        }
    }

    // split alignment up into "paragraphs", each with nColumns
    if (doHTML) os << "<TABLE>\n";
    int paragraphStart, nParags = 0;
    for (paragraphStart=0; (firstCol+paragraphStart)<=lastCol; paragraphStart+=nColumns, ++nParags) {

        // start table row
        if (doHTML)
            os << "<tr><td bgcolor=" << blockBGColors[nParags % nBlockColors] << "><pre>\n";
        else
            if (paragraphStart > 0) os << '\n';

        // do ruler
        int nMarkers = 0, width;
        if (doHTML) os << "<font color=" << rulerColor << '>';
        for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) {
            if ((paragraphStart+i+1)%10 == 0) {
                if (nMarkers == 0)
                    width = leftMargin + i + 1;
                else
                    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';

        // get column colors
        vector < string > columnColors;
        if (doHTML)
            for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i)
                columnColors.resize(columnColors.size()+1,
                    GetColumnColor(firstCol+paragraphStart+i, conservationThreshhold));

        // output each alignment row
        int nDisplayedResidues;
        for (row=0; row<nDisplayRows; ++row) {
            if (options & CAV_ANNOT_BOTTOM) {
                alnRow = row;
                featIndex = row - GetNRows();
            } else {
                featIndex = row;
                alnRow = row - nFeatures;
            }
            isAlnRow = (alnRow >= 0 && alnRow < GetNRows());

            // actual sequence characters; count how many non-gaps in each row
            nDisplayedResidues = 0;
            string rowChars;
            if (isAlnRow) {
                for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) {
                    char ch = textRows[alnRow]->GetCharAt(firstCol+paragraphStart+i);
                    rowChars += ch;
                    if (!IsGap(ch)) ++nDisplayedResidues;
                }
            }

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

            if (isAlnRow) {
                // left start pos (output 1-numbered for humans...)
                if (doHTML) os << "<font color=" << numColor << '>';
                if (nDisplayedResidues > 0)
                    os << RIGHT_JUSTIFY << setw(maxSeqLocStrLength) << (lastShownSeqLocs[alnRow]+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 (columnColors[i] != prevColor) {
                            os << "</font><font color=" << columnColors[i] << '>';
                            prevColor = columnColors[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[alnRow]+nDisplayedResidues+1);
                    if (doHTML) os << "</font>";
                }
                os << '\n';

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

            // print alignment annotation characters
            else {
                // skip number
                os << RIGHT_JUSTIFY << setw(maxSeqLocStrLength) << ' ' << ' ';

                // do characters, but only allow annot where master residue is aligned to something
                for (i=0; i<nColumns && (firstCol+paragraphStart+i)<=lastCol; ++i) {
                    if (IsAligned(textRows[0]->GetCharAt(firstCol+paragraphStart+i))) {
                        masterIndex = indexAlnLocToSeqLocRows[0]->GetSeqLocAt(firstCol+paragraphStart+i);
                        os << ((masterIndex >= 0 && annotLocsByIndex[featIndex][masterIndex])
                            ? alnFeatures[featIndex].featChar : ' ');
                    } else
                        os << ' ';
                }

                os << (doHTML ? "</font>\n" : "\n");
            }
        }

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

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

    // add feature legend
    if (nFeatures > 0) {
        os << (doHTML ? "<BR>\n" : "\n");
        for (featIndex=0; featIndex<nFeatures; ++featIndex)
            if (alnFeatures[featIndex].description)
                os << alnFeatures[featIndex].shortName << ": " << alnFeatures[featIndex].description
                   << (doHTML ? "<BR>\n" : "\n");
    }

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

    // additional sanity check on seqloc markers
    if (firstCol == 0 && lastCol == GetWidth()-1) {
        for (alnRow=0; alnRow<GetNRows(); ++alnRow) {
            if (lastShownSeqLocs[alnRow] !=
                    indexAlnLocToSeqLocRows[alnRow]->sequence->sequenceString.size()-1) {
                ERR_POST(Error << "full display - seqloc markers don't add up");
                break;
            }
        }
        if (alnRow == GetNRows())
            ERR_POST(Info << "full display - seqloc markers add up correctly");
    }

    return CAV_SUCCESS;
}