alngraphic.cpp

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            delete *iter2;
        }
        (*iter)->clear();
    }
    m_AlninfoListList.clear();
}


void CAlnGraphic::AlnGraphicDisplay(CNcbiOstream& out){
    /*Note we can't just show each alnment as we go because we will 
      need to put  all hsp's with the same id on one line*/
   
    TAlnInfoList* alninfo_list = NULL;
    bool is_first_aln = true;
    int num_align = 0;
    int master_len = 0;
    CNodeRef center; 
    CRef<CHTML_table> tbl_box;
    CHTML_tc* tbl_box_tc;

    tbl_box = new CHTML_table;  //draw a box around the graphics
    center = new CHTML_center;  //align all graphic in center
  
    tbl_box->SetCellSpacing(0)->SetCellPadding(10)->SetAttribute("border", "1");    
    tbl_box->SetAttribute("bordercolorlight", "#0000FF");
    tbl_box->SetAttribute("bordercolordark", "#0000FF");
   
    CConstRef<CSeq_id> previous_id, subid, master_id;
    for (CSeq_align_set::Tdata::const_iterator iter = m_AlnSet->Get().begin(); 
         iter != m_AlnSet->Get().end() && num_align < m_NumAlignToShow; 
         iter++, num_align++){
        if(!alninfo_list){
            alninfo_list = new TAlnInfoList; 
        }
        //get start and end seq position for master sequence
        CRange<TSeqPos>* seq_range = new CRange<TSeqPos>((*iter)->GetSeqRange(0));
        //for minus strand
        if(seq_range->GetFrom() > seq_range->GetTo()){
            seq_range->Set(seq_range->GetTo(), seq_range->GetFrom());
        }
        subid = &((*iter)->GetSeq_id(1));
        if(is_first_aln) {
            master_id =  &((*iter)->GetSeq_id(0));
            const CBioseq_Handle& handle = m_Scope->GetBioseqHandle(*master_id);
            if(!handle){
                NCBI_THROW(CException, eUnknown, "Master sequence is not found!");
            }
            master_len = handle.GetBioseqCore()->GetInst().GetLength();
            x_DisplayMaster(master_len, &(*center), &(*tbl_box), tbl_box_tc);
        }
        if(!is_first_aln && !subid->Match(*previous_id)) {
            //this aln is a new id, show result for previous id
            //save ranges for the same seqid
            m_AlninfoListList.push_back(alninfo_list);
            alninfo_list =  new TAlnInfoList;
        }
        SAlignInfo* alninfo = new SAlignInfo;
        alninfo->range = seq_range;
        //get aln info 
        x_GetAlnInfo(**iter, *subid, alninfo);
        alninfo_list->push_back(alninfo);
        is_first_aln = false;
        previous_id = subid;
    }
    
    //save last set of seqs with the same id
    if(alninfo_list){
        m_AlninfoListList.push_back(alninfo_list);
    }
    //merge range for seq with the same id
    ITERATE(TAlnInfoListList, iter, m_AlninfoListList) {
        (*iter)->sort(FromRangeAscendingSort);
        x_MergeSameSeq(**iter);  
    }

    //merge non-overlapping range list so that they can be put on 
    //the same line to compress the results
    if(m_View & eCompactView){
        double pixel_factor = ((double)kMasterPixel)/master_len;

        x_MergeDifferentSeq(pixel_factor);  
    }
    //display the graphic
    x_BuildHtmlTable(master_len, &(*tbl_box), tbl_box_tc);
    center->AppendChild(&(*tbl_box));
    center->Print(out);
    CHTML_hr hr;
    hr.Print(out);
}

//print score legend, master label
void CAlnGraphic::x_PrintTop (CNCBINode* center, CHTML_table* tbl_box, CHTML_tc*& tbl_box_tc){
    if(m_View & eMouseOverInfo){
     
        CRef<CHTML_input> textbox(new CHTML_input("text", "defline"));
        CNodeRef centered_text;       
        textbox->SetAttribute("size", 85);
        textbox->SetAttribute("value", 
                              "Mouse over to see the defline, click to show alignments");
        center->AppendChild(&(*textbox));
      
    }
   
    //score legend graph
    CRef<CHTML_table> tbl(new CHTML_table);
    CHTML_tc* tc;
    tbl->SetCellSpacing(1)->SetCellPadding(0)->SetAttribute("border", "0");
    CRef<CHTML_img> score_margin_img(new CHTML_img(m_ImagePath + kGifWhite,
                                                   kScoreMargin, m_BarHeight));
 
    tc = tbl->InsertAt(0, 0, score_margin_img);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");

    CRef<CHTML_img> score(new CHTML_img(m_ImagePath + kGifScore, kScoreLength,
                                        kScoreHeight));
    tc = tbl->InsertAt(0, 1, score);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");
  
    tbl_box_tc = tbl_box->InsertAt(0, 0, tbl);
    tbl_box_tc->SetAttribute("align", "LEFT");
    tbl_box_tc->SetAttribute("valign", "CENTER");
    //master graph
  
    tbl = new CHTML_table;
    tbl->SetCellSpacing(1)->SetCellPadding(0)->SetAttribute("border", "0");
   
    CRef<CHTML_img> master(new CHTML_img(m_ImagePath + kGifMaster,
                                         kMasterBarLength, kMasterHeight));
    
    tc = tbl->InsertAt(0, 0, master);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");
    tbl_box_tc->AppendChild(&(*tbl));
   
}

void CAlnGraphic::x_DisplayMaster(int master_len, CNCBINode* center, CHTML_table* tbl_box, CHTML_tc*& tbl_box_tc){
    x_PrintTop(&(*center), &(*tbl_box), tbl_box_tc);
 
    //scale 
    CRef<CHTML_table> tbl(new CHTML_table);
    CHTML_tc* tc;
    CRef<CHTML_img> image;
    int column = 0;
    tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute("border", "0");
    image = new CHTML_img(m_ImagePath + kGifWhite, kScoreMargin + kScaleMarginAdj, m_BarHeight);
    tc = tbl->InsertAt(0, column, image);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");
    column ++;
    //first scale 
    image = new CHTML_img(m_ImagePath + kGifScale, kScaleWidth, kScaleHeight);
    tc = tbl->InsertAt(0, column, image);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");
    column ++;

    //second scale mark and on 
    float scale_unit = ((float)(master_len))/(kNumMark - 1);
    int round_number = s_GetRoundNumber(scale_unit);
    int spacer_length;
    double pixel_factor = ((double)kMasterPixel)/master_len;

    for (int i = 1; i*round_number <= master_len; i++) {
        spacer_length = pixel_factor*round_number - kScaleWidth;
        image = new CHTML_img(m_ImagePath + kGifWhite, spacer_length, m_BarHeight);
        tc = tbl->InsertAt(0, column, image);
        tc->SetAttribute("align", "LEFT");
        tc->SetAttribute("valign", "CENTER");
        column ++;  
        image = new CHTML_img(m_ImagePath + kGifScale, kScaleWidth, kScaleHeight);
        tc = tbl->InsertAt(0, column, image);
        tc->SetAttribute("align", "LEFT");
        tc->SetAttribute("valign", "CENTER");
        column ++; 
    }
    tbl_box_tc->AppendChild(&(*tbl));

    //digits 
    //first scale digit
    string digit_str, previous_digitstr;
    int previous_digit;
    column = 0;
    image = new CHTML_img(m_ImagePath + kGifWhite, kScoreMargin, m_BarHeight);
    tbl = new CHTML_table;
    tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute("border", "0");
    tc = tbl->InsertAt(0, column, image);
    tc->SetAttribute("align", "LEFT");
    tc->SetAttribute("valign", "CENTER");
    column ++;
    image = new CHTML_img(m_ImagePath + kDigitGif[0], kDigitWidth, kDigitHeight);
    tc = tbl->InsertAt(0, column, image);
    column ++;
    previous_digit = 0;
    previous_digitstr = NStr::IntToString(0);
    
    //print scale digits from second mark and on
    for (TSeqPos i = 1; i*round_number <= master_len; i++) {
       
        digit_str = NStr::IntToString(i*round_number);        
        spacer_length = pixel_factor*round_number 
            - kDigitWidth*(previous_digitstr.size() 
                           - previous_digitstr.size()/2) 
            - kDigitWidth*(digit_str.size()/2);
        previous_digitstr = digit_str;

        image = new CHTML_img(m_ImagePath + kGifWhite, spacer_length, m_BarHeight);
        tc = tbl->InsertAt(0, column, image);
        tc->SetAttribute("align", "LEFT");
        tc->SetAttribute("valign", "CENTER");
        column ++;
        //digits
        for(size_t j = 0; j < digit_str.size(); j ++){
            string one_digit(1, digit_str[j]); 
            int digit = NStr::StringToInt(one_digit);
            image = new CHTML_img(m_ImagePath + kDigitGif[digit], kDigitWidth, 
                                  kDigitHeight);
            tc = tbl->InsertAt(0, column, image);
            tc->SetAttribute("align", "LEFT");
            tc->SetAttribute("valign", "CENTER");
            column ++;
        }  
    }

    tbl_box_tc->AppendChild(&(*tbl));
    CRef<CHTML_br> br(new CHTML_br);
    tbl_box_tc->AppendChild(br);
}

//alignment bar graph
void CAlnGraphic::x_BuildHtmlTable(int master_len, CHTML_table* tbl_box, CHTML_tc*& tbl_box_tc) {
    CHTML_tc* tc;
    double pixel_factor = ((double)kMasterPixel)/master_len;
    int count = 0;
    //print out each alignment
    ITERATE(TAlnInfoListList, iter, m_AlninfoListList){  //iter =  each line
        if(count > m_NumLine){
            break;
        }
        CRef<CHTML_table> tbl;  //each table represents one line
        CRef<CHTML_img> image;
        CConstRef<CSeq_id> previous_id, current_id;
        CRef<CHTML_a> ad;
        double temp_value ;
        int previous_end = -1;
        int front_margin = 0;
        int bar_length = 0;
        int column = 0;
        if(!(*iter)->empty()){ //table for starting white spacer
            count ++;
            tbl = new CHTML_table;
            tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute("border", "0");  
            image = new CHTML_img(m_ImagePath + kGifWhite, kScoreMargin, m_BarHeight);
            tc = tbl->InsertAt(0, column, image);
            column ++;
            tc->SetAttribute("align", "LEFT");
            tc->SetAttribute("valign", "CENTER");
        }
        ITERATE(TAlnInfoList, iter2, **iter){ //iter2 = each alignments on one line
            current_id = (*iter2)->id;
            //white space in front of this alignment
            temp_value = ((*iter2)->range->GetFrom() - (previous_end + 1))*pixel_factor;
            //rounding to int this way as round() is not portable
            front_margin = temp_value + (temp_value < 0.0 ? -0.5 : 0.5);
            //Need to add white space
            if(temp_value > 0) {
                //Need to show at least one gap
                if(front_margin < 1){
                    front_margin = 1;
                }
                //connecting the alignments with the same id
                if(m_View & eCompactView && !previous_id.Empty() 
                   && previous_id->Match(*current_id)){
                    image = new CHTML_img(m_ImagePath + kGifGrey, front_margin,
                                          kGapHeight);
                } else {
    
                    image = new CHTML_img(m_ImagePath + kGifWhite, front_margin,
                                          m_BarHeight);
                }
                tc = tbl->InsertAt(0, column, image);
                column ++;
                tc->SetAttribute("align", "LEFT");
                tc->SetAttribute("valign", "CENTER");
            }
            previous_end = (*iter2)->range->GetTo();
            previous_id = current_id;
            temp_value = (*iter2)->range->GetLength()*pixel_factor;
            bar_length = temp_value + (temp_value < 0.0 ? -0.5 : 0.5);
            image = new CHTML_img(m_ImagePath + s_GetGif((*iter2)->bits), 
                                  bar_length, m_BarHeight);
            image->SetAttribute("border", 0);
            if(m_View & eMouseOverInfo){
                image->SetAttribute("ONMouseOver", m_MouseOverFormName 
                                    + ".defline.value=" + "'" + (*iter2)->info
                                    + "'");
                image->SetAttribute("ONMOUSEOUT", m_MouseOverFormName + 
                                    ".defline.value='Mouse-over to show defline and scores, click to show alignments'");
            }
            if(m_View & eAnchorLink){
                string acc;
                (*iter2)->id->GetLabel(&acc, CSeq_id::eContent, 0);
                string seqid = (*iter2)->gi == 
                    0 ? acc : NStr::IntToString((*iter2)->gi);
                ad = new CHTML_a("#" + seqid, image);
                tc = tbl->InsertAt(0, column, ad);
            } else {
                tc = tbl->InsertAt(0, column, image);
            }
            column ++;
            tc->SetAttribute("valign", "CENTER");
            tc->SetAttribute("align", "LEFT");
    
        }
        if(!tbl.Empty()){   
            tbl_box_tc->AppendChild(&(*tbl));
            //table for space between bars
            tbl = new CHTML_table;
            image = new CHTML_img(m_ImagePath + kGifWhite, kScoreMargin 
                                  + kScoreLength, kBlankBarHeight);
            tbl->SetCellSpacing(0)->SetCellPadding(0)->SetAttribute("border", "0");  
            tbl->InsertAt(0, 0, image);
            tbl_box_tc->AppendChild(&(*tbl));
        }
    }
}

END_SCOPE(objects)
END_NCBI_SCOPE

/* 
*============================================================
*$Log: alngraphic.cpp,v $
*Revision 1000.0  2004/06/01 19:48:35  gouriano
*PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.2
*
*Revision 1.2  2004/05/21 21:42:51  gorelenk
*Added PCH ncbi_pch.hpp
*
*Revision 1.1  2004/04/30 15:40:41  jianye
*Initial checkin
*

*===========================================================
*/