Example usage for com.lowagie.text FontFactory HELVETICA

Introduction

In this page you can find the example usage for com.lowagie.text FontFactory HELVETICA_BOLD.

Prototype

String HELVETICA_BOLD

To view the source code for com.lowagie.text FontFactory HELVETICA_BOLD.

Click Source Link

Document

This is a possible value of a base 14 type 1 font

Usage

From source file:org.cyberoam.iview.charts.Chart.java

License:Open Source License

public static void generatePDFReport(OutputStream out, int reportID, String applianceID, String startDate,
        String endDate, String limit, int[] deviceIDs, HttpServletRequest request, int reportGroupID,
        LinkedHashMap paramMap) throws Exception {
    float width = 768;
    float height = 1024;
    float rec_hieght = 470;
    Rectangle pagesize = new Rectangle(768, 1024);
    Document document = new Document(pagesize, 30, 30, 30, 30);
    IndexManager indexManager = null;/*from  ww  w . jav  a 2 s .c o m*/
    JFreeChart chart = null;
    SqlReader sqlReader = new SqlReader(false);
    CyberoamLogger.sysLog.debug("reportID:" + reportID);
    CyberoamLogger.sysLog.debug("applianceID:" + applianceID);
    CyberoamLogger.sysLog.debug("startDate:" + startDate);
    CyberoamLogger.sysLog.debug("endDate:" + endDate);
    CyberoamLogger.sysLog.debug("limit:" + limit);

    try {
        //PdfWriter writer = PdfWriter.getInstance(document, response!=null ? response.getOutputStream():new FileOutputStream(pdfFileName));         
        PdfWriter writer = PdfWriter.getInstance(document, out);
        writer.setPageEvent(new Chart());
        document.addAuthor("iView");
        document.addSubject("iView Report");
        document.open();
        PdfContentByte contentByte = writer.getDirectContent();
        //ReportGroupBean reportGroupBean=ReportGroupBean.getRecordbyPrimarykey(reportGroupID);

        //ArrayList reportList=reportGroupBean.getReportIdByReportGroupId(reportGroupID);          
        ReportBean reportBean;
        ResultSetWrapper rsw = null;

        String seperator = System.getProperty("file.separator");
        //         String path=System.getProperty("catalina.home") +seperator+"webapps" +seperator+"ROOT" + seperator + "images" + seperator; 
        String path = InitServlet.contextPath + seperator + "images" + seperator + "iViewPDF.jpg";
        /*          
         *   Loading Image to add into PDF 
         */

        Image iViewImage = Image.getInstance(path);
        iViewImage.scaleAbsolute(750, 900);
        //iViewImage.scaleAbsolute(600,820);
        iViewImage.setAbsolutePosition(10, 10);

        /*Image headerImage= Image.getInstance(path+ "iViewPDFHeader.jpg");
                
        PdfPTable headerTable = new PdfPTable(2);
        PdfPCell cell = new PdfPCell(headerImage);
        headerTable.addCell(cell);         
        HeaderFooter docHeader=null;         
        //document.setHeader(new HeaderFooter(new Phrase(new Chunk())), true);
        */
        document.add(iViewImage);

        document.add(new Paragraph("\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"));

        /*
         *   Generating Table on the First Page of Report providing summary of Content 
         */
        PdfPTable frontPageTable = new PdfPTable(2);

        PdfPCell dataCell;
        String reportName = "";

        Color tableHeadBackColor = new Color(150, 174, 190);
        Color tableContentBackColor = new Color(229, 232, 237);
        Color tableBorderColor = new Color(229, 232, 237);

        dataCell = new PdfPCell(new Phrase(new Chunk("Report Profile",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 16, Font.PLAIN, new Color(255, 255, 255)))));
        dataCell.setBackgroundColor(tableHeadBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);
        if (paramMap != null) {
            reportName = paramMap.get("title").toString();
            paramMap.remove("title");
        }
        if (request != null) {
            ReportGroupBean reportGroupBean = ReportGroupBean.getRecordbyPrimarykey(reportGroupID);
            reportName = getFormattedTitle(request, reportGroupBean, true);
        }
        dataCell = new PdfPCell();

        dataCell.addElement(new Phrase(new Chunk(reportName,
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(255, 255, 255)))));
        //dataCell.addElement(new Phrase(new Chunk(ReportBean.getRecordbyPrimarykey(reportID).getTitle(), FontFactory.getFont(FontFactory.HELVETICA_BOLD, 11, Font.PLAIN, new Color(10,10,10)))));
        if (request != null) {
            dataCell.addElement(new Phrase(new Chunk(reportName + " >> ", FontFactory
                    .getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(255, 255, 255)))));
            dataCell.addElement(
                    new Phrase(new Chunk(ReportBean.getRecordbyPrimarykey(reportID).getTitle(), FontFactory
                            .getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(255, 255, 255)))));
        }
        dataCell.setBackgroundColor(tableHeadBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(new Chunk("Start Date",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(0, 0, 0)))));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(startDate));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(new Chunk("End Date",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(0, 0, 0)))));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(endDate));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(new Chunk("iView Server Time",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(0, 0, 0)))));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        java.util.Date currentDate = new java.util.Date();
        dataCell = new PdfPCell(new Phrase(currentDate.toString()));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        dataCell = new PdfPCell(new Phrase(new Chunk("Device Names (IP Address)",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 12, Font.PLAIN, new Color(0, 0, 0)))));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        DeviceBean deviceBean = null;
        String deviceNameWithIP = "";
        if (deviceIDs != null) {
            for (int i = 0; i < deviceIDs.length; i++) {
                deviceBean = DeviceBean.getRecordbyPrimarykey(deviceIDs[i]);
                if (deviceBean != null) {
                    deviceNameWithIP += " " + (i + 1) + ". " + deviceBean.getName() + " (" + deviceBean.getIp()
                            + ")\n";
                }
            }
        }
        dataCell = new PdfPCell(new Phrase("\n" + deviceNameWithIP + "\n"));
        dataCell.setBackgroundColor(tableContentBackColor);
        dataCell.setBorderColor(tableBorderColor);
        frontPageTable.addCell(dataCell);

        /*
         * Adding Table to PDF      
         */
        document.add(frontPageTable);

        /*
         * Adding Charts and Table to PDF 
         */
        document.newPage();
        reportBean = ReportBean.getRecordbyPrimarykey(reportID);
        String query = null;
        if (request == null) {
            query = PrepareQuery.getQuery(reportBean, startDate, endDate, applianceID, null, null, "0", limit,
                    paramMap);
        } else {
            PrepareQuery prepareQuery = new PrepareQuery();
            query = prepareQuery.getQuery(reportBean, request);
        }
        String searchQuery = "";
        if (request == null) {
            searchQuery = null;
        } else {
            searchQuery = request.getParameter("searchquery");
        }
        if (searchQuery != null && !"".equalsIgnoreCase(searchQuery)) {
            query = query.replaceFirst("where", "where " + searchQuery + " and");
        }
        CyberoamLogger.sysLog.debug("PDF:ReportID:" + reportBean.getReportId() + "Query->" + query);
        try {
            if (query.indexOf("select") == -1 && query.indexOf("SELECT") == -1) {
                indexManager = new IndexManager();
                rsw = indexManager.getSearch(query);
                //rsw=indexManager.getResutSetFromArrayList(searchRecord);
            } else {
                rsw = sqlReader.getInstanceResultSetWrapper(query);
            }
        } catch (org.postgresql.util.PSQLException e) {
            if (query.indexOf("5min_ts_20") > -1) {
                query = query.substring(0, query.indexOf("5min_ts_20")) + "4hr"
                        + query.substring(query.indexOf("5min_ts_20") + 16, query.length());
                CyberoamLogger.appLog.debug("New query : " + query);
                rsw = sqlReader.getInstanceResultSetWrapper(query);
            } else {
                CyberoamLogger.appLog.error("Exeption in AjaxController.java " + e, e);
            }
        } catch (Exception e) {
            CyberoamLogger.appLog.error("Exeption in AjaxController.java " + e, e);
            rsw.close();
        }
        /*
         * PDF Rendering work starts here
         */
        //if(Integer.parseInt(limit)<=10 && query.indexOf("where")>-1){
        if (reportBean.getReportFormatId() != 2) {
            chart = Chart.getChart(reportBean.getReportId(), rsw, null);
            PdfTemplate pdfTemplate = contentByte.createTemplate(width, height);
            Graphics2D graphics2D = pdfTemplate.createGraphics(width, height);
            Rectangle2D rectangle = new Rectangle2D.Double(100, 85, 540, rec_hieght);
            chart.draw(graphics2D, rectangle);
            graphics2D.dispose();
            contentByte.addTemplate(pdfTemplate, 0, 0);

            for (int j = 0; j < (int) (rec_hieght / 16) + 1; j++) {
                document.add(new Paragraph("\n"));
            }
        } else
            document.add(new Paragraph("\n"));

        // Retrieving PdfPTable
        PdfPTable pdfTable = getPdfPTable(reportBean, rsw);
        rsw.close();

        document.add(pdfTable);
        CyberoamLogger.appLog.info("*************Finishing PDF Work****************");
    } catch (Exception e) {

        CyberoamLogger.sysLog.debug("Chart.writeChartToPDF.e" + e.getMessage(), e);
    } finally {
        sqlReader.close();
    }
    document.close();
}

From source file:org.emmanet.controllers.PdfView.java

License:Apache License

@Override
protected void buildPdfDocument(Map map, Document doc, PdfWriter writer, HttpServletRequest request,
        HttpServletResponse response) throws Exception {
    if (map.get("WebRequestsDAO") != null && request.getParameter("type").equals("req")) {
        WebRequestsDAO wrd = new WebRequestsDAO();
        WebRequests wr = new WebRequests();
        wrd = (WebRequestsDAO) map.get("WebRequestsDAO");

        if (wrd.getRegister_interest() != null) {
            if (wrd.getRegister_interest().equals("1")) {
                pdfTitle = "EMMA Strain Interest Registration Form";
                pdfConditions = false;/*w ww .  j a va  2 s  .c o m*/
            } else if (wrd.getRegister_interest().equals("0")) {
                pdfTitle = "EMMA Mutant Request Form";
                pdfConditions = true;
            }
        }

        Paragraph pHead = new Paragraph(pdfTitle + "\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11));
        pHead.setAlignment(Element.ALIGN_CENTER);
        doc.add(pHead);
        doc.add(new Paragraph(pdfTitle + "\nRequest ID:" + wrd.getId_req() + "\n\n",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 20)));
        Paragraph pSubHead = new Paragraph(
                "Following data have been submitted to EMMA on " + wrd.getTimestamp(),
                FontFactory.getFont(FontFactory.HELVETICA, 11));
        pSubHead.setAlignment(Element.ALIGN_CENTER);

        doc.add(pSubHead);
        doc.add(Chunk.NEWLINE);
        // Space padding underline
        Chunk underlined = new Chunk(
                "                                                                                     "
                        + "                                                                       ");
        underlined.setUnderline(new Color(0x00, 0x00, 0x00), 0.0f, 0.2f, 16.0f, 0.0f,
                PdfContentByte.LINE_CAP_BUTT);//Black line
        doc.add(underlined);
        Font font = FontFactory.getFont(FontFactory.HELVETICA_BOLD, 11);
        // Set table cell widths equiv. to 25% and 75%
        float[] widths = { 0.25f, 0.75f };
        PdfPTable table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        PdfPCell cell = new PdfPCell(new Paragraph("Scientist\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        table.addCell("Title");
        table.addCell("" + wrd.getSci_title());
        table.addCell("Firstname");
        table.addCell("" + wrd.getSci_firstname());
        table.addCell("Surname");
        table.addCell("" + wrd.getSci_surname());
        table.addCell("E-mail");
        table.addCell("" + wrd.getSci_e_mail());
        table.addCell("Phone");
        table.addCell("" + wrd.getSci_phone());
        table.addCell("Fax");
        table.addCell("" + wrd.getSci_fax());
        PdfPCell cellShip = new PdfPCell(new Paragraph("\nShipping Contact\n\n", font));
        cellShip.setColspan(2);
        cellShip.setBorder(0);
        table.addCell(cellShip);

        table.addCell("Title");
        table.addCell("" + wrd.getCon_title());
        table.addCell("Firstname");
        table.addCell("" + wrd.getCon_firstname());
        table.addCell("Surname");
        table.addCell("" + wrd.getCon_surname());
        table.addCell("E-mail");
        table.addCell("" + wrd.getCon_e_mail());
        table.addCell("Phone");
        table.addCell("" + wrd.getCon_phone());
        table.addCell("Fax");
        table.addCell("" + wrd.getCon_fax());
        table.addCell("Institution");
        table.addCell("" + wrd.getCon_institution());
        table.addCell("Department");
        table.addCell("" + wrd.getCon_dept());
        table.addCell("Address Line 1");
        table.addCell("" + wrd.getCon_addr_1());
        table.addCell("Address Line 2");
        table.addCell("" + wrd.getCon_addr_2());
        table.addCell("County/province");
        table.addCell("" + wrd.getCon_province());
        table.addCell("Town");
        table.addCell("" + wrd.getCon_town());
        table.addCell("Postcode");
        table.addCell("" + wrd.getCon_postcode());
        table.addCell("Country");
        table.addCell("" + wrd.getCon_country());

        if (!wrd.getRegister_interest().equals("1")) {
            //webrequest is not a roi so these were set above so send them to pdf
            PdfPCell cellBill = new PdfPCell(new Paragraph("\nBilling Details\n\n", font));
            cellBill.setColspan(2);
            cellBill.setBorder(0);
            table.addCell(cellBill);

            table.addCell("VAT reference");
            table.addCell("" + wrd.getBil_vat());
            table.addCell("Purchase Order Number");
            table.addCell("" + wrd.getPO_ref());
            table.addCell("Title");
            table.addCell("" + wrd.getBil_title());
            table.addCell("Firstname");
            table.addCell("" + wrd.getBil_firstname());
            table.addCell("Surname");
            table.addCell("" + wrd.getBil_surname());
            table.addCell("E-mail");
            table.addCell("" + wrd.getBil_e_mail());
            table.addCell("Phone");
            table.addCell("" + wrd.getBil_phone());
            table.addCell("Fax");
            table.addCell("" + wrd.getBil_fax());
            table.addCell("Institution");
            table.addCell("" + wrd.getBil_institution());
            table.addCell("Department");
            table.addCell("" + wrd.getBil_dept());
            table.addCell("Address Line 1");
            table.addCell("" + wrd.getBil_addr_1());
            table.addCell("Address Line 2");
            table.addCell("" + wrd.getBil_addr_2());
            table.addCell("County/province");
            table.addCell("" + wrd.getBil_province());
            table.addCell("Town");
            table.addCell("" + wrd.getBil_town());
            table.addCell("Postcode");
            table.addCell("" + wrd.getBil_postcode());
            table.addCell("Country");
            table.addCell("" + wrd.getBil_country());

            // TODO add europhenome and wtsi_mouse_portal info
        }

        PdfPCell cellStrain = new PdfPCell(new Paragraph("\nStrain Details\n\n", font));
        cellStrain.setColspan(2);
        cellStrain.setBorder(0);

        table.addCell(cellStrain);
        table.addCell("Strain ID");
        table.addCell("" + wrd.getStrain_id());
        table.addCell("Strain name");
        //new String (wrd.getStrain_name().getBytes("UTF-8"));
        //table.addCell("" + wrd.getStrain_name());
        table.addCell("" + new String(wrd.getStrain_name().getBytes("UTF-8")));
        table.addCell("Common Name(s)");
        table.addCell("" + wrd.getCommon_name_s());

        if (wrd.getReq_material() != null) {
            PdfPCell cellMaterial = new PdfPCell(new Paragraph("\nRequested Material\n\n", font));
            cellMaterial.setColspan(2);
            cellMaterial.setBorder(0);

            table.addCell(cellMaterial);
            table.addCell("Material");
            table.addCell("" + wrd.getReq_material());
        }

        if (wrd.getLive_animals() != null) {
            table.addCell("Live Animals");
            table.addCell("Selected");
        }

        if (wrd.getFrozen_emb() != null) {
            table.addCell("Frozen Embryos");
            table.addCell("Selected");
        }

        if (wrd.getFrozen_spe() != null) {
            table.addCell("Frozen Sperm");
            table.addCell("Selected");
        }

        if (pdfConditions) {
            String text = "";
            String text1 = "";
            String text2 = "";
            String header = "";
            String header1 = "";
            String header2 = "";
            if (wrd.getApplication_type().equals("request_only")) {
                text = new StringBuilder().append(text).append(
                        "\nYou have indicated that you have read the conditions and agree to pay the transmittal fee "
                                + "plus shipping costs.")
                        .toString();

                header = new StringBuilder().append(header).append("\nStandard request\n").toString();

            } else if (!wrd.getApplication_type().equals("request_only")) {
                header1 = new StringBuilder().append(header1)
                        .append("\nApplication for Transnational Access Activity").toString();
                if (wrd.getApplication_type().equals("ta_only")) {
                    text1 = new StringBuilder().append(text1).append(
                            "\nYou have indicated that you have read the conditions and have applied for free of charge TA only. "
                                    + "In the case of the TA application being rejected the request process will be terminated.")
                            .toString();
                    header1 = new StringBuilder().append(header1).append(" (TA Option B)\n").toString();
                } else {
                    text1 = new StringBuilder().append(text1).append(
                            "\nYou have indicated that you have read the conditions and have applied for free of charge TA "
                                    + "and have agreed to pay the service charge plus shipping cost if the TA application is rejected.")
                            .toString();
                    header1 = new StringBuilder().append(header1).append(" (TA Option A)\n").toString();
                }

                header2 = new StringBuilder().append(header2).append(
                        "\n\nDescription of project (1/2 page) involving requested EMMA mouse mutant resource. "
                                + "The project description will be used by the Evaluation Committee for selection of applicants:")
                        .toString();
            }

            if (!wrd.getApplication_type().equals("request_only")) {
                //  table.addCell("" + model.get("ta_proj_desc"));
                text2 = new StringBuilder().append(text2).append("\n\n ").append(wrd.getProject_description())
                        .toString();
            }

            if (!wrd.getApplication_type().equals("request_only")) {
                //we have a ta header and text to add
                PdfPCell cellConditions1 = new PdfPCell(new Paragraph(header1, font));

                cellConditions1.setColspan(2);
                cellConditions1.setBorder(0);
                table.addCell(cellConditions1);

                PdfPCell cellConditions2 = new PdfPCell(new Paragraph(text1));

                cellConditions2.setColspan(2);
                cellConditions2.setBorder(0);
                table.addCell(cellConditions2);

                PdfPCell cellConditions3 = new PdfPCell(new Paragraph(header2, font));

                cellConditions3.setColspan(2);
                cellConditions3.setBorder(0);
                table.addCell(cellConditions3);

                PdfPCell cellConditions4 = new PdfPCell(new Paragraph(text2));

                cellConditions4.setColspan(2);
                cellConditions4.setBorder(0);
                table.addCell(cellConditions4);

            } else {

                PdfPCell cellConditions = new PdfPCell(new Paragraph(header, font));
                cellConditions.setColspan(2);
                cellConditions.setBorder(0);
                table.addCell(cellConditions);

                PdfPCell cellConditionsTxt = new PdfPCell(new Paragraph(text));
                cellConditionsTxt.setColspan(2);
                cellConditionsTxt.setBorder(0);
                table.addCell(cellConditionsTxt);
            }
        }
        doc.add(table);
    }

    if (map.get("StrainsDAO") != null && request.getParameter("type").equals("sub")) {
        StrainsDAO sd;
        StrainsManager sm = new StrainsManager();
        PeopleDAO pd;
        PeopleDAO subPDAO = new PeopleDAO();
        PeopleManager pm = new PeopleManager();
        BibliosManager bm = new BibliosManager();

        sd = (StrainsDAO) map.get("StrainsDAO");
        pd = pm.getPerson(sd.getPer_id_per_contact());//For shipping details

        if (sd.getPer_id_per_sub() != null) {
            subPDAO = pm.getPerson(sd.getPer_id_per_sub());
        }

        //RETRIEVE ASSOCIATED SUBMISSION FILES IF PRESENT

        final String submissionID = sd.getSub_id_sub();
        System.out.println("SUBMISSION ID IS::" + submissionID);

        List assocFilesADDITIONAL = new ArrayList();
        List assocFilesSANITARY = new ArrayList();
        List assocFilesCHARACTERISATION = new ArrayList();

        File dir = new File(SUBFORMUPLOAD);
        File[] files;
        files = dir.listFiles(new FilenameFilter() {
            @Override
            public boolean accept(File dir, String name) {
                //only add to list if submission id is conatined within file name (which includes path and file name)
                if (submissionID != null && name.startsWith(submissionID)) {
                    return name.toLowerCase().endsWith(".pdf");
                }
                return false;
            }
        });
        System.out.println("Files size is::" + files.length);
        if (files != null && submissionID != null) {
            for (int i = 0; i < files.length; i++) {
                System.out.println("FILEname VALUE " + i + "==" + files[i].getName());
                String file = files[i].getName();
                if (file.startsWith(submissionID) && file.contains((CharSequence) "ADDITIONAL")) {
                    assocFilesADDITIONAL.add(file);
                    System.out.println("ADDITIONAL file " + file);
                } else if (file.startsWith(submissionID) && file.contains((CharSequence) "SANITARYSTATUS")) {
                    assocFilesSANITARY.add(file);
                    System.out.println("SANITARY file " + file);
                } else {
                    assocFilesCHARACTERISATION.add(file);
                    System.out.println("CHARACTERISATION file " + file);
                }
            }
        }

        ServletContext servletContext = request.getSession().getServletContext();
        URL infrafrontierIconURL = servletContext.getResource("/images/infrafrontier/icon/footerlogo.jpg");
        logger.debug("infrafrontierIconURL = " + infrafrontierIconURL);
        URL emmaIconURL = servletContext.getResource("/images/infrafrontier/icon/emma-logo-soft.png");
        logger.debug("emmaIconURL = " + emmaIconURL);
        Image infrafrontierIcon = Image.getInstance(infrafrontierIconURL);
        Image emmaIcon = Image.getInstance(emmaIconURL);

        pdfTitle = "EMMA Mutant Submission Form";
        doc.add(new Chunk(infrafrontierIcon, 0, 0));
        doc.add(new Chunk(emmaIcon, 320, 0));
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        Paragraph paragraph = new Paragraph(pdfTitle, FontFactory.getFont(FontFactory.HELVETICA_BOLD, 20));
        paragraph.setAlignment(Element.ALIGN_CENTER);
        doc.add(paragraph);

        float[] widths = { 0.25f, 0.75f };
        PdfPTable table = new PdfPTable(widths);
        table.setWidthPercentage(100);
        PdfPCell cell;

        Paragraph pSubHead = new Paragraph(
                "\nThe Following data have been submitted to EMMA on " + sd.getArchiveDAO().getSubmitted(),
                FontFactory.getFont(FontFactory.HELVETICA, 11));
        pSubHead.setAlignment(Element.ALIGN_CENTER);

        doc.add(pSubHead);
        doc.add(Chunk.NEWLINE);
        // Space padding underline
        Chunk underlined = new Chunk(
                "                                                                                     "
                        + "                                                                       ");
        underlined.setUnderline(new Color(0x00, 0x00, 0x00), 0.0f, 0.2f, 16.0f, 0.0f,
                PdfContentByte.LINE_CAP_BUTT);//Black line
        doc.add(underlined);
        Font font = FontFactory.getFont(FontFactory.HELVETICA_BOLD, 11);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Genotype preparation - strain name [actually, synonym] and description
        // Jira request EMMA-586 - use strain.name instead of synonym (requested by Sabine)
        String strainName = sd.getName();
        pSubHead = new Paragraph(strainName + " / " + sd.getEmma_id() + "\n\n",
                FontFactory.getFont(FontFactory.HELVETICA_BOLD, 11));
        pSubHead.setAlignment(Element.ALIGN_CENTER);
        doc.add(pSubHead);

        // Submitter
        cell = new PdfPCell(new Paragraph("\nSubmitter (Steps 1 and 2 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        if (sd.getPer_id_per_sub() != null) {
            table.addCell(cell);
            table.addCell("Title");
            table.addCell("" + subPDAO.getTitle());
            table.addCell("Firstname");
            table.addCell("" + subPDAO.getFirstname());
            table.addCell("Surname");
            table.addCell("" + subPDAO.getSurname());
            table.addCell("E-mail");
            table.addCell("" + subPDAO.getEmail());
            table.addCell("Phone");
            table.addCell("" + subPDAO.getPhone());
            table.addCell("Fax");
            table.addCell("" + subPDAO.getFax());
        }
        if (subPDAO.getLabsDAO() != null) {
            table.addCell("Institution");
            table.addCell("" + subPDAO.getLabsDAO().getName());
            table.addCell("Department");
            table.addCell("" + subPDAO.getLabsDAO().getDept());
            table.addCell("Address Line 1");
            table.addCell("" + subPDAO.getLabsDAO().getAddr_line_1());
            table.addCell("Address Line 2");
            table.addCell("" + subPDAO.getLabsDAO().getAddr_line_2());
            table.addCell("County/province");
            table.addCell("" + subPDAO.getLabsDAO().getProvince());
            table.addCell("Town");
            table.addCell("" + subPDAO.getLabsDAO().getTown());
            table.addCell("Postcode");
            table.addCell("" + subPDAO.getLabsDAO().getPostcode());
            table.addCell("Country");
            table.addCell("" + subPDAO.getLabsDAO().getCountry());
        }
        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Producer
        cell = new PdfPCell(new Paragraph("Producer (Step 3 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        table.addCell("Title");
        table.addCell("" + sd.getPeopleDAO().getTitle());
        table.addCell("Firstname");
        table.addCell("" + sd.getPeopleDAO().getFirstname());
        table.addCell("Surname");
        table.addCell("" + sd.getPeopleDAO().getSurname());
        table.addCell("E-mail");
        table.addCell("" + sd.getPeopleDAO().getEmail());
        table.addCell("Phone");
        table.addCell("" + sd.getPeopleDAO().getPhone());
        table.addCell("Fax");
        table.addCell("" + sd.getPeopleDAO().getFax());
        table.addCell("Institution");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getName());
        table.addCell("Department");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getDept());
        table.addCell("Address Line 1");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getAddr_line_1());
        table.addCell("Address Line 2");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getAddr_line_2());
        table.addCell("County/province");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getProvince());
        table.addCell("Town");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getTown());
        table.addCell("Postcode");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getPostcode());
        table.addCell("Country");
        table.addCell("" + sd.getPeopleDAO().getLabsDAO().getCountry());
        Integer id_ilar = Utils.tryParseInt(sd.getPeopleDAO().getId_ilar());
        if ((id_ilar != null) && (id_ilar.intValue() > 0)) { // If there is a valid ILAR, display it.
            table.addCell("ILAR");
            table.addCell(sd.getPeopleDAO().getIlarDAO().getLabcode());
        }

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Shipper
        cell = new PdfPCell(new Paragraph("\nShipper (Step 4 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        table.addCell("Title");
        table.addCell("" + pd.getTitle());
        table.addCell("Firstname");
        table.addCell("" + pd.getFirstname());
        table.addCell("Surname");
        table.addCell("" + pd.getSurname());
        table.addCell("E-mail");
        table.addCell("" + pd.getEmail());
        table.addCell("Phone");
        table.addCell("" + pd.getPhone());
        table.addCell("Fax");
        table.addCell("" + pd.getFax());
        table.addCell("Institution");
        table.addCell("" + pd.getLabsDAO().getName());
        table.addCell("Department");
        table.addCell("" + pd.getLabsDAO().getDept());
        table.addCell("Address Line 1");
        table.addCell("" + pd.getLabsDAO().getAddr_line_1());
        table.addCell("Address Line 2");
        table.addCell("" + pd.getLabsDAO().getAddr_line_2());
        table.addCell("County/province");
        table.addCell("" + pd.getLabsDAO().getProvince());
        table.addCell("Town");
        table.addCell("" + pd.getLabsDAO().getTown());
        table.addCell("Postcode");
        table.addCell("" + pd.getLabsDAO().getPostcode());
        table.addCell("Country");
        table.addCell("" + pd.getLabsDAO().getCountry());

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        String origBgName = sd.getBackgroundDAO().getName();

        // Genotype
        cell = new PdfPCell(new Paragraph("\nGenotype (Step 5 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        table.addCell("Strain Name");
        table.addCell("" + strainName);

        table.addCell("Genetic description");
        table.addCell("" + cleanNULLS(sd.getCharact_gen(), false));

        table.addCell("Current genetic background");
        table.addCell("" + cleanNULLS(origBgName, false));

        table.addCell("Number of generations backcrossed");
        table.addCell("" + cleanNULLS(sd.getGeneration(), false));

        table.addCell("Number of generations sib-mated");
        table.addCell("" + cleanNULLS(sd.getSibmatings(), false));

        table.addCell("Breeding history");
        table.addCell("" + sd.getMaintenance());

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Genotype - Mutations
        cell = new PdfPCell(new Paragraph("Mutation(s)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        Set sMutations = sd.getMutationsStrainsDAO();

        StringBuffer sDom = new StringBuffer();
        for (Iterator it = sMutations.iterator(); it.hasNext();) {
            MutationsStrainsDAO mutDAO = (MutationsStrainsDAO) it.next();
            if (mutDAO.getMutationsDAO().getDominance() != null) {
                sDom = new StringBuffer(sDom).append(mutDAO.getMutationsDAO().getDominance().toString());
            }

            cell = new PdfPCell(
                    new Paragraph("Type: " + cleanNULLS(mutDAO.getMutationsDAO().getMain_type(), false),
                            FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(
                    new Paragraph("Subtype: " + cleanNULLS(mutDAO.getMutationsDAO().getSub_type(), false),
                            FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "Affected gene: " + cleanNULLS(
                            mutDAO.getMutationsDAO().getAllelesDAO().getGenesDAO().getName(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "MGI of affected gene: " + cleanNULLS(
                            mutDAO.getMutationsDAO().getAllelesDAO().getGenesDAO().getMgi_ref(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "Affected allele: " + cleanNULLS(mutDAO.getMutationsDAO().getAllelesDAO().getName(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "MGI of affected allele: "
                            + cleanNULLS(mutDAO.getMutationsDAO().getAllelesDAO().getMgi_ref(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "Affected chromosome: " + cleanNULLS(
                            mutDAO.getMutationsDAO().getAllelesDAO().getGenesDAO().getChromosome(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "Dominance pattern: " + cleanNULLS(mutDAO.getMutationsDAO().getDominance(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            if (mutDAO.getMutationsDAO().getBackgroundDAO() != null) {
                cell = new PdfPCell(new Paragraph(
                        "Original genetic background: "
                                + cleanNULLS(mutDAO.getMutationsDAO().getBackgroundDAO().getName(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
            } else {
                cell = new PdfPCell(new Paragraph("\n"));
            }
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            if (mutDAO.getMutationsDAO().getCh_ano_name() != null) {
                cell = new PdfPCell(new Paragraph(
                        "Chromosomal anomaly name: "
                                + cleanNULLS(mutDAO.getMutationsDAO().getCh_ano_name(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
            } else {
                cell = new PdfPCell(new Paragraph("\n"));
            }
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            if (mutDAO.getMutationsDAO().getCh_ano_desc() != null) {
                cell = new PdfPCell(new Paragraph(
                        "Chromosomal anomaly description: "
                                + cleanNULLS(mutDAO.getMutationsDAO().getCh_ano_desc(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
            } else {
                cell = new PdfPCell(new Paragraph("\n"));
            }
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph(
                    "ES cell line used: " + cleanNULLS(mutDAO.getMutationsDAO().getTm_esline(), false) + "\n\n",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);
        }

        /* END MUTATIONS*/

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        cell = new PdfPCell(new Paragraph("\nONE mutant strain is defined by its specific set of mutation(s) "
                + "and its specific genetic background. Therefore strains with the same set of mutation(s) but different "
                + "backgrounds do require DISTINCT submission forms (i.e) ONE form for each background\n\n",
                font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Phenotype
        cell = new PdfPCell(new Paragraph("\nPhenotype (Step 6 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("Phenotypic description of homozygous mice\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getPheno_text(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("\nPhenotypic description of heterozygous mice\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getPheno_text_hetero(), true)));
        cell.setColspan(2);
        table.addCell(cell);
        doc.add(table);

        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // References
        List bibliosStrains = bm.bibliosStrains(sd.getId_str());
        String acceptedString = ((!bibliosStrains.isEmpty()) && (bibliosStrains.size() > 0) ? "Yes/Accepted"
                : "No/Not known");
        cell = new PdfPCell(new Paragraph("\nReferences (Step 7 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("Has this mouse mutant strain been published or accepted for publication? "
                        + acceptedString + "\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        for (Iterator it = bibliosStrains.iterator(); it.hasNext();) {
            BibliosStrainsDAO bsdao = (BibliosStrainsDAO) it.next();

            cell = new PdfPCell(
                    new Paragraph("Short description\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            if (bsdao.getBibliosDAO().getNotes() != null) {
                cell = new PdfPCell(new Paragraph("" + cleanNULLS(bsdao.getBibliosDAO().getNotes(), true)));
            } else {
                cell = new PdfPCell(new Paragraph("\n"));
            }
            cell.setColspan(2);
            table.addCell(cell);

            String pubmedId = (bsdao.getBibliosDAO().getPubmed_id() == null ? ""
                    : bsdao.getBibliosDAO().getPubmed_id());
            cell = new PdfPCell(
                    new Paragraph("\nPubMed ID: " + pubmedId, FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph("Title: " + bsdao.getBibliosDAO().getTitle(),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            String authors = "Authors: " + bsdao.getBibliosDAO().getAuthor1();
            if (bsdao.getBibliosDAO().getAuthor2() != null)
                authors = authors + ", " + bsdao.getBibliosDAO().getAuthor2();
            cell = new PdfPCell(new Paragraph(authors, FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph("Journal/Book: " + bsdao.getBibliosDAO().getJournal(),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph("Year: " + cleanNULLS(bsdao.getBibliosDAO().getYear(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph("Volume: " + bsdao.getBibliosDAO().getVolume(),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            cell = new PdfPCell(new Paragraph("Pages: " + bsdao.getBibliosDAO().getPages() + "\n\n",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);
        }
        doc.add(table);

        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Characterization
        cell = new PdfPCell(new Paragraph("\nCharacterization (Step 8 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        cell = new PdfPCell(new Paragraph(
                "By genotyping \n" + "(e.g. sequence of PCR primers and PCR settings,Southern probes and "
                        + "hybridization protocol)\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getChar_genotyping(), true)));
        } else {
            cell = new PdfPCell(new Paragraph("\n"));
        }
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("\nBy phenotyping (e.g. coat colour)\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(
                    new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getChar_phenotyping(), true)));
        } else {
            cell = new PdfPCell(new Paragraph("\n"));
        }
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("\nBy any other means that are not genotyping or phenotyping\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getChar_other(), true)));
        } else {
            cell = new PdfPCell(new Paragraph(""));
        }
        cell.setColspan(2);
        table.addCell(cell);

        //assocFilesCHARACTERISATION

        StringBuffer additionalCharacFiles = new StringBuffer("");
        for (Iterator it = assocFilesCHARACTERISATION.iterator(); it.hasNext();) {
            String fileName = it.next().toString();
            additionalCharacFiles = new StringBuffer(additionalCharacFiles).append("\n        ")
                    .append(fileName);
        }

        cell = new PdfPCell(
                new Paragraph("\nAdditional files uploaded:", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("" + additionalCharacFiles, FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        doc.add(table);

        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);

        // Breeding
        cell = new PdfPCell(new Paragraph("\nBreeding (Step 9 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("Are homozygous mice viable? " + cleanNULLS(sd.getMutant_viable(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        cell = new PdfPCell(
                new Paragraph("Are homozygous mice fertile? " + cleanNULLS(sd.getMutant_fertile(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Are heterozygous/hemizygous mice fertile? " + cleanNULLS(sd.getHethemi_fertile(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Are homozygous matings required? " + cleanNULLS(sd.getRequire_homozygous() + "\n\n", false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph(
                    "" + cleanNULLS(sd.getResiduesDAO().getHomozygous_matings_required_text(), true)));
        } else {
            cell = new PdfPCell(new Paragraph(""));
        }
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "\nAverage age of reproductive maturity (weeks): "
                        + cleanNULLS(sd.getResiduesDAO().getReproductive_maturity_age(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Average age of reproductive decline (months): "
                        + cleanNULLS(sd.getResiduesDAO().getReproductive_decline_age(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Average length of gestation (days): "
                        + cleanNULLS(sd.getResiduesDAO().getGestation_length(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Average number of pups at birth: " + cleanNULLS(sd.getResiduesDAO().getPups_at_birth(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Average number of pups surviving to weaning: "
                        + cleanNULLS(sd.getResiduesDAO().getPups_at_weaning(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Recommended weaning age (days): " + cleanNULLS(sd.getResiduesDAO().getWeaning_age(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Average number of litters in lifetime: "
                        + cleanNULLS(sd.getResiduesDAO().getLitters_in_lifetime(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Breeding performance: " + cleanNULLS(sd.getResiduesDAO().getBreeding_performance(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("Husbandry requirements:\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(
                    new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getAnimal_husbandry() + "\n", true)));
        } else {
            cell = new PdfPCell(new Paragraph(""));
        }
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("\nAre mice immunicompromised? " + cleanNULLS(sd.getImmunocompromised(), false),
                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("\nSanitary status:\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(
                    new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getCurrent_sanitary_status(), true)));
        } else {
            cell = new PdfPCell(new Paragraph("\n"));
        }
        cell.setColspan(2);

        table.addCell(cell);
        cell = new PdfPCell(
                new Paragraph("\nAnimal welfare:\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getWelfare(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("\nRemedial actions:\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getRemedial_actions(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("\nPlease note that under certain circumstances "
                + "(e.g.: long-term cryopreservation by sperm freezing) the strain's original genotype will not "
                + "always be available for future reconstitution of live colonies. Therefore, the original genetic "
                + "background cannot be guaranteed.\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        //assocFilesSANITARY

        StringBuffer additionalSanitaryFiles = new StringBuffer("");
        for (Iterator it = assocFilesSANITARY.iterator(); it.hasNext();) {
            String fileName = it.next().toString();
            additionalSanitaryFiles = new StringBuffer(additionalSanitaryFiles).append("\n        ")
                    .append(fileName);
        }

        cell = new PdfPCell(
                new Paragraph("\nAdditional files uploaded:", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("" + additionalSanitaryFiles, FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        doc.add(table);

        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);
        table.setWidthPercentage(100);
        doc.add(table);

        // Research value
        cell = new PdfPCell(new Paragraph("\n\n\nResearch value (Step 10 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "Does this strain model a human condition or disease? "
                        + cleanNULLS(sd.getHuman_model(), false),
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        Strains_OmimManager strainsOmimManager = new Strains_OmimManager();
        List<Strains_OmimDAO> strains_omimDAOList = strainsOmimManager.findById_Strains(sd.getId_str());

        if (!strains_omimDAOList.isEmpty()) {
            cell = new PdfPCell(
                    new Paragraph("\nOMIM IDs:\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);

            for (Strains_OmimDAO strainsOmimDAO : strains_omimDAOList) {
                cell = new PdfPCell(
                        new Paragraph("" + cleanNULLS(strainsOmimDAO.getOmimDAO().getOmim(), true)));
                cell.setColspan(2);
                table.addCell(cell);
            }
        }

        cell = new PdfPCell(new Paragraph(
                "\n\nIf OMIM IDs are not available, please describe the human condition or disease:\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getHuman_model_desc(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        // Prep for Research areas
        Set cs = sd.getCategoriesStrainsDAO();
        String otherCategory = "";
        StringBuffer categories = new StringBuffer();
        for (Iterator it = cs.iterator(); it.hasNext();) {
            CategoriesStrainsDAO cd = (CategoriesStrainsDAO) it.next();
            if (cd.getCategoriesDAO().getCurated().compareTo("Y") == 0)
                categories.append("\n        ").append(cd.getCategoriesDAO().getMain_cat());
            else
                otherCategory = cd.getCategoriesDAO().getMain_cat();
        }

        cell = new PdfPCell(new Paragraph("\n\nResearch areas:\n        " + categories + "\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        Set sRTools = sd.getRtoolsDAO();
        StringBuffer rtools = new StringBuffer("");
        System.out.println("size of rtoolsdao set is :- " + sRTools.size());
        for (Iterator it = sRTools.iterator(); it.hasNext();) {
            RToolsDAO rtd = (RToolsDAO) it.next();
            rtools = new StringBuffer(rtools).append("\n        ")
                    .append(rtd.getCvrtoolsDAO().getDescription());
            //System.out.println("Rtools set iterator value is: " + rtools);
        }

        if ((otherCategory != null) && (otherCategory.trim().length() > 0)) {
            cell = new PdfPCell(new Paragraph("\n\nOther Research areas:\n\n        " + otherCategory + "\n",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
            cell.setColspan(2);
            cell.setBorder(0);
            table.addCell(cell);
        }
        cell = new PdfPCell(new Paragraph("\n\nResearch tools:\n" + rtools,
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        /* END OF Research value */

        doc.add(table);
        doc.add(Chunk.NEWLINE);
        doc.add(Chunk.NEWLINE);
        doc.add(underlined);
        table = new PdfPTable(widths);

        table.setWidthPercentage(100);

        /* Additional information */

        cell = new PdfPCell(new Paragraph("\n\nAdditional information (Step 11 of 11)\n\n", font));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph(
                    "How many requests for this strain have you received in the last 6 months? "
                            + cleanNULLS(sd.getResiduesDAO().getNumber_of_requests(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        } else {
            cell = new PdfPCell(
                    new Paragraph("How many requests for this strain have you received in the last 6 months? ",
                            FontFactory.getFont(FontFactory.HELVETICA, 11)));
        }

        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph(
                    "Is this strain being deposited with any other institution or biotechnology company? "
                            + cleanNULLS(sd.getResiduesDAO().getDeposited_elsewhere() + "\n\n", false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        } else {
            cell = new PdfPCell(new Paragraph(
                    "Is this strain being deposited with any other institution or biotechnology company? ",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        }
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            if (sd.getResiduesDAO().getIpr_description() != null) {
                cell = new PdfPCell(
                        new Paragraph(cleanNULLS(sd.getResiduesDAO().getDeposited_elsewhere_text(), true)));
                cell.setColspan(2);
                table.addCell(cell);
            }
        }

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph(
                    "\n\nAre other laboratories producing similar strains? "
                            + cleanNULLS(sd.getResiduesDAO().getOther_labos(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        } else {
            cell = new PdfPCell(new Paragraph("\n\nAre other laboratories producing similar strains? ",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        }
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        String IPRights = "";
        if (sd.getResiduesDAO() != null) {
            IPRights = sd.getResiduesDAO().getIp_rights();
        } else {
            //do nothing
        }
        cell = new PdfPCell(new Paragraph(
                "Are there any intellectual property rights or patented technologies linked to this strain? "
                        + IPRights + "\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        if (sd.getResiduesDAO() != null) {
            if (sd.getResiduesDAO().getIpr_description() != null) {
                cell = new PdfPCell(
                        new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getIpr_description(), true)));
                cell.setColspan(2);
                table.addCell(cell);
            }
        }

        cell = new PdfPCell(new Paragraph(
                "\nIs the producer the exclusive owner of this strain? "
                        + cleanNULLS(sd.getExclusive_owner(), false) + "\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph("" + cleanNULLS(sd.getEx_owner_description(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        cell = new PdfPCell(new Paragraph(
                "\nDo you have permission from all owners to deposit this strain in the EMMA repository? "
                        + cleanNULLS(sd.getResiduesDAO().getOwner_permission(), false) + "\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("" + cleanNULLS(sd.getResiduesDAO().getOwner_permission_text(), true)));
        cell.setColspan(2);
        table.addCell(cell);

        String delayedRelease = "";
        if (sd.getResiduesDAO() != null) {
            delayedRelease = cleanNULLS(sd.getResiduesDAO().getDelayed_wanted(), false);
        }
        if (delayedRelease != null && delayedRelease.startsWith("yes")) {
            delayedRelease = new StringBuffer(delayedRelease).append(" (briefly explain below)\n\n").toString();
        }

        cell = new PdfPCell(new Paragraph("\nDo you require delayed release for your strain? " + delayedRelease,
                FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);
        if (delayedRelease != null && delayedRelease.startsWith("yes")) {
            cell = new PdfPCell(new Paragraph("" + sd.getResiduesDAO().getDelayed_description()));
            cell.setColspan(2);
            table.addCell(cell);
        }

        if (sd.getResiduesDAO() != null) {
            cell = new PdfPCell(new Paragraph("\nHow many mice of breeding age could you provide and when?"
                    + "\n\nEstimated date of shipping:\n\nMonth: "
                    + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_month(), false) + "\n\nYear: "
                    + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_year(), false) + "\n\nNumber of males: "
                    + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_males(), false)
                    + "\n\nNumber of females: "
                    + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_females(), false),
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        } else {
            cell = new PdfPCell(new Paragraph(
                    "\n\nHow many mice of breeding age could you provide and when?"
                            + "\n\nEstimated date of shipping:\n\nMonth: " + "\n\nYear: "
                            + "\n\nNumber of males: " + "\n\nNumber of females: ",
                    FontFactory.getFont(FontFactory.HELVETICA, 11)));
        }
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        //assocFilesADDITIONAL

        StringBuffer additionalFiles = new StringBuffer("");
        for (Iterator it = assocFilesADDITIONAL.iterator(); it.hasNext();) {
            String fileName = it.next().toString();
            additionalFiles = new StringBuffer(additionalFiles).append("\n        ").append(fileName);
        }

        cell = new PdfPCell(
                new Paragraph("\nAdditional files uploaded:", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        cell = new PdfPCell(
                new Paragraph("" + additionalFiles, FontFactory.getFont(FontFactory.HELVETICA, 11)));
        cell.setColspan(2);
        cell.setBorder(0);
        table.addCell(cell);

        //            cell = new PdfPCell(new Paragraph("\n\nWere any of the following techniques used in the construction of this mutant?\n\n", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);
        //
        //            if (sd.getResiduesDAO() != null) {
        //                cell = new PdfPCell(new Paragraph("Cre recombinase-loxP technology? " + cleanNULLS(sd.getResiduesDAO().getCrelox(), false), FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            } else {
        //                cell = new PdfPCell(new Paragraph("Cre recombinase-loxP technology? ", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            }
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);
        //
        //            if (sd.getResiduesDAO() != null) {
        //                cell = new PdfPCell(new Paragraph("FLP recombinase technology? " + cleanNULLS(sd.getResiduesDAO().getFlp(), false), FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            } else {
        //                cell = new PdfPCell(new Paragraph("FLP recombinase technology? ", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            }
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);
        //
        //            if (sd.getResiduesDAO() != null) {
        //                cell = new PdfPCell(new Paragraph("TET-system technology? " + cleanNULLS(sd.getResiduesDAO().getTet(), false), FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            } else {
        //                cell = new PdfPCell(new Paragraph("TET-system technology? ", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            }
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);
        //
        //
        //            if (sd.getResiduesDAO() != null) {
        //                cell = new PdfPCell(new Paragraph("\n\nIf the submission request is accepted when could you provide "
        //                        + "10 females and 6 males (5-12 weeks old)?"
        //                        + "\nEstimated date of shipping\nMonth: " + cleanNULLS(sd.getResiduesDAO().getWhen_mice_month(), false) + "\nYear: " + cleanNULLS(sd.getResiduesDAO().getWhen_mice_year(), false), FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            } else {
        //                cell = new PdfPCell(new Paragraph("\n\nIf the submission request is accepted when could you provide "
        //                        + "10 females and 6 males (5-12 weeks old)?"
        //                        + "\nEstimated date of shipping\nMonth: \nYear:", FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            }
        //
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);

        //            if (sd.getResiduesDAO() != null) {
        //                cell = new PdfPCell(new Paragraph("\n\nIf unable to provide this number of mice how many could you provide and when?"
        //                        + "\nEstimated date of shipping\nMonth: " + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_month(), false)
        //                        + "\nYear: " + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_year(), false)
        //                        + "\nNumber of males: " + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_males(), false)
        //                        + "\nNumber of females: " + cleanNULLS(sd.getResiduesDAO().getWhen_how_many_females(), false),
        //                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            } else {
        //                cell = new PdfPCell(new Paragraph("\n\nIf unable to provide this number of mice how many could you provide and when?"
        //                        + "\nEstimated date of shipping\nMonth: "
        //                        + "\nYear: "
        //                        + "\nNumber of males: "
        //                        + "\nNumber of females: ",
        //                        FontFactory.getFont(FontFactory.HELVETICA, 11)));
        //            }
        //            cell.setColspan(2);
        //            cell.setBorder(0);
        //            table.addCell(cell);

        /* END OF ADDITIONAL INFORMATION */
        doc.add(table);

        doc.add(Chunk.NEWLINE);
        // Space padding underline
        underlined = new Chunk(
                "                                                                                     "
                        + "                                                                       ");
        underlined.setUnderline(new Color(0x00, 0x00, 0x00), 0.0f, 0.2f, 16.0f, 0.0f,
                PdfContentByte.LINE_CAP_BUTT);//Black line
        doc.add(underlined);

        pSubHead = new Paragraph("The terms and conditions have been accepted.\n\n",
                FontFactory.getFont(FontFactory.HELVETICA, 11));
        pSubHead.setAlignment(Element.ALIGN_CENTER);
        doc.add(pSubHead);
    }
}

From source file:org.emmanet.controllers.RequestFormController.java