Example usage for com.lowagie.text Table setWidths

List of usage examples for com.lowagie.text Table setWidths

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Introduction

In this page you can find the example usage for com.lowagie.text Table setWidths.

Prototype

public void setWidths(int[] widths) throws DocumentException

Source Link

Document

Sets the widths of the different columns (percentages).

Usage

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the XFR Spectra table/*from ww w.ja  v a 2s. c  o m*/
 * 
 * @param document
 * @throws Exception
 */
private void setXfrSpectraTable(Document document) throws Exception {
    if (slv == null) {// if session is null, no sense to display XFRSpectra
        return;
    }
    document.add(new Paragraph("XRF Spectra:", FONT_TITLE));
    document.add(new Paragraph(" "));
    if (xfeList == null || xfeList.isEmpty()) {
        document.add(new Paragraph("There is no XRF spectra in this report", FONT_DOC));
    } else {
        int NumColumnsXRF = 6;
        Table tableXRF = new Table(NumColumnsXRF);
        int headerwidthsSessionXRF[] = { 15, 15, 15, 15, 15, 25 }; // percentage
        int headerwidthsMXPressXRF[] = { 16, 16, 15, 15, 15, 8, 17 }; // percentage
        tableXRF.setWidths(headerwidthsSessionXRF);
        // Column crystalClass added only for IFX proposal in case of
        // MXPress experiment
        if (proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX)) {
            tableXRF = new Table(NumColumnsXRF + 1);
            tableXRF.setWidths(headerwidthsMXPressXRF);
        }

        tableXRF.setWidth(100); // percentage
        tableXRF.setPadding(3);
        tableXRF.setCellsFitPage(true);
        tableXRF.getDefaultCell().setBorderWidth(1);
        tableXRF.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

        // XRF Spectra Header

        tableXRF.getDefaultCell().setGrayFill(GREY_FILL_HEADER);
        tableXRF.addCell(new Paragraph("Energy\n(keV)", FONT_DOC_BOLD));
        tableXRF.addCell(new Paragraph("Exposure Time\n(s)", FONT_DOC_BOLD));
        tableXRF.addCell(new Paragraph("Beam size Hor.\n(" + Constants.MICRO + "m)", FONT_DOC_BOLD));
        tableXRF.addCell(new Paragraph("Beam size Ver.\n(" + Constants.MICRO + "m)", FONT_DOC_BOLD));
        tableXRF.addCell(new Paragraph("Transm. Factor\n(%)", FONT_DOC_BOLD));
        // Column crystalClass only for IFX proposal in case of MXPress
        // experiment
        if (proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX))
            tableXRF.addCell(new Paragraph("Crystal class", FONT_DOC_BOLD));
        tableXRF.addCell(new Paragraph("Comments", FONT_DOC_BOLD));
        tableXRF.getDefaultCell().setGrayFill(GREY_FILL_DATA);
        tableXRF.getDefaultCell().setBorderWidth(1);

        // XRF Spectra Rows
        Iterator<XFEFluorescenceSpectrum3VO> itES = xfeList.iterator();
        while (itES.hasNext()) {
            XFEFluorescenceSpectrum3VO col = itES.next();
            if (col.getEnergy() != null)
                tableXRF.addCell(new Paragraph(col.getEnergy().toString(), FONT_DOC));
            else
                tableXRF.addCell("");

            if (col.getExposureTime() != null)
                tableXRF.addCell(new Paragraph(col.getExposureTime().toString(), FONT_DOC));
            else
                tableXRF.addCell("");

            if (col.getBeamSizeHorizontal() != null)
                tableXRF.addCell(new Paragraph(col.getBeamSizeHorizontal().toString(), FONT_DOC));
            else
                tableXRF.addCell("");

            if (col.getBeamSizeVertical() != null)
                tableXRF.addCell(new Paragraph(col.getBeamSizeVertical().toString(), FONT_DOC));
            else
                tableXRF.addCell("");

            if (col.getBeamTransmission() != null)
                tableXRF.addCell(new Paragraph(col.getBeamTransmission().toString(), FONT_DOC));
            else
                tableXRF.addCell("");

            if (proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX)) {
                // if (col.getCrystalClass()!= null) tableXRF.addCell(new
                // Paragraph(col.getCrystalClass().toString(), new
                // Font(Font.HELVETICA, 8)));
                // else tableXRF.addCell("");
                if (col.getCrystalClass() != null) {
                    int idCC = getCrystalClassIndex(listOfCrystalClass,
                            col.getCrystalClass().trim().toUpperCase());
                    if (idCC == -1) {
                        tableXRF.addCell(new Paragraph(col.getCrystalClass().toString(), FONT_DOC));
                    } else
                        tableXRF.addCell(
                                new Paragraph(listOfCrystalClass.get(idCC).getCrystalClassName(), FONT_DOC));
                } else
                    tableXRF.addCell("");
            }

            tableXRF.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT);
            if (col.getComments() != null)
                tableXRF.addCell(new Paragraph(col.getComments().toString(), FONT_DOC));
            else
                tableXRF.addCell("");
            tableXRF.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

        }
        document.add(tableXRF);
    }
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the summary - IFX proposal//from  www.jav  a 2  s .c  o m
 * 
 * @param document
 * @throws Exception
 */
private void setSummary(Document document) throws Exception {
    if (proposalCode.toLowerCase().equals(Constants.PROPOSAL_CODE_FX) && name == null) {
        document.add(new Paragraph(" "));
        document.add(new Paragraph("Summary:", FONT_TITLE));
        document.add(new Paragraph(" "));

        int NumColumnsCC = 2;
        Table tableCC = new Table(NumColumnsCC);
        int headerwidthsCC[] = { 30, 15 }; // percentage
        tableCC.setWidths(headerwidthsCC);

        tableCC.setWidth(50); // percentage
        tableCC.setPadding(3);
        tableCC.setCellsFitPage(true);
        tableCC.getDefaultCell().setBorderWidth(1);
        tableCC.getDefaultCell().setGrayFill(GREY_FILL_HEADER);
        tableCC.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);
        tableCC.addCell(new Paragraph("Crystal class", FONT_DOC_BOLD));
        tableCC.addCell(new Paragraph("Number of crystals", FONT_DOC_BOLD));
        tableCC.getDefaultCell().setGrayFill(GREY_FILL_DATA);

        int nbCC = listOfCrystalClass.size();
        for (int cc = 0; cc < nbCC; cc++) {
            if (listOfNbCrystalPerClass.get(cc) > 0) {
                tableCC.addCell(new Paragraph(listOfCrystalClass.get(cc).getCrystalClassName() + " ("
                        + listOfCrystalClass.get(cc).getCrystalClassCode() + ")", FONT_DOC));
                tableCC.addCell(new Paragraph(listOfNbCrystalPerClass.get(cc).toString(), FONT_DOC));
            }
            LOG.debug("classe " + listOfCrystalClass.get(cc).getCrystalClassCode() + ": "
                    + listOfNbCrystalPerClass.get(cc).toString());
        }

        document.add(tableCC);

        // total
        // int nbPuckScreen = nbCrystal3;
        // int nbTotal = nbCrystal1 + nbCrystal2 + nbCrystalT;
        int nbPuckScreen = listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "PS"));
        // nbTotal = C+CR+T+SC+SCR
        int nbTotal = listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "C"))
                + listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "SC"))
                + listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "T"))
                + listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "CR"))
                + listOfNbCrystalPerClass.get(getCrystalClassIndex(listOfCrystalClass, "SCR"));
        document.add(new Paragraph(" "));
        document.add(new Paragraph("Total number of tests: " + new String(new Integer(nbTotal).toString()),
                FONT_DOC));
        document.add(new Paragraph("Nb of puck screens: " + new String(new Integer(nbPuckScreen).toString()),
                FONT_DOC));
        document.add(new Paragraph(
                "Total number of samples: " + new String(new Integer(nbTotal + (nbPuckScreen * 10)).toString()),
                FONT_DOC));
    }
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set a table for a sessionDataObject//w  ww .j  a  v  a  2  s .c  om
 * 
 * @param document
 * @param sessionDataObject
 * @param mRequest
 */
private void setDetailSessionObjectTable(Document document, SessionDataObjectInformation sessionDataObject,
        HttpServletRequest mRequest) {
    try {
        int nbCol = 6;
        int nbRows = 5;
        List<Param> listParam = sessionDataObject.getListParameters();
        int idParam = 0;
        int nbParam = listParam.size();
        nbRows = Math.max(nbRows, nbParam);
        boolean secondGraph = sessionDataObject.getGraph2Path() != null
                && !sessionDataObject.getGraph2Path().isEmpty();
        if (secondGraph)
            nbCol += 1;

        Table table = new Table(nbCol);

        int l = 0;

        int[] headersWidth = new int[nbCol];

        headersWidth[l++] = 10; // def
        headersWidth[l++] = 6; // parameters title
        headersWidth[l++] = 6; // parameters value
        headersWidth[l++] = 12; // Thumbnail
        headersWidth[l++] = 12; // Snapshot
        headersWidth[l++] = 22; // Graph
        if (secondGraph)
            headersWidth[l++] = 22; // Graph2
        table.setWidths(headersWidth);

        table.setWidth(100); // percentage
        table.setPadding(1);
        table.setCellsFitPage(true);
        table.setTableFitsPage(true);
        table.setBorderWidth(1);
        table.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);
        // no header
        // first Row
        // firstCell: def : date
        SimpleDateFormat formatter = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
        String collectTime = formatter.format(sessionDataObject.getDataTime());
        Cell c = getCellValue(collectTime);
        c.setBorderWidthBottom(0);
        table.addCell(c);
        // second Cell param
        setCellParam(table, listParam, idParam++, 1);
        // third Cell : thumbnail
        Cell cellThumbnail = getCellImage(sessionDataObject.getImageThumbnailPath());
        cellThumbnail.setRowspan(nbRows);
        cellThumbnail.setBorderWidth(0);
        table.addCell(cellThumbnail);
        // 4 Cell : snapshot
        Cell cellSnapshot = getCellImage(sessionDataObject.getCrystalSnapshotPath());
        cellSnapshot.setRowspan(nbRows);
        cellSnapshot.setBorderWidth(0);
        table.addCell(cellSnapshot);
        // 5 Cell : graph
        Cell cellGraph = getCellGraph(sessionDataObject);
        cellGraph.setRowspan(nbRows);
        cellGraph.setBorderWidth(0);
        table.addCell(cellGraph);
        // 6 Cell : graph2
        if (secondGraph) {
            Cell cellGraph2 = getCellImage(sessionDataObject.getGraph2Path());
            cellGraph2.setRowspan(nbRows);
            cellGraph2.setBorderWidth(0);
            table.addCell(cellGraph2);
        }

        // second row
        Cell c2 = getCellValue(sessionDataObject.getImagePrefix() + " " + sessionDataObject.getRunNumber());
        c2.setBorderWidth(0);
        table.addCell(c2);
        // param2
        setCellParam(table, listParam, idParam++, 1);

        // third row
        Cell c3 = getCellValue(sessionDataObject.getExperimentType());
        c3.setBorderWidth(0);
        table.addCell(c3);
        // param3
        setCellParam(table, listParam, idParam++, 1);

        // 4 row
        Cell c4 = getCellValue(sessionDataObject.getSampleNameProtein());
        c4.setBorderWidth(0);
        table.addCell(c4);
        // param4
        setCellParam(table, listParam, idParam++, 1);

        // 5 row
        Cell c5 = new Cell();
        c5.setHorizontalAlignment(Element.ALIGN_LEFT);
        c5.add(new Paragraph(sessionDataObject.getComments(), FONT_DOC_ITALIC));
        c5.setBorderWidth(0);
        c5.setRowspan(nbRows - 4);
        table.addCell(c5);
        // param4
        setCellParam(table, listParam, idParam++, 1);

        for (int i = 5; i < nbRows; i++) {
            setCellParam(table, listParam, idParam++, 1);
        }

        // results
        // workflow result status
        if (sessionDataObject.isWorkflow()) {
            Cell resultCell = getWorkflowResult(sessionDataObject.getWorkflow(), mRequest);
            resultCell.setHorizontalAlignment(Element.ALIGN_LEFT);
            resultCell.setColspan(nbCol);
            table.addCell(resultCell);
        }
        // collect OSC
        if ((sessionDataObject.isDataCollection()
                && !sessionDataObject.getDataCollection().getDataCollectionGroupVO().getExperimentType()
                        .equals(Constants.EXPERIMENT_TYPE_CHARACTERIZATION))) {
            DataCollectionExporter dcExporter = new DataCollectionExporter(df2, df3, proposalCode,
                    proposalNumber, mRequest);
            DataCollection3VO dataCollection = sessionDataObject.getDataCollection();
            DataCollectionInformation dcInfo = dcExporter.getDataCollectionInformation(dataCollection,
                    getSampleRankingVO(dataCollection.getDataCollectionId()),
                    getAutoProcRankingVO(dataCollection.getDataCollectionId()));
            Cell resultCell = getAutoProcResultStatus(dcInfo);
            resultCell.setColspan(nbCol);
            resultCell.setHorizontalAlignment(Element.ALIGN_LEFT);
            table.addCell(resultCell);
            document.add(table);
            document.add(new Paragraph(" ", VERY_SMALL_FONT));

            setAutoProcResultsTable(document, dcInfo);
        } else if (sessionDataObject.isWorkflow() && sessionDataObject.getWorkflow().isMXPressEOIA()) { // MXPRESS
            // wf
            DataCollectionExporter dcExporter = new DataCollectionExporter(df2, df3, proposalCode,
                    proposalNumber, mRequest);
            DataCollection3VO dataCollection = sessionDataObject.getListDataCollection().get(0);
            DataCollectionInformation dcInfo = dcExporter.getDataCollectionInformation(dataCollection,
                    getSampleRankingVO(dataCollection.getDataCollectionId()),
                    getAutoProcRankingVO(dataCollection.getDataCollectionId()));
            Cell resultCell = getAutoProcResultStatus(dcInfo);
            resultCell.setHorizontalAlignment(Element.ALIGN_LEFT);
            resultCell.setColspan(nbCol);
            table.addCell(resultCell);

            document.add(table);
            document.add(new Paragraph(" ", VERY_SMALL_FONT));

            setAutoProcResultsTable(document, dcInfo);
        } else if ((sessionDataObject.isDataCollection()
                && sessionDataObject.getDataCollection().getDataCollectionGroupVO().getExperimentType()
                        .equals(Constants.EXPERIMENT_TYPE_CHARACTERIZATION))) { // Characterization
            DataCollectionExporter dcExporter = new DataCollectionExporter(df2, df3, proposalCode,
                    proposalNumber, mRequest);
            DataCollection3VO dataCollection = sessionDataObject.getDataCollection();
            DataCollectionInformation dcInfo = dcExporter.getDataCollectionInformation(dataCollection,
                    getSampleRankingVO(dataCollection.getDataCollectionId()),
                    getAutoProcRankingVO(dataCollection.getDataCollectionId()));
            Cell resultCell = getCharacterizationResultStatus(dcInfo, mRequest);
            resultCell.setColspan(nbCol);
            resultCell.setHorizontalAlignment(Element.ALIGN_LEFT);
            table.addCell(resultCell);
            document.add(table);
            document.add(new Paragraph(" ", VERY_SMALL_FONT));

            setStrategyTable2(document, dcInfo);
        } else {
            List<Param> listResults = sessionDataObject.getListResults();
            if (listResults != null) {
                int nbResults = listResults.size();
                for (int j = 0; j < nbResults; j++) {
                    setCellParam(table, listResults, j, 2);
                    Cell eCell = getEmptyCell(nbCol - 3);
                    eCell.setBorderWidth(0);
                    table.addCell(eCell);
                }
            }
            document.add(table);
            document.add(new Paragraph(" ", FONT_SPACE));
        }

    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the EDNA Table/*from  w  w  w.j av a2s  .  com*/
 * 
 * @param document
 * @param dcInfo
 * @throws Exception
 */
private void setEDNATable(Document document, DataCollectionInformation dcInfo) throws Exception {
    if (dcInfo.getSpacegroup() != "") {
        int noCol = 4;
        Table tableEDNA = new Table(noCol);
        int headerEDNA[] = { 10, 10, 10, 10 }; // percentage
        tableEDNA.setWidths(headerEDNA);
        tableEDNA.setWidth(70); // percentage
        tableEDNA.setPadding(3);
        tableEDNA.setCellsFitPage(true);
        tableEDNA.setTableFitsPage(true);
        // tableEDNA.getDefaultCell().setBorderWidth(1);
        tableEDNA.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);
        // EDNA Header
        tableEDNA.getDefaultCell().setBackgroundColor(BLUE_COLOR);
        tableEDNA.addCell(new Paragraph("Space Group", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Unit Cell", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Mosaicity\n(" + Constants.ANGSTROM + ")", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Ranking Resolution\n(" + Constants.ANGSTROM + ")", FONT_DOC_BOLD));
        tableEDNA.getDefaultCell().setBorderWidth(1);
        tableEDNA.getDefaultCell().setBackgroundColor(WHITE_COLOR);
        // EDNA data
        String unitCell = dcInfo.getCellA() + " (" + dcInfo.getCellAlpha() + ")\n" + dcInfo.getCellB() + " ("
                + dcInfo.getCellBeta() + ")\n" + dcInfo.getCellC() + " (" + dcInfo.getCellGamma() + ")";

        tableEDNA.addCell(new Paragraph(dcInfo.getSpacegroup(), FONT_DOC));
        tableEDNA.addCell(new Paragraph(unitCell, FONT_DOC));
        tableEDNA.addCell(new Paragraph(dcInfo.getMosaicity(), FONT_DOC));
        tableEDNA.addCell(new Paragraph(dcInfo.getResObserved(), FONT_DOC));
        //

        document.add(tableEDNA);
        document.add(new Paragraph(" ", VERY_SMALL_FONT));
    }
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

private void setEDNATable2(Document document, DataCollectionInformation dcInfo) throws Exception {
    if (dcInfo.getSpacegroup() != "") {
        int noCol = 4;
        Table tableEDNA = new Table(noCol);
        int headerEDNA[] = { 10, 10, 10, 10 }; // percentage
        tableEDNA.setWidths(headerEDNA);
        tableEDNA.setWidth(100); // percentage
        tableEDNA.setPadding(3);//from   w  w  w . j av  a 2 s.  co m
        tableEDNA.setCellsFitPage(true);
        tableEDNA.setTableFitsPage(true);
        // tableEDNA.getDefaultCell().setBorderWidth(1);
        tableEDNA.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);
        // EDNA Header
        tableEDNA.getDefaultCell().setGrayFill(GREY_FILL_HEADER);
        tableEDNA.addCell(new Paragraph("Space Group", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Unit Cell (a, b, c, alpha, beta, gamma)", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Mosaicity (" + Constants.DEGREE + ")", FONT_DOC_BOLD));
        tableEDNA.addCell(new Paragraph("Ranking Resolution (" + Constants.ANGSTROM + ")", FONT_DOC_BOLD));
        tableEDNA.getDefaultCell().setBorderWidth(1);
        tableEDNA.getDefaultCell().setBackgroundColor(WHITE_COLOR);
        // EDNA data
        String unitCell = dcInfo.getCellA() + ", " + dcInfo.getCellB() + ", " + dcInfo.getCellC() + "\n"
                + dcInfo.getCellAlpha() + ", " + dcInfo.getCellBeta() + ", " + dcInfo.getCellGamma();
        tableEDNA.addCell(new Paragraph(dcInfo.getSpacegroup(), FONT_DOC));
        tableEDNA.addCell(new Paragraph(unitCell, FONT_DOC));
        tableEDNA.addCell(new Paragraph(dcInfo.getMosaicity(), FONT_DOC));
        tableEDNA.addCell(new Paragraph(dcInfo.getResObserved(), FONT_DOC));
        //

        document.add(tableEDNA);
        document.add(new Paragraph(" ", VERY_SMALL_FONT));
    }
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the strategy table and wedge & subwedge strategy tables
 * /*  ww w .  j  a v  a2s  .c o  m*/
 * @param document
 * @param dcInfo
 * @throws Exception
 */
private void setStrategyTable(Document document, DataCollectionInformation dcInfo) throws Exception {
    // ------------------------------------------- Strategy Wedge
    // ------------------------------------------------
    List<StrategyWedgeInformation> strategyWedgeInformationList = dcInfo.getListStrategyWedgeInformation();
    for (Iterator<StrategyWedgeInformation> i = strategyWedgeInformationList.iterator(); i.hasNext();) {
        document.add(new Paragraph(" ", VERY_SMALL_FONT));
        StrategyWedgeInformation swi = i.next();
        Table strategyWedgeTable = new Table(10);
        int headerStrategyWedge[] = { 8, 10, 10, 10, 10, 10, 10, 10, 10, 20 }; // percentage
        strategyWedgeTable.setWidths(headerStrategyWedge);
        strategyWedgeTable.setWidth(100);
        strategyWedgeTable.setCellsFitPage(true);
        strategyWedgeTable.setTableFitsPage(true);
        strategyWedgeTable.setPadding(0);
        strategyWedgeTable.getDefaultCell().setBorderWidth(0);
        strategyWedgeTable.setBorderWidth(0);
        strategyWedgeTable.getDefaultCell().setBackgroundColor(WEDGE_COLOR);

        strategyWedgeTable.addCell(new Paragraph("Wedge number", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Resolution\n(" + Constants.ANGSTROM + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Completeness", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Multiplicity", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Total dose", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Number of Images", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Phi\n(" + Constants.DEGREE + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Kappa\n(" + Constants.DEGREE + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Wavelength", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Comments", FONT_DOC_BOLD));

        strategyWedgeTable.getDefaultCell().setBackgroundColor(WHITE_COLOR);
        // rows
        strategyWedgeTable.addCell(new Paragraph(swi.getWedgeNumber(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getResolution(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getCompleteness(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getMultiplicity(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getDoseTotal(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getNumberOfImages(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getPhi(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getKappa(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getWavelength(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getComments(), FONT_DOC));

        document.add(strategyWedgeTable);

        // --- strategy sub wedge
        if (swi.getListStrategySubWedgeInformation().size() > 0) {
            document.add(new Paragraph(" ", VERY_SMALL_FONT));

            Table strategySubWedgeTable = new Table(12);
            int headerStrategySubWedge[] = { 8, 15, 10, 10, 10, 10, 10, 10, 10, 8, 8, 20 }; // percentage
            strategySubWedgeTable.setWidths(headerStrategySubWedge);
            strategySubWedgeTable.setWidth(80);
            strategySubWedgeTable.setCellsFitPage(true);
            strategySubWedgeTable.setTableFitsPage(true);
            strategySubWedgeTable.setPadding(0);
            strategySubWedgeTable.getDefaultCell().setBorderWidth(0);
            strategySubWedgeTable.setBorderWidth(0);
            strategySubWedgeTable.getDefaultCell().setBackgroundColor(SUBWEDGE_COLOR);

            strategySubWedgeTable.addCell(new Paragraph("Sub Wedge number", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Rotation axis", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Axis start", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Axis end", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Exposure time", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Transmission", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Oscillation Range", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Completeness", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Multiplicity", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Total dose", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Number of images", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Comments", FONT_DOC_BOLD));

            strategySubWedgeTable.getDefaultCell().setBackgroundColor(WHITE_COLOR);
            // rows
            for (Iterator<StrategySubWedgeInformation> s = swi.getListStrategySubWedgeInformation()
                    .iterator(); s.hasNext();) {
                StrategySubWedgeInformation sswi = s.next();
                strategySubWedgeTable.addCell(new Paragraph(sswi.getSubWedgeNumber(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getRotationAxis(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getAxisStart(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getAxisEnd(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getExposureTime(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getTransmission(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getOscillationRange(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getCompleteness(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getMultiplicity(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getDoseTotal(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getNumberOfImages(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getComments(), FONT_DOC));
            }
            document.add(strategySubWedgeTable);
        }
    }
    document.add(new Paragraph(" ", VERY_SMALL_FONT));
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the strategy table and wedge & subwedge strategy tables copy from
 * setStrategyTable, waiting for feedback that we can remove the old reports
 * and the first method/* w w  w.  ja  v  a 2 s .c  om*/
 * 
 * @param document
 * @param dcInfo
 * @throws Exception
 */
private void setStrategyTable2(Document document, DataCollectionInformation dcInfo) throws Exception {
    // ------------------------------------------- Strategy Wedge
    // ------------------------------------------------
    List<StrategyWedgeInformation> strategyWedgeInformationList = dcInfo.getListStrategyWedgeInformation();
    for (Iterator<StrategyWedgeInformation> i = strategyWedgeInformationList.iterator(); i.hasNext();) {
        document.add(new Paragraph(" ", VERY_SMALL_FONT));
        StrategyWedgeInformation swi = i.next();
        Table strategyWedgeTable = new Table(10);
        int headerStrategyWedge[] = { 8, 10, 10, 10, 10, 10, 10, 10, 10, 20 }; // percentage
        strategyWedgeTable.setWidths(headerStrategyWedge);
        strategyWedgeTable.setWidth(100);
        strategyWedgeTable.setCellsFitPage(true);
        strategyWedgeTable.setTableFitsPage(true);
        strategyWedgeTable.setPadding(1);
        strategyWedgeTable.getDefaultCell().setBorderWidth(1);
        strategyWedgeTable.setBorderWidth(1);
        strategyWedgeTable.getDefaultCell().setBackgroundColor(LIGHT_GREY_COLOR);
        strategyWedgeTable.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

        strategyWedgeTable.addCell(new Paragraph("Wedge number", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Resolution (" + Constants.ANGSTROM + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Completeness", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Multiplicity", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Total dose", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Number of Images", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Phi (" + Constants.DEGREE + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Kappa (" + Constants.DEGREE + ")", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Wavelength", FONT_DOC_BOLD));
        strategyWedgeTable.addCell(new Paragraph("Comments", FONT_DOC_BOLD));

        strategyWedgeTable.getDefaultCell().setBackgroundColor(WHITE_COLOR);
        // rows
        strategyWedgeTable.addCell(new Paragraph(swi.getWedgeNumber(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getResolution(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getCompleteness(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getMultiplicity(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getDoseTotal(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getNumberOfImages(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getPhi(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getKappa(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getWavelength(), FONT_DOC));
        strategyWedgeTable.addCell(new Paragraph(swi.getComments(), FONT_DOC));

        document.add(strategyWedgeTable);

        // --- strategy sub wedge
        if (swi.getListStrategySubWedgeInformation().size() > 0) {
            document.add(new Paragraph(" ", VERY_SMALL_FONT));

            Table strategySubWedgeTable = new Table(12);
            int headerStrategySubWedge[] = { 8, 15, 10, 10, 10, 10, 10, 10, 10, 8, 8, 20 }; // percentage
            strategySubWedgeTable.setWidths(headerStrategySubWedge);
            strategySubWedgeTable.setWidth(97);
            strategySubWedgeTable.setCellsFitPage(true);
            strategySubWedgeTable.setTableFitsPage(true);
            strategySubWedgeTable.setPadding(1);
            strategySubWedgeTable.getDefaultCell().setBorderWidth(1);
            strategySubWedgeTable.setBorderWidth(1);
            strategySubWedgeTable.getDefaultCell().setBackgroundColor(LIGHT_GREY_COLOR);
            strategySubWedgeTable.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

            strategySubWedgeTable.addCell(new Paragraph("Sub Wedge number", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Rotation axis", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Axis start", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Axis end", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Exposure time", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Transmission", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Oscillation Range", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Completeness", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Multiplicity", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Total dose", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Number of images", FONT_DOC_BOLD));
            strategySubWedgeTable.addCell(new Paragraph("Comments", FONT_DOC_BOLD));

            strategySubWedgeTable.getDefaultCell().setBackgroundColor(WHITE_COLOR);
            // rows
            for (Iterator<StrategySubWedgeInformation> s = swi.getListStrategySubWedgeInformation()
                    .iterator(); s.hasNext();) {
                StrategySubWedgeInformation sswi = s.next();
                strategySubWedgeTable.addCell(new Paragraph(sswi.getSubWedgeNumber(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getRotationAxis(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getAxisStart(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getAxisEnd(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getExposureTime(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getTransmission(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getOscillationRange(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getCompleteness(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getMultiplicity(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getDoseTotal(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getNumberOfImages(), FONT_DOC));
                strategySubWedgeTable.addCell(new Paragraph(sswi.getComments(), FONT_DOC));
            }
            document.add(strategySubWedgeTable);
        }
    }
    document.add(new Paragraph(" ", VERY_SMALL_FONT));
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the table for a given MXPressO/*from   w ww  . j a va2s .c  om*/
 * 
 * @param document
 * @param dataCollectionGroupVO
 * @param mRequest
 * @param lastCollectOSC
 * @param nextToLastCollectChar
 * @throws Exception
 */
private void setMXPressOTable(Document document, DataCollectionGroup3VO dataCollectionGroupVO,
        HttpServletRequest mRequest, DataCollection3VO lastCollectOSC, DataCollection3VO nextToLastCollectChar)
        throws Exception {
    if (dataCollectionGroupVO != null) {

        DataCollectionExporter dcExporter = new DataCollectionExporter(df2, df3, proposalCode, proposalNumber,
                mRequest);
        if (lastCollectOSC != null) {

            DataCollectionInformation dcInfo = dcExporter.getDataCollectionInformation(lastCollectOSC,
                    getSampleRankingVO(lastCollectOSC.getDataCollectionId()),
                    getAutoProcRankingVO(lastCollectOSC.getDataCollectionId()));

            int noCol = 3;
            Table tableWF = new Table(noCol);
            int[] headersWidthWF = new int[noCol];
            int l = 0;

            headersWidthWF[l++] = 27; // snapshot
            headersWidthWF[l++] = 24; // map 1
            headersWidthWF[l++] = 51; // map2
            // tableWF.setWidths(headersWidthWF);

            tableWF.setWidth(100); // percentage
            tableWF.setPadding(1);
            tableWF.setCellsFitPage(true);
            tableWF.setTableFitsPage(true);
            tableWF.getDefaultCell().setBorderWidth(1);
            tableWF.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);
            // first row: protein acronym and sample name (or image prefix)
            // and startTime
            String collectName = lastCollectOSC.getImagePrefix();
            if (dataCollectionGroupVO.getBlSampleVO() != null
                    && dataCollectionGroupVO.getBlSampleVO().getCrystalVO() != null) {
                collectName = dataCollectionGroupVO.getBlSampleVO().getCrystalVO().getProteinVO().getAcronym()
                        + "-" + dataCollectionGroupVO.getBlSampleVO().getName();
            }
            tableWF.addCell(new Paragraph(collectName, FONT_DOC));

            String collectTime = lastCollectOSC.getStartTime().toString();
            Cell c = new Cell(new Paragraph(collectTime, FONT_DOC));
            c.setColspan(2);
            tableWF.addCell(c);

            // second row: first snapshot + cartography graphes (2 mesh)
            // first snapshot
            String imgCrystal = dcInfo.getPathJpgCrystal3();
            Cell cellCrystalImage = getCellImage(imgCrystal);
            tableWF.addCell(cellCrystalImage);
            // workflowMesh cartography
            Workflow3VO mxExpressOWF = dataCollectionGroupVO.getWorkflowVO();
            List<WorkflowMesh3VO> listWFMesh = new ArrayList<WorkflowMesh3VO>();
            Ejb3ServiceLocator ejb3ServiceLocator = Ejb3ServiceLocator.getInstance();
            WorkflowMesh3Service workflowMeshService = (WorkflowMesh3Service) ejb3ServiceLocator
                    .getLocalService(WorkflowMesh3Service.class);
            listWFMesh = workflowMeshService.findByWorkflowId(mxExpressOWF.getWorkflowId());

            if (listWFMesh != null && listWFMesh.size() > 0) {
                Cell cellImg1 = getMeshMapCell(listWFMesh.get(0));
                if (cellImg1 == null) {
                    tableWF.addCell(new Paragraph("Image not found", FONT_DOC));
                } else {
                    tableWF.addCell(cellImg1);
                }
                if (listWFMesh.size() > 1) {
                    Cell cellImg2 = getMeshMapCell(listWFMesh.get(1));
                    if (cellImg2 == null) {
                        tableWF.addCell(new Paragraph("Image not found", FONT_DOC));
                    } else {
                        tableWF.addCell(cellImg2);
                    }
                } else
                    tableWF.addCell(new Paragraph("No Workflow found", FONT_DOC));
            } else {
                tableWF.addCell(new Paragraph("No Workflow found", FONT_DOC));
                tableWF.addCell(new Paragraph("No Workflow found", FONT_DOC));
            }

            //
            // third row:
            // autoprocessing results
            Cell resultCell = getAutoProcResultStatus(dcInfo);
            resultCell.setColspan(3);
            resultCell.setHorizontalAlignment(Element.ALIGN_LEFT);
            tableWF.addCell(resultCell);

            Integer idDc = -1;
            for (int k = 0; k < dataCollectionList.size(); k++) {
                DataCollection3VO dcVo = dataCollectionList.get(k);
                if (dcVo.getDataCollectionId().equals(lastCollectOSC.getDataCollectionId())) {
                    idDc = k;
                    break;
                }
            }

            if (idDc != -1) {
                AutoProc3VO[] autoProcs = wrapper.getAutoProcs();
                AutoProcScalingStatistics3VO[] autoProcsOverall = wrapper.getScalingStatsOverall();
                AutoProcScalingStatistics3VO[] autoProcsInner = wrapper.getScalingStatsInner();
                AutoProcScalingStatistics3VO[] autoProcsOuter = wrapper.getScalingStatsOuter();

                AutoProc3VO autoProcValue = autoProcs[idDc];
                AutoProcScalingStatistics3VO autoProcOverall = autoProcsOverall[idDc];
                AutoProcScalingStatistics3VO autoProcInner = autoProcsInner[idDc];
                AutoProcScalingStatistics3VO autoProcOuter = autoProcsOuter[idDc];
                if (autoProcValue == null) {
                    Cell cNo = new Cell(new Paragraph("No autoprocessing results found", FONT_DOC));
                    cNo.setColspan(3);
                    cNo.setHorizontalAlignment(Element.ALIGN_LEFT);
                    tableWF.addCell(cNo);
                    document.add(tableWF);
                } else {
                    int noColSPG = 5;
                    Table tableSPG = new Table(noColSPG);
                    int[] headersWidth = new int[noColSPG];
                    int i = 0;

                    headersWidth[i++] = 7; // space group
                    headersWidth[i++] = 10; // completeness
                    headersWidth[i++] = 9; // resolution
                    headersWidth[i++] = 9; // rsymm
                    headersWidth[i++] = 12; // unit cell
                    tableSPG.setWidths(headersWidth);

                    tableSPG.setWidth(100); // percentage
                    tableSPG.setPadding(3);
                    tableSPG.setCellsFitPage(true);
                    tableSPG.setTableFitsPage(true);
                    tableSPG.getDefaultCell().setBorderWidth(1);
                    tableSPG.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

                    tableSPG.getDefaultCell().setGrayFill(GREY_FILL_HEADER);
                    tableSPG.addCell(new Paragraph("Space Group", FONT_DOC_BOLD));
                    tableSPG.addCell(new Paragraph("Completeness (Inner, Outer, Overall)", FONT_DOC_BOLD));
                    tableSPG.addCell(new Paragraph("Resolution", FONT_DOC_BOLD));
                    tableSPG.addCell(new Paragraph("Rsymm (Inner, Outer, Overall)", FONT_DOC_BOLD));
                    tableSPG.addCell(new Paragraph("Unit Cell (a, b, c, alpha, beta, gamma)", FONT_DOC_BOLD));

                    tableSPG.getDefaultCell().setGrayFill(GREY_FILL_DATA);

                    // space group
                    if (autoProcValue != null && autoProcValue.getSpaceGroup() != null) {
                        Paragraph p = new Paragraph(autoProcValue.getSpaceGroup(), FONT_DOC);
                        tableSPG.addCell(p);
                    } else
                        tableSPG.addCell("");

                    // completeness, rsymm, processed resolution
                    String completenessString = new String();
                    String rSymmString = new String();
                    String resolutionString = new String();

                    if (autoProcOverall != null && autoProcInner != null && autoProcOuter != null) {
                        completenessString += df2.format(autoProcInner.getCompleteness()) + "\n"
                                + df2.format(autoProcOuter.getCompleteness()) + "\n"
                                + df2.format(autoProcOverall.getCompleteness());
                        rSymmString += (autoProcInner.getRmerge() == null ? ""
                                : df2.format(autoProcInner.getRmerge()))
                                + "\n"
                                + (autoProcOuter.getRmerge() == null ? ""
                                        : df2.format(autoProcOuter.getRmerge()))
                                + "\n" + (autoProcOverall.getRmerge() == null ? ""
                                        : df2.format(autoProcOverall.getRmerge()));
                        resolutionString += autoProcInner.getResolutionLimitLow() + " - "
                                + autoProcInner.getResolutionLimitHigh() + "\n"
                                + autoProcOuter.getResolutionLimitLow() + " - "
                                + autoProcOuter.getResolutionLimitHigh() + "\n"
                                + autoProcOverall.getResolutionLimitLow() + " - "
                                + autoProcOverall.getResolutionLimitHigh();
                    }
                    tableSPG.addCell(new Paragraph(completenessString, FONT_DOC));
                    tableSPG.addCell(new Paragraph(resolutionString, FONT_DOC));
                    tableSPG.addCell(new Paragraph(rSymmString, FONT_DOC));

                    // unit cell
                    if (autoProcValue != null && autoProcValue.getSpaceGroup() != null) {
                        tableSPG.addCell(new Paragraph("" + autoProcValue.getRefinedCellA() + ", "
                                + autoProcValue.getRefinedCellB() + ", " + autoProcValue.getRefinedCellC()
                                + "\n" + autoProcValue.getRefinedCellAlpha() + ", "
                                + autoProcValue.getRefinedCellBeta() + ", "
                                + autoProcValue.getRefinedCellGamma(), FONT_DOC));
                    } else {
                        tableSPG.addCell("");
                    }

                    document.add(tableWF);
                    document.add(new Paragraph("Best autoprocessing result", FONT_DOC));
                    document.add(tableSPG);
                } // end autoProc null
            } // end idDc -1

            //
            document.add(new Paragraph(" ", FONT_SPACE));

        } // end lastCollect null
        if (nextToLastCollectChar != null) {
            DataCollectionInformation dcInfo = dcExporter.getDataCollectionInformation(nextToLastCollectChar,
                    getSampleRankingVO(nextToLastCollectChar.getDataCollectionId()),
                    getAutoProcRankingVO(nextToLastCollectChar.getDataCollectionId()));

            if (dcInfo.getSpacegroup() != "") {
                document.add(new Paragraph("EDNA characterisation output and collect strategy", FONT_DOC));
            }
            setEDNATable2(document, dcInfo);
            setStrategyTable2(document, dcInfo);
        }
    } // end dataCollectionGroup null
}

From source file:ispyb.client.mx.collection.PdfRtfExporter.java

License:Open Source License

/**
 * set the autoproc results table, if no autoProc add a cell at the end of
 * topTable//from   w  w w  .j  a  v  a 2s .c  o m
 * 
 * @param document
 * @param topTable
 * @param collect
 * @throws Exception
 */
private void setAutoProcResultsTable(Document document, DataCollectionInformation collect) throws Exception {
    Integer idDc = -1;
    for (int k = 0; k < dataCollectionList.size(); k++) {
        DataCollection3VO dcVo = dataCollectionList.get(k);
        if (dcVo.getDataCollectionId().equals(collect.getDataCollectionId())) {
            idDc = k;
            break;
        }
    }

    if (idDc != -1) {
        AutoProc3VO[] autoProcs = wrapper.getAutoProcs();
        AutoProcScalingStatistics3VO[] autoProcsOverall = wrapper.getScalingStatsOverall();
        AutoProcScalingStatistics3VO[] autoProcsInner = wrapper.getScalingStatsInner();
        AutoProcScalingStatistics3VO[] autoProcsOuter = wrapper.getScalingStatsOuter();

        AutoProc3VO autoProcValue = autoProcs[idDc];
        AutoProcScalingStatistics3VO autoProcOverall = autoProcsOverall[idDc];
        AutoProcScalingStatistics3VO autoProcInner = autoProcsInner[idDc];
        AutoProcScalingStatistics3VO autoProcOuter = autoProcsOuter[idDc];
        if (autoProcValue == null) {
            // Cell cNo = new Cell(new
            // Paragraph("No autoprocessing results found", FONT_DOC));
            // cNo.setHorizontalAlignment(Element.ALIGN_LEFT);
            // Table tableNR = new Table(1);
            // tableNR.setWidth(100); // percentage
            // tableNR.setPadding(3);
            // tableNR.setCellsFitPage(true);
            // tableNR.setTableFitsPage(true);
            // tableNR.getDefaultCell().setBorderWidth(1);
            // tableNR.getDefaultCell().setHorizontalAlignment(Element.ALIGN_LEFT);
            // tableNR.addCell(cNo);
            // document.add(tableNR);
        } else {
            int noColSPG = 5;
            Table tableSPG = new Table(noColSPG);
            int[] headersWidth = new int[noColSPG];
            int i = 0;

            headersWidth[i++] = 7; // space group
            headersWidth[i++] = 10; // completeness
            headersWidth[i++] = 9; // resolution
            headersWidth[i++] = 9; // rsymm
            headersWidth[i++] = 12; // unit cell
            tableSPG.setWidths(headersWidth);

            tableSPG.setWidth(100); // percentage
            tableSPG.setPadding(3);
            tableSPG.setCellsFitPage(true);
            tableSPG.setTableFitsPage(true);
            tableSPG.getDefaultCell().setBorderWidth(1);
            tableSPG.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER);

            tableSPG.getDefaultCell().setGrayFill(GREY_FILL_HEADER);
            tableSPG.addCell(new Paragraph("Space Group", FONT_DOC_BOLD));
            tableSPG.addCell(new Paragraph("Completeness (Inner, Outer, Overall)", FONT_DOC_BOLD));
            tableSPG.addCell(new Paragraph("Resolution", FONT_DOC_BOLD));
            tableSPG.addCell(new Paragraph("Rsymm (Inner, Outer, Overall)", FONT_DOC_BOLD));
            tableSPG.addCell(new Paragraph("Unit Cell (a, b, c, alpha, beta, gamma)", FONT_DOC_BOLD));

            tableSPG.getDefaultCell().setGrayFill(GREY_FILL_DATA);

            // space group
            if (autoProcValue != null && autoProcValue.getSpaceGroup() != null) {
                Paragraph p = new Paragraph(autoProcValue.getSpaceGroup(), FONT_DOC);
                tableSPG.addCell(p);
            } else
                tableSPG.addCell("");

            // completeness, rsymm, processed resolution
            String completenessString = new String();
            String rSymmString = new String();
            String resolutionString = new String();

            if (autoProcOverall != null && autoProcInner != null && autoProcOuter != null) {
                completenessString += df2.format(autoProcInner.getCompleteness()) + "\n"
                        + df2.format(autoProcOuter.getCompleteness()) + "\n"
                        + df2.format(autoProcOverall.getCompleteness());
                rSymmString += (autoProcInner.getRmerge() == null ? "" : df2.format(autoProcInner.getRmerge()))
                        + "\n"
                        + (autoProcOuter.getRmerge() == null ? "" : df2.format(autoProcOuter.getRmerge()))
                        + "\n"
                        + (autoProcOverall.getRmerge() == null ? "" : df2.format(autoProcOverall.getRmerge()));
                resolutionString += autoProcInner.getResolutionLimitLow() + " - "
                        + autoProcInner.getResolutionLimitHigh() + "\n" + autoProcOuter.getResolutionLimitLow()
                        + " - " + autoProcOuter.getResolutionLimitHigh() + "\n"
                        + autoProcOverall.getResolutionLimitLow() + " - "
                        + autoProcOverall.getResolutionLimitHigh();
            }
            tableSPG.addCell(new Paragraph(completenessString, FONT_DOC));
            tableSPG.addCell(new Paragraph(resolutionString, FONT_DOC));
            tableSPG.addCell(new Paragraph(rSymmString, FONT_DOC));

            // unit cell
            if (autoProcValue != null && autoProcValue.getSpaceGroup() != null) {
                tableSPG.addCell(new Paragraph("" + autoProcValue.getRefinedCellA() + ", "
                        + autoProcValue.getRefinedCellB() + ", " + autoProcValue.getRefinedCellC() + "\n"
                        + autoProcValue.getRefinedCellAlpha() + ", " + autoProcValue.getRefinedCellBeta() + ", "
                        + autoProcValue.getRefinedCellGamma(), FONT_DOC));
            } else {
                tableSPG.addCell("");
            }
            document.add(tableSPG);
        } // end autoProc null
    } // end idDc -1

    //
    document.add(new Paragraph(" ", FONT_SPACE));
}

From source file:jp.ac.utokyo.rcast.karkinos.graph.GetReadsStatsChart.java

License:Apache License

private static Object getSummaryTable(ReadsSummary readsSummary, String readsStat) {

    try {/*from www  .j  a v  a  2 s . c  o  m*/

        ReadsCounter normal = readsSummary.getNormalCounter();
        ReadsCounter tumor = readsSummary.getTumorCounter();

        Table table = new Table(3);
        int[] width = new int[] { 60, 20, 20 };
        table.setWidths(width);

        // row1
        table.addCell("reads stats/");
        table.addCell("normal");
        table.addCell("tumor");

        // // row
        if (readsStat != null) {

            String[] sa = readsStat.split(",");
            String normalfile = sa[0];
            Properties np = getProp(normalfile);
            String tumorfile = sa[1];
            Properties tp = getProp(tumorfile);
            // datamap.put("total", total);
            // datamap.put("passfilter", passfilter);
            // datamap.put("mapped", mapped);
            // datamap.put("nonduplicate", nonduplicate);
            // datamap.put("duplicate", duplicate);
            // //datamap.put("identityLow", identityLow);
            // datamap.put("unique", unique);
            // datamap.put("proper", proper);
            // datamap.put("properOrunique", properOrunique);
            // datamap.put("bincount", 1l);
            // datamap.put("afterrealgin", afterrealgin);
            // datamap.put("identityLow", identityLow);
            String[] keys = new String[] { "total", "passfilter", "mapped", "nonduplicate", "duplicate",
                    "unique", "proper", "properOrunique", "afterrealgin", "identityLow" };
            for (String key : keys) {
                if (np.containsKey(key)) {

                    // row2
                    String kyeDisp = key.replaceAll("Or", " or ");
                    table.addCell(kyeDisp + " tags");
                    table.addCell(format(np.getProperty(key)));
                    table.addCell(format(tp.getProperty(key)));

                    if (key.equals("duplicate")) {

                        try {
                            // row 13
                            table.addCell("duplicate (%)");
                            table.addCell(
                                    format(getParcent(np.getProperty(key), np.getProperty("nonduplicate")))
                                            + "%");
                            table.addCell(
                                    format(getParcent(tp.getProperty(key), tp.getProperty("nonduplicate")))
                                            + "%");
                        } catch (Exception ex) {
                        }
                    }
                }
            }

        }

        // row
        table.addCell("Total used tags");
        table.addCell(format(normal.getTotalmap()));
        table.addCell(format(tumor.getTotalmap()));

        // row4
        table.addCell("Target tags");
        table.addCell(format(normal.getTotalOnTarget()));
        table.addCell(format(tumor.getTotalOnTarget()));
        // row5
        table.addCell("Target unique tags");
        table.addCell(format(normal.getTotalUniqueOntarget()));
        table.addCell(format(tumor.getTotalUniqueOntarget()));

        if (readsSummary.isPairStats()) {

            // row6
            table.addCell("First reads");
            table.addCell(format(normal.getFirstReads()));
            table.addCell(format(tumor.getFirstReads()));
            // row7
            table.addCell("Second reads");
            table.addCell(format(normal.getSecondReads()));
            table.addCell(format(tumor.getSecondReads()));
            // row8
            table.addCell("Both mapped");
            table.addCell(format(normal.getBothmap()));
            table.addCell(format(tumor.getBothmap()));
            // row9
            table.addCell("Proper reads");
            table.addCell(format(normal.getPropermap()));
            table.addCell(format(tumor.getPropermap()));
            // row10
            table.addCell("mean library size");
            table.addCell(format(normal.getMeanInsertSize()));
            table.addCell(format(tumor.getMeanInsertSize()));

        }

        // // row11
        // row 12
        table.addCell("mean depth");
        table.addCell(format(readsSummary.getNormalDepth().getMeanDepth()));
        table.addCell(format(readsSummary.getTumorDepth().getMeanDepth()));

        table.addCell("total covered region");
        table.addCell(format(readsSummary.getNormalDepth().getTotal()));
        table.addCell(format(readsSummary.getTumorDepth().getTotal()));

        // row 13
        table.addCell("On target(%)");
        table.addCell(format(normal.onTargetParcent()) + "%");
        table.addCell(format(tumor.onTargetParcent()) + "%");

        table.addCell("more than X20(%)");
        table.addCell(format(getX20percent(readsSummary.getNormalDepth())) + "%");
        table.addCell(format(getX20percent(readsSummary.getTumorDepth())) + "%");

        table.addCell("mean depth CDS");
        table.addCell(format(readsSummary.getNormalDepth().getMeanCDSDepth()));
        table.addCell(format(readsSummary.getTumorDepth().getMeanCDSDepth()));

        table.addCell("more than X10(%) CDS");
        table.addCell(format(readsSummary.getNormalDepth().getOver10X()) + "%");
        table.addCell(format(readsSummary.getTumorDepth().getOver10X()) + "%");

        table.addCell("more than X20(%) CDS");
        table.addCell(format(readsSummary.getNormalDepth().getOver20X()) + "%");
        table.addCell(format(readsSummary.getTumorDepth().getOver20X()) + "%");

        return table;

    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    return null;

}