Examples with Section com.lowagie.text.Section used on opensource projects

Example 6 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeSubDomainsEquationsAsText.

protected void writeSubDomainsEquationsAsText(Section mathDescSection, MathDescription mathDesc) throws DocumentException {
    Enumeration<SubDomain> subDomains = mathDesc.getSubDomains();
    Section volDomains = mathDescSection.addSection("Volume Domains", mathDescSection.depth() + 1);
    Section memDomains = mathDescSection.addSection("Membrane Domains", mathDescSection.depth() + 1);
    Section filDomains = mathDescSection.addSection("Filament Domains", mathDescSection.depth() + 1);
    while (subDomains.hasMoreElements()) {
        Section tempSection = null;
        SubDomain subDomain = subDomains.nextElement();
        if (subDomain instanceof CompartmentSubDomain) {
            tempSection = volDomains.addSection(subDomain.getName(), volDomains.depth() + 1);
        } else if (subDomain instanceof MembraneSubDomain) {
            tempSection = memDomains.addSection(subDomain.getName(), memDomains.depth() + 1);
        } else if (subDomain instanceof FilamentSubDomain) {
            tempSection = filDomains.addSection(subDomain.getName(), filDomains.depth() + 1);
        }
        Enumeration<Equation> equationsList = subDomain.getEquations();
        while (equationsList.hasMoreElements()) {
            Equation equ = equationsList.nextElement();
            writeEquation(tempSection, equ);
        }
        if (subDomain.getFastSystem() != null) {
            writeFastSystem(tempSection, subDomain.getFastSystem());
        }
        if (subDomain instanceof MembraneSubDomain) {
            Enumeration<JumpCondition> jcList = ((MembraneSubDomain) subDomain).getJumpConditions();
            while (jcList.hasMoreElements()) {
                JumpCondition jc = jcList.nextElement();
                writeJumpCondition(tempSection, jc);
            }
        }
    }
    if (volDomains.isEmpty()) {
        mathDescSection.remove(volDomains);
    }
    if (memDomains.isEmpty()) {
        mathDescSection.remove(memDomains);
    }
    if (filDomains.isEmpty()) {
        mathDescSection.remove(filDomains);
    }
}

Example 7 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeSimulation.

// container can be a chapter or a section of a chapter.
protected void writeSimulation(Section container, Simulation sim) throws DocumentException {
    if (sim == null) {
        return;
    }
    Section simSection = container.addSection(sim.getName(), container.numberDepth() + 1);
    writeMetadata(simSection, sim.getName(), sim.getDescription(), null, "Simulation ");
    // add overriden params
    Table overParamTable = null;
    MathOverrides mo = sim.getMathOverrides();
    if (mo != null) {
        String[] constants = mo.getOverridenConstantNames();
        for (int i = 0; i < constants.length; i++) {
            String actualStr = "", defStr = "";
            Expression tempExp = mo.getDefaultExpression(constants[i]);
            if (tempExp != null) {
                defStr = tempExp.infix();
            }
            if (mo.isScan(constants[i])) {
                actualStr = mo.getConstantArraySpec(constants[i]).toString();
            } else {
                tempExp = mo.getActualExpression(constants[i], 0);
                if (tempExp != null) {
                    actualStr = tempExp.infix();
                }
            }
            if (overParamTable == null) {
                overParamTable = getTable(3, 75, 1, 3, 3);
                overParamTable.setAlignment(Table.ALIGN_LEFT);
                overParamTable.addCell(createCell("Overriden Parameters", getBold(DEF_HEADER_FONT_SIZE), 3, 1, Element.ALIGN_CENTER, true));
                overParamTable.addCell(createHeaderCell("Name", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Actual Value", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Default Value", getBold(), 1));
            }
            overParamTable.addCell(createCell(constants[i], getFont()));
            overParamTable.addCell(createCell(actualStr, getFont()));
            overParamTable.addCell(createCell(defStr, getFont()));
        }
    }
    if (overParamTable != null) {
        simSection.add(overParamTable);
    }
    // add spatial details
    // sim.isSpatial();
    Table meshTable = null;
    MeshSpecification mesh = sim.getMeshSpecification();
    if (mesh != null) {
        Geometry geom = mesh.getGeometry();
        Extent extent = geom.getExtent();
        String extentStr = "(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")";
        ISize meshSize = mesh.getSamplingSize();
        String meshSizeStr = "(" + meshSize.getX() + ", " + meshSize.getY() + ", " + meshSize.getZ() + ")";
        meshTable = getTable(2, 75, 1, 3, 3);
        meshTable.setAlignment(Table.ALIGN_LEFT);
        meshTable.addCell(createCell("Geometry Setting", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        meshTable.addCell(createCell("Geometry Size (um)", getFont()));
        meshTable.addCell(createCell(extentStr, getFont()));
        meshTable.addCell(createCell("Mesh Size (elements)", getFont()));
        meshTable.addCell(createCell(meshSizeStr, getFont()));
    }
    if (meshTable != null) {
        simSection.add(meshTable);
    }
    // write advanced sim settings
    Table simAdvTable = null;
    SolverTaskDescription solverDesc = sim.getSolverTaskDescription();
    if (solverDesc != null) {
        String solverName = solverDesc.getSolverDescription().getDisplayLabel();
        simAdvTable = getTable(2, 75, 1, 3, 3);
        simAdvTable.setAlignment(Table.ALIGN_LEFT);
        simAdvTable.addCell(createCell("Advanced Settings", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        simAdvTable.addCell(createCell("Solver Name", getFont()));
        simAdvTable.addCell(createCell(solverName, getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Starting", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getStartingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Ending", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getEndingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Min", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMinimumTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Default", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getDefaultTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Max", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMaximumTimeStep(), getFont()));
        ErrorTolerance et = solverDesc.getErrorTolerance();
        if (et != null) {
            simAdvTable.addCell(createCell("Error Tolerance - Absolute", getFont()));
            simAdvTable.addCell(createCell("" + et.getAbsoluteErrorTolerance(), getFont()));
            simAdvTable.addCell(createCell("Error Tolerance - Relative", getFont()));
            simAdvTable.addCell(createCell("" + et.getRelativeErrorTolerance(), getFont()));
        }
        OutputTimeSpec ots = solverDesc.getOutputTimeSpec();
        if (ots.isDefault()) {
            simAdvTable.addCell(createCell("Keep Every", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepEvery(), getFont()));
            simAdvTable.addCell(createCell("Keep At Most", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepAtMost(), getFont()));
        } else if (ots.isUniform()) {
            simAdvTable.addCell(createCell("Output Time Step", getFont()));
            simAdvTable.addCell(createCell("" + ((UniformOutputTimeSpec) ots).getOutputTimeStep(), getFont()));
        } else if (ots.isExplicit()) {
            simAdvTable.addCell(createCell("Output Time Points", getFont()));
            simAdvTable.addCell(createCell("" + ((ExplicitOutputTimeSpec) ots).toCommaSeperatedOneLineOfString(), getFont()));
        }
        simAdvTable.addCell(createCell("Use Symbolic Jacobian (T/F)", getFont()));
        simAdvTable.addCell(createCell((solverDesc.getUseSymbolicJacobian() ? " T " : " F "), getFont()));
        Constant sp = solverDesc.getSensitivityParameter();
        if (sp != null) {
            simAdvTable.addCell(createCell("Sensitivity Analysis Param", getFont()));
            simAdvTable.addCell(createCell(sp.getName(), getFont()));
        }
    }
    if (simAdvTable != null) {
        simSection.add(simAdvTable);
    }
}

Example 8 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeModel.

// model description ignored.
protected void writeModel(Chapter physioChapter, Model model) throws DocumentException {
    Section structSection = null;
    // add structures image
    // if (model.getNumStructures() > 0) {
    // try {
    // ByteArrayOutputStream bos = generateDocStructureImage(model, ITextWriter.LOW_RESOLUTION);
    // structSection = physioChapter.addSection("Structures For: " + model.getName(), physioChapter.numberDepth() + 1);
    // addImage(structSection, bos);
    // } catch(Exception e) {
    // System.err.println("Unable to add structures image for model: " + model.getName());
    // e.printStackTrace();
    // }
    // }
    // write structures
    Table structTable = null;
    for (int i = 0; i < model.getNumStructures(); i++) {
        if (structTable == null) {
            structTable = getTable(4, 100, 1, 3, 3);
            structTable.addCell(createCell("Structures", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
            structTable.addCell(createHeaderCell("Name", getFont(), 1));
            structTable.addCell(createHeaderCell("Type", getFont(), 1));
            structTable.addCell(createHeaderCell("Inside", getFont(), 1));
            structTable.addCell(createHeaderCell("Outside", getFont(), 1));
            structTable.endHeaders();
        }
        writeStructure(model, model.getStructure(i), structTable);
    }
    // if (structTable != null) {
    // structSection.add(structTable);
    // }
    // write reactions
    writeReactions(physioChapter, model);
}

Example 9 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeReactionContext.

// ReactionContext - SpeciesContextSpec: ignored boundary conditions.
protected void writeReactionContext(Section simContextSection, SimulationContext simContext) throws DocumentException {
    ReactionContext rc = simContext.getReactionContext();
    if (rc == null) {
        return;
    }
    Section rcSection = null;
    // add reaction specs
    ReactionSpec[] reactionSpecs = rc.getReactionSpecs();
    Table reactionSpecTable = null;
    for (int i = 0; i < reactionSpecs.length; i++) {
        if (i == 0) {
            reactionSpecTable = getTable(4, 100, 1, 3, 3);
            // reactionSpecTable.setTableFitsPage(true);
            reactionSpecTable.addCell(createCell("Reaction Mapping", getBold(DEF_HEADER_FONT_SIZE), 4, 1, Element.ALIGN_CENTER, true));
            reactionSpecTable.addCell(createHeaderCell("Name", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Type", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Enabled (T/F)", getBold(), 1));
            reactionSpecTable.addCell(createHeaderCell("Fast (T/F)", getBold(), 1));
            reactionSpecTable.endHeaders();
        }
        String reactionName = reactionSpecs[i].getReactionStep().getName();
        String reactionType = reactionSpecs[i].getReactionStep().getDisplayType();
        reactionSpecTable.addCell(createCell(reactionName, getFont()));
        reactionSpecTable.addCell(createCell(reactionType, getFont()));
        reactionSpecTable.addCell(createCell((reactionSpecs[i].isExcluded() ? " F " : " T "), getFont()));
        reactionSpecTable.addCell(createCell((reactionSpecs[i].isFast() ? " T " : " F "), getFont()));
    }
    if (reactionSpecTable != null) {
        rcSection = simContextSection.addSection("Reaction Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        rcSection.add(reactionSpecTable);
    }
    // add species context specs
    SpeciesContextSpec[] speciesContSpecs = rc.getSpeciesContextSpecs();
    Table speciesSpecTable = null;
    int[] widths = { 2, 2, 4, 4, 1 };
    for (int i = 0; i < speciesContSpecs.length; i++) {
        if (i == 0) {
            speciesSpecTable = getTable(5, 100, 1, 3, 3);
            speciesSpecTable.addCell(createCell("Initial Conditions", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            speciesSpecTable.addCell(createHeaderCell("Species", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Structure", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Initial Conc.", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Diffusion Const.", getBold(), 1));
            speciesSpecTable.addCell(createHeaderCell("Fixed (T/F)", getBold(), 1));
            speciesSpecTable.endHeaders();
        }
        String speciesName = speciesContSpecs[i].getSpeciesContext().getSpecies().getCommonName();
        String structName = speciesContSpecs[i].getSpeciesContext().getStructure().getName();
        String diff = speciesContSpecs[i].getDiffusionParameter().getExpression().infix();
        VCUnitDefinition diffUnit = speciesContSpecs[i].getDiffusionParameter().getUnitDefinition();
        SpeciesContextSpecParameter initParam = speciesContSpecs[i].getInitialConditionParameter();
        String initConc = initParam == null ? "" : initParam.getExpression().infix();
        VCUnitDefinition initConcUnit = initParam == null ? null : initParam.getUnitDefinition();
        speciesSpecTable.addCell(createCell(speciesName, getFont()));
        speciesSpecTable.addCell(createCell(structName, getFont()));
        speciesSpecTable.addCell(createCell(initConc + (initConcUnit == null ? "" : "   " + initConcUnit.getSymbolUnicode()), getFont()));
        speciesSpecTable.addCell(createCell(diff + (diffUnit == null ? "" : "   " + diffUnit.getSymbolUnicode()), getFont()));
        speciesSpecTable.addCell(createCell((speciesContSpecs[i].isConstant() ? " T " : " F "), getFont()));
    }
    if (speciesSpecTable != null) {
        if (rcSection == null) {
            rcSection = simContextSection.addSection("Reaction Mapping For " + simContext.getName(), simContextSection.numberDepth() + 1);
        }
        speciesSpecTable.setWidths(widths);
        rcSection.add(speciesSpecTable);
    }
}

Example 10 with Section

use of com.lowagie.text.Section in project vcell by virtualcell.

the class ITextWriter method writeReactions.

// each reaction has its own table, ordered by the structures.
protected void writeReactions(Chapter physioChapter, Model model) throws DocumentException {
    if (model == null) {
        return;
    }
    Paragraph reactionParagraph = new Paragraph();
    reactionParagraph.add(new Chunk("Structures and Reactions Diagram").setLocalDestination(model.getName()));
    Section reactionDiagramSection = physioChapter.addSection(reactionParagraph, physioChapter.numberDepth() + 1);
    try {
        addImage(reactionDiagramSection, encodeJPEG(generateDocReactionsImage(model, null)));
    } catch (Exception e) {
        e.printStackTrace();
        throw new DocumentException(e.getClass().getName() + ": " + e.getMessage());
    }
    for (int i = 0; i < model.getNumStructures(); i++) {
        ReactionStep[] reactionSteps = model.getReactionSteps();
        ReactionStep rs = null;
        Table modifierTable = null;
        Table reactionTable = null;
        boolean firstTime = true;
        Section reactStructSection = null;
        for (int j = 0; j < reactionSteps.length; j++) {
            if (reactionSteps[j].getStructure() == model.getStructure(i)) {
                // can also use structureName1.equals(structureName2)
                if (firstTime) {
                    Paragraph linkParagraph = new Paragraph();
                    linkParagraph.add(new Chunk("Reaction(s) in " + model.getStructure(i).getName()).setLocalDestination(model.getStructure(i).getName()));
                    reactStructSection = physioChapter.addSection(linkParagraph, physioChapter.numberDepth() + 1);
                    firstTime = false;
                }
                rs = reactionSteps[j];
                String type;
                if (rs instanceof SimpleReaction) {
                    type = "Reaction";
                } else {
                    type = "Flux";
                }
                // write Reaction equation as a table
                // Get the image arrow cell depending on type of reactionStep : MassAction => double arrow, otherwise, forward arrow
                boolean bReversible = false;
                if (rs.getKinetics() instanceof MassActionKinetics) {
                    bReversible = true;
                }
                Cell arrowImageCell = getReactionArrowImageCell(bReversible);
                // Get reactants and products strings
                ReactionCanvas rc = new ReactionCanvas();
                rc.setReactionStep(rs);
                ReactionCanvasDisplaySpec rcdSpec = rc.getReactionCanvasDisplaySpec();
                String reactants = rcdSpec.getLeftText();
                String products = rcdSpec.getRightText();
                // Create table and add cells for reactants, arrow(s) images, products
                int[] widths = { 8, 1, 8 };
                reactionTable = getTable(3, 100, 0, 2, 2);
                // Add reactants as cell
                Cell tableCell = createCell(reactants, getBold());
                tableCell.setHorizontalAlignment(Cell.ALIGN_RIGHT);
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // add arrow(s) image as cell
                if (arrowImageCell != null) {
                    arrowImageCell.setHorizontalAlignment(Cell.ALIGN_CENTER);
                    arrowImageCell.setBorderColor(Color.white);
                    reactionTable.addCell(arrowImageCell);
                }
                // add products as cell
                tableCell = createCell(products, getBold());
                tableCell.setBorderColor(Color.white);
                reactionTable.addCell(tableCell);
                // reactionTable.setBorderColor(Color.white);
                reactionTable.setWidths(widths);
                // Identify modifiers,
                ReactionParticipant[] rpArr = rs.getReactionParticipants();
                Vector<ReactionParticipant> modifiersVector = new Vector<ReactionParticipant>();
                for (int k = 0; k < rpArr.length; k += 1) {
                    if (rpArr[k] instanceof Catalyst) {
                        modifiersVector.add(rpArr[k]);
                    }
                }
                // Write the modifiers in a separate table, if present
                if (modifiersVector.size() > 0) {
                    modifierTable = getTable(1, 50, 0, 1, 1);
                    modifierTable.addCell(createCell("Modifiers List", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    StringBuffer modifierNames = new StringBuffer();
                    for (int k = 0; k < modifiersVector.size(); k++) {
                        modifierNames.append(((Catalyst) modifiersVector.elementAt(k)).getName() + "\n");
                    }
                    modifierTable.addCell(createCell(modifierNames.toString().trim(), getFont()));
                    modifiersVector.removeAllElements();
                }
                Section reactionSection = reactStructSection.addSection(type + " " + rs.getName(), reactStructSection.numberDepth() + 1);
                // Annotation
                VCMetaData vcMetaData = rs.getModel().getVcMetaData();
                if (vcMetaData.getFreeTextAnnotation(rs) != null) {
                    Table annotTable = getTable(1, 100, 1, 3, 3);
                    annotTable.addCell(createCell("Reaction Annotation", getBold(DEF_HEADER_FONT_SIZE), 1, 1, Element.ALIGN_CENTER, true));
                    annotTable.addCell(createCell(vcMetaData.getFreeTextAnnotation(rs), getFont()));
                    reactionSection.add(annotTable);
                // reactionSection.add(new Paragraph("\""+rs.getAnnotation()+"\""));
                }
                // reaction table
                if (reactionTable != null) {
                    reactionSection.add(reactionTable);
                    // re-set reactionTable
                    reactionTable = null;
                }
                if (modifierTable != null) {
                    reactionSection.add(modifierTable);
                    modifierTable = null;
                }
                // Write kinetics parameters, etc. in a table
                writeKineticsParams(reactionSection, rs);
            }
        }
    }
}