Created two examples as tests

vcell-core/pom.xml

@@ -171,6 +171,11 @@
 			</exclusions>
 
 		</dependency>
+		<dependency>
+			<groupId>org.jfree</groupId>
+			<artifactId>jfreechart</artifactId>
+			<version>1.5.5</version>
+		</dependency>
 		<dependency>
 			<groupId>org.jgrapht</groupId>
 			<artifactId>jgrapht-core</artifactId>

vcell-core/src/main/java/cbit/vcell/publish/ITextWriter.java

@@ -20,10 +20,10 @@
 import java.awt.image.IndexColorModel;
 import java.awt.image.WritableRaster;
 import java.awt.print.PageFormat;
-import java.io.ByteArrayOutputStream;
-import java.io.FileOutputStream;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
 import javax.imageio.IIOImage;
@@ -905,20 +905,40 @@ protected void createDocument(PageFormat pageFormat) {
         this.document = new Document(pageSize, (float) marginL, (float) marginR, (float) marginT, (float) marginB);
     }
 
+    public void writePlotImageDocument(String docTitle, FileOutputStream fos, PageFormat pageFormat, BufferedImage... plotImages) throws DocumentException, IOException {
+        if (plotImages == null) throw new IllegalArgumentException("No plot images provided");
+        if (fos == null) throw new IllegalArgumentException("No outputstream for plot-document provided");
+        if (pageFormat == null) throw new IllegalArgumentException("No page format provided");
+
+        this.createDocument(pageFormat);
+        this.createDocWriter(fos);
+        this.document.addTitle(docTitle);
+        this.document.addCreator("Virtual Cell");
+        this.document.addCreationDate();
+        this.document.open();
+        for (BufferedImage plotImage : plotImages){
+            com.lowagie.text.Image image = com.lowagie.text.Image.getInstance(plotImage, null);
+            image.setAlignment(Table.ALIGN_LEFT);
+            this.document.add(image);
+            if (this.document.getPageNumber() != plotImages.length) this.document.newPage();
+        }
+        this.document.close();
+    }
+
 
-    public void writeBioModel(BioModel biomodel, FileOutputStream fos, PageFormat pageFormat) throws Exception {
+    public void writeBioModel(BioModel biomodel, FileOutputStream fos, PageFormat pageFormat) throws DocumentException {
 
         writeBioModel(biomodel, fos, pageFormat, PublishPreferences.DEFAULT_BIO_PREF);
     }
 
 
-    public void writeBioModel(BioModel bioModel, FileOutputStream fos, PageFormat pageFormat, PublishPreferences preferences) throws Exception {
+    public void writeBioModel(BioModel bioModel, FileOutputStream fos, PageFormat pageFormat, PublishPreferences preferences) throws DocumentException {
 
         if (bioModel == null || fos == null || pageFormat == null || preferences == null) {
             throw new IllegalArgumentException("One or more null params while publishing BioModel.");
         }
-        createDocument(pageFormat);
-        createDocWriter(fos);
+        this.createDocument(pageFormat);
+        this.createDocWriter(fos);
         // Add metadata before you open the document...
         String name = bioModel.getName().trim();
         String userName = "Unknown";
@@ -2079,7 +2099,7 @@ protected void writeSimulation(Section container, Simulation sim) throws Documen
 
     //SimulationContext: ignored the constraints (steady/unsteady).
 //Electrical Stimulus: ignored the Ground Electrode,   
-    protected void writeSimulationContext(Chapter simContextsChapter, SimulationContext simContext, PublishPreferences preferences) throws Exception {
+    protected void writeSimulationContext(Chapter simContextsChapter, SimulationContext simContext, PublishPreferences preferences) throws DocumentException {
 
         Section simContextSection = simContextsChapter.addSection("Application: " + simContext.getName(), simContextsChapter.getNumberDepth() + 1);
         writeMetadata(simContextSection, simContext.getName(), simContext.getDescription(), null, "Application ");

vcell-core/src/main/java/org/vcell/plotting/Results2DLinePlot.java

@@ -0,0 +1,67 @@
+package org.vcell.plotting;
+
+import java.io.File;
+
+/**
+ * Stores all relevant info to create a 2D plot, and lazily builds a PDF on request
+ */
+public class Results2DLinePlot implements ResultsLinePlot {
+    private String plotTitle;
+    private double[] xData, yData;
+    private String xLabel, yLabel;
+
+    public Results2DLinePlot(){
+        this.plotTitle = "";
+        this.xData = new double[0];
+        this.yData = new double[0];
+        this.xLabel = "";
+        this.yLabel = "";
+    }
+
+    @Override
+    public void setTitle(String newTitle) {
+        this.plotTitle = newTitle;
+    }
+
+    @Override
+    public String getTitle() {
+        return this.plotTitle;
+    }
+
+    public void setXData(double[] newXData){
+        this.xData = newXData;
+    }
+
+    public double[] getXData(){
+        return this.xData;
+    }
+
+    public void setYData(double[] newYData){
+        this.yData = newYData;
+    }
+
+    public double[] getYData(){
+        return this.yData;
+    }
+
+    public void setXLabel(String newXLabel){
+        this.xLabel = newXLabel;
+    }
+
+    public String getXLabel(){
+        return this.xLabel;
+    }
+
+    public void setYLabel(String newYLabel){
+        this.yLabel = newYLabel;
+    }
+
+    public String getYLabel(){
+        return this.yLabel;
+    }
+
+    @Override
+    public void generatePdf(String desiredFileName, File desiredParentDirectory) {
+
+    }
+}

vcell-core/src/main/java/org/vcell/plotting/ResultsLinePlot.java

@@ -0,0 +1,29 @@
+package org.vcell.plotting;
+
+import java.io.File;
+
+/**
+ * Describes the basic functionality all LinePlots displaying simulation results should have.
+ */
+public interface ResultsLinePlot {
+
+    /**
+     * Generates a PDF copy of the current plot state, and exports it as PDF at the desired location.
+     * @param desiredFileName name of the plot file; needs no file suffix: ".pdf" will be appended.
+     * @param desiredParentDirectory directory to place the new pdf into.
+     */
+    void generatePdf(String desiredFileName, File desiredParentDirectory);
+
+    /**
+     * Setter for the title of the plot
+     * @param newTitle the desired new title as a String
+     */
+    void setTitle(String newTitle);
+
+    /**
+     * Getter for the title of the plot
+     * @return the title as a String
+     */
+    String getTitle();
+
+}

vcell-core/src/test/java/org/vcell/plotting/TestJFreeChartLibrary.java

@@ -0,0 +1,149 @@
+package org.vcell.plotting;
+
+import cbit.vcell.publish.PDFWriter;
+import com.lowagie.text.DocumentException;
+import org.jfree.chart.*;
+import org.jfree.chart.labels.StandardXYItemLabelGenerator;
+import org.jfree.chart.labels.XYItemLabelGenerator;
+import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.category.LineAndShapeRenderer;
+import org.jfree.data.*;
+import org.jfree.data.xy.*;
+import org.jfree.data.category.CategoryDataset;
+import org.jfree.data.general.DefaultKeyedValues2DDataset;
+
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
+import org.vcell.sbml.BMDB_SBML_Files;
+import org.vcell.util.Pair;
+import scala.collection.immutable.Page;
+
+import java.awt.*;
+import java.awt.image.BufferedImage;
+import java.awt.print.PageFormat;
+import java.awt.print.Paper;
+import java.io.*;
+import java.nio.charset.StandardCharsets;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.List;
+
+
+@Tag("Fast")
+public class TestJFreeChartLibrary {
+
+    private static List<XYDataItem> testData = List.of(
+        new XYDataItem(0.0, 0.0),
+        new XYDataItem(0.5, 0.25),
+        new XYDataItem(1.0, 1.0),
+        new XYDataItem(1.5, 2.25),
+        new XYDataItem(2.0, 4.0),
+        new XYDataItem(2.5, 6.25),
+        new XYDataItem(3.0, 9.0),
+        new XYDataItem(3.5, 12.25),
+        new XYDataItem(4.0, 16.0),
+        new XYDataItem(4.5, 20.25),
+        new XYDataItem(5.0, 25.0),
+        new XYDataItem(5.5, 30.25)
+    );
+
+    @Test
+    public void testDirectChartCreation() throws IOException, DocumentException {
+        PageFormat pageFormat = TestJFreeChartLibrary.generateAlternatePageFormat();
+
+        // Build Chart
+        XYSeries xySeries = new XYSeries("Ka+", true, false); // The "key" field is what to name the curve itself, when shown in a Legend
+        for (XYDataItem valuePair: TestJFreeChartLibrary.testData){
+            xySeries.add(valuePair);
+        }
+        XYDataset dataset2D = new XYSeriesCollection(xySeries);
+        this.generateChart(dataset2D, pageFormat, "Time");
+    }
+
+    @Test
+    public void testDirectChartCreationFromCSV() throws IOException, DocumentException {
+        PageFormat pageFormat = TestJFreeChartLibrary.generateAlternatePageFormat();
+        Pair<String, XYDataset> datasetPair = TestJFreeChartLibrary.csvToXYDataset();
+        this.generateChart(datasetPair.two, pageFormat, datasetPair.one);
+    }
+
+    private void generateChart(XYDataset dataset2D, PageFormat pageFormat, String xAxisLabel) throws IOException, DocumentException {
+        int AXIS_LABEL_FONT_SIZE = 15;
+        String yAxisLabel = "";
+        JFreeChart chart = ChartFactory.createXYLineChart("Test Sim Results", xAxisLabel, yAxisLabel, dataset2D);
+
+        // Tweak Chart so it looks better
+        chart.setBorderVisible(true);
+        XYPlot chartPlot = chart.getXYPlot();
+        chartPlot.getDomainAxis().setLabelFont(new Font(xAxisLabel, Font.PLAIN, AXIS_LABEL_FONT_SIZE));
+        chartPlot.getRangeAxis().setLabelFont(new Font(yAxisLabel, Font.PLAIN, AXIS_LABEL_FONT_SIZE));
+        if (dataset2D.getItemCount(0) <= 10) { // if it's too crowded, having data point labels is bad
+            for (int i = 0; i < dataset2D.getSeriesCount(); i++){
+                //DecimalFormat decimalformat1 = new DecimalFormat("##");
+                chartPlot.getRenderer().setSeriesItemLabelGenerator(0,
+                        new StandardXYItemLabelGenerator("({1}, {2})"));
+                chartPlot.getRenderer().setSeriesItemLabelFont(i, new Font(null, Font.PLAIN, 8));
+                chartPlot.getRenderer().setSeriesItemLabelsVisible(i, true);
+            }
+        }
+
+        // Prepare for export
+        PDFWriter pdfWriter = new PDFWriter();
+
+        File testfile = File.createTempFile("VCell::TestJFreeChartLibrary::testDirectChartCreation::", ".pdf");
+        if (!testfile.exists()) throw new IllegalArgumentException("Unable to create the testfile, somehow.");
+        try (FileOutputStream fos = new FileOutputStream(testfile)){
+            BufferedImage bfi = chart.createBufferedImage((int)pageFormat.getImageableWidth(), (int)pageFormat.getImageableHeight());
+            pdfWriter.writePlotImageDocument("Test Document", fos, pageFormat, bfi);
+        }
+    }
+
+    private static PageFormat generateAlternatePageFormat(){
+        java.awt.print.PageFormat pageFormat = java.awt.print.PrinterJob.getPrinterJob().defaultPage();
+        Paper alternatePaper = new Paper(); // We want to try and increase the margins
+        double altOriginX = alternatePaper.getImageableX() / 2, altOriginY = alternatePaper.getImageableY() / 2;
+        double altWidth = alternatePaper.getWidth() - 2 * altOriginX, altHeight = alternatePaper.getHeight() - 2 * altOriginY;
+        alternatePaper.setImageableArea(altOriginX, altOriginY, altWidth, altHeight);
+        pageFormat.setPaper(alternatePaper);
+        pageFormat.setOrientation(PageFormat.LANDSCAPE);
+        return pageFormat;
+    }
+
+    private static Pair<String, XYDataset> csvToXYDataset() throws IOException {
+        String CSV_DATA_FILE_LOCAL_PATH = "plot2d_SimpleSimulation.csv";
+        InputStream inputStream = TestJFreeChartLibrary.class.getResourceAsStream(CSV_DATA_FILE_LOCAL_PATH);
+        if (inputStream == null)
+            throw new FileNotFoundException(String.format("can not find `%s`; maybe it moved?", CSV_DATA_FILE_LOCAL_PATH));
+        XYSeriesCollection dataset2D = new XYSeriesCollection();
+        List<String> linesOfData;
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(inputStream, StandardCharsets.UTF_8))){
+            linesOfData = br.lines().toList();
+        }
+        String[] indepDataParts = linesOfData.get(linesOfData.size() - 1).split(",");
+        List<Double> xSeriesData = new ArrayList<>();
+        for (int partNum = 3; partNum < indepDataParts.length; partNum++){ // Skip first three; no need for them
+            xSeriesData.add(Double.parseDouble(indepDataParts[partNum]));
+        }
+
+        for (int lineNum = 0; lineNum < linesOfData.size() - 1; lineNum++){ // Skip last line; that's our independent-var data
+            XYSeries series = getXySeries(linesOfData, lineNum, xSeriesData);
+            dataset2D.addSeries(series);
+        }
+
+        return new Pair<>(indepDataParts[2], dataset2D);
+    }
+
+    private static XYSeries getXySeries(List<String> linesOfData, int lineNum, List<Double> xSeriesData) {
+        String[] parts = linesOfData.get(lineNum).split(",");
+        String ySeriesName = parts[2];
+        XYSeries series = new XYSeries(ySeriesName, true);
+        if (parts.length - 3 != xSeriesData.size()) throw new RuntimeException("Mismatched data length!");
+        for (int partNum = 3; partNum < parts.length; partNum++){ // Skip first two; third we've already grabbed
+            double xData = xSeriesData.get(partNum - 3), yData = Double.parseDouble(parts[partNum]);
+            series.add(xData, yData);
+        }
+        return series;
+    }
+}