Switch To Markdown

Instead of long strings within the Java file the text is written within a markdown file, parsed into HTML, and then rendered by the JTextPane.

view-simulation-results/pom.xml

@@ -157,6 +157,12 @@
             <artifactId>jsoup</artifactId>
             <version>1.16.1</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.commonmark</groupId>
+            <artifactId>commonmark</artifactId>
+            <version>0.20.0</version>
+        </dependency>
     </dependencies>
 
 </project>

view-simulation-results/src/main/java/org/vcell/N5/UI/HelpExplanation.java

@@ -1,41 +1,57 @@
 package org.vcell.N5.UI;
 
+import org.commonmark.node.Node;
+import org.commonmark.parser.Parser;
+import org.commonmark.renderer.html.HtmlRenderer;
+
 import javax.swing.*;
+import java.awt.*;
+import java.io.FileReader;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 
 public class HelpExplanation {
     private JDialog jDialog;
 
     public HelpExplanation(){
-        JPanel helperPanel = new JPanel();
-        JTextArea textArea = new JTextArea();
-
-        String intro = "The VCell application can export the simulations it creates into multiple formats. The format type .N5 is stored remotely on VCell servers,"
-                + "and allows for other applications such as ImageJ to access the results of these simulations, perform some type of analysis, and never have to save"
-                + "the simulation results locally. \n\n\n";
-
-        String accessingSimulationResults = "There are three methods for accessing simulation results within this plugin. \n"
-                + "1. Copy the export link from the VCell app, click the 'Remote Files' button, paste the link in the text box then open it. This method is best for"
-                + "when you need to save a set of exports for the long term future. \n"
-                + "2. Click the recent export button to open the most recent simulation you exported in the N5 format. \n"
-                + "3. Open the export table and open any export within that table using the open button. The tables information is stored locally on your computer so"
-                + "if your computers drive fails the table will be empty, but any links saved elsewhere can still be used. \n\n\n";
+        int height = 400;
+        int width = 700;
 
-        String n5AndDataSet = "N5 files are one to one with simulations within VCell in terms of grouping."
-                +"Data sets are the grouping category for different export variances. For example with simulation A, if you decide to export only 2 of 3 variables, that"
-                + " would be one dataset. For that same simulation if you decide to 1 variable that would be a completely different dataset. "
-                + "Now with simulation B, if you decide to export 2 of 3 variables that would be a different N5 file and a different dataset.";
-
-        textArea.setText("Intro: \n" + intro + "Accessing Simulation Results: \n" + accessingSimulationResults + "N5 and Datasets: \n" + n5AndDataSet);
+        JPanel helperPanel = new JPanel();
+        JTextPane textArea = new JTextPane();
+
+        Parser parser = Parser.builder().build();
+        String md;
+        URL mdPath = ClassLoader.getSystemClassLoader().getResource("Help.md");
+        try {
+            md = new String(Files.readAllBytes(Paths.get(mdPath.getPath())));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+        Node node = parser.parse(md);
+        HtmlRenderer renderer = HtmlRenderer.builder().build();
+        String text = renderer.render(node);
+//        textArea.setText("Intro: \n" + intro + "Accessing Simulation Results: \n" + accessingSimulationResults + "N5 and Datasets: \n" + n5AndDataSet);
+        textArea.setContentType("text/html");
+        textArea.setSize(width, height);
+        textArea.setPreferredSize(new Dimension(width, height));
+        textArea.setText(text);
         textArea.setEditable(false);
-        textArea.setLineWrap(true);
-        textArea.setWrapStyleWord(true);
-        textArea.setSize(600, 600);
-        helperPanel.add(textArea);
+//        textArea.setLineWrap(true);
+//        textArea.setWrapStyleWord(true);
+        JScrollPane scrollPane = new JScrollPane(textArea);
+        scrollPane.setSize(width, height);
+        helperPanel.setSize(width, height);
+        helperPanel.add(scrollPane);
+
 
         JOptionPane pane = new JOptionPane(helperPanel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[]{"Close"});
         jDialog = pane.createDialog("Helper Menu");
         jDialog.setModal(false);
-        jDialog.setResizable(true);
+        jDialog.setPreferredSize(new Dimension(width, height));
+//        jDialog.setResizable(true);
     }
 
     public void displayHelpMenu(){

view-simulation-results/src/main/resources/Help.md

@@ -0,0 +1,28 @@
+### Intro
+The VCell application can export the simulations it creates into multiple formats.
+The .N5 format type is stored remotely on VCell servers, allowing other applications, such as ImageJ,
+to access the results of these simulations, perform various types of analyses,
+and avoid the need to save the simulation results locally.
+
+### Accessing Simulation Results
+There are three methods for accessing simulation results within this plugin:
+
+1. Copy the export link from the VCell app, click the 'Remote Files' button, paste the link in the text box, and then open it.
+This method is best when you need to save a set of exports for the long term future.
+
+2. Click the recent export button to open the most recent simulation you exported in the N5 format.
+
+3. Open the export table and access any export within that table using the open button. The table's information
+is stored locally on your computer. If your computer's drive fails, the table will be empty, but any links
+saved elsewhere can still be used.
+
+
+### N5 and Datasets
+N5 files correspond one-to-one with simulations within VCell in terms of grouping. 
+Data sets serve as the grouping category for different export variances.
+For example, with simulation A, if you choose to export only 2 of 3 variables,
+that constitutes one dataset. In the same simulation, if you decide to export just 1 variable,
+that would be an entirely different dataset.
+
+Now, considering simulation B, if you choose to export 2 of 3 variables, it results in a different N5 file and a distinct dataset.
+