add loguserplot as a JVM option

uk/ac/sanger/artemis/components/GraphMenu.java

@@ -46,6 +46,7 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.io.IOException;
 import java.io.File;
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.List;
 import java.util.Vector;
@@ -170,7 +171,7 @@ public class GraphMenu extends JMenu
         {
           try
           {
-            addUserPlot (null);
+            addUserPlot ((uk.ac.sanger.artemis.util.Document)null, false);
             adjustSplitPane(true);
           }
           catch(java.lang.OutOfMemoryError emem)
@@ -245,34 +246,24 @@ public class GraphMenu extends JMenu
     }
     
     // add user plots from the command line JVM option
-    if(System.getProperty("userplot"+ (index > 0 ? index : "")) != null)
+    if(System.getProperty("userplot"+ (index > 0 ? index : "")) != null ||
+       System.getProperty("loguserplot"+ (index > 0 ? index : "")) != null)
     {
-      String plots[] = System.getProperty("userplot"+ (index > 0 ? index : "")).split("[\\s,]");
+      String plots[] = new String[]{};
+      if(System.getProperty("userplot"+ (index > 0 ? index : "")) != null)
+        plots = System.getProperty("userplot"+ (index > 0 ? index : "")).split("[\\s,]");
+      
+      String logplots[] = new String[]{};
+      if(System.getProperty("loguserplot"+ (index > 0 ? index : "")) != null)
+        logplots = System.getProperty("loguserplot"+ (index > 0 ? index : "")).split("[\\s,]");
       try
       {
         for(int i=0;i<plots.length; i++)
-        {
-          if(plots[i].startsWith("http:") ||
-             plots[i].startsWith("file:") ||
-             plots[i].startsWith("ftp:"))
-          {
-            uk.ac.sanger.artemis.util.Document document =
-              new uk.ac.sanger.artemis.util.URLDocument (new URL(plots[i]));
-            addUserPlot (document);
-          }
-          else
-          {
-            File f = new File(plots[i]);
-            if(f.exists())
-            {
-              uk.ac.sanger.artemis.util.Document document =
-                new uk.ac.sanger.artemis.util.FileDocument (f);
-              addUserPlot (document);
-            }
-            else
-              System.err.println(plots[i]+" not found.");
-          }
-        }
+          addUserPlot (plots[i], false);
+        
+        for(int i=0;i<logplots.length; i++)
+          addUserPlot (logplots[i], true);
+
         splitPane.setDividerSize(3);
         splitPane.setDividerLocation(150);
       }
@@ -559,12 +550,27 @@ public class GraphMenu extends JMenu
     return true;
   }
   
+  private void addUserPlot (final String plot, final boolean isLog) throws MalformedURLException
+  {
+    if (plot.startsWith("http:") || plot.startsWith("file:") || plot.startsWith("ftp:"))
+      addUserPlot(new uk.ac.sanger.artemis.util.URLDocument(new URL(plot)), isLog);
+    else
+    {
+      File f = new File(plot);
+      if (f.exists())
+        addUserPlot(new uk.ac.sanger.artemis.util.FileDocument(f), isLog);
+      else
+        System.err.println(plot + " not found.");
+    }
+  }
+  
   /**
    *  Add a UserDataAlgorithm to the display.
    **/
-  private void addUserPlot (uk.ac.sanger.artemis.util.Document document) 
+  private void addUserPlot (uk.ac.sanger.artemis.util.Document document,
+                            boolean isLog) 
   {
-    final JCheckBox logTransform = new JCheckBox("Use log(data+1)", false);
+    final JCheckBox logTransform = new JCheckBox("Use log(data+1)", isLog);
     if (document == null)
     {
       final JFrame frame = Utilities.getComponentFrame(base_plot_group);