X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=af638c8296de7ea596a8eccfe3138dfe092312a9;hb=refs%2Fheads%2Ffeature%2FJAL-629_--output_-_means_output_to_STDOUT;hp=e4f9ec61be47c93a4bd46ba36c6cbd1c104ce732;hpb=388622051f3d669942d9df63557c7a1401d7ff6d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e4f9ec6..af638c8 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -91,6 +91,7 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -138,9 +139,9 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
-  public ArgParser argparser = null;
+  private ArgParser argparser = null;
 
-  public BootstrapArgs bootstrapArgs = null;
+  private BootstrapArgs bootstrapArgs = null;
 
   private boolean QUIET = false;
 
@@ -273,7 +274,7 @@ public class Jalview
      * 
      */
     {
-      System.out.println("not in js");
+      Console.outPrintln("not in js");
     }
 
     // BH - for event debugging in JavaScript (Java mode only)
@@ -382,29 +383,30 @@ public class Jalview
       }.start();
     }
 
-    if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
+    if (!quiet() || !bootstrapArgs.outputToStdout()
+            || bootstrapArgs.contains(Arg.VERSION))
     {
-      System.out.println(
+      Console.outPrintln(
               "Java version: " + System.getProperty("java.version"));
-      System.out.println("Java home: " + System.getProperty("java.home"));
-      System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+      Console.outPrintln("Java home: " + System.getProperty("java.home"));
+      Console.outPrintln("Java arch: " + System.getProperty("os.arch") + " "
               + System.getProperty("os.name") + " "
               + System.getProperty("os.version"));
 
       String val = System.getProperty("sys.install4jVersion");
       if (val != null)
       {
-        System.out.println("Install4j version: " + val);
+        Console.outPrintln("Install4j version: " + val);
       }
       val = System.getProperty("installer_template_version");
       if (val != null)
       {
-        System.out.println("Install4j template version: " + val);
+        Console.outPrintln("Install4j template version: " + val);
       }
       val = System.getProperty("launcher_version");
       if (val != null)
       {
-        System.out.println("Launcher version: " + val);
+        Console.outPrintln("Launcher version: " + val);
       }
     }
 
@@ -462,6 +464,7 @@ public class Jalview
     // register SIGTERM listener
     Runtime.getRuntime().addShutdownHook(new Thread()
     {
+      @Override
       public void run()
       {
         Console.debug("Running shutdown hook");
@@ -508,7 +511,7 @@ public class Jalview
     Cache.loadProperties(usrPropsFile);
     if (usrPropsFile != null)
     {
-      System.out.println(
+      Console.outPrintln(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
       testoutput(bootstrapArgs, Arg.PROPS,
               "test/jalview/bin/testProps.jvprops", usrPropsFile);
@@ -540,7 +543,7 @@ public class Jalview
       {
         List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
                 .getList(Arg.HELP);
-        System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+        Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
                 .collect(Collectors.toList())));
         Jalview.exit(null, 0);
       }
@@ -550,7 +553,7 @@ public class Jalview
          * Now using new usage statement.
         showUsage();
         */
-        System.out.println(Arg.usage());
+        Console.outPrintln(Arg.usage());
         Jalview.exit(null, 0);
       }
 
@@ -580,13 +583,13 @@ public class Jalview
         try
         {
           Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-          System.out.println(
+          Console.outPrintln(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
           testoutput(bootstrapArgs, Arg.JABAWS,
                   "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
         } catch (MalformedURLException e)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Invalid jabaws parameter: " + jabawsUrl + " ignored");
         }
       }
@@ -616,7 +619,8 @@ public class Jalview
       }
       else
       {
-        System.out.println("Executing setprop argument: " + setprop);
+        jalview.bin.Console
+                .errPrintln("Executing setprop argument: " + setprop);
         if (Platform.isJS())
         {
           Cache.setProperty(setprop.substring(0, p),
@@ -632,8 +636,7 @@ public class Jalview
     {
       headless = true;
     }
-    System.setProperty("http.agent",
-            "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+    System.setProperty("http.agent", HttpUtils.getUserAgent());
 
     try
     {
@@ -749,7 +752,7 @@ public class Jalview
         }
         else
         {
-          System.out.println("CMD [-nousagestats] executed successfully!");
+          Console.outPrintln("CMD [-nousagestats] executed successfully!");
           testoutput(argparser, Arg.NOUSAGESTATS);
         }
 
@@ -765,7 +768,7 @@ public class Jalview
             // questionnaire
             Console.debug("Starting questionnaire url at " + url);
             desktop.checkForQuestionnaire(url);
-            System.out.println("CMD questionnaire[-" + url
+            Console.outPrintln("CMD questionnaire[-" + url
                     + "] executed successfully!");
           }
           else
@@ -786,8 +789,8 @@ public class Jalview
         }
         else
         {
-          System.out
-                  .println("CMD [-noquestionnaire] executed successfully!");
+          Console.outPrintln(
+                  "CMD [-noquestionnaire] executed successfully!");
           testoutput(argparser, Arg.QUESTIONNAIRE);
         }
 
@@ -808,7 +811,9 @@ public class Jalview
     }
     // Run Commands from cli
     cmds = new Commands(argparser, headlessArg);
+    cmds.processArgs();
     boolean commandsSuccess = cmds.argsWereParsed();
+
     if (commandsSuccess)
     {
       if (headlessArg)
@@ -876,7 +881,7 @@ public class Jalview
                         .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("CMD [-open " + file + "] executed successfully!");
+      Console.outPrintln("CMD [-open " + file + "] executed successfully!");
 
       if (!Platform.isJS())
       /**
@@ -913,7 +918,7 @@ public class Jalview
               format);
       if (af == null)
       {
-        System.out.println("error");
+        Console.outPrintln("error");
       }
       else
       {
@@ -928,7 +933,7 @@ public class Jalview
 
           if (cs != null)
           {
-            System.out.println(
+            Console.outPrintln(
                     "CMD [-colour " + data + "] executed successfully!");
           }
           af.changeColour(cs);
@@ -940,8 +945,8 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD groups[-" + data + "]  executed successfully!");
         }
         data = aparser.getValue("features", true);
@@ -949,8 +954,8 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD [-features " + data + "]  executed successfully!");
         }
 
@@ -958,8 +963,8 @@ public class Jalview
         if (data != null)
         {
           af.loadJalviewDataFile(data, null, null, null);
-          // System.out.println("Added " + data);
-          System.out.println(
+          // Console.outPrintln("Added " + data);
+          Console.outPrintln(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
         // set or clear the sortbytree flag.
@@ -968,7 +973,7 @@ public class Jalview
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
           {
-            System.out.println("CMD [-sortbytree] executed successfully!");
+            Console.outPrintln("CMD [-sortbytree] executed successfully!");
           }
         }
         if (aparser.contains("no-annotation"))
@@ -976,7 +981,7 @@ public class Jalview
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
           {
-            System.out.println("CMD no-annotation executed successfully!");
+            Console.outPrintln("CMD no-annotation executed successfully!");
           }
         }
         if (aparser.contains("nosortbytree"))
@@ -984,8 +989,8 @@ public class Jalview
           af.getViewport().setSortByTree(false);
           if (!af.getViewport().getSortByTree())
           {
-            System.out
-                    .println("CMD [-nosortbytree] executed successfully!");
+            Console.outPrintln(
+                    "CMD [-nosortbytree] executed successfully!");
           }
         }
         data = aparser.getValue("tree", true);
@@ -993,7 +998,7 @@ public class Jalview
         {
           try
           {
-            System.out.println(
+            Console.outPrintln(
                     "CMD [-tree " + data + "] executed successfully!");
             NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
@@ -1001,125 +1006,135 @@ public class Jalview
                     .setCurrentTree(af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
-            System.err.println("Couldn't add tree " + data);
+            jalview.bin.Console.errPrintln("Couldn't add tree " + data);
             ex.printStackTrace(System.err);
           }
         }
-        
+
         if (groovyscript != null)
         {
           // Execute the groovy script after we've done all the rendering stuff
           // and before any images or figures are generated.
-          System.out.println("Executing script " + groovyscript);
+          Console.outPrintln("Executing script " + groovyscript);
           executeGroovyScript(groovyscript, af);
-          System.out.println("CMD groovy[" + groovyscript
+          Console.outPrintln("CMD groovy[" + groovyscript
                   + "] executed successfully!");
           groovyscript = null;
         }
         String imageName = "unnamed.png";
         while (aparser.getSize() > 1)
         {
-          String outputFormat = aparser.nextValue();
-          file = aparser.nextValue();
-
-          if (outputFormat.equalsIgnoreCase("png"))
-          {
-            af.createPNG(new File(file));
-            imageName = (new File(file)).getName();
-            System.out.println("Creating PNG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("svg"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            af.createSVG(imageFile);
-            System.out.println("Creating SVG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("html"))
+          try
           {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-            htmlSVG.exportHTML(file);
+            String outputFormat = aparser.nextValue();
+            file = aparser.nextValue();
 
-            System.out.println("Creating HTML image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
-          {
-            if (file == null)
+            if (outputFormat.equalsIgnoreCase("png"))
             {
-              System.err.println("The output html file must not be null");
-              return;
+              Console.outPrintln("Creating PNG image: " + file);
+              af.createPNG(new File(file));
+              imageName = (new File(file)).getName();
+              continue;
             }
-            try
+            else if (outputFormat.equalsIgnoreCase("svg"))
             {
-              BioJsHTMLOutput.refreshVersionInfo(
-                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-            } catch (URISyntaxException e)
+              Console.outPrintln("Creating SVG image: " + file);
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              af.createSVG(imageFile);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("html"))
             {
-              e.printStackTrace();
+              File imageFile = new File(file);
+              imageName = imageFile.getName();
+              HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+
+              Console.outPrintln("Creating HTML image: " + file);
+              htmlSVG.exportHTML(file);
+              continue;
             }
-            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-            bjs.exportHTML(file);
-            System.out
-                    .println("Creating BioJS MSA Viwer HTML file: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("imgMap"))
-          {
-            af.createImageMap(new File(file), imageName);
-            System.out.println("Creating image map: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("eps"))
-          {
-            File outputFile = new File(file);
-            System.out.println(
-                    "Creating EPS file: " + outputFile.getAbsolutePath());
-            af.createEPS(outputFile);
-            continue;
-          }
-          FileFormatI outFormat = null;
-          try
-          {
-            outFormat = FileFormats.getInstance().forName(outputFormat);
-          } catch (Exception formatP)
-          {
-            System.out.println("Couldn't parse " + outFormat
-                    + " as a valid Jalview format string.");
-          }
-          if (outFormat != null)
-          {
-            if (!outFormat.isWritable())
+            else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+            {
+              if (file == null)
+              {
+                jalview.bin.Console.errPrintln(
+                        "The output html file must not be null");
+                return;
+              }
+              try
+              {
+                BioJsHTMLOutput.refreshVersionInfo(
+                        BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+              } catch (URISyntaxException e)
+              {
+                e.printStackTrace();
+              }
+              BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+              Console.outPrintln(
+                      "Creating BioJS MSA Viwer HTML file: " + file);
+              bjs.exportHTML(file);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("imgMap"))
+            {
+              Console.outPrintln("Creating image map: " + file);
+              af.createImageMap(new File(file), imageName);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("eps"))
+            {
+              File outputFile = new File(file);
+              Console.outPrintln(
+                      "Creating EPS file: " + outputFile.getAbsolutePath());
+              af.createEPS(outputFile);
+              continue;
+            }
+
+            FileFormatI outFormat = null;
+            try
             {
-              System.out.println(
-                      "This version of Jalview does not support alignment export as "
-                              + outputFormat);
+              outFormat = FileFormats.getInstance().forName(outputFormat);
+            } catch (Exception formatP)
+            {
+              Console.outPrintln("Couldn't parse " + outFormat
+                      + " as a valid Jalview format string.");
             }
-            else
+            if (outFormat != null)
             {
-              af.saveAlignment(file, outFormat);
-              if (af.isSaveAlignmentSuccessful())
+              if (!outFormat.isWritable())
               {
-                System.out.println("Written alignment in "
-                        + outFormat.getName() + " format to " + file);
+                Console.outPrintln(
+                        "This version of Jalview does not support alignment export as "
+                                + outputFormat);
               }
               else
               {
-                System.out.println("Error writing file " + file + " in "
-                        + outFormat.getName() + " format!!");
+                af.saveAlignment(file, outFormat);
+                if (af.isSaveAlignmentSuccessful())
+                {
+                  Console.outPrintln("Written alignment in "
+                          + outFormat.getName() + " format to " + file);
+                }
+                else
+                {
+                  Console.outPrintln("Error writing file " + file + " in "
+                          + outFormat.getName() + " format!!");
+                }
               }
             }
+          } catch (ImageOutputException ioexc)
+          {
+            Console.outPrintln(
+                    "Unexpected error whilst exporting image to " + file);
+            ioexc.printStackTrace();
           }
 
         }
 
         while (aparser.getSize() > 0)
         {
-          System.out.println("Unknown arg: " + aparser.nextValue());
+          Console.outPrintln("Unknown arg: " + aparser.nextValue());
         }
       }
     }
@@ -1187,12 +1202,12 @@ public class Jalview
     {
       if (Cache.groovyJarsPresent())
       {
-        System.out.println("Executing script " + groovyscript);
+        Console.outPrintln("Executing script " + groovyscript);
         executeGroovyScript(groovyscript, startUpAlframe);
       }
       else
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                         + groovyscript);
       }
@@ -1210,93 +1225,102 @@ public class Jalview
 
   private static void setLookAndFeel()
   {
-    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
-    // "mac" or "flat"
-    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
-    // try Quaqua/Vaqua.
-    String lafProp = System.getProperty("laf");
-    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
-    String laf = "none";
-    if (lafProp != null)
-    {
-      laf = lafProp;
-    }
-    else if (lafSetting != null)
-    {
-      laf = lafSetting;
-    }
-    boolean lafSet = false;
-    switch (laf)
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-    case "crossplatform":
-      lafSet = setCrossPlatformLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "system":
-      lafSet = setSystemLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "gtk":
-      lafSet = setGtkLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "metal":
-      lafSet = setMetalLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
-      }
-      break;
-    case "nimbus":
-      lafSet = setNimbusLookAndFeel();
-      if (!lafSet)
-      {
-        Console.error("Could not set requested laf=" + laf);
+      // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+      // "mac" or "flat"
+      // If not set (or chosen laf fails), use the normal SystemLaF and if on
+      // Mac,
+      // try Quaqua/Vaqua.
+      String lafProp = System.getProperty("laf");
+      String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+      String laf = "none";
+      if (lafProp != null)
+      {
+        laf = lafProp;
       }
-      break;
-    case "flat":
-      lafSet = setFlatLookAndFeel();
-      if (!lafSet)
+      else if (lafSetting != null)
       {
-        Console.error("Could not set requested laf=" + laf);
+        laf = lafSetting;
       }
-      break;
-    case "mac":
-      lafSet = setMacLookAndFeel();
-      if (!lafSet)
+      boolean lafSet = false;
+      switch (laf)
       {
-        Console.error("Could not set requested laf=" + laf);
+      case "crossplatform":
+        lafSet = setCrossPlatformLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "system":
+        lafSet = setSystemLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "gtk":
+        lafSet = setGtkLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "metal":
+        lafSet = setMetalLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "nimbus":
+        lafSet = setNimbusLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "flat":
+        lafSet = setFlatLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "mac":
+        lafSet = setMacLookAndFeel();
+        if (!lafSet)
+        {
+          Console.error("Could not set requested laf=" + laf);
+        }
+        break;
+      case "none":
+        break;
+      default:
+        Console.error("Requested laf=" + laf + " not implemented");
       }
-      break;
-    case "none":
-      break;
-    default:
-      Console.error("Requested laf=" + laf + " not implemented");
-    }
-    if (!lafSet)
-    {
-      // Flatlaf default for everyone!
-      lafSet = setFlatLookAndFeel();
       if (!lafSet)
       {
-        setSystemLookAndFeel();
-      }
-      if (Platform.isLinux())
-      {
-        setLinuxLookAndFeel();
-      }
-      if (Platform.isMac())
-      {
-        setMacLookAndFeel();
+        // Flatlaf default for everyone!
+        lafSet = setFlatLookAndFeel();
+        if (!lafSet)
+        {
+          setSystemLookAndFeel();
+        }
+        if (Platform.isLinux())
+        {
+          setLinuxLookAndFeel();
+        }
+        if (Platform.isMac())
+        {
+          setMacLookAndFeel();
+        }
       }
     }
   }
@@ -1528,7 +1552,7 @@ public class Jalview
   /*
   private static void showUsage()
   {
-    System.out.println(
+    jalview.bin.Console.outPrintln(
             "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
                     + "-nodisplay\tRun Jalview without User Interface.\n"
                     + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
@@ -1554,7 +1578,7 @@ public class Jalview
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                     + "-noquestionnaire\tTurn off questionnaire check.\n"
                     + "-nonews\tTurn off check for Jalview news.\n"
-                    + "-nousagestats\tTurn off google analytics tracking for this session.\n"
+                    + "-nousagestats\tTurn off analytics tracking for this session.\n"
                     + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                     // +
                     // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
@@ -1576,18 +1600,16 @@ public class Jalview
      * start a User Config prompt asking if we can log usage statistics.
      */
     PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
-            "USAGESTATS", "Jalview Usage Statistics",
-            "Do you want to help make Jalview better by enabling "
-                    + "the collection of usage statistics with Google Analytics ?"
-                    + "\n\n(you can enable or disable usage tracking in the preferences)",
+            "USAGESTATS",
+            MessageManager.getString("prompt.plausible_analytics_title"),
+            MessageManager.getString("prompt.plausible_analytics"),
             new Runnable()
             {
               @Override
               public void run()
               {
-                Console.debug(
-                        "Initialising googletracker for usage stats.");
-                Cache.initGoogleTracker();
+                Console.debug("Initialising analytics for usage stats.");
+                Cache.initAnalytics();
                 Console.debug("Tracking enabled.");
               }
             }, new Runnable()
@@ -1595,7 +1617,7 @@ public class Jalview
               @Override
               public void run()
               {
-                Console.debug("Not enabling Google Tracking.");
+                Console.debug("Not enabling analytics.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);
@@ -1641,9 +1663,10 @@ public class Jalview
 
       } catch (Exception ex)
       {
-        System.err.println("Failed to read from STDIN into tempfile "
-                + ((tfile == null) ? "(tempfile wasn't created)"
-                        : tfile.toString()));
+        jalview.bin.Console
+                .errPrintln("Failed to read from STDIN into tempfile "
+                        + ((tfile == null) ? "(tempfile wasn't created)"
+                                : tfile.toString()));
         ex.printStackTrace();
         return;
       }
@@ -1652,7 +1675,7 @@ public class Jalview
         sfile = tfile.toURI().toURL();
       } catch (Exception x)
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
                         + tfile.toURI());
         x.printStackTrace();
@@ -1669,17 +1692,20 @@ public class Jalview
         tfile = new File(groovyscript);
         if (!tfile.exists())
         {
-          System.err.println("File '" + groovyscript + "' does not exist.");
+          jalview.bin.Console.errPrintln(
+                  "File '" + groovyscript + "' does not exist.");
           return;
         }
         if (!tfile.canRead())
         {
-          System.err.println("File '" + groovyscript + "' cannot be read.");
+          jalview.bin.Console.errPrintln(
+                  "File '" + groovyscript + "' cannot be read.");
           return;
         }
         if (tfile.length() < 1)
         {
-          System.err.println("File '" + groovyscript + "' is empty.");
+          jalview.bin.Console
+                  .errPrintln("File '" + groovyscript + "' is empty.");
           return;
         }
         try
@@ -1687,7 +1713,7 @@ public class Jalview
           sfile = tfile.getAbsoluteFile().toURI().toURL();
         } catch (Exception ex)
         {
-          System.err.println("Failed to create a file URL for "
+          jalview.bin.Console.errPrintln("Failed to create a file URL for "
                   + tfile.getAbsoluteFile());
           return;
         }
@@ -1712,8 +1738,9 @@ public class Jalview
       }
     } catch (Exception e)
     {
-      System.err.println("Exception Whilst trying to execute file " + sfile
-              + " as a groovy script.");
+      jalview.bin.Console
+              .errPrintln("Exception Whilst trying to execute file " + sfile
+                      + " as a groovy script.");
       e.printStackTrace(System.err);
 
     }
@@ -1755,7 +1782,7 @@ public class Jalview
     Jalview.currentAlignFrame = currentAlignFrame;
   }
 
-  protected Commands getCommands()
+  public Commands getCommands()
   {
     return cmds;
   }
@@ -1769,11 +1796,11 @@ public class Jalview
       {
         if (exitcode == 0)
         {
-          System.out.println(message);
+          Console.outPrintln(message);
         }
         else
         {
-          System.err.println(message);
+          jalview.bin.Console.errPrintln(message);
         }
       }
     }
@@ -1865,7 +1892,7 @@ public class Jalview
     if (yes && ((s1 == null && s2 == null)
             || (s1 != null && s1.equals(s2))))
     {
-      System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+      Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
               + "' was set");
     }
   }
@@ -1923,6 +1950,17 @@ public class Jalview
     {
       message = a.argString() + (yes ? " was set" : " was not set");
     }
-    System.out.println("[TESTOUTPUT] arg " + message);
+    Console.outPrintln("[TESTOUTPUT] arg " + message);
+  }
+
+  public ArgParser getArgParser()
+  {
+    return argparser;
+  }
+
+  public BootstrapArgs getBootstrapArgs()
+  {
+    return bootstrapArgs;
   }
+
 }