X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=362b15eb1fb880171a91d11df281be28c544bd5f;hb=c9f21b2f940ed83ee018f7651302e7d3cea489c5;hp=fc6d23e52363bb33943c4bd4b73b000b4e14585d;hpb=ee684c859bd7cddaa517a81cf11e168d4596ddbe;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fc6d23e..362b15e 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -24,6 +24,8 @@ import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.lang.reflect.Constructor;
+import java.net.MalformedURLException;
+import java.net.URI;
 import java.net.URL;
 import java.net.URLDecoder;
 import java.security.AllPermission;
@@ -81,8 +83,9 @@ public class Jalview
             + System.getProperty("os.version"));
     if (new Platform().isAMac())
     {
-    	System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview");
-    	System.setProperty("apple.laf.useScreenMenuBar", "true");
+      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+              "Jalview");
+      System.setProperty("apple.laf.useScreenMenuBar", "true");
     }
 
     ArgsParser aparser = new ArgsParser(args);
@@ -179,6 +182,7 @@ public class Jalview
     if (!headless)
     {
       desktop = new Desktop();
+      desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -246,7 +250,8 @@ public class Jalview
       {
         try
         {
-          String viprotocol = Jalview.checkProtocol(vamsasImport);
+          String viprotocol = jalview.io.AppletFormatAdapter
+                  .checkProtocol(vamsasImport);
           if (viprotocol == jalview.io.FormatAdapter.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
@@ -314,9 +319,15 @@ public class Jalview
         }
       }
     }
+    long progress = -1;
     // Finally, deal with the remaining input data.
     if (file != null)
     {
+      if (!headless)
+      {
+        desktop.setProgressBar("Processing commandline arguments...",
+                progress = System.currentTimeMillis());
+      }
       System.out.println("Opening file: " + file);
 
       if (!file.startsWith("http://"))
@@ -331,7 +342,7 @@ public class Jalview
         }
       }
 
-      protocol = checkProtocol(file);
+      protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
 
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
@@ -340,158 +351,164 @@ public class Jalview
       if (af == null)
       {
         System.out.println("error");
-        return;
       }
-
-      data = aparser.getValue("colour", true);
-      if (data != null)
+      else
       {
-        data.replaceAll("%20", " ");
 
-        jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
-                .getColour(af.getViewport().getAlignment(), data);
-
-        if (cs == null)
+        data = aparser.getValue("colour", true);
+        if (data != null)
         {
-          jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-                  "white");
-          ucs.parseAppletParameter(data);
-          cs = ucs;
-        }
+          data.replaceAll("%20", " ");
 
-        System.out.println("colour is " + data);
-        af.changeColour(cs);
-      }
+          jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+                  .getColour(af.getViewport().getAlignment(), data);
 
-      // Must maintain ability to use the groups flag
-      data = aparser.getValue("groups", true);
-      if (data != null)
-      {
-        af.parseFeaturesFile(data, checkProtocol(data));
-        System.out.println("Added " + data);
-      }
-      data = aparser.getValue("features", true);
-      if (data != null)
-      {
-        af.parseFeaturesFile(data, checkProtocol(data));
-        System.out.println("Added " + data);
-      }
-
-      data = aparser.getValue("annotations", true);
-      if (data != null)
-      {
-        af.loadJalviewDataFile(data);
-        System.out.println("Added " + data);
-      }
-      // set or clear the sortbytree flag.
-      if (aparser.contains("sortbytree"))
-      {
-        af.getViewport().setSortByTree(true);
-      }
-      if (aparser.contains("nosortbytree"))
-      {
-        af.getViewport().setSortByTree(false);
-      }
-      data = aparser.getValue("tree", true);
-      if (data != null)
-      {
-        jalview.io.NewickFile fin = null;
-        try
-        {
-          fin = new jalview.io.NewickFile(data, checkProtocol(data));
-          if (fin != null)
+          if (cs == null)
           {
-            af.getViewport().setCurrentTree(
-                    af.ShowNewickTree(fin, data).getTree());
-            System.out.println("Added tree " + data);
+            jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+                    "white");
+            ucs.parseAppletParameter(data);
+            cs = ucs;
           }
-        } catch (IOException ex)
-        {
-          System.err.println("Couldn't add tree " + data);
-          ex.printStackTrace(System.err);
-        }
-      }
-      // todo - load PDB structure to alignment
-      // (associate with identical sequence in alignment, or a specified
-      // sequence)
 
-      getFeatures = checkDasArguments(aparser);
-      if (af != null && getFeatures != null)
-      {
-        FeatureFetcher ff = startFeatureFetching(getFeatures);
-        if (ff != null)
-          while (!ff.allFinished() || af.operationInProgress())
-          {
-            // wait around until fetching is finished.
-            try
-            {
-              Thread.sleep(100);
-            } catch (Exception e)
-            {
+          System.out.println("colour is " + data);
+          af.changeColour(cs);
+        }
 
-            }
-          }
-        getFeatures = null; // have retrieved features - forget them now.
-      }
-      if (groovyscript != null)
-      {
-        // Execute the groovy script after we've done all the rendering stuff
-        // and before any images or figures are generated.
-        if (jalview.bin.Cache.groovyJarsPresent())
+        // Must maintain ability to use the groups flag
+        data = aparser.getValue("groups", true);
+        if (data != null)
         {
-          System.out.println("Executing script " + groovyscript);
-          executeGroovyScript(groovyscript, desktop);
+          af.parseFeaturesFile(data,
+                  jalview.io.AppletFormatAdapter.checkProtocol(data));
+          System.out.println("Added " + data);
         }
-        else
+        data = aparser.getValue("features", true);
+        if (data != null)
         {
-          System.err
-                  .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
-                          + groovyscript);
+          af.parseFeaturesFile(data,
+                  jalview.io.AppletFormatAdapter.checkProtocol(data));
+          System.out.println("Added " + data);
         }
-        groovyscript = null;
-      }
-      String imageName = "unnamed.png";
-      while (aparser.getSize() > 1)
-      {
-        format = aparser.nextValue();
-        file = aparser.nextValue();
 
-        if (format.equalsIgnoreCase("png"))
+        data = aparser.getValue("annotations", true);
+        if (data != null)
         {
-          af.createPNG(new java.io.File(file));
-          imageName = (new java.io.File(file)).getName();
-          System.out.println("Creating PNG image: " + file);
-          continue;
+          af.loadJalviewDataFile(data, null, null, null);
+          System.out.println("Added " + data);
         }
-        else if (format.equalsIgnoreCase("imgMap"))
+        // set or clear the sortbytree flag.
+        if (aparser.contains("sortbytree"))
         {
-          af.createImageMap(new java.io.File(file), imageName);
-          System.out.println("Creating image map: " + file);
-          continue;
+          af.getViewport().setSortByTree(true);
         }
-        else if (format.equalsIgnoreCase("eps"))
+        if (aparser.contains("nosortbytree"))
         {
-          System.out.println("Creating EPS file: " + file);
-          af.createEPS(new java.io.File(file));
-          continue;
+          af.getViewport().setSortByTree(false);
         }
+        data = aparser.getValue("tree", true);
+        if (data != null)
+        {
+          jalview.io.NewickFile fin = null;
+          try
+          {
+            fin = new jalview.io.NewickFile(data,
+                    jalview.io.AppletFormatAdapter.checkProtocol(data));
+            if (fin != null)
+            {
+              af.getViewport().setCurrentTree(
+                      af.ShowNewickTree(fin, data).getTree());
+              System.out.println("Added tree " + data);
+            }
+          } catch (IOException ex)
+          {
+            System.err.println("Couldn't add tree " + data);
+            ex.printStackTrace(System.err);
+          }
+        }
+        // TODO - load PDB structure(s) to alignment JAL-629
+        // (associate with identical sequence in alignment, or a specified
+        // sequence)
 
-        if (af.saveAlignment(file, format))
+        getFeatures = checkDasArguments(aparser);
+        if (af != null && getFeatures != null)
         {
-          System.out.println("Written alignment in " + format
-                  + " format to " + file);
+          FeatureFetcher ff = startFeatureFetching(getFeatures);
+          if (ff != null)
+            while (!ff.allFinished() || af.operationInProgress())
+            {
+              // wait around until fetching is finished.
+              try
+              {
+                Thread.sleep(100);
+              } catch (Exception e)
+              {
+
+              }
+            }
+          getFeatures = null; // have retrieved features - forget them now.
         }
-        else
+        if (groovyscript != null)
         {
-          System.out.println("Error writing file " + file + " in " + format
-                  + " format!!");
+          // Execute the groovy script after we've done all the rendering stuff
+          // and before any images or figures are generated.
+          if (jalview.bin.Cache.groovyJarsPresent())
+          {
+            System.out.println("Executing script " + groovyscript);
+            executeGroovyScript(groovyscript, new Object[]
+            { desktop, af });
+          }
+          else
+          {
+            System.err
+                    .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+                            + groovyscript);
+          }
+          groovyscript = null;
         }
+        String imageName = "unnamed.png";
+        while (aparser.getSize() > 1)
+        {
+          format = aparser.nextValue();
+          file = aparser.nextValue();
 
-      }
+          if (format.equalsIgnoreCase("png"))
+          {
+            af.createPNG(new java.io.File(file));
+            imageName = (new java.io.File(file)).getName();
+            System.out.println("Creating PNG image: " + file);
+            continue;
+          }
+          else if (format.equalsIgnoreCase("imgMap"))
+          {
+            af.createImageMap(new java.io.File(file), imageName);
+            System.out.println("Creating image map: " + file);
+            continue;
+          }
+          else if (format.equalsIgnoreCase("eps"))
+          {
+            System.out.println("Creating EPS file: " + file);
+            af.createEPS(new java.io.File(file));
+            continue;
+          }
 
-      while (aparser.getSize() > 0)
-      {
-        System.out.println("Unknown arg: " + aparser.nextValue());
+          if (af.saveAlignment(file, format))
+          {
+            System.out.println("Written alignment in " + format
+                    + " format to " + file);
+          }
+          else
+          {
+            System.out.println("Error writing file " + file + " in "
+                    + format + " format!!");
+          }
+
+        }
+
+        while (aparser.getSize() > 0)
+        {
+          System.out.println("Unknown arg: " + aparser.nextValue());
+        }
       }
     }
     AlignFrame startUpAlframe = null;
@@ -501,8 +518,18 @@ public class Jalview
     if (!headless && file == null && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
-      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
-              "http://www.jalview.org/examples/exampleFile_2_3.jar");
+      file = jalview.bin.Cache.getDefault(
+              "STARTUP_FILE",
+              jalview.bin.Cache.getDefault("www.jalview.org",
+                      "http://www.jalview.org")
+                      + "/examples/exampleFile_2_7.jar");
+      if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+      {
+        // hardwire upgrade of the startup file
+        file.replace("_2_3.jar", "_2_7.jar");
+        // and remove the stale setting
+        jalview.bin.Cache.removeProperty("STARTUP_FILE");
+      }
 
       protocol = "File";
 
@@ -536,13 +563,14 @@ public class Jalview
         startFeatureFetching(getFeatures);
       }
     }
-    // execute a groovy script.
+    // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
       {
         System.out.println("Executing script " + groovyscript);
-        executeGroovyScript(groovyscript, desktop);
+        executeGroovyScript(groovyscript, new Object[]
+        { desktop, startUpAlframe });
       }
       else
       {
@@ -551,8 +579,15 @@ public class Jalview
                         + groovyscript);
       }
     }
-
-    // Once all other stuff is done, execute any groovy scripts (in order)
+    // and finally, turn off batch mode indicator - if the desktop still exists
+    if (desktop != null)
+    {
+      if (progress != -1)
+      {
+        desktop.setProgressBar(null, progress);
+      }
+      desktop.setInBatchMode(false);
+    }
   }
 
   private static void startUsageStats(final Desktop desktop)
@@ -583,7 +618,7 @@ public class Jalview
                 Cache.log.info("Not enabling Google Tracking.");
               }
             }, null, true);
-    SwingUtilities.invokeLater(prompter);
+    desktop.addDialogThread(prompter);
   }
 
   /**
@@ -596,22 +631,29 @@ public class Jalview
    *          'Jalview' object.
    */
   private static void executeGroovyScript(String groovyscript,
-          Object jalviewContext)
+          Object[] jalviewContext)
   {
     if (jalviewContext == null)
     {
       System.err
               .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
     }
-    File sfile = null;
+    /**
+     * for scripts contained in files
+     */
+    File tfile = null;
+    /**
+     * script's URI
+     */
+    URL sfile = null;
     if (groovyscript.trim().equals("STDIN"))
     {
       // read from stdin into a tempfile and execute it
       try
       {
-        sfile = File.createTempFile("jalview", "groovy");
+        tfile = File.createTempFile("jalview", "groovy");
         PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
-                new FileOutputStream(sfile)));
+                new FileOutputStream(tfile)));
         BufferedReader br = new BufferedReader(
                 new java.io.InputStreamReader(System.in));
         String line = null;
@@ -626,30 +668,56 @@ public class Jalview
       } catch (Exception ex)
       {
         System.err.println("Failed to read from STDIN into tempfile "
-                + ((sfile == null) ? "(tempfile wasn't created)" : sfile
+                + ((tfile == null) ? "(tempfile wasn't created)" : tfile
                         .toString()));
         ex.printStackTrace();
         return;
       }
+      try
+      {
+        sfile = tfile.toURI().toURL();
+      } catch (Exception x)
+      {
+        System.err
+                .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+                        + tfile.toURI());
+        x.printStackTrace();
+        return;
+      }
     }
     else
     {
-      sfile = new File(groovyscript);
-    }
-    if (!sfile.exists())
-    {
-      System.err.println("File '" + groovyscript + "' does not exist.");
-      return;
-    }
-    if (!sfile.canRead())
-    {
-      System.err.println("File '" + groovyscript + "' cannot be read.");
-      return;
-    }
-    if (sfile.length() < 1)
-    {
-      System.err.println("File '" + groovyscript + "' is empty.");
-      return;
+      try
+      {
+        sfile = new URI(groovyscript).toURL();
+      } catch (Exception x)
+      {
+        tfile = new File(groovyscript);
+        if (!tfile.exists())
+        {
+          System.err.println("File '" + groovyscript + "' does not exist.");
+          return;
+        }
+        if (!tfile.canRead())
+        {
+          System.err.println("File '" + groovyscript + "' cannot be read.");
+          return;
+        }
+        if (tfile.length() < 1)
+        {
+          System.err.println("File '" + groovyscript + "' is empty.");
+          return;
+        }
+        try
+        {
+          sfile = tfile.getAbsoluteFile().toURI().toURL();
+        } catch (Exception ex)
+        {
+          System.err.println("Failed to create a file URL for "
+                  + tfile.getAbsoluteFile());
+          return;
+        }
+      }
     }
     boolean success = false;
     try
@@ -665,25 +733,61 @@ public class Jalview
        * = new Binding(); binding.setVariable("input", "world");
        * gse.run("hello.groovy", binding); </code>
        */
-      ClassLoader cl = jalviewContext.getClass().getClassLoader();
+      Class[] bspec;
+      Object[] binding;
+      int blen = ((jalviewContext[0] == null) ? 0 : 1)
+              + ((jalviewContext[1] == null) ? 0 : 1);
+      String cnames[] = new String[]
+      { "Jalview", "currentAlFrame" };
+      bspec = new Class[blen * 2];
+      binding = new Object[blen * 2];
+      blen = 0;
+      ClassLoader cl = null;
+      Map vbinding = new Hashtable();
+      for (int jc = 0; jc < jalviewContext.length; jc++)
+      {
+        if (jalviewContext[jc] != null)
+        {
+          if (cl == null)
+          {
+            cl = jalviewContext[jc].getClass().getClassLoader();
+          }
+          bspec[blen * 2] = String.class;
+          bspec[blen * 2 + 1] = Object.class;
+          binding[blen * 2] = cnames[jc];
+          binding[blen * 2 + 1] = jalviewContext[jc];
+          vbinding.put(cnames[jc], jalviewContext[jc]);
+          blen++;
+        }
+      }
       Class gbindingc = cl.loadClass("groovy.lang.Binding");
-      Constructor gbcons = gbindingc.getConstructor(null);
-      Object gbinding = gbcons.newInstance(null);
-      java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
-              new Class[]
-              { String.class, Object.class });
-      setvar.invoke(gbinding, new Object[]
-      { "Jalview", jalviewContext });
+      Constructor gbcons;
+      Object gbinding;
+      try
+      {
+        gbcons = gbindingc.getConstructor(Map.class);
+        gbinding = gbcons.newInstance(vbinding);
+      } catch (NoSuchMethodException x)
+      {
+        // old style binding config - using series of string/object values to
+        // setVariable.
+        gbcons = gbindingc.getConstructor(null);
+        gbinding = gbcons.newInstance(null);
+        java.lang.reflect.Method setvar = gbindingc.getMethod(
+                "setVariable", bspec);
+        setvar.invoke(gbinding, binding);
+      }
+      ;
       Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
       Constructor gseccons = gsec.getConstructor(new Class[]
       { URL[].class }); // String[].class });
       Object gse = gseccons.newInstance(new Object[]
       { new URL[]
-      { sfile.toURL() } }); // .toString() } });
+      { sfile } }); // .toString() } });
       java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
       { String.class, gbindingc });
       run.invoke(gse, new Object[]
-      { sfile.getName(), gbinding });
+      { sfile.toString(), gbinding });
       success = true;
     } catch (Exception e)
     {
@@ -696,7 +800,7 @@ public class Jalview
     {
       // delete temp file that we made - but only if it was successfully
       // executed
-      sfile.delete();
+      tfile.delete();
     }
   }
 
@@ -786,17 +890,6 @@ public class Jalview
     }
     return ff;
   }
-
-  private static String checkProtocol(String file)
-  {
-    String protocol = jalview.io.FormatAdapter.FILE;
-
-    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
-    {
-      protocol = jalview.io.FormatAdapter.URL;
-    }
-    return protocol;
-  }
 }
 
 /**