X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=fcee9e1f35b2719dc7ef82162277802e604bc33a;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=e5a22e046d5dc23600c27803038c53521432b4d1;hpb=afcdc36e5f65333f8ff9ca3229b6cffdb27edca7;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e5a22e0..fcee9e1 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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.io.BioJsHTMLOutput;
 import jalview.io.HtmlSvgOutput;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -45,11 +46,12 @@ import java.security.CodeSource;
 import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.UIManager;
+import javax.swing.UnsupportedLookAndFeelException;
 
 /**
  * Main class for Jalview Application <br>
@@ -80,11 +82,6 @@ public class Jalview
   }
 
   /**
-   * Put protein=true for get a protein example
-   */
-  private static boolean protein = false;
-
-  /**
    * main class for Jalview application
    * 
    * @param args
@@ -97,12 +94,6 @@ public class Jalview
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + 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");
-    }
 
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
@@ -118,7 +109,14 @@ public class Jalview
       System.setProperty("java.awt.headless", "true");
       headless = true;
     }
-    Cache.loadProperties(aparser.getValue("props")); // must do this before
+    String usrPropsFile = aparser.getValue("props");
+    Cache.loadProperties(usrPropsFile); // must do this before
+    if (usrPropsFile != null)
+    {
+      System.out.println("CMD [-props " + usrPropsFile
+              + "] executed successfully!");
+    }
+
     // anything else!
 
     final String jabawsUrl = aparser.getValue("jabaws");
@@ -127,6 +125,8 @@ public class Jalview
       try
       {
         Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+        System.out.println("CMD [-jabaws " + jabawsUrl
+                + "] executed successfully!");
       } catch (MalformedURLException e)
       {
         System.err.println("Invalid jabaws parameter: " + jabawsUrl
@@ -178,6 +178,21 @@ public class Jalview
     } catch (Exception ex)
     {
     }
+    if (new Platform().isAMac())
+    {
+      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+              "Jalview");
+      System.setProperty("apple.laf.useScreenMenuBar", "true");
+      try
+      {
+        UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
+                .getLookAndFeel());
+      } catch (UnsupportedLookAndFeelException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
+    }
 
     if (!headless)
     {
@@ -189,6 +204,11 @@ public class Jalview
       {
         startUsageStats(desktop);
       }
+      else
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+
       if (!aparser.contains("noquestionnaire"))
       {
         String url = aparser.getValue("questionnaire");
@@ -198,6 +218,8 @@ public class Jalview
           // questionnaire
           Cache.log.debug("Starting questionnaire url at " + url);
           desktop.checkForQuestionnaire(url);
+          System.out.println("CMD questionnaire[-" + url
+                  + "] executed successfully!");
         }
         else
         {
@@ -216,11 +238,20 @@ public class Jalview
           }
         }
       }
+      else
+      {
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
+      }
       desktop.checkForNews();
     }
 
+    if (!isHeadlessMode())
+    {
+      BioJsHTMLOutput.updateBioJS();
+    }
+
     String file = null, protocol = null, format = null, data = null;
-    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
     Vector getFeatures = null; // vector of das source nicknames to fetch
     // features from
     // loading is done.
@@ -326,10 +357,11 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
+        desktop.setProgressBar(MessageManager
+                .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("Opening file: " + file);
+      System.out.println("CMD [-open " + file + "] executed successfully!");
 
       if (!file.startsWith("http://"))
       {
@@ -355,7 +387,7 @@ public class Jalview
       }
       else
       {
-
+        Desktop.setCurrentAlignFrame(af);
         data = aparser.getValue("colour", true);
         if (data != null)
         {
@@ -371,8 +403,11 @@ public class Jalview
             ucs.parseAppletParameter(data);
             cs = ucs;
           }
-
-          System.out.println("colour is " + data);
+          else
+          {
+            System.out.println("CMD [-color " + data
+                    + "] executed successfully!");
+          }
           af.changeColour(cs);
         }
 
@@ -382,30 +417,53 @@ public class Jalview
         {
           af.parseFeaturesFile(data,
                   jalview.io.AppletFormatAdapter.checkProtocol(data));
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD groups[-" + data
+                  + "]  executed successfully!");
         }
         data = aparser.getValue("features", true);
         if (data != null)
         {
           af.parseFeaturesFile(data,
                   jalview.io.AppletFormatAdapter.checkProtocol(data));
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD [-features " + data
+                  + "]  executed successfully!");
         }
 
         data = aparser.getValue("annotations", true);
         if (data != null)
         {
           af.loadJalviewDataFile(data, null, null, null);
-          System.out.println("Added " + data);
+          // System.out.println("Added " + data);
+          System.out.println("CMD [-annotations " + data
+                  + "] executed successfully!");
         }
         // set or clear the sortbytree flag.
         if (aparser.contains("sortbytree"))
         {
           af.getViewport().setSortByTree(true);
+          if (af.getViewport().getSortByTree())
+          {
+            System.out.println("CMD [-sortbytree] executed successfully!");
+          }
+        }
+        if (aparser.contains("no-annotation"))
+        {
+          af.getViewport().setShowAnnotation(false);
+          if (!af.getViewport().isShowAnnotation())
+          {
+            System.out.println("CMD no-annotation executed successfully!");
+          }
         }
         if (aparser.contains("nosortbytree"))
         {
           af.getViewport().setSortByTree(false);
+          if (!af.getViewport().getSortByTree())
+          {
+            System.out
+                    .println("CMD [-nosortbytree] executed successfully!");
+          }
         }
         data = aparser.getValue("tree", true);
         if (data != null)
@@ -413,13 +471,14 @@ public class Jalview
           jalview.io.NewickFile fin = null;
           try
           {
+            System.out.println("CMD [-tree " + data
+                    + "] executed successfully!");
             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)
           {
@@ -458,8 +517,10 @@ public class Jalview
           if (jalview.bin.Cache.groovyJarsPresent())
           {
             System.out.println("Executing script " + groovyscript);
-            executeGroovyScript(groovyscript, new Object[]
-            { desktop, af });
+            executeGroovyScript(groovyscript, new Object[] { desktop, af });
+
+            System.out.println("CMD groovy[" + groovyscript
+                    + "] executed successfully!");
           }
           else
           {
@@ -506,8 +567,10 @@ public class Jalview
           }
           else if (format.equalsIgnoreCase("eps"))
           {
-            System.out.println("Creating EPS file: " + file);
-            af.createEPS(new java.io.File(file));
+            File outputFile = new java.io.File(file);
+            System.out.println("Creating EPS file: "
+                    + outputFile.getAbsolutePath());
+            af.createEPS(outputFile);
             continue;
           }
 
@@ -536,8 +599,7 @@ public class Jalview
     // ////////////////////
 
     if (!headless && file == null && vamsasImport == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
-            && protein == true)
+            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
       file = jalview.bin.Cache.getDefault(
               "STARTUP_FILE",
@@ -590,8 +652,8 @@ public class Jalview
       if (jalview.bin.Cache.groovyJarsPresent())
       {
         System.out.println("Executing script " + groovyscript);
-        executeGroovyScript(groovyscript, new Object[]
-        { desktop, startUpAlframe });
+        executeGroovyScript(groovyscript, new Object[] { desktop,
+            startUpAlframe });
       }
       else
       {
@@ -628,6 +690,7 @@ public class Jalview
                     + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
                     + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
                     + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
                     + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
                     + "-png FILE\tCreate PNG image FILE from alignment.\n"
                     + "-svg FILE\tCreate SVG image FILE from alignment.\n"
@@ -669,7 +732,7 @@ public class Jalview
               public void run()
               {
                 Cache.log
-                        .info("Initialising googletracker for usage stats.");
+                        .debug("Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
                 Cache.log.debug("Tracking enabled.");
               }
@@ -677,7 +740,7 @@ public class Jalview
             {
               public void run()
               {
-                Cache.log.info("Not enabling Google Tracking.");
+                Cache.log.debug("Not enabling Google Tracking.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);
@@ -795,17 +858,16 @@ public class Jalview
        * = new Binding(); binding.setVariable("input", "world");
        * gse.run("hello.groovy", binding); </code>
        */
-      Class[] bspec;
+      Class<?>[] bspec;
       Object[] binding;
       int blen = ((jalviewContext[0] == null) ? 0 : 1)
               + ((jalviewContext[1] == null) ? 0 : 1);
-      String cnames[] = new String[]
-      { "Jalview", "currentAlFrame" };
+      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();
+      Map<String, Object> vbinding = new HashMap<String, Object>();
       for (int jc = 0; jc < jalviewContext.length; jc++)
       {
         if (jalviewContext[jc] != null)
@@ -822,8 +884,8 @@ public class Jalview
           blen++;
         }
       }
-      Class gbindingc = cl.loadClass("groovy.lang.Binding");
-      Constructor gbcons;
+      Class<?> gbindingc = cl.loadClass("groovy.lang.Binding");
+      Constructor<?> gbcons;
       Object gbinding;
       try
       {
@@ -833,23 +895,23 @@ public class Jalview
       {
         // old style binding config - using series of string/object values to
         // setVariable.
-        gbcons = gbindingc.getConstructor(null);
-        gbinding = gbcons.newInstance(null);
+        gbcons = gbindingc.getConstructor();
+        gbinding = gbcons.newInstance();
         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 } }); // .toString() } });
-      java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
-      { String.class, gbindingc });
-      run.invoke(gse, new Object[]
-      { sfile.toString(), gbinding });
+
+      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 } }); // .toString()
+                                                                  // } });
+      java.lang.reflect.Method run = gsec.getMethod("run", new Class[] {
+          String.class, gbindingc });
+      run.invoke(gse, new Object[] { sfile.toString(), gbinding });
       success = true;
     } catch (Exception e)
     {
@@ -914,6 +976,8 @@ public class Jalview
         }
         source.addElement(nickname);
       }
+      System.out.println("CMD [-dasserver " + data
+              + "] executed successfully!");
     } // loop until no more server entries are found.
     if (locsources != null && locsources.indexOf('|') > -1)
     {
@@ -941,7 +1005,7 @@ public class Jalview
   private static FeatureFetcher startFeatureFetching(final Vector dasSources)
   {
     FeatureFetcher ff = new FeatureFetcher();
-    AlignFrame afs[] = Desktop.getAlignframes();
+    AlignFrame afs[] = Desktop.getAlignFrames();
     if (afs == null || afs.length == 0)
     {
       return null;
@@ -952,6 +1016,16 @@ public class Jalview
     }
     return ff;
   }
+
+  public static boolean isHeadlessMode()
+  {
+    String isheadless = System.getProperty("java.awt.headless");
+    if (isheadless != null && isheadless.equalsIgnoreCase("true"))
+    {
+      return true;
+    }
+    return false;
+  }
 }
 
 /**
@@ -1103,7 +1177,8 @@ class FeatureFetcher
           running++;
         }
 
-        af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
+        af.setProgressBar(MessageManager
+                .getString("status.das_features_being_retrived"), id);
         af.featureSettings_actionPerformed(null);
         af.featureSettings.fetchDasFeatures(dasSources, true);
         af.setProgressBar(null, id);
@@ -1120,4 +1195,4 @@ class FeatureFetcher
     return queued == 0 && running == 0;
   }
 
-};
+}