X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3c694646faeb8e2a3d2353b0024c345c11053956;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=8ad4cbd0e0568353cd79e4fa85dcaeff3d01d7ec;hpb=e9c752522f4b0b9ef072e7c1f198f9ec59de957d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8ad4cbd..3c69464 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -240,8 +240,7 @@ public class Jalview
       }
       else
       {
-        System.err
-.println("CMD [-noquestionnaire] executed successfully!");
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
       desktop.checkForNews();
     }
@@ -358,7 +357,8 @@ 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("CMD [-open " + file + "] executed successfully!");
@@ -387,7 +387,7 @@ public class Jalview
       }
       else
       {
-
+        Desktop.setCurrentAlignFrame(af);
         data = aparser.getValue("colour", true);
         if (data != null)
         {
@@ -445,8 +445,7 @@ public class Jalview
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
           {
-            System.out
-.println("CMD [-sortbytree] executed successfully!");
+            System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
         if (aparser.contains("no-annotation"))
@@ -454,8 +453,7 @@ public class Jalview
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
           {
-            System.out
-.println("CMD no-annotation executed successfully!");
+            System.out.println("CMD no-annotation executed successfully!");
           }
         }
         if (aparser.contains("nosortbytree"))
@@ -519,8 +517,7 @@ 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!");
@@ -655,8 +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
       {
@@ -693,6 +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"
@@ -864,8 +862,7 @@ public class Jalview
       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;
@@ -906,15 +903,15 @@ public class Jalview
       }
 
       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 });
+      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)
     {
@@ -1180,7 +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);