X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;fp=src%2Fjalview%2Fbin%2FJalview.java;h=dfd092491d058527ca31061c3030c908d2d06825;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=177d56f782e65c9a75af73d6e25e0d976e6980fb;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 177d56f..dfd0924 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -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!");
@@ -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
       {
@@ -865,8 +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;
@@ -907,15 +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)
     {
@@ -1181,7 +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);