X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3c694646faeb8e2a3d2353b0024c345c11053956;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=ff1b18099190bfec774bd1928ba20fc8a9325edd;hpb=4e7511345e2d3b5c0ec47c280bf5582073c86c1e;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff1b180..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 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -22,6 +22,8 @@ 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;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -44,11 +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>
@@ -91,12 +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;
@@ -112,7 +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");
@@ -121,6 +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
@@ -172,6 +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)
     {
@@ -183,6 +204,11 @@ public class Jalview
       {
         startUsageStats(desktop);
       }
+      else
+      {
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+
       if (!aparser.contains("noquestionnaire"))
       {
         String url = aparser.getValue("questionnaire");
@@ -192,6 +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
         {
@@ -210,11 +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.
@@ -320,10 +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://"))
       {
@@ -349,7 +387,7 @@ public class Jalview
       }
       else
       {
-
+        Desktop.setCurrentAlignFrame(af);
         data = aparser.getValue("colour", true);
         if (data != null)
         {
@@ -365,8 +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);
         }
 
@@ -376,30 +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)
@@ -407,13 +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)
           {
@@ -452,8 +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
           {
@@ -484,6 +551,14 @@ public class Jalview
             System.out.println("Creating SVG image: " + file);
             continue;
           }
+          else if (format.equalsIgnoreCase("html"))
+          {
+            File imageFile = new java.io.File(file);
+            imageName = imageFile.getName();
+            new HtmlSvgOutput(new java.io.File(file), af.alignPanel);
+            System.out.println("Creating HTML image: " + file);
+            continue;
+          }
           else if (format.equalsIgnoreCase("imgMap"))
           {
             af.createImageMap(new java.io.File(file), imageName);
@@ -492,8 +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;
           }
 
@@ -575,8 +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
       {
@@ -613,8 +690,11 @@ 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"
+                    + "-html FILE\tCreate HTML file from alignment.\n"
                     + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
                     + "-eps FILE\tCreate EPS file FILE from alignment.\n"
                     + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
@@ -778,17 +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)
@@ -805,8 +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
       {
@@ -816,23 +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)
     {
@@ -897,6 +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)
     {
@@ -924,7 +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;
@@ -935,6 +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;
+  }
 }
 
 /**
@@ -1086,7 +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);
@@ -1103,4 +1195,4 @@ class FeatureFetcher
     return queued == 0 && running == 0;
   }
 
-};
+}