X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ba9c5b0919efc4baf4a53b434f629b836cc134c7;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=ba418fea51e49088d8db149ec45d125637d15c92;hpb=1213d49ca3df8f48360da857121805d088c13aab;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ba418fe..ba9c5b0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -73,6 +73,8 @@ import jalview.bin.argparser.Arg.Opt;
 import jalview.bin.argparser.Arg.Type;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.BootstrapArgs;
+import jalview.bin.groovy.JalviewObject;
+import jalview.bin.groovy.JalviewObjectI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -98,6 +100,8 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
 import jalview.util.HttpUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
 import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -118,7 +122,7 @@ import jalview.ws.jws2.Jws2Discoverer;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview
+public class Jalview implements JalviewObjectI
 {
   static
   {
@@ -138,7 +142,7 @@ public class Jalview
 
   protected Commands cmds;
 
-  public static AlignFrame currentAlignFrame;
+  public AlignFrame currentAlignFrame = null;
 
   private ArgParser argparser = null;
 
@@ -204,7 +208,7 @@ public class Jalview
     public void addFetcher(final AlignFrame af,
             final Vector<String> dasSources)
     {
-      final long id = System.currentTimeMillis();
+      final long id = IdUtils.newId(IdType.PROGRESS);
       queued++;
       final FeatureFetcher us = this;
       new Thread(new Runnable()
@@ -447,7 +451,7 @@ public class Jalview
       }
       else if (bootstrapArgs.contains(Arg.DEBUG))
       {
-        logLevel = "DEBUG";
+        logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
       }
       if (logLevel == null && !(bootstrapProperties == null))
       {
@@ -835,36 +839,40 @@ public class Jalview
     }
 
     // Run Commands from cli
-    cmds = new Commands(argparser, headlessArg);
-    cmds.processArgs();
-    boolean commandsSuccess = cmds.argsWereParsed();
-
-    if (commandsSuccess)
+    boolean commandsSuccess = false;
+    if (!(argparser.isMixedStyle() || argparser.isOldStyle()))
     {
-      if (headlessArg)
+      cmds = new Commands(argparser, headlessArg);
+      cmds.processArgs();
+      commandsSuccess = cmds.argsWereParsed();
+
+      if (commandsSuccess)
       {
-        if (argparser.getBoolean(Arg.NOQUIT))
-        {
-          Console.warn(
-                  "Completed " + Arg.HEADLESS.getName() + " commands, but "
-                          + Arg.NOQUIT + " is set so not quitting!");
-        }
-        else
+        if (headlessArg)
         {
-          Jalview.exit("Successfully completed commands in headless mode",
-                  ExitCode.OK);
+          if (argparser.getBoolean(Arg.NOQUIT))
+          {
+            Console.warn("Completed " + Arg.HEADLESS.getName()
+                    + " commands, but " + Arg.NOQUIT
+                    + " is set so not quitting!");
+          }
+          else
+          {
+            Jalview.exit("Successfully completed commands in headless mode",
+                    ExitCode.OK);
+          }
         }
+        Console.info("Successfully completed commands");
       }
-      Console.info("Successfully completed commands");
-    }
-    else
-    {
-      if (headlessArg)
+      else
       {
-        Jalview.exit("Error when running Commands in headless mode",
-                ExitCode.ERROR_RUNNING_COMMANDS);
+        if (headlessArg)
+        {
+          Jalview.exit("Error when running Commands in headless mode",
+                  ExitCode.ERROR_RUNNING_COMMANDS);
+        }
+        Console.warn("Error when running commands");
       }
-      Console.warn("Error when running commands");
     }
 
     // Check if JVM and compile version might cause problems and log if it
@@ -905,7 +913,7 @@ public class Jalview
         desktop.setProgressBar(
                 MessageManager
                         .getString("status.processing_commandline_args"),
-                progress = System.currentTimeMillis());
+                progress = IdUtils.newId(IdType.PROGRESS));
       }
       Console.outPrintln("CMD [-open " + file + "] executed successfully!");
 
@@ -1749,12 +1757,11 @@ public class Jalview
     }
     try
     {
+      JalviewObjectI j = new JalviewObject(this);
       Map<String, java.lang.Object> vbinding = new HashMap<>();
-      vbinding.put("Jalview", this);
-      if (af != null)
-      {
-        vbinding.put("currentAlFrame", af);
-      }
+      vbinding.put(JalviewObjectI.jalviewObjectName, j);
+      vbinding.put(JalviewObjectI.currentAlFrameName,
+              af != null ? af : getCurrentAlignFrame());
       Binding gbinding = new Binding(vbinding);
       GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
       gse.run(sfile.toString(), gbinding);
@@ -1770,7 +1777,6 @@ public class Jalview
               .errPrintln("Exception Whilst trying to execute file " + sfile
                       + " as a groovy script.");
       e.printStackTrace(System.err);
-
     }
   }
 
@@ -1784,30 +1790,32 @@ public class Jalview
     return false;
   }
 
+  @Override
   public AlignFrame[] getAlignFrames()
   {
     return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
-            : Desktop.getAlignFrames();
-
+            : Desktop.getDesktopAlignFrames();
   }
 
   /**
    * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
    */
+  @Override
   public void quit()
   {
     // System.exit will run the shutdownHook first
     Jalview.exit("Quitting now. Bye!", ExitCode.OK);
   }
 
-  public static AlignFrame getCurrentAlignFrame()
+  @Override
+  public AlignFrame getCurrentAlignFrame()
   {
-    return Jalview.currentAlignFrame;
+    return currentAlignFrame;
   }
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  public void setCurrentAlignFrame(AlignFrame af)
   {
-    Jalview.currentAlignFrame = currentAlignFrame;
+    this.currentAlignFrame = af;
   }
 
   public Commands getCommands()
@@ -1859,7 +1867,7 @@ public class Jalview
     // only add new ones to the end of the list (to preserve ordinal values)
     OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
     INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
-    ERROR_RUNNING_COMMANDS, NO_LOGGING;
+    ERROR_RUNNING_COMMANDS, NO_LOGGING, GROOVY_ERROR;
   }
 
   /******************************
@@ -2064,7 +2072,7 @@ public class Jalview
         String cont = MessageManager.getString("label.continue");
 
         Desktop.instance.nonBlockingDialog(title, warning, url, cont,
-                JvOptionPane.WARNING_MESSAGE, false, true, true, 2000);
+                JvOptionPane.WARNING_MESSAGE, false, true, true, 30000);
       }
     }
     if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)