JAL-4409 JAL-4160 Don't let getdown turn jalviewX:// URIs into absolute local file...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b7d15e5..6d28da1 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import java.awt.Color;
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
@@ -73,6 +74,8 @@ 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;
@@ -101,6 +104,7 @@ import jalview.util.HttpUtils;
 import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UserAgent;
 import jalview.ws.jws2.Jws2Discoverer;
 
 /**
@@ -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;
 
@@ -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))
       {
@@ -637,19 +641,17 @@ public class Jalview
     {
       headless = true;
     }
-    System.setProperty("http.agent", HttpUtils.getUserAgent());
+    System.setProperty("http.agent", UserAgent.getUserAgent());
 
     try
     {
       Console.initLogger();
-    } catch (
-
-    NoClassDefFoundError error)
+    } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
       String message = "\nEssential logging libraries not found."
               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
-      Jalview.exit(message, ExitCode.OK);
+      Jalview.exit(message, ExitCode.NO_LOGGING);
     }
     desktop = null;
 
@@ -938,9 +940,12 @@ public class Jalview
       try
       {
         format = new IdentifyFile().identify(file, protocol);
-      } catch (FileFormatException e1)
+      } catch (FileNotFoundException e)
       {
-        // TODO ?
+        Console.error("File at '" + file + "' not found", e);
+      } catch (FileFormatException e)
+      {
+        Console.error("File '" + file + "' format not recognised", e);
       }
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -1211,9 +1216,12 @@ public class Jalview
         try
         {
           format = new IdentifyFile().identify(file, protocol);
+        } catch (FileNotFoundException e)
+        {
+          Console.error("File at '" + file + "' not found", e);
         } catch (FileFormatException e)
         {
-          // TODO what?
+          Console.error("File '" + file + "' format not recognised", e);
         }
       }
 
@@ -1633,8 +1641,7 @@ public class Jalview
     PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
             "USAGESTATS",
             MessageManager.getString("prompt.analytics_title"),
-            MessageManager.getString("prompt.analytics"),
-            new Runnable()
+            MessageManager.getString("prompt.analytics"), new Runnable()
             {
               @Override
               public void run()
@@ -1752,12 +1759,11 @@ 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);
@@ -1773,7 +1779,6 @@ public class Jalview
               .errPrintln("Exception Whilst trying to execute file " + sfile
                       + " as a groovy script.");
       e.printStackTrace(System.err);
-
     }
   }
 
@@ -1787,30 +1792,32 @@ 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()
@@ -1862,7 +1869,7 @@ 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;
+    ERROR_RUNNING_COMMANDS, NO_LOGGING, GROOVY_ERROR;
   }
 
   /******************************
@@ -2041,8 +2048,8 @@ public class Jalview
               j.getArgParser().getMixedExamples());
       String quit = MessageManager.getString("action.quit");
 
-      Desktop.instance.nonBlockingDialog(title, warning, quit,
-              JvOptionPane.WARNING_MESSAGE, false, true);
+      Desktop.instance.nonBlockingDialog(title, warning, null, quit,
+              JvOptionPane.WARNING_MESSAGE, false, false, true, 30000);
 
       Jalview.exit(
               "Exiting due to mixed old and new command line arguments.",
@@ -2066,8 +2073,8 @@ public class Jalview
       {
         String cont = MessageManager.getString("label.continue");
 
-        Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
-                JvOptionPane.WARNING_MESSAGE, false, true, true);
+        Desktop.instance.nonBlockingDialog(title, warning, url, cont,
+                JvOptionPane.WARNING_MESSAGE, false, true, true, 30000);
       }
     }
     if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
@@ -2087,7 +2094,7 @@ public class Jalview
                 Math.max(message.length(), Math.min(60, shortest)),
                 Math.min(errors.size(), 20), title, message,
                 j.getCommands().errorsToString(), ok,
-                JvOptionPane.WARNING_MESSAGE, true, false, true);
+                JvOptionPane.WARNING_MESSAGE, true, false, true, -1);
       }
     }
   }