Jalview 2.6 source licence

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 23b18b0..6910f28 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -19,6 +19,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.io.*;
+import jalview.ws.params.ParamManager;
 
 import java.awt.*;
 import java.awt.datatransfer.*;
@@ -54,7 +55,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private class JalviewChangeSupport implements PropertyChangeListener
   {
-    @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
       // Handle change events - most are simply routed to other sources
@@ -414,6 +414,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         iw = (int) (iw * sw);
         iy = (int) (iy * sh);
         ih = (int) (ih * sh);
+        while (ix>=screenSize.width) {
+          jalview.bin.Cache.log.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+          ix-=screenSize.width;
+        }
+        while (iy>=screenSize.height) {
+          jalview.bin.Cache.log.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+                    iy-=screenSize.height;
+        }
         jalview.bin.Cache.log.debug("Got last known dimensions for "
                 + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
                 + " height:" + ih);
@@ -1177,13 +1185,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       java.io.File choice = chooser.getSelectedFile();
-      JProgressBar progpanel = addProgressPanel("Saving jalview project "
-              + choice.getName());
+      setProgressBar("Saving jalview project "
+              + choice.getName(), choice.hashCode());
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
       // TODO catch and handle errors for savestate
-      new Jalview2XML().SaveState(choice);
-      removeProgressPanel(progpanel);
-
+      try {
+        new Jalview2XML().SaveState(choice);
+      } catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Whilst saving current state to "+choice.getName(), oom);
+      }
+      catch (Exception ex)
+      {
+        Cache.log.error("Problems whilst trying to save to "+choice.getName(),ex);
+        JOptionPane.showMessageDialog(this, "Error whilst saving current state to "+choice.getName(), "Couldn't save project", JOptionPane.WARNING_MESSAGE);
+      }
+      setProgressBar(null, choice.hashCode());
+      
     }
   }
 
@@ -1206,13 +1224,27 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      String choice = chooser.getSelectedFile().getAbsolutePath();
-      setProgressBar("loading jalview project "
-              + chooser.getSelectedFile().getName(), choice.hashCode());
+      final String choice = chooser.getSelectedFile().getAbsolutePath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
-      new Jalview2XML().LoadJalviewAlign(choice);
+      new Thread(new Runnable() {
+        public void run() {
+          setProgressBar("loading jalview project "
+              + choice, choice.hashCode());
+          try {
+      new Jalview2XML().LoadJalviewAlign(choice); } 
+      catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Whilst loading project from "+choice, oom);
+      }
+      catch (Exception ex)
+      {
+        Cache.log.error("Problems whilst loading project from "+choice,ex);
+        JOptionPane.showMessageDialog(Desktop.desktop, "Error whilst loading project from "+choice, "Couldn't load project", JOptionPane.WARNING_MESSAGE);
+      }
       setProgressBar(null, choice.hashCode());
+        }
+      }).start();
     }
   }
 
@@ -2088,6 +2120,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     return v_client;
 
   }
+  /**
+   * flag set if jalview GUI is being operated programmatically
+   */
+  private boolean inBatchMode=false;
+
+  /**
+   * check if jalview GUI is being operated programmatically
+   * @return inBatchMode
+   */
+  public boolean isInBatchMode()
+  {
+    return inBatchMode;
+  }
+
+  /**
+   * set flag if jalview GUI is being operated programmatically
+   * @param inBatchMode 
+   */
+  public void setInBatchMode(boolean inBatchMode)
+  {
+    this.inBatchMode = inBatchMode;
+  }
+
 
   public void startServiceDiscovery()
   {
@@ -2113,7 +2168,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     try
     {
-      if (Cache.getDefault("SHOW_ENVISION2_SERVICES", true))
+      if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
       {
         // EnfinEnvision web service menu entries are rebuild every time the
         // menu is shown, so no changeSupport events are needed.
@@ -2153,4 +2208,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
   }
 
+  /**
+   * start a thread to open a URL in the configured browser. Pops up a warning dialog to the user if there is an exception when calling out to the browser to open the URL.
+   * @param url
+   */
+  public static void showUrl(final String url)
+  {
+    new Thread(new Runnable() {
+      public void run() {
+        try {
+          jalview.util.BrowserLauncher.openURL(url);
+        } catch (Exception ex)
+        {    
+          JOptionPane
+                  .showInternalMessageDialog(
+                          Desktop.desktop,
+                          "Unixers: Couldn't find default web browser."
+                                  + "\nAdd the full path to your browser in Preferences.",
+                          "Web browser not found", JOptionPane.WARNING_MESSAGE);
+
+          ex.printStackTrace();
+        }
+      }
+    }).start();    
+  }
+
+  public static WsParamSetManager wsparamManager = null;
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager==null)
+    {
+      wsparamManager = new WsParamSetManager();
+    }
+    return wsparamManager;
+  }
+
 }