X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=ef48bf96dc2d9a23dfcdbde129b1c3978f13f1ac;hb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;hp=631c7fe0920e2a4fcb749bf117bfb3ce555b9b74;hpb=117479142a51c5ab468ba4120815cb8436648dfd;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 631c7fe..ef48bf9 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.bin;
@@ -1390,8 +1392,7 @@ public class JalviewLite extends Applet implements
       }
       else
       {
-        throw new Error(
-                "Invalid separator parameter - must be non-zero length");
+        throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
       }
     }
     int r = 255;
@@ -1480,36 +1481,44 @@ public class JalviewLite extends Applet implements
       callInitCallback();
     }
   }
+
   private void initLiveConnect()
   {
     // try really hard to get the liveConnect thing working
-    boolean notFailed=false;
-    int tries=0;
-    while (notFailed && tries<10) {
-      if (tries>0)
+    boolean notFailed = false;
+    int tries = 0;
+    while (!notFailed && tries < 10)
+    {
+      if (tries > 0)
       {
         System.err.println("LiveConnect request thread going to sleep.");
       }
-      try {
-        Thread.sleep(700*(1+tries));
+      try
+      {
+        Thread.sleep(700 * (1 + tries));
+      } catch (InterruptedException q)
+      {
       }
-      catch (InterruptedException q) {};
-      if (tries++>0)
+      ;
+      if (tries++ > 0)
       {
         System.err.println("LiveConnect request thread woken up.");
       }
-      try {
+      try
+      {
         JSObject scriptObject = JSObject.getWindow(this);
-        if (scriptObject.eval("navigator")!=null)
+        if (scriptObject.eval("navigator") != null)
         {
-          notFailed=true;
+          notFailed = true;
         }
       } catch (JSException jsex)
       {
-        System.err.println("Attempt "+tries+" to access LiveConnect javascript failed.");
+        System.err.println("Attempt " + tries
+                + " to access LiveConnect javascript failed.");
       }
     }
   }
+
   private void callInitCallback()
   {
     String initjscallback = getParameter("oninit");
@@ -1528,7 +1537,7 @@ public class JalviewLite extends Applet implements
       {
       }
       ;
-      // try really hard to let the browser plugin know we want liveconnect 
+      // try really hard to let the browser plugin know we want liveconnect
       initLiveConnect();
 
       if (scriptObject != null)
@@ -1645,15 +1654,19 @@ public class JalviewLite extends Applet implements
       g.setColor(Color.cyan);
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.red);
-      g.drawString(MessageManager.getString("label.jalview_cannot_open_file"), 5, 15);
+      g.drawString(
+              MessageManager.getString("label.jalview_cannot_open_file"),
+              5, 15);
       g.drawString("\"" + file + "\"", 5, 30);
     }
     else if (embedded)
     {
       g.setColor(Color.black);
       g.setFont(new Font("Arial", Font.BOLD, 24));
-      g.drawString(MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30);
-      g.drawString(MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2);
+      g.drawString(MessageManager.getString("label.jalview_applet"), 50,
+              getSize().height / 2 - 30);
+      g.drawString(MessageManager.getString("label.loading_data") + "...",
+              50, getSize().height / 2);
     }
   }
 
@@ -1860,10 +1873,14 @@ public class JalviewLite extends Applet implements
 
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)
         {
-          newAlignFrame.setTitle(MessageManager.formatMessage("label.sequences_from", new String[]{applet.getDocumentBase().toString()}));
+          newAlignFrame.setTitle(MessageManager.formatMessage(
+                  "label.sequences_from", new String[]
+                  { applet.getDocumentBase().toString() }));
         }
 
-        newAlignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String []{file}));
+        newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+                "label.successfully_loaded_file", new String[]
+                { file }));
 
         String treeFile = applet.getParameter("tree");
         if (treeFile == null)
@@ -1961,7 +1978,7 @@ public class JalviewLite extends Applet implements
         param = applet.getParameter("showFeatureSettings");
         if (param != null && param.equalsIgnoreCase("true"))
         {
-          newAlignFrame.viewport.showSequenceFeatures(true);
+          newAlignFrame.viewport.setShowSequenceFeatures(true);
           new FeatureSettings(newAlignFrame.alignPanel);
         }
 
@@ -2059,10 +2076,12 @@ public class JalviewLite extends Applet implements
             {
               String sequence = applet.getParameter("PDBSEQ");
               if (sequence != null)
+              {
                 seqs = new SequenceI[]
                 { matcher == null ? (Sequence) newAlignFrame
                         .getAlignViewport().getAlignment()
                         .findName(sequence) : matcher.findIdMatch(sequence) };
+              }
 
             }
             else
@@ -2122,6 +2141,8 @@ public class JalviewLite extends Applet implements
                 if (seqs[i] != null)
                 {
                   ((Sequence) seqs[i]).addPDBId(pdb);
+                  StructureSelectionManager.getStructureSelectionManager(
+                          applet).registerPDBEntry(pdb);
                 }
                 else
                 {
@@ -2306,7 +2327,9 @@ public class JalviewLite extends Applet implements
     // note separator local variable intentionally masks object field
     int seplen = separator.length();
     if (list == null || list.equals("") || list.equals(separator))
+    {
       return null;
+    }
     java.util.Vector jv = new Vector();
     int cp = 0, pos;
     while ((pos = list.indexOf(separator, cp)) > cp)