Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dbdc23f..cdfed1d 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -63,6 +63,7 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -1202,11 +1203,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public String outputAnnotations(boolean displayTextbox)
   {
-    String annotation = new AnnotationFile().printAnnotations(
-            viewport.showAnnotation ? viewport.getAlignment()
-                    .getAlignmentAnnotation() : null, viewport
-                    .getAlignment().getGroups(), ((Alignment) viewport
-                    .getAlignment()).alignmentProperties);
+    String annotation = new AnnotationFile()
+            .printAnnotationsForView(viewport);
 
     if (displayTextbox)
     {
@@ -1282,7 +1280,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     StringBuffer url = new StringBuffer(jalviewServletURL);
 
-    url.append("?open="
+    // allow servlet parameters to be passed in applet parameter
+    String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
+            : "?";
+    url.append(firstSep);
+
+    url.append("open="
             + appendProtocol(viewport.applet.getParameter("file")));
 
     if (viewport.applet.getParameter("features") != null)
@@ -1692,11 +1695,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       copiedHiddenColumns = new Vector();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
-              .size(); i++)
+      for (int[] region : viewport.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) viewport.getColumnSelection()
-                .getHiddenColumns().elementAt(i);
 
         copiedHiddenColumns.addElement(new int[]
         { region[0] - hiddenOffset, region[1] - hiddenOffset });
@@ -3642,7 +3642,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         return null;
       }
     }
-    ExtJmol jmv = null;
+    AAStructureBindingModel jmv = null;
     // TODO: search for a jmv that involves viewer
     if (jmv == null)
     { // create a new viewer/jalview binding.