Applet has hidden regions

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2b53d76..e1d8ce8 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -38,7 +38,6 @@ public class AlignFrame extends Frame implements ActionListener,
   public AlignViewport viewport;\r
   int NEW_WINDOW_WIDTH = 700;\r
   int NEW_WINDOW_HEIGHT = 500;\r
-  jalview.bin.JalviewLite applet;\r
 \r
   String jalviewServletURL;\r
 \r
@@ -58,7 +57,6 @@ public class AlignFrame extends Frame implements ActionListener,
       ex.printStackTrace();\r
     }\r
 \r
-    this.applet = applet;\r
     viewport = new AlignViewport(al, applet);\r
     alignPanel = new AlignmentPanel(this, viewport);\r
 \r
@@ -515,25 +513,25 @@ public void itemStateChanged(ItemEvent evt)
     StringBuffer url = new StringBuffer(jalviewServletURL);\r
 \r
     url.append("?open="+\r
-               appendProtocol( applet.getParameter("file") ) );\r
+               appendProtocol( viewport.applet.getParameter("file") ) );\r
 \r
-    if(applet.getParameter("features")!=null)\r
+    if(viewport.applet.getParameter("features")!=null)\r
     {\r
       url.append( "&features=" );\r
-      url.append( appendProtocol( applet.getParameter("features") ) );\r
+      url.append( appendProtocol( viewport.applet.getParameter("features") ) );\r
     }\r
 \r
-    if(applet.getParameter("defaultColour")!=null)\r
+    if(viewport.applet.getParameter("defaultColour")!=null)\r
     {\r
       url.append("&colour=" +\r
-                 removeWhiteSpace(applet.getParameter("defaultColour"))\r
+                 removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
           );\r
     }\r
 \r
-    if(applet.getParameter("userDefinedColour")!=null)\r
+    if(viewport.applet.getParameter("userDefinedColour")!=null)\r
     {\r
       url.append( "&colour=" +\r
-                 removeWhiteSpace( applet.getParameter("userDefinedColour") )\r
+                 removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") )\r
          );\r
     }\r
 \r
@@ -562,7 +560,7 @@ public void itemStateChanged(ItemEvent evt)
        new URL(url);\r
     }catch(java.net.MalformedURLException ex)\r
     {\r
-      url = applet.getCodeBase()+url;\r
+      url = viewport.applet.getCodeBase()+url;\r
     }\r
     return url;\r
   }\r
@@ -570,7 +568,7 @@ public void itemStateChanged(ItemEvent evt)
   public void closeMenuItem_actionPerformed()\r
   {\r
     PaintRefresher.components.remove(viewport.alignment);\r
-    if(PaintRefresher.components.size()==0 && applet==null)\r
+    if(PaintRefresher.components.size()==0 && viewport.applet==null)\r
       System.exit(0);\r
 \r
     this.dispose();\r
@@ -820,7 +818,7 @@ public void itemStateChanged(ItemEvent evt)
           newtitle = newtitle.concat("- from " + getTitle());\r
         }\r
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
-                                       applet,\r
+                                       viewport.applet,\r
                                        newtitle,\r
                                        false);\r
 \r
@@ -1749,7 +1747,7 @@ public void itemStateChanged(ItemEvent evt)
 \r
   public void showURL(String url, String target)\r
   {\r
-    if (applet == null)\r
+    if (viewport.applet == null)\r
     {\r
       System.out.println("Not running as applet - no browser available.");\r
     }\r
@@ -1758,7 +1756,7 @@ public void itemStateChanged(ItemEvent evt)
       try\r
       {\r
         System.out.println("Show url: "+url);\r
-        applet.getAppletContext().showDocument(new java.net.URL(url),\r
+        viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
                                                target);\r
       }\r
       catch (Exception ex)\r
@@ -2185,16 +2183,16 @@ public void itemStateChanged(ItemEvent evt)
     fileMenu.remove(closeMenuItem);\r
     fileMenu.remove(3); // Seperator\r
 \r
-    applet.setLayout(new BorderLayout());\r
-    applet.add(embeddedMenu, BorderLayout.NORTH);\r
-    applet.add(statusBar, BorderLayout.SOUTH);\r
-   // applet.validate();\r
+    viewport.applet.setLayout(new BorderLayout());\r
+    viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+    viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+   // viewport.applet.validate();\r
 \r
-    alignPanel.setSize(applet.size().width, applet.size().height\r
+    alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
 \r
-     applet.add(alignPanel, BorderLayout.CENTER);\r
-     applet.validate();\r
+     viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+     viewport.applet.validate();\r
 \r
   }\r
 \r