Remove system.out

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 78c175b..8e54ba9 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -36,8 +36,8 @@ public class AlignFrame extends Frame implements ActionListener,
 {\r
   public AlignmentPanel alignPanel;\r
   public AlignViewport viewport;\r
-  int NEW_WINDOW_WIDTH = 700;\r
-  int NEW_WINDOW_HEIGHT = 500;\r
+  int DEFAULT_WIDTH = 700;\r
+  int DEFAULT_HEIGHT = 500;\r
 \r
   String jalviewServletURL;\r
 \r
@@ -91,13 +91,13 @@ public class AlignFrame extends Frame implements ActionListener,
         if (param != null)\r
         {\r
           int width = Integer.parseInt(param);\r
-          NEW_WINDOW_WIDTH = width;\r
+          DEFAULT_WIDTH = width;\r
         }\r
         param = applet.getParameter("windowHeight");\r
         if (param != null)\r
         {\r
           int height = Integer.parseInt(param);\r
-          NEW_WINDOW_HEIGHT = height;\r
+          DEFAULT_HEIGHT = height;\r
         }\r
       }\r
       catch (Exception ex)\r
@@ -132,8 +132,8 @@ public class AlignFrame extends Frame implements ActionListener,
    else\r
    {\r
      add(alignPanel, BorderLayout.CENTER);\r
-     jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH,\r
-                                      NEW_WINDOW_HEIGHT);\r
+     jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+                                      DEFAULT_HEIGHT);\r
    }\r
    alignPanel.validate();\r
    alignPanel.repaint();\r
@@ -260,7 +260,10 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_SPACE:\r
         if(viewport.cursorMode)\r
         {\r
-          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown());\r
+          alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+                                                || evt.isShiftDown()\r
+                                                || evt.isAltDown()\r
+              );\r
         }\r
         break;\r
 \r
@@ -268,7 +271,10 @@ public class AlignFrame extends Frame implements ActionListener,
       case KeyEvent.VK_BACK_SPACE:\r
         if(viewport.cursorMode)\r
         {\r
-          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown());\r
+          alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+                                                || evt.isShiftDown()\r
+                                                || evt.isAltDown()\r
+              );\r
         }\r
        else\r
         {\r
@@ -362,8 +368,23 @@ public class AlignFrame extends Frame implements ActionListener,
         alignPanel.repaint();\r
         break;\r
       }\r
-\r
-    }\r
+      case KeyEvent.VK_PAGE_UP:\r
+        if (viewport.wrapAlignment)\r
+          alignPanel.scrollUp(true);\r
+        else\r
+          alignPanel.setScrollValues(viewport.startRes,\r
+                                     viewport.startSeq\r
+                                     - viewport.endSeq + viewport.startSeq);\r
+        break;\r
+      case KeyEvent.VK_PAGE_DOWN:\r
+        if (viewport.wrapAlignment)\r
+          alignPanel.scrollUp(false);\r
+        else\r
+          alignPanel.setScrollValues(viewport.startRes,\r
+                                     viewport.startSeq\r
+                                     + viewport.endSeq - viewport.startSeq);\r
+        break;\r
+      }\r
   }\r
   public void keyReleased(KeyEvent evt)\r
   {}\r
@@ -583,6 +604,12 @@ public void itemStateChanged(ItemEvent evt)
       url.append( appendProtocol( viewport.applet.getParameter("annotations") ) );\r
     }\r
 \r
+    if(viewport.applet.getParameter("jnetfile")!=null)\r
+    {\r
+      url.append( "&annotations=" );\r
+      url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) );\r
+    }\r
+\r
     if(viewport.applet.getParameter("defaultColour")!=null)\r
     {\r
       url.append("&colour=" +\r
@@ -919,8 +946,8 @@ public void itemStateChanged(ItemEvent evt)
         }\r
 \r
 \r
-        jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
-                                         NEW_WINDOW_HEIGHT);\r
+        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+                                         DEFAULT_HEIGHT);\r
       }\r
       else\r
       {\r
@@ -1220,7 +1247,7 @@ public void itemStateChanged(ItemEvent evt)
                           viewport.alignment.getWidth());\r
       }\r
 \r
-      cs.setConsensus(viewport.vconsensus);\r
+      cs.setConsensus(viewport.hconsensus);\r
       if (cs.conservationApplied())\r
       {\r
         Alignment al = (Alignment) viewport.alignment;\r
@@ -1460,7 +1487,7 @@ public void itemStateChanged(ItemEvent evt)
         cs.setConservation(null);\r
       }\r
 \r
-      cs.setConsensus(viewport.vconsensus);\r
+      cs.setConsensus(viewport.hconsensus);\r
 \r
     }\r
     viewport.setGlobalColourScheme(cs);\r