update author list in license for (JAL-826)

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 30026ef..9b91255 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -65,6 +65,7 @@ import jalview.schemes.HelixColourScheme;
 import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -401,7 +402,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     || evt.isShiftDown() || evt.isAltDown());
           }
           break;
-
+          
+        //case KeyEvent.VK_A:
+       //      if (viewport.cursorMode)
+       //     {
+       //              alignPanel.seqPanel.insertNucAtCursor(false,"A");
+       //              //System.out.println("A");
+       //     }
+       //      break;
+        /*     
+        case KeyEvent.VK_CLOSE_BRACKET:
+               if (viewport.cursorMode)
+            {
+                       System.out.println("closing bracket");
+            }
+               break;
+         */
         case KeyEvent.VK_DELETE:
         case KeyEvent.VK_BACK_SPACE:
           if (!viewport.cursorMode)
@@ -574,6 +590,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
+      ap.av.updateStrucConsensus(ap);
     }
   }
 
@@ -645,11 +662,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
+    rnahelicesColour.setEnabled(nucleotide);
+    purinePyrimidineColour.setEnabled(nucleotide);
     // Remember AlignFrame always starts as protein
-    if (!nucleotide)
-    {
-      calculateMenu.remove(calculateMenu.getItemCount() - 2);
-    }
+    //if (!nucleotide)
+   // {
+   //   showTr
+   //   calculateMenu.remove(calculateMenu.getItemCount() - 2);
+   // }
   }
 
   /**
@@ -701,7 +721,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
     autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
-
+    listenToViewSelections.setSelected(av.followSelection);
+    rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
+    rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
 
     updateEditMenuBar();
@@ -2967,10 +2989,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     changeColour(new NucleotideColourScheme());
   }
 
+  public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new PurinePyrimidineColourScheme());
+  }
+  /*
+  public void covariationColour_actionPerformed(ActionEvent e)
+  {
+    changeColour(new CovariationColourScheme(viewport.alignment.getAlignmentAnnotation()[0]));
+  }
+  */
   public void annotationColour_actionPerformed(ActionEvent e)
   {
     new AnnotationColourChooser(viewport, alignPanel);
   }
+  
+  public void rnahelicesColour_actionPerformed(ActionEvent e)
+  {
+    new RNAHelicesColourChooser(viewport, alignPanel);
+  }
 
   /**
    * DOCUMENT ME!
@@ -3427,6 +3464,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.sortByTree = sortByTree.isSelected();
   }
 
+  @Override
+  protected void listenToViewSelections_actionPerformed(ActionEvent e)
+  {
+    viewport.followSelection = listenToViewSelections.isSelected();
+  }
   /**
    * DOCUMENT ME!
    *