X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=32f9514ecb7a9d464a5055aa861c9065a2750e35;hb=9a05eeccaf18e0c82cd183f0b84a8be42bf181c7;hp=60d3e06065c5e0a2398a74255dd52a5d5253dbfd;hpb=f7bce11fb6036cd7f94e17c9f136970984a9402a;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 60d3e06..32f9514 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -93,6 +93,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
   boolean mouseDragging = false;
 
   boolean MAC = false;
+  
+  //for editing cursor
+  int cursorX = 0;
+  int cursorY = 0;
 
   /**
    * Creates a new AnnotationPanel object.
@@ -454,15 +458,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       }
 
       JPopupMenu pop = new JPopupMenu("Structure type");
-      JMenuItem item = new JMenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(STEM);
-      item.addActionListener(this);
-      pop.add(item);
+      JMenuItem item;
+      /*
+       * Just display the needed structure options
+       */
+      if(av.alignment.isNucleotide()==true){
+    	  item = new JMenuItem(STEM);
+    	  item.addActionListener(this);
+    	  pop.add(item); 
+      }else{
+    	  item = new JMenuItem(HELIX);
+    	  item.addActionListener(this);
+    	  pop.add(item);
+    	  item = new JMenuItem(SHEET);
+    	  item.addActionListener(this);
+    	  pop.add(item); 	  
+      }
       item = new JMenuItem(LABEL);
       item.addActionListener(this);
       pop.add(item);
@@ -655,7 +666,35 @@ public class AnnotationPanel extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
+	  if(activeRow !=-1){
+	    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();	    	   
+	    AlignmentAnnotation anot = aa[activeRow];
+	    
+	    if(anot.description.equals("secondary structure")){
+	    	System.out.println(anot.description+" "+anot.getRNAStruc());	   
+	    }
+	  }
   }
+	  
+	  public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1)
+	  {
+	    int pady = av.charHeight / 5;
+	    int charOffset = 0;
+	    graphics.setColor(Color.black);
+	    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+	    if (av.validCharWidth)
+	    {
+	      graphics.setColor(Color.white);
+
+	      char s = seq.getCharAt(res);
+
+	      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+	      graphics.drawString(String.valueOf(s), charOffset + x1,
+	              (y1 + av.charHeight) - pady);
+	    }
+
+	  }
 
   /**
    * DOCUMENT ME!