v2

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 2b67500..7e6e3a1 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,18 +1,18 @@
 /*
  * 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.
- * 
+ *
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  * PURPOSE.  See the GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
@@ -21,14 +21,11 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.font.LineMetrics;
-import java.awt.geom.AffineTransform;
+import java.awt.image.BufferedImage;
 
-import jalview.analysis.AAFrequency;
 import jalview.datamodel.*;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ColourSchemeI;
 
 public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener,
         ActionListener, MouseListener, MouseMotionListener
@@ -41,19 +38,24 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   Vector activeRes;
 
-  static String HELIX = "Helix";
+  final String HELIX = "Helix";
 
-  static String SHEET = "Sheet";
+  final String SHEET = "Sheet";
 
-  static String LABEL = "Label";
+  /**
+   * For RNA secondary structure "stems" aka helices
+   */
+  final String STEM = "RNA Helix";
+
+  final String LABEL = "Label";
 
-  static String REMOVE = "Remove Annotation";
+  final String REMOVE = "Remove Annotation";
 
-  static String COLOUR = "Colour";
+  final String COLOUR = "Colour";
 
-  static Color HELIX_COLOUR = Color.red.darker();
+  final Color HELIX_COLOUR = Color.red.darker();
 
-  static Color SHEET_COLOUR = Color.green.darker().darker();
+  final Color SHEET_COLOUR = Color.green.darker().darker();
 
   Image image;
 
@@ -101,16 +103,18 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     renderer = new AnnotationRenderer();
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
   }
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
@@ -207,6 +211,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
         symbol = "\u03B2";
       }
 
+      // Added by LML to color stems
+      else if (evt.getActionCommand().equals(STEM))
+      {
+        type = 'S';
+        symbol = "\u03C3";
+      }
+
       if (!aa[activeRow].hasIcons)
       {
         aa[activeRow].hasIcons = true;
@@ -260,6 +271,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
       return null;
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
@@ -304,12 +316,23 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
       }
 
       PopupMenu pop = new PopupMenu("Structure type");
-      MenuItem item = new MenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new MenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
+      MenuItem item;
+      /*
+       * Just display the needed structure options
+       */
+      if (av.getAlignment().isNucleotide() == true)
+      {
+        item = new MenuItem(STEM);
+        item.addActionListener(this);
+        pop.add(item);
+      } else {
+        item = new MenuItem(HELIX);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new MenuItem(SHEET);
+        item.addActionListener(this);
+        pop.add(item);
+      }
       item = new MenuItem(LABEL);
       item.addActionListener(this);
       pop.add(item);
@@ -333,6 +356,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     ap.scalePanel.mousePressed(evt);
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     graphStretch = -1;
@@ -346,12 +370,14 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     ap.scalePanel.mouseReleased(evt);
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
   boolean needValidating = false;
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (graphStretch > -1)
@@ -373,6 +399,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     }
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
@@ -417,11 +444,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     ap.scalePanel.mouseEntered(evt);
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     ap.scalePanel.mouseExited(evt);
@@ -526,11 +555,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     activeRes.addElement(String.valueOf(i));
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     Dimension d = getSize();
@@ -598,7 +629,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param g
    *          DOCUMENT ME!
    * @param startRes
@@ -636,7 +667,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen
     renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
     g.translate(0, +scrollOffset);
   }
-  
+
   int scrollOffset = 0;
 
   public void setScrollOffset(int value)