X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=d642c14ddb2ecbdac3ee72960cd737de8214f87a;hb=8d44c38e7028bcce53c0370dec67baa5d8d209c9;hp=4b9fa679f5d1254be3eca9543abcd27bc1f82bb5;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 4b9fa67..d642c14 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,16 +20,30 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
 public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         AdjustmentListener, ActionListener, MouseListener,
         MouseMotionListener
@@ -40,8 +54,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   int activeRow = -1;
 
-  Vector activeRes;
-
   final String HELIX = "Helix";
 
   final String SHEET = "Sheet";
@@ -138,15 +150,17 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     String label = "";
     if (av.getColumnSelection() != null
-            && av.getColumnSelection().size() > 0
+            && !av.getColumnSelection().isEmpty()
             && anot[av.getColumnSelection().getMin()] != null)
+    {
       label = anot[av.getColumnSelection().getMin()].displayCharacter;
+    }
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int sel : av.getColumnSelection().getSelected())
       {
-        anot[av.getColumnSelection().columnAt(i)] = null;
+        anot[sel] = null;
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -163,12 +177,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         aa[activeRow].hasText = true;
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -185,12 +199,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
       Color col = udc.getColor();
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
@@ -244,19 +258,20 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         }
       }
 
-      for (int i = 0; i < av.getColumnSelection().size(); i++)
+      for (int index : av.getColumnSelection().getSelected())
       {
-        int index = av.getColumnSelection().columnAt(i);
-
         if (!av.getColumnSelection().isVisible(index))
+        {
           continue;
+        }
 
         if (anot[index] == null)
         {
           anot[index] = new Annotation(label, "", type, 0);
         }
 
-        anot[index].secondaryStructure = type;
+        anot[index].secondaryStructure = type != 'S' ? type : label
+                .length() == 0 ? ' ' : label.charAt(0);
         anot[index].displayCharacter = label;
       }
     }
@@ -276,9 +291,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
             ap.alignFrame, "Enter Label", 400, 200, true);
 
     if (dialog.accept)
+    {
       return dialog.getName();
+    }
     else
+    {
       return null;
+    }
   }
 
   @Override
@@ -361,11 +380,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return;
     }
 
-    if (aa == null)
-    {
-      return;
-    }
-
     ap.scalePanel.mousePressed(evt);
   }
 
@@ -511,15 +525,6 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
         }
       }
     }
-
-    if (activeRes == null)
-    {
-      activeRes = new Vector();
-      activeRes.addElement(String.valueOf(i));
-      return;
-    }
-
-    activeRes.addElement(String.valueOf(i));
   }
 
   @Override
@@ -572,13 +577,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return;
     }
 
-    gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
-            * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getSize().height,
+            -horizontal * av.getCharWidth(), 0);
     int sr = av.startRes, er = av.endRes + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
-      transX = (er - sr - horizontal) * av.charWidth;
+      transX = (er - sr - horizontal) * av.getCharWidth();
       sr = er - horizontal;
     }
     else if (horizontal < 0)
@@ -612,7 +617,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     g.setFont(ofont);
 
     g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+    g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+            getSize().height);
 
     if (fm == null)
     {
@@ -681,6 +687,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return bounds;
     }
     else
+    {
       return null;
+    }
   }
 }