X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=3d54ae1b429067d07ae13e8310a8d34f9f427f64;hb=4608f763ad15fdb8b093d205985fb3b4d7077471;hp=635535c052cdbfe21a5b5429f4300010066c6757;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 635535c..3d54ae1 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,13 +1,13 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 
  * 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 
@@ -21,7 +21,6 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.image.BufferedImage;
 
 import jalview.datamodel.*;
 import jalview.util.ParseHtmlBodyAndLinks;
@@ -107,7 +106,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
   int getSelectedRow(int y)
   {
     int row = -2;
-    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     if (aa == null)
     {
@@ -228,7 +228,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
     if (row > -1)
     {
-      ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.getAlignment().getAlignmentAnnotation()[row].getDescription(true), true, "\n");
+      ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+              av.getAlignment().getAlignmentAnnotation()[row]
+                      .getDescription(true),
+              true, "\n");
       if (tooltip == null)
       {
         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
@@ -290,7 +293,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
         ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
                 - dif));
         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
-                ap.annotationPanel.calcPanelHeight());
+                av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
         ap.setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -334,7 +337,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
       int end = getSelectedRow(evt.getY() + scrollOffset);
 
-      if (start>-1 && start != end)
+      if (start > -1 && start != end)
       {
         // Swap these annotations
         AlignmentAnnotation startAA = ap.av.getAlignment()
@@ -391,11 +394,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       return;
     }
-    dragCancelled=false;
+    dragCancelled = false;
     // todo: move below to mouseClicked ?
     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 
-    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
@@ -505,7 +509,28 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
+
               popup.add(cprofl);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      "Normalise Group Logo",
+                      aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setshowSequenceLogo(true);
+                  aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
             else
             {
@@ -522,6 +547,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowConsensusHistogram(chist.getState());
+                  ap.alignFrame.showConsensusHistogram.setState(chist
+                          .getState()); // TODO: implement
+                                        // ap.updateGUI()/alignFrame.updateGUI
+                                        // for applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
@@ -540,11 +569,40 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowSequenceLogo(cprof.getState());
+                  ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+                                                                             // implement
+                                                                             // ap.updateGUI()/alignFrame.updateGUI
+                                                                             // for
+                                                                             // applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
               popup.add(cprof);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      "Normalise Logo", av.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowSequenceLogo(true);
+                  ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+                                                                              // implement
+                                                                              // ap.updateGUI()/alignFrame.updateGUI
+                                                                              // for
+                                                                              // applet
+                  av.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
 
             item = new MenuItem(COPYCONS_SEQ);
@@ -646,7 +704,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
   {
     int w = getSize().width;
     int h = getSize().height;
-    if (image == null || w != image.getWidth(this) || h!=image.getHeight(this) )
+    if (image == null || w != image.getWidth(this)
+            || h != image.getHeight(this))
     {
       image = createImage(w, ap.annotationPanel.getSize().height);
     }
@@ -703,7 +762,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               dragEvent.getY());
     }
 
-    if ((aa == null) || (aa.length < 1))
+    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
     {
       g.setColor(Color.black);
       g.drawString("Right click", 2, 8);