JAL-1153 new runtime property set to first non-null annotation element colour

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 0826924..6d32c04 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.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.
  * 
@@ -143,7 +143,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   void getSelectedRow(int y)
   {
     int height = 0;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
     selectedRow = -2;
     if (aa != null)
     {
@@ -175,20 +175,20 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
-              null, new Annotation[ap.av.alignment.getWidth()]);
+              null, new Annotation[ap.av.getAlignment().getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
         return;
       }
 
-      ap.av.alignment.addAnnotation(newAnnotation);
-      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      ap.av.getAlignment().addAnnotation(newAnnotation);
+      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
@@ -201,7 +201,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     }
     else if (evt.getActionCommand().equals(DELETE))
     {
-      ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+      ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
     }
     else if (evt.getActionCommand().equals(SHOWALL))
     {
@@ -305,16 +305,16 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (start != end)
     {
       // Swap these annotations
-      AlignmentAnnotation startAA = ap.av.alignment
+      AlignmentAnnotation startAA = ap.av.getAlignment()
               .getAlignmentAnnotation()[start];
       if (end == -1)
       {
-        end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+        end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
       }
-      AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+      AlignmentAnnotation endAA = ap.av.getAlignment().getAlignmentAnnotation()[end];
 
-      ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-      ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+      ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
     }
 
     resizePanel = false;
@@ -402,9 +402,9 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     getSelectedRow(evt.getY() - scrollOffset);
 
     if (selectedRow > -1
-            && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+            && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
     {
-      AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
+      AlignmentAnnotation aa = ap.av.getAlignment().getAlignmentAnnotation()[selectedRow];
       
       StringBuffer desc = new StringBuffer();
       if (aa.description != null
@@ -460,7 +460,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
       if (selectedRow > -1 && selectedRow < aa.length)
@@ -630,6 +630,28 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             }
           });
           pop.add(cprofl);
+          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+                  "Normalise Group Logo",
+                  aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+          cproflnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+              // automatically enable logo display if we're clicked
+              aaa.groupRef.setshowSequenceLogo(true);
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cproflnorm);
         }
         else
         {
@@ -646,6 +668,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // can be
               // updated.
               av.setShowConsensusHistogram(chist.getState());
+              ap.alignFrame.setMenusForViewport();
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
@@ -664,11 +687,32 @@ public class AnnotationLabels extends JPanel implements MouseListener,
               // can be
               // updated.
               av.setShowSequenceLogo(cprof.getState());
+              ap.alignFrame.setMenusForViewport();
               ap.repaint();
               // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
             }
           });
           pop.add(cprof);
+          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+                  "Normalise Logo", av.isNormaliseSequenceLogo());
+          cprofnorm.addActionListener(new ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowSequenceLogo(true);
+              av.setNormaliseSequenceLogo(cprofnorm.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprofnorm);
         }
         final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
         consclipbrd.addActionListener(this);
@@ -700,7 +744,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       sq.setDatasetSequence(dseqs[0]);
     }
     Alignment ds = new Alignment(dseqs);
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
               sq.getLength(), seqs);
@@ -713,7 +757,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
             .setContents(new StringSelection(output), Desktop.instance);
 
     Vector hiddenColumns = null;
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       hiddenColumns = new Vector();
       for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
@@ -782,7 +826,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
     int x = 0;