add partial button fix to annotation and statistics output

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

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index ce87c72..445ee11 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -74,6 +74,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
           .compile("<");
 
+
   String TOGGLE_LABELSCALE = MessageManager
           .getString("label.scale_label_to_column");
 
@@ -435,25 +436,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           pop.add(item);
         }
       }
-      else if (label.indexOf("Consensus") > -1
-              || label.indexOf("Information Content") > -1)
+      else if (label.indexOf("Consensus") > -1)
       {
-        // identifier for type of histogram and/or logo to be shown
-        int type = 2;
-        if (label.indexOf("Consensus") > -1)
-        {
-          type = 0;
-        }
-        else if (label.indexOf("Information Content") > -1)
-        {
-          type = 1;
-        }
+
 
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for
         final AlignmentAnnotation aaa = aa[selectedRow];
-        if (type == 0)
-        {
+
         final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
                   MessageManager.getString("label.ignore_gaps_consensus"),
                 (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
@@ -480,37 +470,6 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           }
         });
         pop.add(cbmi);
-        }
-        if (type == 1)
-        {
-          final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                  "Ignore Below Background Frequency",
-                  (aa[selectedRow].groupRef != null)
-                          ? aa[selectedRow].groupRef
-                                  .getIgnoreBelowBackground()
-                          : ap.av.isIgnoreBelowBackground());
-
-          cbmi.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              if (aaa.groupRef != null)
-              {
-                // TODO: pass on reference to ap so the view can be updated.
-                aaa.groupRef.setIgnoreBelowBackground(cbmi.getState());
-                ap.getAnnotationPanel()
-                        .paint(ap.getAnnotationPanel().getGraphics());
-              }
-              else
-              {
-                ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
-              }
-              ap.alignmentChanged();
-            }
-          });
-          pop.add(cbmi);
-        }
         // av and sequencegroup need to implement same interface for
         if (aaa.groupRef != null)
         {
@@ -649,6 +608,178 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
+      else if (label.indexOf("Information Content") > -1) // TODO create labels
+                                                          // in message resource
+                                                          // for these
+      {
+        pop.addSeparator();
+        final AlignmentAnnotation aaa = aa[selectedRow];
+
+        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+                "Ignore Below Background Frequency",
+                (aa[selectedRow].groupRef != null)
+                        ? aa[selectedRow].groupRef
+                                .getIgnoreBelowBackground()
+                        : ap.av.isIgnoreBelowBackground());
+
+        cbmi.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            if (aaa.groupRef != null)
+            {
+              // TODO: pass on reference to ap so the view can be updated.
+              aaa.groupRef.setIgnoreBelowBackground(cbmi.getState());
+              ap.getAnnotationPanel()
+                      .paint(ap.getAnnotationPanel().getGraphics());
+            }
+            else
+            {
+              ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+            }
+            ap.alignmentChanged();
+          }
+        });
+        pop.add(cbmi);
+        if (aaa.groupRef != null)
+        {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.show_group_histogram"),
+                  aa[selectedRow].groupRef.isShowInformationHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setShowInformationHistogram(chist.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.show_group_logo"),
+                  aa[selectedRow].groupRef.isShowHMMSequenceLogo());
+          cprofl.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprofl);
+          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.normalise_group_logo"),
+                  aa[selectedRow].groupRef.isNormaliseHMMSequenceLogo());
+          cproflnorm.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              aaa.groupRef
+                      .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+              // automatically enable logo display if we're clicked
+              aaa.groupRef.setshowHMMSequenceLogo(true);
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cproflnorm);
+        }
+        else
+        {
+          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.show_histogram"),
+                  av.isShowInformationHistogram());
+          chist.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowInformationHistogram(chist.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(chist);
+          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.show_logo"),
+                  av.isShowHMMSequenceLogo());
+          cprof.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowHMMSequenceLogo(cprof.getState());
+              ap.alignFrame.setMenusForViewport();
+              ap.repaint();
+              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+            }
+          });
+          pop.add(cprof);
+          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+                  MessageManager.getString("label.normalise_logo"),
+                  av.isNormaliseHMMSequenceLogo());
+          cprofnorm.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // TODO: pass on reference
+              // to ap
+              // so the
+              // view
+              // can be
+              // updated.
+              av.setShowHMMSequenceLogo(true);
+              av.setNormaliseHMMSequenceLogo(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);
+        pop.add(consclipbrd);
+      }
     }
     pop.show(this, evt.getX(), evt.getY());
   }