X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;fp=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=8aac7dcb60a87acc19e2b55dcbb2974b41914426;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=6da6cc385caf32f6b639565cf2948367b37d2298;hpb=9e31a59b947882325ffe614bd71fb732d7952a23;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6da6cc3..8aac7dc 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -34,6 +34,7 @@ import jalview.io.FormatAdapter;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.workers.InformationThread;
 
 import java.awt.Color;
 import java.awt.Cursor;
@@ -352,6 +353,10 @@ public class AnnotationLabels extends JPanel
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
+
+    final AlignmentAnnotation ann = aa[selectedRow];
+    final boolean isSequenceAnnotation = ann.sequenceRef != null;
+
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -361,9 +366,9 @@ public class AnnotationLabels extends JPanel
     // JAL-1264 hide all sequence-specific annotations of this type
     if (selectedRow < aa.length)
     {
-      if (aa[selectedRow].sequenceRef != null)
+      if (isSequenceAnnotation)
       {
-        final String label = aa[selectedRow].label;
+        final String label = ann.label;
         JMenuItem hideType = new JMenuItem();
         String text = MessageManager.getString("label.hide_all") + " "
                 + label;
@@ -398,16 +403,17 @@ public class AnnotationLabels extends JPanel
     // property methods
     if (selectedRow < aa.length)
     {
-      final String label = aa[selectedRow].label;
-      if (!aa[selectedRow].autoCalculated)
+      final String label = ann.label;
+      if (!(ann.autoCalculated)
+              && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
       {
-        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+        if (ann.graph == AlignmentAnnotation.NO_GRAPH)
         {
           // display formatting settings for this row.
           pop.addSeparator();
           // av and sequencegroup need to implement same interface for
           item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
-                  aa[selectedRow].scaleColLabel);
+                  ann.scaleColLabel);
           item.addActionListener(this);
           pop.add(item);
         }
@@ -420,11 +426,169 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
+      else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        addHmmerMenu(pop, ann);
+      }
     }
     pop.show(this, evt.getX(), evt.getY());
   }
 
   /**
+   * Adds context menu options for (alignment or group) Hmmer annotation
+   * 
+   * @param pop
+   * @param ann
+   */
+  protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+  {
+    final boolean isGroupAnnotation = ann.groupRef != null;
+    pop.addSeparator();
+    final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+            MessageManager.getString(
+                    "label.ignore_below_background_frequency"),
+            isGroupAnnotation
+                    ? ann.groupRef
+                            .isIgnoreBelowBackground()
+                    : ap.av.isIgnoreBelowBackground());
+    cbmi.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (isGroupAnnotation)
+        {
+          if (!ann.groupRef.isUseInfoLetterHeight())
+          {
+            ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+            // todo and recompute group annotation
+          }
+        }
+        else if (!ap.av.isInfoLetterHeight())
+        {
+          ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+          // todo and recompute annotation
+        }
+        ap.alignmentChanged(); // todo not like this
+      }
+    });
+    pop.add(cbmi);
+    final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+            MessageManager.getString("label.use_info_for_height"),
+            isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+                    : ap.av.isInfoLetterHeight());
+    letterHeight.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (isGroupAnnotation)
+        {
+          ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+          ann.groupRef.setIgnoreBelowBackground(true);
+          // todo and recompute group annotation
+        }
+        else
+        {
+          ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+          ap.av.setIgnoreBelowBackground(true, ap);
+          // todo and recompute annotation
+        }
+        ap.alignmentChanged();
+      }
+    });
+    pop.add(letterHeight);
+    if (isGroupAnnotation)
+    {
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_histogram"),
+              ann.groupRef.isShowInformationHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setShowInformationHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_logo"),
+              ann.groupRef.isShowHMMSequenceLogo());
+      cprofl.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofl);
+      final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_group_logo"),
+              ann.groupRef.isNormaliseHMMSequenceLogo());
+      cproflnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef
+                  .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+          // automatically enable logo display if we're clicked
+          ann.groupRef.setShowHMMSequenceLogo(true);
+          ap.repaint();
+        }
+      });
+      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)
+        {
+          av.setShowInformationHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      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)
+        {
+          av.setShowHMMSequenceLogo(cprof.getState());
+          ap.repaint();
+        }
+      });
+      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)
+        {
+          av.setShowHMMSequenceLogo(true);
+          av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofnorm);
+    }
+  }
+
+  /**
    * A helper method that adds menu options for calculation and visualisation of
    * group and/or alignment consensus annotation to a popup menu. This is
    * designed to be reusable for either unwrapped mode (popup menu is shown on
@@ -925,7 +1089,6 @@ public class AnnotationLabels extends JPanel
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
-
         }
       }
       return;
@@ -997,7 +1160,6 @@ public class AnnotationLabels extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
-
     int width = getWidth();
     if (width == 0)
     {
@@ -1012,7 +1174,6 @@ public class AnnotationLabels extends JPanel
     }
 
     drawComponent(g2, true, width);
-
   }
 
   /**