X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=09624a80ac779a1cab0f2aef87cf56793575441e;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=9976604510dc300563812202b05c64ae553cd668;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 9976604..09624a8 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -36,6 +36,7 @@ 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;
@@ -353,6 +354,8 @@ 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);
@@ -400,7 +403,8 @@ public class AnnotationLabels extends JPanel
     if (selectedRow < aa.length)
     {
       final String label = aa[selectedRow].label;
-      if (!aa[selectedRow].autoCalculated)
+      if (!(aa[selectedRow].autoCalculated)
+              && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
       {
         if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
         {
@@ -408,7 +412,7 @@ public class AnnotationLabels extends JPanel
           pop.addSeparator();
           // av and sequencegroup need to implement same interface for
           item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
-                  aa[selectedRow].scaleColLabel);
+        		  aa[selectedRow].scaleColLabel);
           item.addActionListener(this);
           pop.add(item);
         }
@@ -421,11 +425,169 @@ 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
@@ -971,7 +1133,7 @@ public class AnnotationLabels extends JPanel
             seqs, omitHidden, alignmentStartEnd);
 
     Toolkit.getDefaultToolkit().getSystemClipboard()
-            .setContents(new StringSelection(output), Desktop.instance);
+            .setContents(new StringSelection(output), Desktop.getInstance());
 
     HiddenColumns hiddenColumns = null;
 
@@ -981,20 +1143,12 @@ public class AnnotationLabels extends JPanel
               av.getAlignment().getHiddenColumns());
     }
 
-    Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
-                                                        // of a consensus
-                                                        // sequence ? need to
-                                                        // flag
-        // sequence as special.
+    // what is the dataset of a consensus sequence? 
+    // need to flag sequence as special.
+    Desktop.getInstance().jalviewClipboard = new Object[] { seqs, ds, 
         hiddenColumns };
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param g1
-   *          DOCUMENT ME!
-   */
   @Override
   public void paintComponent(Graphics g)
   {