X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=30d57e0a3326e6837761655f27963a0ec3d90e9c;hb=0201d2b630e06a75fd9522f24863e9cecf8810fd;hp=e01615acc80b96921d7fc73035d80a84ee11adaf;hpb=1d37661bae76ec6d499ff50a88ea249b8b33430e;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index e01615a..30d57e0 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -31,6 +31,8 @@ public class FeatureSettings extends Panel implements ItemListener,
   final AlignmentPanel ap;
   final AlignViewport av;
   final Frame frame;
+  Panel groupPanel;
+  Panel featurePanel = new Panel();
 
   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
   {
@@ -40,9 +42,22 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     setTableData();
 
+    this.setLayout(new BorderLayout());
+    ScrollPane sp = new ScrollPane();
+    sp.add(featurePanel);
+    add(sp, BorderLayout.CENTER);
+    if(groupPanel!=null)
+    {
+      sp = new ScrollPane();
+      sp.add(groupPanel);
+
+      add(sp, BorderLayout.NORTH);
+      sp.validate();
+      sp.setSize( 100, 55);
+    }
     frame = new Frame();
     frame.add(this);
-    int height = this.getComponentCount()*50;
+    int height = featurePanel.getComponentCount()*50 ;
     if (height>400)
       height = 400;
 
@@ -52,68 +67,92 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   void setTableData()
   {
+    if(fr.featureGroups==null)
+      fr.featureGroups = new Hashtable();
+    else
+      fr.featureGroups.clear();
+
     Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
+    Enumeration tmpfeatures;
     SequenceFeature sf;
 
     for (int i = 0; i < av.alignment.getHeight(); i++)
     {
-      features = av.alignment.getSequenceAt(i).getSequenceFeatures();
-      if (features == null)
+      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
         continue;
 
-      e = features.elements();
-      while (e.hasMoreElements())
+      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures().elements();
+      while (tmpfeatures.hasMoreElements())
       {
-        sf = (SequenceFeature) e.nextElement();
+        sf = (SequenceFeature) tmpfeatures.nextElement();
         if (!allFeatures.contains(sf.getType()))
         {
           allFeatures.addElement(sf.getType());
+          Color col = fr.getColour(sf.getType());
+          boolean displayed = true;
+          if (fr.featuresDisplayed != null)
+            displayed = fr.featuresDisplayed.contains(sf.getType());
+
+          Checkbox check = new Checkbox(sf.getType(), displayed);
+          check.addMouseListener(this);
+          check.addMouseMotionListener(this);
+          check.setBackground(col);
+          check.addItemListener(this);
+          featurePanel.add(check);
+        }
+        if(sf.getFeatureGroup()!=null
+           && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+        {
+          fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
+          if(groupPanel==null)
+            groupPanel = new Panel();
+
+          Checkbox check = new Checkbox(sf.getFeatureGroup(), true);
+          check.setFont(new Font("Serif", Font.BOLD, 12));
+          check.addItemListener(this);
+          groupPanel.add(check);
         }
       }
     }
 
-    int fSize = allFeatures.size();
-
-    String type;
-    this.setLayout(new GridLayout(fSize, 2, 10,5));
-
-    for (int i = 0; i < fSize; i++)
-    {
-      type = allFeatures.elementAt(i).toString();
-      Color col = fr.getColour(type);
-      boolean displayed = true;
-      if(fr.featuresDisplayed!=null)
-        displayed = fr.featuresDisplayed.contains(type);
-
-      Checkbox check = new Checkbox(type, displayed);
-      check.addMouseListener(this);
-      check.addMouseMotionListener(this);
-      check.setBackground(col);
-      check.addItemListener(this);
-      add(check);
-    }
-    validate();
+    featurePanel.setLayout(new GridLayout(allFeatures.size(), 2, 10,5));
+    featurePanel.validate();
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
-    Component [] comps = this.getComponents();
-    int cSize = comps.length;
-
-    Object [][] data = new Object[cSize][3];
-
-    for(int i=0; i<cSize; i++)
+    if(evt!=null)
     {
-      Checkbox check = (Checkbox)comps[i];
-      data[i][0] = check.getLabel();
-      data[i][1] = fr.getColour(check.getLabel());
-      data[i][2] = new Boolean(check.getState());
+      //Is the source a top level featureGroup?
+      Checkbox source = (Checkbox) evt.getSource();
+      if (fr.featureGroups.containsKey(source.getLabel()))
+      {
+        fr.featureGroups.put(source.getLabel(), new Boolean(source.getState()));
+        ap.seqPanel.seqCanvas.repaint();
+        if (ap.overviewPanel != null)
+          ap.overviewPanel.updateOverviewImage();
+
+        return;
+      }
     }
 
-    fr.setFeaturePriority(data);
-    ap.seqPanel.seqCanvas.repaint();
+      Component[] comps = featurePanel.getComponents();
+      int cSize = comps.length;
+
+      Object[][] data = new Object[cSize][3];
+
+      for (int i = 0; i < cSize; i++)
+      {
+        Checkbox check = (Checkbox) comps[i];
+        data[i][0] = check.getLabel();
+        data[i][1] = fr.getColour(check.getLabel());
+        data[i][2] = new Boolean(check.getState());
+      }
+
+      fr.setFeaturePriority(data);
+      ap.seqPanel.seqCanvas.repaint();
+      if (ap.overviewPanel != null)
+        ap.overviewPanel.updateOverviewImage();
   }
 
   Checkbox selectedCheck;
@@ -136,17 +175,18 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     int height = evt.getY()+evt.getComponent().getLocation().y;
 
+
     if(height > this.getSize().height)
      {
-       comp = this.getComponent(this.getComponentCount()-1);
+       comp = featurePanel.getComponent(featurePanel.getComponentCount()-1);
      }
      else if(height < 0)
      {
-       comp = this.getComponent(0);
+       comp = featurePanel.getComponent(0);
      }
      else
      {
-       comp = this.getComponentAt(evt.getX(),
+       comp = featurePanel.getComponentAt(evt.getX(),
                                   evt.getY() +
                                   evt.getComponent().getLocation().y);
      }
@@ -157,16 +197,17 @@ public class FeatureSettings extends Panel implements ItemListener,
     if (selectedCheck != null && target != null && selectedCheck != target)
     {
       int targetIndex = -1;
-      for(int i=0; i<this.getComponentCount(); i++)
+      for(int i=0; i<featurePanel.getComponentCount(); i++)
       {
-          if(target==this.getComponent(i))
+          if(target==featurePanel.getComponent(i))
           { targetIndex = i; break; }
       }
 
 
-      this.remove(selectedCheck);
-      this.add(selectedCheck, targetIndex);
-      validate();
+      featurePanel.remove(selectedCheck);
+      featurePanel.add(selectedCheck, targetIndex);
+      featurePanel.validate();
+      itemStateChanged(null);
     }
   }