From 22b9e04a8351aef1cb23a66d898502601499b673 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Feb 2006 15:49:43 +0000
Subject: [PATCH] FeatureGroups added

---
 src/jalview/gui/FeatureRenderer.java |   15 +++++++++++-
 src/jalview/gui/FeatureSettings.java |   45 +++++++++++++++++++++++++++++++---
 2 files changed, 56 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 69ecf14..22789a1 100755
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -46,6 +46,11 @@ public class FeatureRenderer
     // to be added, in the correct order or rendering
     Vector featuresDisplayed = null;
 
+    // A higher level for grouping features of a
+   // particular type
+    Hashtable featureGroups = null;
+
+
     /**
      * Creates a new FeatureRenderer object.
      *
@@ -98,7 +103,7 @@ public class FeatureRenderer
                              int start, int end, int x1, int y1, int width, int height)
     {
 
-//System.out.println(start+" "+end+" "+x1+" "+y1);
+        //System.out.println(start+" "+end+" "+x1+" "+y1);
       if (seq.getDatasetSequence().getSequenceFeatures() == null
           || seq.getDatasetSequence().getSequenceFeatures().size()==0)
         return;
@@ -135,6 +140,14 @@ public class FeatureRenderer
           if (!type.equals(sf.getType()))
             continue;
 
+          if(featureGroups!=null
+             && sf.getFeatureGroup()!=null
+             && featureGroups.containsKey(sf.getFeatureGroup())
+             && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())
+          {
+            continue;
+          }
+
           if (sf.getBegin() > seq.getEnd())
             continue;
 
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 47cedd3..eb74454 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -39,6 +39,7 @@ public class FeatureSettings extends JPanel
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
+  JPanel groupPanel;
 
   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
   {
@@ -122,6 +123,8 @@ public class FeatureSettings extends JPanel
     JPanel bigPanel = new JPanel(new BorderLayout());
     bigPanel.add(transPanel, BorderLayout.SOUTH);
     bigPanel.add(scrollPane, BorderLayout.CENTER);
+    if(groupPanel!=null)
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
 
     add(bigPanel, BorderLayout.CENTER);
     add(buttonPanel, BorderLayout.SOUTH);
@@ -131,6 +134,11 @@ public class FeatureSettings extends JPanel
 
   void setTableData()
   {
+    if (fr.featureGroups == null)
+      fr.featureGroups = new Hashtable();
+    else
+      fr.featureGroups.clear();
+
     Vector allFeatures = new Vector();
     Vector features;
     Enumeration e;
@@ -147,6 +155,32 @@ public class FeatureSettings extends JPanel
     while (e.hasMoreElements())
     {
       sf = (SequenceFeature) e.nextElement();
+      if(sf.getFeatureGroup()!=null
+          && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+       {
+         fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
+         if(groupPanel==null)
+            groupPanel = new JPanel();
+
+          final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true);
+          check.setFont(new Font("Serif", Font.BOLD, 12));
+          check.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent evt)
+                {
+                  if (fr.featureGroups.containsKey(check.getText()))
+                  {
+                    fr.featureGroups.put(check.getText(),
+                                         new Boolean(check.isSelected()));
+                    ap.seqPanel.seqCanvas.repaint();
+                    if (ap.overviewPanel != null)
+                      ap.overviewPanel.updateOverviewImage();
+                  }
+
+                }
+              });
+          groupPanel.add(check);
+       }
       if (!allFeatures.contains(sf.getType()))
       {
         allFeatures.addElement(sf.getType());
@@ -155,9 +189,14 @@ public class FeatureSettings extends JPanel
   }
     if(allFeatures.size()<1)
      {
-       try{
-         frame.setClosed(true);
-       }catch(Exception ex){}
+       try
+       { frame.setClosed(true);  }
+       catch (Exception ex){}
+
+       JOptionPane.showInternalMessageDialog(
+           Desktop.desktop, "No features have been added to this alignment!",
+           "No Sequence Features", JOptionPane.WARNING_MESSAGE);
+
        return;
      }
 
-- 
1.7.10.2