JAL-1432 updated copyright notices

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 9b2dba6..1191abd 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -118,8 +119,10 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     if (groupPanel != null)
     {
-      groupPanel.setLayout(new GridLayout(fr.featureGroups.size() / 4 + 1,
-              4));
+      groupPanel
+              .setLayout(new GridLayout(
+                      (fr.featureGroups.size() - fr.hiddenGroups.size()) / 4 + 1,
+                      4));
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -261,7 +264,8 @@ public class FeatureSettings extends Panel implements ItemListener,
       rdrw = true;
       groupPanel.removeAll();
     }
-
+    // TODO: JAL-964 - smoothly incorporate new group entries if panel already
+    // displayed and new groups present
     Enumeration gps = fr.featureGroups.keys();
     while (gps.hasMoreElements())
     {
@@ -273,6 +277,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       check.addMouseListener(this);
       check.setFont(new Font("Serif", Font.BOLD, 12));
       check.addItemListener(this);
+      check.setVisible(fr.hiddenGroups.contains(group));
       groupPanel.add(check);
     }
     if (rdrw)
@@ -288,15 +293,15 @@ public class FeatureSettings extends Panel implements ItemListener,
     SequenceFeature[] tmpfeatures;
     String group = null, type;
     Vector visibleChecks = new Vector();
-
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment = av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)
+      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {