From 8ac25f08dacd4759548f62332004288b0e86fdee Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 9 Jan 2019 16:31:20 +0000
Subject: [PATCH] JAL-3184 restore group visibility on Cancel in Feature
 Settings

---
 src/jalview/gui/FeatureSettings.java               |   30 +++++++++++++++++---
 .../seqfeatures/FeatureRendererModel.java          |   20 ++++++-------
 2 files changed, 35 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1358c8f..c310c47 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -62,6 +62,7 @@ import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
@@ -135,6 +136,10 @@ public class FeatureSettings extends JPanel
 
   private Map<String, FeatureMatcherSetI> originalFilters;
 
+  private List<String> originalVisibleGroups;
+
+  private List<String> originalHiddenGroups;
+
   final JInternalFrame frame;
 
   JScrollPane scrollPane = new JScrollPane();
@@ -187,6 +192,10 @@ public class FeatureSettings extends JPanel
 
     originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
 
+    originalVisibleGroups = new ArrayList<>(fr.getGroups(true));
+
+    originalHiddenGroups = new ArrayList<>(fr.getGroups(false));
+
     try
     {
       jbInit();
@@ -1236,10 +1245,7 @@ public class FeatureSettings extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        fr.setTransparency(originalTransparency);
-        fr.setFeatureFilters(originalFilters);
-        updateFeatureRenderer(originalData);
-        close();
+        cancel();
       }
     });
 
@@ -1321,6 +1327,22 @@ public class FeatureSettings extends JPanel
     this.add(settingsPane);
   }
 
+  /**
+   * Restores feature type and group visibility, and any filters and
+   * transparency setting, to the values when this dialog was opened. Note this
+   * won't affect any feature types or groups which were added while the dialog
+   * was open.
+   */
+  void cancel()
+  {
+    fr.setTransparency(originalTransparency);
+    fr.setFeatureFilters(originalFilters);
+    fr.setGroupVisibility(originalVisibleGroups, true);
+    fr.setGroupVisibility(originalHiddenGroups, false);
+    updateFeatureRenderer(originalData);
+    close();
+  }
+
   // ///////////////////////////////////////////////////////////////////////
   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
   // ///////////////////////////////////////////////////////////////////////
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 553f813..186b57b 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -43,6 +43,7 @@ import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 
@@ -859,30 +860,27 @@ public abstract class FeatureRendererModel
   }
 
   /**
-   * get visible or invisible groups
+   * Answers a (possibly empty) list of visible or invisible feature groups
    * 
    * @param visible
-   *          true to return visible groups, false to return hidden ones.
-   * @return list of groups
+   *          true to return visible groups, false to return hidden ones
+   * @return
    */
   @Override
   public List<String> getGroups(boolean visible)
   {
+    List<String> groups = new ArrayList<>();
     if (featureGroups != null)
     {
-      List<String> gp = new ArrayList<>();
-
-      for (String grp : featureGroups.keySet())
+      for (Entry<String, Boolean> grp : featureGroups.entrySet())
       {
-        Boolean state = featureGroups.get(grp);
-        if (state.booleanValue() == visible)
+        if (grp.getValue() == visible)
         {
-          gp.add(grp);
+          groups.add(grp.getKey());
         }
       }
-      return gp;
     }
-    return null;
+    return groups;
   }
 
   @Override
-- 
1.7.10.2