X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=0478a766625598d98b441ae857dc9f6a4746e5c1;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=39249cc28cf17f2df670e575295c98f3e0527833;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
old mode 100755
new mode 100644
index 39249cc..0478a76
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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;
 
@@ -23,10 +24,10 @@ import java.awt.*;
 
 import java.awt.event.*;
 
-import jalview.appletgui.FeatureSettings.MyCheckbox;
 import jalview.datamodel.*;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -84,17 +85,19 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     featureGroups = fr.featureGroups;
     featureColours = fr.featureColours;
     transparency = fr.transparency;
-    if (av!=null && fr.av!=null && fr.av!=av)
+    if (av != null && fr.av != null && fr.av != av)
     {
-      if (fr.av.featuresDisplayed!=null)
+      if (fr.av.featuresDisplayed != null)
       {
-        if (av.featuresDisplayed==null)
+        if (av.featuresDisplayed == null)
         {
           av.featuresDisplayed = new Hashtable();
-        } else {
+        }
+        else
+        {
           av.featuresDisplayed.clear();
         }
-        Enumeration en=fr.av.featuresDisplayed.keys();
+        Enumeration en = fr.av.featuresDisplayed.keys();
         while (en.hasMoreElements())
         {
           av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
@@ -193,7 +196,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
           g.setColor(Color.black);
           Font f = new Font("Verdana", Font.PLAIN, 10);
           g.setFont(f);
-          g.drawString("Label", 0, 0);
+          g.drawString(MessageManager.getString("label.label"), 0, 0);
         }
         else
         {
@@ -363,7 +366,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     }
     else
     {
-      dialog.ok.setLabel("Amend");
+      dialog.ok.setLabel(MessageManager.getString("label.amend"));
       dialog.buttonPanel.add(deleteButton, 1);
       deleteButton.addActionListener(new ActionListener()
       {
@@ -786,10 +789,10 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     av.featuresDisplayed = new Hashtable();
     Vector allfeatures = new Vector();
     minmax = new Hashtable();
-
-    for (int i = 0; i < av.alignment.getHeight(); i++)
+    AlignmentI alignment = av.getAlignment();
+    for (int i = 0; i < alignment.getHeight(); i++)
     {
-      SequenceFeature[] features = av.alignment.getSequenceAt(i)
+      SequenceFeature[] features = alignment.getSequenceAt(i)
               .getSequenceFeatures();
 
       if (features == null)
@@ -1064,9 +1067,9 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
       for (int i = 0; i < toset.length; i++)
       {
         Object st = featureGroups.get(toset[i]);
+        featureGroups.put(toset[i], new Boolean(visible));
         if (st != null)
         {
-          featureGroups.put(toset[i], new Boolean(visible));
           rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
         }
       }
@@ -1090,6 +1093,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     }
   }
 
+  ArrayList<String> hiddenGroups = new ArrayList<String>();
+
   /**
    * analyse alignment for groups and hash tables (used to be embedded in
    * FeatureSettings.setTableData)
@@ -1103,29 +1108,34 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       featureGroups = new Hashtable();
     }
-    Vector allFeatures = new Vector();
-    Vector allGroups = new Vector();
+    hiddenGroups = new ArrayList<String>();
+    hiddenGroups.addAll(featureGroups.keySet());
+    ArrayList allFeatures = new ArrayList();
+    ArrayList allGroups = new ArrayList();
     SequenceFeature[] tmpfeatures;
     String group;
-    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;
       }
 
       alignmentHasFeatures = true;
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {
         if (tmpfeatures[index].getFeatureGroup() != null)
         {
           group = tmpfeatures[index].featureGroup;
+          // Remove group from the hiddenGroup list
+          hiddenGroups.remove(group);
           if (!allGroups.contains(group))
           {
-            allGroups.addElement(group);
+            allGroups.add(group);
 
             boolean visible = true;
             if (featureGroups.containsKey(group))
@@ -1141,7 +1151,7 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
 
         if (!allFeatures.contains(tmpfeatures[index].getType()))
         {
-          allFeatures.addElement(tmpfeatures[index].getType());
+          allFeatures.add(tmpfeatures[index].getType());
         }
         index++;
       }
@@ -1170,16 +1180,17 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     Vector allFeatures = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
-    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;
       }
 
       alignmentHasFeatures = true;
 
-      tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();
+      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
       int index = 0;
       while (index < tmpfeatures.length)
       {