X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=8d1255c15d4dbf70bb74fd7c9dbb11cb01e77a83;hb=72b3f05a1157da32ada5aea139139996dddea219;hp=e0dad5878f30f7ade0d395355ceeccace472c120;hpb=648f0d7f48b5865bd43b5edbe71f5e483f0cc455;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e0dad58..8d1255c 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.Conservation;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.SequenceStructureBinding;
+import jalview.api.FeatureRenderer;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -90,9 +91,12 @@ import java.awt.event.WindowEvent;
 import java.io.IOException;
 import java.net.URL;
 import java.net.URLEncoder;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -286,7 +290,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       featuresFile = new jalview.io.FeaturesFile(file, type)
               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
-                      .getFeatureRenderer().featureColours, featureLinks,
+                      .getFeatureRenderer().getFeatureColours(), featureLinks,
                       true, viewport.applet.getDefaultParameter(
                               "relaxedidmatch", false));
     } catch (Exception ex)
@@ -305,6 +309,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         viewport.setShowSequenceFeatures(true);
         sequenceFeatures.setState(true);
       }
+      if (alignPanel.seqPanel.seqCanvas.fr != null)
+      {
+        // update the min/max ranges where necessary
+        alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
+      }
       if (viewport.featureSettings != null)
       {
         viewport.featureSettings.refreshTable();
@@ -1201,20 +1210,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Hashtable getDisplayedFeatureCols()
+  private Map<String,Object> getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
-            && viewport.featuresDisplayed != null)
+            && viewport.getFeaturesDisplayed()!= null)
     {
-      FeatureRenderer fr = alignPanel.getFeatureRenderer();
-      Hashtable fcols = new Hashtable();
-      Enumeration en = viewport.featuresDisplayed.keys();
-      while (en.hasMoreElements())
-      {
-        Object col = en.nextElement();
-        fcols.put(col, fr.featureColours.get(col));
-      }
-      return fcols;
+      return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
+      
     }
     return null;
   }
@@ -1418,6 +1420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   /**
    * TODO: JAL-1104
    */
+  @Override
   public void addHistoryItem(CommandI command)
   {
     if (command.getSize() > 0)
@@ -2240,7 +2243,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {
-      return fr.getGroups();
+      List gps = fr.getFeatureGroups();
+      int p=0;
+      String[] _gps = new String[gps.size()];
+      for (Object gp:gps)
+      {
+        _gps[p++] = gp.toString();
+      }
+      return _gps;
     }
     return null;
   }
@@ -2258,7 +2268,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {
-      return fr.getGroups(visible);
+      List gps = fr.getGroups(visible);
+      int p=0;
+      String[] _gps = new String[gps.size()];
+      for (Object gp:gps)
+      {
+        _gps[p++] = gp.toString();
+      }
+      return _gps;
     }
     return null;
   }
@@ -2279,7 +2296,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (alignPanel != null
             && (fr = alignPanel.getFeatureRenderer()) != null)
     {
-      fr.setGroupState(groups, state);
+      
+      fr.setGroupVisibility((List)Arrays.asList(groups), state);
       alignPanel.seqPanel.seqCanvas.repaint();
       if (alignPanel.overviewPanel != null)
       {