X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=86d8b3004d79a3ed19a6e28dfdc625ed94f43f56;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=03f15d3ddccf4f1d084095d7bf38ef0b130dcf7e;hpb=8f49ecb042d47e8eda13869f7581fd340191f46b;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 03f15d3..86d8b30 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -84,17 +84,19 @@ 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);
@@ -786,10 +788,10 @@ 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)
@@ -1090,7 +1092,8 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     }
   }
 
-  ArrayList<String> hiddenGroups=new ArrayList<String>();
+  ArrayList<String> hiddenGroups = new ArrayList<String>();
+
   /**
    * analyse alignment for groups and hash tables (used to be embedded in
    * FeatureSettings.setTableData)
@@ -1104,22 +1107,23 @@ public class FeatureRenderer implements jalview.api.FeatureRenderer
     {
       featureGroups = new Hashtable();
     }
-    hiddenGroups =new ArrayList<String>();
+    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)
       {
@@ -1175,16 +1179,17 @@ 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)
       {