X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=bf2408c79e2ec7d4ff1ff9888861bbe86019a582;hb=3d4ead4880755ec949de0300c232544ba965e60d;hp=8a6cb610f5aa912868e80269de8c1a2f291c1d88;hpb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 8a6cb61..bf2408c 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -27,9 +27,11 @@ import jalview.datamodel.features.FeatureSourceI;
 import jalview.datamodel.features.FeatureSources;
 import jalview.util.StringUtils;
 
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Map.Entry;
+import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
@@ -97,6 +99,11 @@ public class SequenceFeature implements FeatureLocationI
    */
   private String source;
 
+  // for Overview sort:
+  public int index;
+
+  public SequenceFeature containedBy;
+
   /**
    * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
    * otherDetails map, so the new and original SequenceFeature may reference the
@@ -643,9 +650,13 @@ public class SequenceFeature implements FeatureLocationI
         {
           /*
            * expand values in a Map attribute across separate lines
+           * copy to a TreeMap for alphabetical ordering
            */
-          Map<?, ?> values = (Map<?, ?>) value;
-          for (Entry<?, ?> e : values.entrySet())
+          Map<String, Object> values = (Map<String, Object>) value;
+          SortedMap<String, Object> sm = new TreeMap<>(
+                  String.CASE_INSENSITIVE_ORDER);
+          sm.putAll(values);
+          for (Entry<?, ?> e : sm.entrySet())
           {
             sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
                     .getValue().toString()));
@@ -731,3 +742,21 @@ public class SequenceFeature implements FeatureLocationI
     source = theSource;
   }
 }
+
+class SFSortByEnd implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getEnd() - b.getEnd();
+  }
+}
+
+class SFSortByBegin implements Comparator<SequenceFeature>
+{
+  @Override
+  public int compare(SequenceFeature a, SequenceFeature b)
+  {
+    return a.getBegin() - b.getBegin();
+  }
+}