X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=6f514203088bf246329d5d629b62cd0bbfeaa165;hb=5e37267b48b75b90d264e7ab04ae1bc4a0155e3e;hp=8a6cb610f5aa912868e80269de8c1a2f291c1d88;hpb=8ace2707dd1c5cfbb1688efa265fd0afcec35def;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 8a6cb61..6f51420 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -27,12 +27,16 @@ 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;
 
+import intervalstore.api.IntervalI;
+
 /**
  * A class that models a single contiguous feature on a sequence. If flag
  * 'contactFeature' is true, the start and end positions are interpreted instead
@@ -215,10 +219,20 @@ public class SequenceFeature implements FeatureLocationI
   @Override
   public boolean equals(Object o)
   {
-    return equals(o, false);
+    return (o != null && (o instanceof SequenceFeature)
+            && equalsInterval((SequenceFeature) o));
   }
 
   /**
+   * Having determined that this is in fact a SequenceFeature, now check it for
+   * equivalence. Overridden in CrossRef; used by IntervalStore (possibly).
+   */
+  @Override
+  public boolean equalsInterval(IntervalI sf)
+  {
+    return equals((SequenceFeature) sf, false);
+  }
+  /**
    * Overloaded method allows the equality test to optionally ignore the
    * 'Parent' attribute of a feature. This supports avoiding adding many
    * superficially duplicate 'exon' or CDS features to genomic or protein
@@ -228,14 +242,8 @@ public class SequenceFeature implements FeatureLocationI
    * @param ignoreParent
    * @return
    */
-  public boolean equals(Object o, boolean ignoreParent)
+  public boolean equals(SequenceFeature sf, boolean ignoreParent)
   {
-    if (o == null || !(o instanceof SequenceFeature))
-    {
-      return false;
-    }
-
-    SequenceFeature sf = (SequenceFeature) o;
     boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
             : score == sf.score;
     if (begin != sf.begin || end != sf.end || !sameScore)
@@ -643,9 +651,13 @@ 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()));
@@ -730,4 +742,24 @@ 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();
+  }
 }