X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=30e0929e7f4d7573fd481e54da13608fa8666018;hb=b74cdec4b07000bee431a7cca86a948f44d3ffbe;hp=bf2408c79e2ec7d4ff1ff9888861bbe86019a582;hpb=3d4ead4880755ec949de0300c232544ba965e60d;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index bf2408c..30e0929 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -35,6 +35,8 @@ 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
@@ -99,11 +101,6 @@ 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
@@ -222,10 +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 sf != null && 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
@@ -235,47 +242,19 @@ 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)
-    {
-      return false;
-    }
-
-    if (getStrand() != sf.getStrand())
-    {
-      return false;
-    }
-
-    if (!(type + description + featureGroup + getPhase()).equals(
-            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
-    {
-      return false;
-    }
-    if (!equalAttribute(getValue("ID"), sf.getValue("ID")))
-    {
-      return false;
-    }
-    if (!equalAttribute(getValue("Name"), sf.getValue("Name")))
-    {
-      return false;
-    }
-    if (!ignoreParent)
-    {
-      if (!equalAttribute(getValue("Parent"), sf.getValue("Parent")))
-      {
-        return false;
-      }
-    }
-    return true;
+    return (begin == sf.begin && end == sf.end
+            && getStrand() == sf.getStrand()
+            && (Float.isNaN(score) ? Float.isNaN(sf.score)
+                    : score == sf.score)
+            && (type + description + featureGroup + getPhase())
+                    .equals(sf.type + sf.description + sf.featureGroup
+                            + sf.getPhase())
+            && equalAttribute(getValue("ID"), sf.getValue("ID"))
+            && equalAttribute(getValue("Name"), sf.getValue("Name"))
+            && (ignoreParent || equalAttribute(getValue("Parent"),
+                    sf.getValue("Parent"))));
   }
 
   /**
@@ -741,6 +720,8 @@ public class SequenceFeature implements FeatureLocationI
   {
     source = theSource;
   }
+
+ 
 }
 
 class SFSortByEnd implements Comparator<SequenceFeature>