X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=1f2e639cc89408d90056c4c1298a083d406c5474;hb=refs%2Fheads%2Fbug%2FJAL-3487-splash-JS;hp=34565c666d198e45b90b41ad9cd507e6de6648f6;hpb=8eb8ed34a9bbd66087433ca6a3d41b4fe2553d6a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 34565c6..1f2e639 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -27,6 +27,7 @@ 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;
@@ -216,7 +217,8 @@ public class SequenceFeature implements FeatureLocationI
   @Override
   public boolean equals(Object o)
   {
-    return equals(o, false);
+    return (o instanceof SequenceFeature
+            && equals((SequenceFeature) o, false));
   }
 
   /**
@@ -229,47 +231,19 @@ 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"))));
   }
 
   /**
@@ -735,4 +709,24 @@ 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();
+  }
 }