Index: lucene/spatial/src/java/org/apache/lucene/spatial/prefix/ContainsPrefixTreeFilter.java
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- lucene/spatial/src/java/org/apache/lucene/spatial/prefix/ContainsPrefixTreeFilter.java	(revision 1493637)
+++ lucene/spatial/src/java/org/apache/lucene/spatial/prefix/ContainsPrefixTreeFilter.java	(revision )
@@ -41,6 +41,15 @@
  */
 public class ContainsPrefixTreeFilter extends AbstractPrefixTreeFilter {
 
+  /**
+   * If the spatial data for a document is comprised of multiple overlapping or adjacent parts,
+   * it might fail to match a query shape when doing the CONTAINS predicate when the sum of
+   * those shapes contain the query shape but none do individually.  Set this to false to
+   * increase performance if you don't care about that circumstance (such as if your indexed
+   * data doesn't even have such conditions).  See LUCENE-5062.
+   */
+  protected boolean supportMultiOverlappingIndexedShapes = true;
+
   public ContainsPrefixTreeFilter(Shape queryShape, String fieldName, SpatialPrefixTree grid, int detailLevel) {
     super(queryShape, fieldName, grid, detailLevel);
   }
@@ -65,18 +74,25 @@
       if (termsEnum == null)//signals all done
         return null;
 
-      //Leaf docs match all query shape
+      // Leaf docs match all query shape
       SmallDocSet leafDocs = getLeafDocs(cell, acceptContains);
 
-      // Get the AND of all child results
+      // Get the AND of all child results (into combinedSubResults)
       SmallDocSet combinedSubResults = null;
-      Collection<Cell> subCells = cell.getSubCells(queryShape);
+      //   Optimization: use null subCellsFilter when we know cell is within the query shape.
+      Shape subCellsFilter = queryShape;
+      if (cell.getLevel() != 0 && ((cell.getShapeRel() == null || cell.getShapeRel() == SpatialRelation.WITHIN))) {
+        subCellsFilter = null;
+        assert cell.getShape().relate(queryShape) == SpatialRelation.WITHIN;
+      }
+      Collection <Cell> subCells = cell.getSubCells(subCellsFilter);
       for (Cell subCell : subCells) {
         if (!seekExact(subCell))
           combinedSubResults = null;
         else if (subCell.getLevel() == detailLevel)
           combinedSubResults = getDocs(subCell, acceptContains);
-        else if (subCell.getShapeRel() == SpatialRelation.WITHIN)
+        else if (!supportMultiOverlappingIndexedShapes &&
+            subCell.getShapeRel() == SpatialRelation.WITHIN)
           combinedSubResults = getLeafDocs(subCell, acceptContains);
         else
           combinedSubResults = visit(subCell, acceptContains); //recursion
@@ -90,7 +106,7 @@
       if (combinedSubResults != null) {
         if (leafDocs == null)
           return combinedSubResults;
-        return leafDocs.union(combinedSubResults);
+        return leafDocs.union(combinedSubResults);//union is 'or'
       }
       return leafDocs;
     }
@@ -109,8 +125,12 @@
       return collectDocs(acceptContains);
     }
 
+    private Cell lastLeaf = null;//just for assertion
+
     private SmallDocSet getLeafDocs(Cell leafCell, Bits acceptContains) throws IOException {
       assert new BytesRef(leafCell.getTokenBytes()).equals(termBytes);
+      assert ! leafCell.equals(lastLeaf);//don't call for same leaf again
+      lastLeaf = leafCell;
 
       BytesRef nextTerm = termsEnum.next();
       if (nextTerm == null) {
Index: lucene/spatial/src/test/org/apache/lucene/spatial/prefix/SpatialOpRecursivePrefixTreeTest.java
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
--- lucene/spatial/src/test/org/apache/lucene/spatial/prefix/SpatialOpRecursivePrefixTreeTest.java	(revision 1493637)
+++ lucene/spatial/src/test/org/apache/lucene/spatial/prefix/SpatialOpRecursivePrefixTreeTest.java	(revision )
@@ -18,6 +18,7 @@
  */
 
 import com.carrotsearch.randomizedtesting.annotations.Repeat;
+import com.carrotsearch.randomizedtesting.annotations.Seed;
 import com.spatial4j.core.context.SpatialContext;
 import com.spatial4j.core.shape.Point;
 import com.spatial4j.core.shape.Rectangle;
@@ -111,6 +112,17 @@
   }
 
   @Test
+  public void testContainsPairOverlap() throws IOException {
+    mySetup(3);
+    adoc("0", new ShapePair(ctx.makeRectangle(0, 33, -128, 128), ctx.makeRectangle(33, 128, -128, 128), true));
+    commit();
+    Query query = strategy.makeQuery(new SpatialArgs(SpatialOperation.Contains,
+        ctx.makeRectangle(0, 128, -16, 128)));
+    SearchResults searchResults = executeQuery(query, 1);
+    assertEquals(1, searchResults.numFound);
+  }
+
+  @Test
   public void testWithinDisjointParts() throws IOException {
     mySetup(7);
     //one shape comprised of two parts, quite separated apart
@@ -184,10 +196,10 @@
       Shape indexedShape;
       Shape indexedShapeGS; //(grid-snapped)
       int R = random().nextInt(12);
-      if (R == 0) {//1 in 10
+      if (R == 0) {//1 in 12
         indexedShape = null; //no shape for this doc
         indexedShapeGS = null;
-      } else if (R % 4 == 0) {//3 in 12
+      } else if (R % 3 == 0) {//4-1 in 12
         //comprised of more than one shape
         Rectangle shape1 = randomRectangle();
         Rectangle shape2 = randomRectangle();