When testing for a polygon I want to get back all fences that are either completely or partly contained in my polygon. Therefore I test if the returned fences are within my polygon or are not disjoint.

polygon_snippet.java

@ApiMethod(name = "polygon", httpMethod = "post", path = "polygon")
    public ArrayList < MyFence > queryPolygon(@Named("group") String group, MyPolyLine polyline) {
        ArrayList < MyFence > fences = new ArrayList < MyFence > ();

        //Get index from Memcache
        MemcacheService syncCache = MemcacheServiceFactory.getMemcacheService();
        STRtree index = (STRtree) syncCache.get(group); // read from cache
        if (index != null) {
            //Create coordinate array.
            double[][] points = polyline.getCoordinates();
            Coordinate[] coordinates = new Coordinate[points.length];
            int i = 0;
            for (double[] point: points) {
                Coordinate coordinate = new Coordinate(point[0], point[1]);
                coordinates[i++] = coordinate;
            }
            //Create polygon.
            GeometryFactory fact = new GeometryFactory();
            LinearRing linear = new GeometryFactory().createLinearRing(coordinates);
            Polygon polygon = new Polygon(linear, null, fact);

            List < MyPolygon > items = index.query(polygon.getEnvelopeInternal());
            if (!items.isEmpty()) {
                for (MyPolygon poly: items) {
                    if (polygon.contains(poly) || !polygon.disjoint(poly)) {
                        long id = poly.getID();
                        MyFence newFence = new MyFence();
                        newFence.setId(id);
                        fences.add(newFence);
                    }
                }
            }
        } else {
            try {
                MyIndex.buildIndex(group);
            } catch (IOException e) {
                e.printStackTrace();
            }
        }

        return fences;
    }