FeatureIndexManager indexManager = null;
FeatureIndexResults results = null;

try (GeoPackage geoPackage = GeoPackageManager.open("pot_WEG_Luebz_linie.gpkg")) {
  indexManager = new FeatureIndexManager(geoPackage, "pot_WEG_Luebz_linie");
  if (!indexManager.isIndexed()) {
    indexManager.setIndexLocation(FeatureIndexType.RTREE);
    indexManager.index();
  }

  Double minX = 33302120.0;
  Double minY = 5923548.0;
  Double maxX = 33303206.0;
  Double maxY = 5925394.0;

  RTreeIndexTableDao rTreeIndexTableDao = indexManager.getRTreeIndexTableDao();

  StringBuilder whereBuilder = new StringBuilder();

  whereBuilder.append(rTreeIndexTableDao.buildWhere(RTreeIndexExtension.COLUMN_MIN_X, minX, "<="));
  whereBuilder.append(" AND ");
  whereBuilder.append(rTreeIndexTableDao.buildWhere(RTreeIndexExtension.COLUMN_MIN_Y, minY, "<="));
  whereBuilder.append(" AND ");
  whereBuilder.append(rTreeIndexTableDao.buildWhere(RTreeIndexExtension.COLUMN_MAX_X, maxX, ">="));
  whereBuilder.append(" AND ");
  whereBuilder.append(rTreeIndexTableDao.buildWhere(RTreeIndexExtension.COLUMN_MAX_Y, maxY, ">="));

  String whereBounds = whereBuilder.toString();
FeatureIndexManager
  Double tolerance = rTreeIndexTableDao.getTolerance();

  minX -= tolerance;
  maxX += tolerance;
  minY -= tolerance;
  maxY += tolerance;

  String[] whereArgs = rTreeIndexTableDao.buildWhereArgs(new Object[] { maxX, maxY, minX, minY });

  String where = rTreeIndexTableDao.getFeatureDao().buildWhereIn(rTreeIndexTableDao.queryIdsSQL(whereBounds), null);

  FeatureResultSet featureResultSet = rTreeIndexTableDao.getFeatureDao().queryForChunk(where, whereArgs, "fid", 5, 0);

  int count = 0;
  try {
    while (featureResultSet.moveToNext()) {
      FeatureRow featureRow = featureResultSet.getRow();
      GeoPackageGeometryData geometryData = featureRow.getGeometry();
      if (geometryData != null && !geometryData.isEmpty()) {
        count++;
      }`
    }
  } finally {
    featureResultSet.close();
  }
  System.out.println("count=" + count);
} finally {
  if (results != null) {
    results.close();
  }
  if (indexManager != null) {
    indexManager.close();
  }
}