http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/QueryVariableNormalizer.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/QueryVariableNormalizer.java
 
b/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/QueryVariableNormalizer.java
deleted file mode 100644
index a3e6e04..0000000
--- 
a/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/QueryVariableNormalizer.java
+++ /dev/null
@@ -1,1180 +0,0 @@
-package mvm.rya.indexing.pcj.matching;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- * 
- *   http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-
-import org.openrdf.model.Literal;
-import org.openrdf.model.Value;
-import org.openrdf.model.impl.ValueFactoryImpl;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.NAryValueOperator;
-import org.openrdf.query.algebra.ProjectionElem;
-import org.openrdf.query.algebra.ProjectionElemList;
-import org.openrdf.query.algebra.QueryModelNode;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.ValueConstant;
-import org.openrdf.query.algebra.ValueExpr;
-import org.openrdf.query.algebra.Var;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-import com.google.common.collect.Lists;
-import com.google.common.collect.Maps;
-
-public class QueryVariableNormalizer {
-
-    
-    /**
-     * @param tuple1
-     *            tuple expression from a parsed query
-     * @param tuple2
-     *            tuple expression from a parsed query (the proposed index 
whose
-     *            variables are to be relabeled)
-     * @return list of all possible tuples obtained by substituting the
-     *         variables of proposed index with the variables from query
-     * @throws Exception
-     * @throws IllegalArgumentException
-     */
-    public static List<TupleExpr> getNormalizedIndex(TupleExpr tuple1, 
TupleExpr tuple2) throws Exception {
-
-        List<QueryModelNode> nodes1, nodes2;
-        TreeMap<String, List<QueryModelNode>> queryMap1, indexMap1;
-        List<HashMap<String, String>> varChanges = new 
ArrayList<HashMap<String, String>>();
-        List<TupleExpr> tupleList = new ArrayList<TupleExpr>();
-        
-       
-
-        // if tuples are equal, no need to do anything
-        if (tuple1.equals(tuple2)) {
-            tupleList.add((TupleExpr) tuple1.clone());
-            return tupleList;
-        }
-
-        
-        NormalizeQueryVisitor tupNVis = new NormalizeQueryVisitor(false);
-        NormalizeQueryVisitor indexNVis = new NormalizeQueryVisitor(true);
-        tuple1.visit(tupNVis);
-        tuple2.visit(indexNVis);
-        
-        
-        TupleExpr tuple;
-        queryMap1 = tupNVis.getMap();
-        indexMap1 = indexNVis.getMap();
-
-        // TreeMaps that used for comparators
-        TreeMap<String, Integer>[] trees = (TreeMap<String, Integer>[]) new 
TreeMap[4];
-        for (int i = 0; i < 4; i++) {
-            trees[i] = new TreeMap<String, Integer>();
-        }
-
-        trees[0] = tupNVis.getKeyMap(); // query tuple variable count
-        trees[2] = indexNVis.getKeyMap(); // index tuple variable count
-         
-      
-        // if query does not contain as many constant Vars as index,
-        // normalization not possible.
-//        if (!(trees[0].keySet().size() >= trees[2].keySet().size())) {
-//            System.out.println("In here:1");
-//            return tupleList;
-//        }
-
-        // sort keys according to size of associated StatementPattern list
-        // this optimization ensures that initial list of HashMaps (possible
-        // variable substitutions)
-        // is as small as possible
-        // Maybe add additional criteria to comparator taking into account size
-        // of query bin lists
-        Set<String> keys = indexMap1.keySet();
-        List<String> keyList = new ArrayList<String>(keys);
-        Collections.sort(keyList, new ConstantKeyComp(indexMap1, queryMap1));
-
-        // iterate through constant values associated with smaller tuple,
-        // check that larger tuple constants these constants, and use lists
-        // of associated statement patterns to begin to construct variable
-        // substitutions
-        // that are consistent
-
-        for (String s : keyList) {
-            if (queryMap1.containsKey(s)) {
-                nodes1 = queryMap1.get(s);
-                nodes2 = indexMap1.get(s);
-                
-
-                if (!(nodes1.size() >= nodes2.size())) {
-//                    System.out.println("In here: 2");
-//                    System.out.println("Node lists are " + nodes1 + " and " +
-//                            nodes2);
-                    return tupleList;
-                }
-
-                trees[1] = getListVarCnt(nodes1, tupNVis.getVariableMap()); // 
query
-                                                                          // 
list
-                                                                          // 
variable
-                                                                          // 
count
-                trees[3] = getListVarCnt(nodes2, indexNVis.getVariableMap()); 
// index
-                                                                          // 
list
-                                                                          // 
variable
-                                                                          // 
count
-                Collections.sort(nodes1, new CountComp(trees[1], trees[0]));
-                Collections.sort(nodes2, new CountComp(trees[3], trees[2]));
-
-                varChanges = statementCompare(nodes1, nodes2, varChanges, 
trees);
-
-                if (varChanges.size() == 0) {
-                    return tupleList;
-                }
-            }
-
-            else {
-                return tupleList;
-            }
-
-        }
-
-        List<QueryModelNode> filters2 = indexNVis.getFilters();
-        // determine if index contains filters whose variables need to be 
relabeled
-        if (filters2.size() != 0) {
-            List<QueryModelNode> filters1 = tupNVis.getFilters();
-            // only attempt to normalize variables if query contains more 
filters than index
-            if (filters1.size() >= filters2.size()) {
-                Collections.sort(filters1, new FilterComp());
-                Collections.sort(filters2, new FilterComp());
-
-                varChanges = statementCompare(filters1, filters2, varChanges, 
trees);
-
-            }
-        }
-
-        List<HashMap<String, String>> varChangeSet = new 
ArrayList<HashMap<String, String>>();
-
-        for (HashMap<String, String> s : varChanges) {
-            if (!varChangeSet.contains(s)) {
-                varChangeSet.add(s);
-            }
-
-        }
-
-        
-        ValueMapVisitor valMapVis = new ValueMapVisitor();
-        tuple1.visit(valMapVis);
-        Map<String, Value> valMap = valMapVis.getValueMap();
-        
-
-        for (HashMap<String, String> s : varChangeSet) {
-            //System.out.println(s);
-            tuple = tuple2.clone();
-            replaceTupleVariables(s, tuple, valMap);
-            tupleList.add(tuple);
-        }
-
-        return tupleList;
-
-    }
-
-    /**
-     * Produces a list of all possible substitutions stored in HashMaps that 
are
-     * consistent with the two lists of statement patterns
-     * 
-     * @param qArray
-     *            list of Statement nodes from query tuple
-     * @param iArray
-     *            list of Statement nodes from index tuple
-     * @param hMaps
-     *            HashMap containing variable substitutions
-     * @param trees
-     *            TreeMaps used for statement pattern node ordering
-     * @return
-     */
-    private static List<HashMap<String, String>> 
statementCompare(List<QueryModelNode> qArray,
-            List<QueryModelNode> iArray, List<HashMap<String, String>> hMaps, 
TreeMap<String, Integer>[] trees) {
-
-        if (hMaps.size() == 0) {
-            HashMap<HashMap<String, String>, Boolean> mapConsistent = new 
HashMap<HashMap<String, String>, Boolean>();
-            HashMap<String, String> hMap = new HashMap<String, String>();
-            mapConsistent.put(hMap, false);
-            evaluateMap(qArray, iArray, hMap, hMaps, mapConsistent, trees);
-
-            return hMaps;
-        }
-
-        else {
-
-            ArrayList<HashMap<String, String>> tempMaps = 
Lists.newArrayList(hMaps);
-            HashMap<HashMap<String, String>, Boolean> mapConsistent = new 
HashMap<HashMap<String, String>, Boolean>();
-            for (HashMap<String, String> s : hMaps) {
-                mapConsistent.put(s, false);
-            }
-            for (HashMap<String, String> s : hMaps) {
-                evaluateMap(qArray, iArray, s, tempMaps, mapConsistent, trees);
-            }
-
-            return tempMaps;
-
-        }
-    }
-
-   
-    /**
-     * Adds or removes HashMap substitution schemes to the list of 
substitutions
-     * schemes depending on whether or not they are consistent with the two
-     * lists of statement patterns
-     * 
-     * @param qArray
-     *            List of StatementPatterns associated with query array
-     * @param iArray
-     *            List of StatementPatterns associated with index array
-     * @param hMap
-     *            HashMap of substitutions to be analyzed for consistent and
-     *            added or removed
-     * @param hMaps
-     *            List of HashMaps containing substitution schemes
-     * @param trees
-     *            Array of TreeMaps used for comparison of StatementPattern
-     *            nodes
-     */
-    private static void evaluateMap(List<QueryModelNode> qArray, 
List<QueryModelNode> iArray,
-            HashMap<String, String> hMap, List<HashMap<String, String>> hMaps,
-            HashMap<HashMap<String, String>, Boolean> mapConsistent, 
TreeMap<String, Integer>[] trees) throws IllegalArgumentException {
-
-        // if all nodes in indexArray have been exhausted, add map of 
substitutions to
-        // list of possible substitution schemes.
-        if (iArray.size() == 0) {
-            if (!hMaps.contains(hMap)) {
-                hMaps.add(hMap);
-            }
-            mapConsistent.put(hMap, true);
-            return;
-        }
-
-        // for a given constant key, iterate through possible combinations of 
statement pattern nodes contained in associated query list and
-        // index list to generate all possible substitution schemes.
-        for (int i = 0; i < iArray.size(); i++) {
-            for (int j = 0; j < qArray.size(); j++) {
-                //System.out.println("Query list is " + qArray+ " and index 
list is " + iArray);
-                
-                QueryModelNode node1 = qArray.get(j);
-                QueryModelNode node2 = iArray.get(i);
-                // if lists contain statement patterns, check to see if two 
given statement patterns have same structure
-                // independent of variables names (same constants in same 
place, non constant Vars in same place)
-                if ((node1 instanceof StatementPattern) && (node2 instanceof 
StatementPattern)) {
-                    if (genConstantCompare((StatementPattern) node1, 
(StatementPattern) node2)) {
-
-                        List<Var> variables1 = 
((StatementPattern)node1).getVarList();
-                        List<Var> variables2 =  
((StatementPattern)node2).getVarList();
-                        
-                        List<List<String>> vars = genGetCommonVars(variables1, 
variables2);
-                        List<String> vars1 = vars.get(0);
-                        List<String> vars2 = vars.get(1);
-
-                        if (listConsistent(vars1, vars2, hMap)) {
-
-                            HashMap<String, String> hashMap = 
Maps.newHashMap(hMap);
-                            putVars(vars1, vars2, hashMap);
-
-                            List<QueryModelNode> queryArray = 
Lists.newArrayList(qArray);
-                            List<QueryModelNode> indexArray = 
Lists.newArrayList(iArray);
-
-                            indexArray.remove(i);
-                            queryArray.remove(j);
-
-                            evaluateMap(queryArray, indexArray, hashMap, 
hMaps, mapConsistent, trees);
-                        }
-                    }
-                } // if lists contain filters, see if filters have same 
structure independent of variables names
-                //(check that conditions are same independent of variable 
names).
-                else if ((node1 instanceof Filter) && (node2 instanceof 
Filter)) {
-                    try {
-                        if (filterCompare((Filter) node1, (Filter) node2)) {
-
-                            List<QueryModelNode> variables1 = 
FilterVarValueCollector.process(((Filter) node1).getCondition());
-                            List<QueryModelNode> variables2 = 
FilterVarValueCollector.process(((Filter) node2).getCondition());
-                            
-                            List<List<String>> vars = 
filterCommonVars(variables1, variables2);
-                            List<String> vars1 = vars.get(0);
-                            List<String> vars2 = vars.get(1);
-                            
-                            if (listConsistent(vars1, vars2, hMap)) {
-
-                                HashMap<String, String> hashMap = 
Maps.newHashMap(hMap);
-                                putVars(vars1, vars2, hashMap);
-
-                                List<QueryModelNode> queryArray = 
Lists.newArrayList(qArray);
-                                List<QueryModelNode> indexArray = 
Lists.newArrayList(iArray);
-
-                                indexArray.remove(i);
-                                queryArray.remove(j);
-
-                                evaluateMap(queryArray, indexArray, hashMap, 
hMaps, mapConsistent, trees);
-                            }
-
-                        }
-                    } catch (Exception e) {
-                        System.out.println("Invalid Filter! " + e);
-                    }
-
-                } else {
-                    throw new IllegalArgumentException("Invalid query tree.");
-                }
-
-            }
-        }
-        if (mapConsistent.containsKey(hMap))
-            if (mapConsistent.get(hMap) == false) {
-                hMaps.remove(hMap);
-            }
-        return;
-
-    }
-
-
-    
-    
-    private static List<List<String>> genGetCommonVars(List<Var> vars1, 
List<Var> vars2) {
-        
-        
-        List<List<String>> varList = Lists.newArrayList();
-        List<String> varList1 = Lists.newArrayList();
-        List<String> varList2 = Lists.newArrayList();
-        
-
-        
-        for (int i = 0; i < vars1.size(); i++) {
-
-            if (!vars1.get(i).isConstant() && !vars2.get(i).isConstant()) {
-
-                varList1.add(vars1.get(i).getName());
-                varList2.add(vars2.get(i).getName());
-
-            } else if(vars1.get(i).isConstant() && !vars2.get(i).isConstant()) 
{
-                varList1.add(vars1.get(i).getName());
-                varList2.add(vars2.get(i).getName());  
-            }
-
-        }
-        
-        varList.add(varList1);
-        varList.add(varList2);
-
-        return varList;
-    }
-    
-    
- private static List<List<String>> filterCommonVars(List<QueryModelNode> 
vars1, List<QueryModelNode> vars2) {
-        
-        
-        List<List<String>> varList = Lists.newArrayList();
-        List<String> varList1 = Lists.newArrayList();
-        List<String> varList2 = Lists.newArrayList();
-        
-
-        
-        for (int i = 0; i < vars1.size(); i++) {
-
-            if ((vars1.get(i) instanceof ValueConstant) && (vars2.get(i) 
instanceof Var)) {
-                
-                ValueConstant vc = (ValueConstant) vars1.get(i);
-                String s = vc.getValue().toString();
-                if(vc.getValue() instanceof Literal) {
-                    s = s.substring(1, s.length() - 1);
-                } 
-                s = "-const-" + s;
-                varList1.add(s);
-                varList2.add(((Var)vars2.get(i)).getName());
-            } else if(!(vars1.get(i) instanceof ValueConstant)){
-                if (!((Var) vars1.get(i)).isConstant() && (vars2.get(i) 
instanceof Var)
-                        && !((Var) vars2.get(i)).isConstant()) {
-                    varList1.add(((Var) vars1.get(i)).getName());
-                    varList2.add(((Var) vars2.get(i)).getName());
-                } else if (((Var) vars1.get(i)).isConstant() && (vars2.get(i) 
instanceof Var)
-                        && !((Var) vars2.get(i)).isConstant()) {
-                    varList1.add(((Var) vars1.get(i)).getName());
-                    varList2.add(((Var) vars2.get(i)).getName());
-                }
-            }
-
-        }
-        
-        varList.add(varList1);
-        varList.add(varList2);
-
-        return varList;
-    }
-    
-    
-    
-    private static boolean genConstantCompare(StatementPattern queryNode, 
StatementPattern indexNode) {
-        
-        
-
-        ArrayList<Var> vars1 = (ArrayList<Var>) queryNode.getVarList();
-        ArrayList<Var> vars2 = (ArrayList<Var>) indexNode.getVarList();
-
-        
-        for (int i = 0; i < vars1.size(); i++) {
-
-            if (vars1.get(i).isConstant() && vars2.get(i).isConstant()) {
-
-                if (!vars1.get(i).equals(vars2.get(i))) {
-                    return false;
-
-                }
-
-            } else if(!vars1.get(i).isConstant() && vars2.get(i).isConstant() 
) {
-                    return false;
-            }
-
-        }
-
-        return true;
-
-    }
-        
-    
-    
-    
-    /**
-     * Method checks that substituting val for key is consistent with
-     * substitutions in hMap
-     * 
-     * @param val
-     *            substituting variable
-     * @param key
-     *            variable to be substituted for
-     * @param hMap
-     *            HashMap containing the substitutions to be made
-     * @return true if the proposed substitution is consistent with hMap, and
-     *         false otherwise
-     */
-    private static boolean checkVariables(String val, String key, 
HashMap<String, String> hMap) {
-
-        if (!hMap.containsKey(key) && !hMap.containsValue(val)) {
-
-            return true;
-        } else if (!hMap.containsKey(key) && hMap.containsValue(val) || 
hMap.containsKey(key)
-                && !hMap.containsValue(val)) {
-
-            return false;
-        } else {
-
-            if (hMap.get(key).equals(val)) {
-                return true;
-            } else
-                return false;
-
-        }
-
-    }
-
-    
-    
-   
-    
-    
-    // given two lists of variables and a HashMap, checks to see if 
substituting variable names in varList1
-    // for variable names in varList2 is consistent with map.
-    private static boolean listConsistent(List<String> varList1, List<String> 
varList2, HashMap<String, String> hMap) {
-
-        for (int k = 0; k < varList1.size(); k++) {
-
-            String s1 = varList1.get(k);
-            String s2 = varList2.get(k);
-            if (!checkVariables(s1, s2, hMap)) {
-                return false;
-            }
-        }
-        return true;
-
-    }
-
-    
-    // given two lists of variables and a HashMap, substitutes variable names 
in varList1
-    // for variable names in varList2 by updating map.
-    private static void putVars(List<String> varList1, List<String> varList2, 
HashMap<String, String> hashMap) {
-
-        for (int k = 0; k < varList1.size(); k++) {
-            String s1 = varList1.get(k);
-            String s2 = varList2.get(k);
-            if (!hashMap.containsKey(s2)) {
-
-                hashMap.put(s2, s1);
-            }
-        }
-
-    }
-
-   
-    /**
-     * @param filter1
-     * @param filter2
-     * @return true if filter2 is equal to filter1 once variables in filter2 
are replaced with variables and constants
-     * occurring in same position in filter1 (allows filter1 to contain 
constants where filter2 contains variables)
-     * @throws Exception
-     */
-    private static boolean filterCompare(Filter filter1, Filter filter2) 
throws Exception {
-
-        NodeCollector nc1 = new NodeCollector();
-        NodeCollector nc2 = new NodeCollector();
-
-        filter1.getCondition().visit(nc1);
-        filter2.getCondition().visit(nc2);
-
-        List<QueryModelNode> nodeList1 = nc1.getNodes();
-        List<QueryModelNode> nodeList2 = nc2.getNodes();
-
-        if (nodeList1.size() != nodeList2.size()) {
-            return false;
-        }
-
-        for (int i = 0; i < nodeList1.size(); i++) {
-            if ((nodeList1.get(i) instanceof ValueConstant) && 
(nodeList2.get(i) instanceof Var)) {
-                continue;
-            } else {
-                if (nodeList1.get(i).getClass() != 
nodeList2.get(i).getClass()) {
-                    return false;
-                }
-            }
-        }
-
-        return true;
-
-    }
-
-    /**
-     * Given a HashMap containing variable substitutions and a tuple, this
-     * method uses a visitor to iterate through the tuple and make the 
necessary
-     * substitutions
-     * 
-     * @param varChanges
-     * @param tuple
-     * @throws Exception
-     */
-    private static void replaceTupleVariables(HashMap<String, String> 
varChanges, TupleExpr tuple, Map<String,Value> valMap) throws Exception {
-
-        TupleVarRenamer visitor = new TupleVarRenamer(varChanges, valMap);
-        tuple.visit(visitor);
-    }
-
-    /**
-     * Given a list of StatementPattern nodes and a TreeMap containing the
-     * variables in the tuple, this method counts the number of occurrences of
-     * each variable in the given list
-     * 
-     * @param list
-     *            List of StatementPattern nodes
-     * @param cnt
-     *            TreeMap whose keys are tuple variables and whose value is 0
-     * @return TreeMap whose keys are tuple variables and whose value is the
-     *         number of times variable appears in list
-     */
-    private static TreeMap<String, Integer> getListVarCnt(List<QueryModelNode> 
list, TreeMap<String, Integer> cnt) {
-
-        int count = 0;
-
-        for (QueryModelNode qNode : list) {
-            List<String> vars = VarCollector.process(qNode);
-            for (String s : vars) {
-                count = cnt.get(s);
-                count++;
-                cnt.put(s, count);
-            }
-
-        }
-
-        return cnt;
-
-    }
-
-    /**
-     * Given a StatementPattern and two TreeMaps containing the variable counts
-     * associated with an associated list and tuple, this method assigns a
-     * number to the StatementPattern node which is determined by the number of
-     * times its variables (non-constant Vars) appear in the list and 
throughout
-     * the tuple
-     * 
-     * @param sp
-     *            StatementPattern node
-     * @param listCount
-     *            TreeMap with variable count info associated with list
-     * @param tupCount
-     *            TreeMap with variable count info associated with tuple
-     * @return count info associated with StatementPattern node
-     */
-    private static int getSpCount(QueryModelNode sp, TreeMap<String, Integer> 
listCount,
-            TreeMap<String, Integer> tupCount) {
-
-        int spCount = 0;
-
-        List<String> vars = VarCollector.process(sp);
-        for (String var : vars) {
-            spCount = spCount + listCount.get(var) + tupCount.get(var);
-        }
-        return spCount;
-
-    }
-
-    /**
-     * @return NormalizedQueryVisitor
-     */
-    public static NormalizeQueryVisitor getVisitor(boolean isIndex) {
-        return new NormalizeQueryVisitor(isIndex);
-
-    }
-
-   
-    // ********************Definition of Comparators****************
-    // *************************************************************
-    public static class CountComp implements Comparator<QueryModelNode> {
-
-        private TreeMap<String, Integer> lCount, tupleCount;
-
-        public CountComp(TreeMap<String, Integer> lCount, TreeMap<String, 
Integer> tupleCount) {
-
-            this.lCount = lCount;
-            this.tupleCount = tupleCount;
-        }
-
-        // compares StatementPattern nodes based on frequency at which their
-        // variables appear in other StatementPattern nodes in associated
-        // tuple and list
-
-        public int compare(QueryModelNode sp1, QueryModelNode sp2) {
-
-            return -(getSpCount(sp1, lCount, tupleCount) - getSpCount(sp2, 
lCount, tupleCount));
-        }
-
-    }
-
-    // comparator to sort constant key list according to size of associated
-    // StatementPattern array
-    public static class ConstantKeyComp implements Comparator<String> {
-
-        private TreeMap<String, List<QueryModelNode>> indexMap, queryMap;
-
-        public ConstantKeyComp(TreeMap<String, List<QueryModelNode>> indexMap,
-                TreeMap<String, List<QueryModelNode>> queryMap) {
-
-            this.indexMap = indexMap;
-            this.queryMap = queryMap;
-
-        }
-
-        // Compare method to sort keys of HashMap<String,
-        // ArrayList<StatementPattern>
-        // for index based on whether key also appears in query Map--if key 
does
-        // not appear
-        // in query map, key is given value 0 so it is moved to front when key
-        // list is sorted.
-        // If key appears in query map, key is assigned value that is the sum 
of
-        // the size of the associated
-        // lists in index map and query map.
-
-        public int compare(String key1, String key2) {
-
-            int len1 = 0;
-            int len2 = 0;
-
-            if (queryMap.containsKey(key1) && indexMap.containsKey(key1))
-                len1 = indexMap.get(key1).size() + queryMap.get(key1).size();
-            if (queryMap.containsKey(key2) && indexMap.containsKey(key2))
-                len2 = indexMap.get(key2).size() + queryMap.get(key2).size();
-
-            return (len1 - len2);
-
-        }
-
-    }
-
-    public static class FilterComp implements Comparator<QueryModelNode> {
-
-        public int compare(QueryModelNode q1, QueryModelNode q2) {
-
-            int size1 = VarCollector.process(q1).size();
-            int size2 = VarCollector.process(q2).size();
-
-            return size1 - size2;
-
-        }
-
-    }
-
-    // ******************** Definition of Visitors*****************
-    // ************************************************************
-
-    
-
-    public static class ValueMapVisitor extends 
QueryModelVisitorBase<Exception> {
-
-        
-        private Map<String, Value> valMap = Maps.newHashMap();
-
-       
-        
-        public Map<String, Value> getValueMap() {
-            return valMap;
-        }
-
-        public void meet(Var var) {
-            if (var.isConstant()) {
-                valMap.put(var.getName(),var.getValue());
-            }
-            
-            
-        }
-
-        public void meet(ValueConstant val) {
-
-            String s = val.getValue().toString();
-            
-            if (val.getValue() instanceof Literal) {
-                s = s.substring(1, s.length() - 1);
-            }
-            
-            s = "-const-" + s;
-            valMap.put(s, val.getValue());
-        }
-
-    }
-    
-    
-    
-    
-    
-    
-    
-    public static class NodeCollector extends QueryModelVisitorBase<Exception> 
{
-
-        
-        private List<QueryModelNode> nodes = Lists.newArrayList();
-
-        public List<QueryModelNode> getNodes() {
-            return nodes;
-        }
-
-        @Override
-        public void meetNode(QueryModelNode node) throws Exception {
-            nodes.add(node);
-            super.meetNode(node);
-        }
-
-    }
-
-    public static class SpVarReNamer extends 
QueryModelVisitorBase<RuntimeException> {
-
-        private final HashMap<String, String> hMap;
-        private Map<String, Value> valMap;
-        private final ValueFactoryImpl vf = new ValueFactoryImpl();
-
-        public SpVarReNamer(HashMap<String, String> hMap, Map<String, Value> 
valMap) {
-            this.valMap = valMap;
-            this.hMap = hMap;
-        }
-
-        public void meet(Var var) {
-            if (!var.isConstant() && hMap.containsKey(var.getName())) {
-                String val = hMap.get(var.getName());
-                if (val.startsWith("-const-")) {
-                   var.setName(val);
-                   var.setValue(valMap.get(val));
-                   var.setAnonymous(true); //TODO this might be a hack -- when 
are Vars not anonymous?
-                } else {
-                    var.setName(val);
-                }
-            }
-        }
-
-    }
-    
-    
-    
-    
-    public static class FilterVarReNamer extends 
QueryModelVisitorBase<RuntimeException> {
-
-        private final HashMap<String, String> hMap;
-        private Map<String, Value> valMap;
-        private final ValueFactoryImpl vf = new ValueFactoryImpl();
-
-        public FilterVarReNamer(HashMap<String, String> hMap, Map<String, 
Value> valMap) {
-            this.valMap = valMap;
-            this.hMap = hMap;
-        }
-
-        @Override
-        public void meet(Var var) {
-            
-            if (!(var.getParentNode() instanceof NAryValueOperator)) {
-                if (!var.isConstant() && hMap.containsKey(var.getName())) {
-                    String val = hMap.get(var.getName());
-                    if (val.startsWith("-const-")) {
-                        var.replaceWith(new ValueConstant(valMap.get(val)));
-                    } else {
-                        var.setName(val);
-                    }
-                }
-            }
-        }
-        
-        
-        
-        @Override
-        public void meetNAryValueOperator(NAryValueOperator node) {
-
-            List<ValueExpr> oldValues = node.getArguments();
-            List<ValueExpr> newValues = Lists.newArrayList();
-
-            for (ValueExpr v : oldValues) {
-                if (v instanceof Var) {
-                    Var var = (Var) v;
-                    if (!(var.isConstant() && 
hMap.containsKey(var.getName()))) {
-                        String val = hMap.get(var.getName());
-                        if (val.startsWith("-const-")) {
-                            newValues.add(new ValueConstant(valMap.get(val)));
-                        } else {
-                            var.setName(val);
-                            newValues.add(var);
-                        }
-                    }
-                } else {
-                    newValues.add(v);
-                }
-            }
-            
-            node.setArguments(newValues);
-
-        }
-        
-
-    }
-    
-    
-    
-
-    public static class TupleVarRenamer extends 
QueryModelVisitorBase<RuntimeException> {
-
-        private final HashMap<String, String> varChanges;
-        private Map<String, Value> valMap;
-
-        public TupleVarRenamer(HashMap<String, String> varChanges, Map<String, 
Value> valMap) {
-            this.varChanges = varChanges;
-            this.valMap = valMap;
-        }
-
-        @Override
-        public void meet(ProjectionElemList node) {
-            List<ProjectionElem> proj = node.getElements();
-            for (ProjectionElem s : proj) {
-                if (varChanges.containsKey(s.getSourceName())) {
-                    String name = s.getSourceName();
-                    s.setSourceName(varChanges.get(name));
-                    s.setTargetName(varChanges.get(name));
-                   
-                }
-            }
-
-        }
-        
-        
-        @Override
-       public void meet(StatementPattern node) {
-           SpVarReNamer spv = new SpVarReNamer(varChanges, valMap);
-           node.visit(spv);
-       }
-       
-       
-       @Override
-       public void meet(Filter node) {
-           FilterVarReNamer fvr = new FilterVarReNamer(varChanges, valMap);
-           node.getCondition().visit(fvr);
-           node.getArg().visit(this);
-           
-       }
-        
-        
-
-    }
-
-    public static class VarCollector extends 
QueryModelVisitorBase<RuntimeException> {
-
-        public static List<String> process(QueryModelNode node) {
-            VarCollector collector = new VarCollector();
-            node.visit(collector);
-            return collector.getVarNames();
-        }
-        
-        public static List<Var> processVar(QueryModelNode node) {
-            VarCollector collector = new VarCollector();
-            node.visit(collector);
-            return collector.getVars();
-        }
-
-        private List<String> varNames = new ArrayList<String>();
-        private List<Var> vars = Lists.newArrayList();
-
-        public List<String> getVarNames() {
-            return varNames;
-        }
-        
-        public List<Var> getVars() {
-            return vars;
-        }
-
-        @Override
-        public void meet(Var var) {
-            if (!var.hasValue()) {
-                varNames.add(var.getName());
-            }
-            vars.add(var);
-        }
-    }
-    
-    public static class FilterVarValueCollector extends 
QueryModelVisitorBase<RuntimeException> {
-
-        public static List<QueryModelNode> process(QueryModelNode node) {
-            FilterVarValueCollector collector = new FilterVarValueCollector();
-            node.visit(collector);
-            return collector.getVars();
-        }
-        
-      
-       
-        private List<QueryModelNode> vars = Lists.newArrayList();
-
-        
-        public List<QueryModelNode> getVars() {
-            return vars;
-        }
-
-        @Override
-        public void meet(Var node) {
-            vars.add(node);
-        }
-        
-        @Override
-        public void meet(ValueConstant node) {
-            vars.add(node);
-        }
-        
-        
-        
-    }
-    
-    
-    
-
-    public static class NormalizeQueryVisitor extends 
QueryModelVisitorBase<Exception> {
-
-        private TreeMap<String, List<QueryModelNode>> map = new 
TreeMap<String, List<QueryModelNode>>();
-        private TreeMap<String, Integer> varMap = new TreeMap<String, 
Integer>();
-        private TreeMap<String, Integer> emptyVarMap = new TreeMap<String, 
Integer>();
-        private List<StatementPattern> statementList = new 
ArrayList<StatementPattern>();
-        private List<QueryModelNode> filters = new ArrayList<QueryModelNode>();
-        private boolean isIndex;
-        
-        
-        
-        public NormalizeQueryVisitor(boolean isIndex) {
-            this.isIndex = isIndex;
-        }
-        
-        
-        
-        private TreeMap<String, List<QueryModelNode>> getMap() {
-
-            return map;
-
-        }
-        
-
-        private TreeMap<String, Integer> getKeyMap() {
-
-            return varMap;
-        }
-
-        private TreeMap<String, Integer> getVariableMap() {
-            return emptyVarMap;
-        }
-
-        public List<StatementPattern> getStatementPatterns() {
-            return statementList;
-        }
-        
-
-        private List<QueryModelNode> getFilters() {
-
-            return filters;
-        }
-
-        @Override
-        public void meet(StatementPattern node) throws Exception {
-
-            statementList.add(node);
-
-            String s = "";
-            String t = "";
-
-            Var node1 = node.getSubjectVar();
-            Var node2 = node.getObjectVar();
-            Var node3 = node.getPredicateVar();
-            Var node4 = node.getContextVar();
-            
-            String s1 = "";
-            String s2 = "";
-            String s3 = "";
-            String s4 = "";
-            
-            
-            if (node1.isConstant())
-                s1 = node1.getName().substring(7);
-
-            if (node2.isConstant())
-                s2 = node2.getName().substring(7);
-
-            if (node3.isConstant())
-                s3 = node3.getName().substring(7);
-
-            if (node4 != null) {
-                if (node4.isConstant())
-                    s4 = node4.getName().substring(7);
-            }
-
-            if ((s1+s2+s3).length() == 0) {
-                s = "Nonconstant nodes have no variables.";
-            }
-              
-            List<QueryModelNode> nodes;
-            
-            
-            if (s.length() > 0) {
-       
-                if (map.containsKey(s)) {
-                    nodes = map.get(s);
-                    nodes.add(node);
-                } else {
-                    nodes = new ArrayList<QueryModelNode>();
-                    nodes.add(node);
-                }
-                
-                map.put(s, nodes);
-                
-            } else {
-
-                if (isIndex) {
-
-                    t = s1 + s2 + s3 + s4;
-
-                    if (map.containsKey(t)) {
-                        nodes = map.get(t);
-                        nodes.add(node);
-                    } else {
-                        nodes = new ArrayList<QueryModelNode>();
-                        nodes.add(node);
-                    }
-
-                    map.put(t, nodes);
-
-                } else {
-
-                    String[] comps = new String[4];
-                    comps[0] = s1;
-                    comps[1] = s2;
-                    comps[2] = s3;
-                    comps[3] = s4;
-
-                    for (int i = 0; i < 3; i++) {
-                        if (comps[i].length() != 0) {
-                            if (map.containsKey(comps[i] + comps[3])) {
-                                nodes = map.get(comps[i] + comps[3]);
-                                nodes.add(node);
-                            } else {
-                                nodes = new ArrayList<QueryModelNode>();
-                                nodes.add(node);
-                            }
-
-                            map.put(comps[i] + comps[3], nodes);
-
-                            for (int j = i + 1; j < 3; j++) {
-                                if (comps[j].length() != 0) {
-                                    if (map.containsKey(comps[i] + comps[j] + 
comps[3])) {
-                                        nodes = map.get(comps[i] + comps[j] + 
comps[3]);
-                                        nodes.add(node);
-                                    } else {
-                                        nodes = new 
ArrayList<QueryModelNode>();
-                                        nodes.add(node);
-                                    }
-                                    map.put(comps[i] + comps[j] + comps[3], 
nodes);
-                                }
-
-                            }
-                        }
-                    }
-
-                    if (s1.length() != 0 && s2.length() != 0 && s3.length() != 
0) {
-                        if (map.containsKey(s1 + s2 + s3 + s4)) {
-                            nodes = map.get(s1 + s2 + s3 + s4);
-                            nodes.add(node);
-                        } else {
-                            nodes = new ArrayList<QueryModelNode>();
-                            nodes.add(node);
-                        }
-                        map.put(s1 + s2 + s3 + s4, nodes);
-                    }
-                }
-            }
-           
-            super.meet(node);
-
-        }
-
-        @Override
-        public void meet(Var node) throws Exception {
-
-            int count = 1;
-
-            if (!node.isConstant()) {
-                if (varMap.containsKey(node.getName())) {
-                    count = varMap.get(node.getName());
-                    count++;
-                    varMap.put(node.getName(), count);
-                } else
-                    varMap.put(node.getName(), 1);
-
-                if (!emptyVarMap.containsKey(node.getName()))
-                    emptyVarMap.put(node.getName(), 0);
-
-            }
-            super.meet(node);
-        }
-
-        public void meet(Filter filter) throws Exception {
-            filters.add(filter);
-            super.meet(filter);
-        }
-
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/TopOfQueryFilterRelocator.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/TopOfQueryFilterRelocator.java
 
b/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/TopOfQueryFilterRelocator.java
deleted file mode 100644
index 71e119e..0000000
--- 
a/extras/indexing/src/main/java/mvm/rya/indexing/pcj/matching/TopOfQueryFilterRelocator.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package mvm.rya.indexing.pcj.matching;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.Projection;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.ValueExpr;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-/**
- *     Class consisting of a single utility method for relocating filters.
- *
- */
-public class TopOfQueryFilterRelocator  {
-
-
-       /**
-        *
-        * This method moves the Filters of a specified {@link TupleExpr}
-        * to the top of the TupleExpr.
-        *
-        * @param query - query whose filters will be relocated
-        * @return - TupleExpr with filters relocated to top
-        */
-       public static TupleExpr moveFiltersToTop(TupleExpr query) {
-
-               ProjectionAndFilterGatherer fg = new 
ProjectionAndFilterGatherer();
-               query.visit(fg);
-               List<ValueExpr> filterCond = new ArrayList<>(fg.filterCond);
-               Projection projection = fg.projection;
-
-               if(filterCond.size() == 0) {
-                       return query;
-               }
-
-               Filter first = new Filter();
-               first.setCondition(filterCond.remove(0));
-               Filter current = first;
-               for(ValueExpr cond: filterCond) {
-                       Filter filter = new Filter(null, cond);
-                       current.setArg(filter);
-                       current = filter;
-               }
-
-               TupleExpr te = projection.getArg();
-               projection.setArg(first);
-               current.setArg(te);
-
-               return query;
-
-       }
-
-
-       static class ProjectionAndFilterGatherer extends 
QueryModelVisitorBase<RuntimeException> {
-
-               Set<ValueExpr> filterCond = new HashSet<>();
-               Projection projection;
-
-
-               @Override
-               public void meet(Projection node) {
-                       this.projection = node;
-                       node.getArg().visit(this);
-               }
-
-               @Override
-               public void meet(Filter node) {
-                       filterCond.add(node.getCondition());
-                       node.replaceWith(node.getArg());
-               }
-
-       }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailConfig.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailConfig.java 
b/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailConfig.java
deleted file mode 100644
index d66fdd7..0000000
--- 
a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailConfig.java
+++ /dev/null
@@ -1,165 +0,0 @@
-package mvm.rya.sail.config;
-
-import org.openrdf.model.Graph;
-import org.openrdf.model.Literal;
-import org.openrdf.model.Resource;
-import org.openrdf.model.URI;
-import org.openrdf.model.ValueFactory;
-import org.openrdf.model.impl.ValueFactoryImpl;
-import org.openrdf.model.util.GraphUtil;
-import org.openrdf.model.util.GraphUtilException;
-import org.openrdf.sail.config.SailConfigException;
-import org.openrdf.sail.config.SailImplConfigBase;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-
-/**
- * @deprecated Use {@link AccumuloRdfConfiguration} instead.
- */
-@Deprecated
-public class RyaAccumuloSailConfig extends SailImplConfigBase {
-
-    public static final String NAMESPACE = 
"http://rya.apache.org/RyaAccumuloSail/Config#";;
-
-    public static final URI INSTANCE;
-    public static final URI USER;
-    public static final URI PASSWORD;
-    public static final URI ZOOKEEPERS;
-    public static final URI IS_MOCK;
-
-    static {
-        final ValueFactory factory = ValueFactoryImpl.getInstance();
-        USER = factory.createURI(NAMESPACE, "user");
-        PASSWORD = factory.createURI(NAMESPACE, "password");
-        INSTANCE = factory.createURI(NAMESPACE, "instance");
-        ZOOKEEPERS = factory.createURI(NAMESPACE, "zookeepers");
-        IS_MOCK = factory.createURI(NAMESPACE, "isMock");
-    }
-
-    private String user = "root";
-    private String password = "root";
-    private String instance = "dev";
-    private String zookeepers = "zoo1,zoo2,zoo3";
-    private boolean isMock = false;
-
-    public RyaAccumuloSailConfig() {
-        super(RyaAccumuloSailFactory.SAIL_TYPE);
-    }
-
-    public String getUser() {
-        return user;
-    }
-
-    public void setUser(final String user) {
-        this.user = user;
-    }
-
-    public String getPassword() {
-        return password;
-    }
-
-    public void setPassword(final String password) {
-        this.password = password;
-    }
-
-    public String getInstance() {
-        return instance;
-    }
-
-    public void setInstance(final String instance) {
-        this.instance = instance;
-    }
-
-    public String getZookeepers() {
-        return zookeepers;
-    }
-
-    public void setZookeepers(final String zookeepers) {
-        this.zookeepers = zookeepers;
-    }
-
-    public boolean isMock() {
-        return isMock;
-    }
-
-    public void setMock(final boolean isMock) {
-        this.isMock = isMock;
-    }
-
-    public AccumuloRdfConfiguration toRdfConfiguation() {
-        final AccumuloRdfConfiguration conf = new AccumuloRdfConfiguration();
-        return conf;
-    }
-
-    @Override
-    public void validate() throws SailConfigException {
-        super.validate();
-    }
-
-    @Override
-    public Resource export(final Graph graph) {
-        final Resource implNode = super.export(graph);
-
-        @SuppressWarnings("deprecation")
-        final
-        ValueFactory v = graph.getValueFactory();
-
-        graph.add(implNode, USER, v.createLiteral(user));
-        graph.add(implNode, PASSWORD, v.createLiteral(password));
-        graph.add(implNode, INSTANCE, v.createLiteral(instance));
-        graph.add(implNode, ZOOKEEPERS, v.createLiteral(zookeepers));
-        graph.add(implNode, IS_MOCK, v.createLiteral(isMock));
-
-        return implNode;
-    }
-
-    @Override
-    public void parse(final Graph graph, final Resource implNode) throws 
SailConfigException {
-        super.parse(graph, implNode);
-        System.out.println("parsing");
-
-        try {
-            final Literal userLit = GraphUtil.getOptionalObjectLiteral(graph, 
implNode, USER);
-            if (userLit != null) {
-                setUser(userLit.getLabel());
-            }
-            final Literal pwdLit = GraphUtil.getOptionalObjectLiteral(graph, 
implNode, PASSWORD);
-            if (pwdLit != null) {
-                setPassword(pwdLit.getLabel());
-            }
-            final Literal instLit = GraphUtil.getOptionalObjectLiteral(graph, 
implNode, INSTANCE);
-            if (instLit != null) {
-                setInstance(instLit.getLabel());
-            }
-            final Literal zooLit = GraphUtil.getOptionalObjectLiteral(graph, 
implNode, ZOOKEEPERS);
-            if (zooLit != null) {
-                setZookeepers(zooLit.getLabel());
-            }
-            final Literal mockLit = GraphUtil.getOptionalObjectLiteral(graph, 
implNode, IS_MOCK);
-            if (mockLit != null) {
-                setMock(Boolean.parseBoolean(mockLit.getLabel()));
-            }
-        } catch (final GraphUtilException e) {
-            throw new SailConfigException(e.getMessage(), e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailFactory.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailFactory.java 
b/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailFactory.java
deleted file mode 100644
index 83641bd..0000000
--- 
a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaAccumuloSailFactory.java
+++ /dev/null
@@ -1,95 +0,0 @@
-package mvm.rya.sail.config;
-
-import org.apache.accumulo.core.client.AccumuloException;
-import org.apache.accumulo.core.client.AccumuloSecurityException;
-import org.apache.accumulo.core.client.Connector;
-import org.apache.accumulo.core.client.Instance;
-import org.apache.accumulo.core.client.ZooKeeperInstance;
-import org.apache.accumulo.core.client.mock.MockInstance;
-import org.apache.accumulo.core.client.security.tokens.PasswordToken;
-import org.openrdf.sail.Sail;
-import org.openrdf.sail.config.SailConfigException;
-import org.openrdf.sail.config.SailFactory;
-import org.openrdf.sail.config.SailImplConfig;
-
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *   http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.accumulo.AccumuloRyaDAO;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-import mvm.rya.rdftriplestore.RdfCloudTripleStore;
-
-/**
- * @deprecated Use {@link RyaSailFactory} instead.
- */
-@Deprecated
-public class RyaAccumuloSailFactory implements SailFactory {
-
-    public static final String SAIL_TYPE = "rya:RyaAccumuloSail";
-
-    @Override
-    public SailImplConfig getConfig() {
-        return new RyaAccumuloSailConfig();
-    }
-
-    @Override
-    public Sail getSail(final SailImplConfig config) throws 
SailConfigException {
-        try {
-            final RdfCloudTripleStore store = new RdfCloudTripleStore();
-            final RyaAccumuloSailConfig cbconfig = (RyaAccumuloSailConfig) 
config;
-
-            final String instanceName = cbconfig.getInstance();
-            final String zooKeepers = cbconfig.getZookeepers();
-
-            Instance i;
-            if (cbconfig.isMock()) {
-                i = new MockInstance(instanceName);
-            } else {
-                i = new ZooKeeperInstance(instanceName, zooKeepers);
-            }
-
-            final String user = cbconfig.getUser();
-            final String pass = cbconfig.getPassword();
-
-            final Connector connector = i.getConnector(user, new 
PasswordToken(pass));
-            final AccumuloRyaDAO crdfdao = new AccumuloRyaDAO();
-            crdfdao.setConnector(connector);
-
-            final AccumuloRdfConfiguration conf = cbconfig.toRdfConfiguation();
-            ConfigUtils.setIndexers(conf);
-            conf.setDisplayQueryPlan(true);
-
-            crdfdao.setConf(conf);
-            crdfdao.init();
-            store.setRyaDAO(crdfdao);
-
-            return store;
-        } catch (RyaDAOException | AccumuloException | 
AccumuloSecurityException e) {
-            throw new SailConfigException(e);
-        }
-    }
-
-    @Override
-    public String getSailType() {
-        return SAIL_TYPE;
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java 
b/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
deleted file mode 100644
index d3c891c..0000000
--- a/extras/indexing/src/main/java/mvm/rya/sail/config/RyaSailFactory.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements.  See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership.  The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License.  You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied.  See the License for the
- * specific language governing permissions and limitations
- * under the License.
- */
-package mvm.rya.sail.config;
-
-import static java.util.Objects.requireNonNull;
-
-import java.net.UnknownHostException;
-import java.util.Objects;
-
-import org.apache.accumulo.core.client.AccumuloException;
-import org.apache.accumulo.core.client.AccumuloSecurityException;
-import org.apache.accumulo.core.client.Connector;
-import org.apache.accumulo.core.client.Instance;
-import org.apache.accumulo.core.client.security.tokens.PasswordToken;
-import org.apache.hadoop.conf.Configuration;
-import org.openrdf.sail.Sail;
-import org.openrdf.sail.SailException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.mongodb.MongoClient;
-
-import mvm.rya.accumulo.AccumuloRdfConfiguration;
-import mvm.rya.accumulo.AccumuloRyaDAO;
-import mvm.rya.accumulo.instance.AccumuloRyaInstanceDetailsRepository;
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-import mvm.rya.api.instance.RyaDetailsToConfiguration;
-import mvm.rya.api.layout.TablePrefixLayoutStrategy;
-import mvm.rya.api.persist.RyaDAO;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.indexing.accumulo.ConfigUtils;
-import mvm.rya.mongodb.MongoConnectorFactory;
-import mvm.rya.mongodb.MongoDBRdfConfiguration;
-import mvm.rya.mongodb.MongoDBRyaDAO;
-import mvm.rya.mongodb.instance.MongoRyaInstanceDetailsRepository;
-import mvm.rya.rdftriplestore.RdfCloudTripleStore;
-import mvm.rya.rdftriplestore.inference.InferenceEngine;
-import mvm.rya.rdftriplestore.inference.InferenceEngineException;
-
-public class RyaSailFactory {
-    private static final Logger LOG = 
LoggerFactory.getLogger(RyaSailFactory.class);
-
-    /**
-     * Creates an instance of {@link Sail} that is attached to a Rya instance.
-     *
-     * @param conf - Configures how the Sail object will be constructed. (not 
null)
-     * @return A {@link Sail} object that is backed by a Rya datastore.
-     * @throws SailException The object could not be created.
-     */
-    public static Sail getInstance(final Configuration conf) throws 
AccumuloException,
-        AccumuloSecurityException, RyaDAOException, InferenceEngineException, 
SailException {
-        requireNonNull(conf);
-        return getRyaSail(conf);
-    }
-
-    private static Sail getRyaSail(final Configuration config) throws 
InferenceEngineException, RyaDAOException, AccumuloException, 
AccumuloSecurityException, SailException {
-        final RdfCloudTripleStore store = new RdfCloudTripleStore();
-        final RyaDAO<?> dao;
-        final RdfCloudTripleStoreConfiguration rdfConfig;
-
-        final String user;
-        final String pswd;
-        // XXX Should(?) be MongoDBRdfConfiguration.MONGO_COLLECTION_PREFIX 
inside the if below. RYA-135
-        final String ryaInstance = 
config.get(RdfCloudTripleStoreConfiguration.CONF_TBL_PREFIX);
-        Objects.requireNonNull(ryaInstance, "RyaInstance or table prefix is 
missing from configuration."+RdfCloudTripleStoreConfiguration.CONF_TBL_PREFIX);
-
-        if(ConfigUtils.getUseMongo(config)) {
-            final MongoDBRdfConfiguration mongoConfig = new 
MongoDBRdfConfiguration(config);
-            rdfConfig = mongoConfig;
-            final MongoClient client = 
MongoConnectorFactory.getMongoClient(config);
-            try {
-                final MongoRyaInstanceDetailsRepository ryaDetailsRepo = new 
MongoRyaInstanceDetailsRepository(client, mongoConfig.getCollectionName());
-                
RyaDetailsToConfiguration.addRyaDetailsToConfiguration(ryaDetailsRepo.getRyaInstanceDetails(),
 mongoConfig);
-            } catch (final RyaDetailsRepositoryException e) {
-               LOG.info("Instance does not have a rya details collection, 
skipping.");
-           }            dao = getMongoDAO((MongoDBRdfConfiguration)rdfConfig, 
client);
-        } else {
-            rdfConfig = new AccumuloRdfConfiguration(config);
-            user = rdfConfig.get(ConfigUtils.CLOUDBASE_USER);
-            pswd = rdfConfig.get(ConfigUtils.CLOUDBASE_PASSWORD);
-            Objects.requireNonNull(user, "Accumulo user name is missing from 
configuration."+ConfigUtils.CLOUDBASE_USER);
-            Objects.requireNonNull(pswd, "Accumulo user password is missing 
from configuration."+ConfigUtils.CLOUDBASE_PASSWORD);
-            rdfConfig.setTableLayoutStrategy( new 
TablePrefixLayoutStrategy(ryaInstance) );
-            updateAccumuloConfig((AccumuloRdfConfiguration) rdfConfig, user, 
pswd, ryaInstance);
-            dao = getAccumuloDAO((AccumuloRdfConfiguration)rdfConfig);
-        }
-        store.setRyaDAO(dao);
-        rdfConfig.setTablePrefix(ryaInstance);
-
-        if (rdfConfig.isInfer()){
-            final InferenceEngine inferenceEngine = new InferenceEngine();
-            inferenceEngine.setConf(rdfConfig);
-            inferenceEngine.setRyaDAO(dao);
-            inferenceEngine.init();
-            store.setInferenceEngine(inferenceEngine);
-        }
-
-        store.initialize();
-
-        return store;
-    }
-
-    private static MongoDBRyaDAO getMongoDAO(final MongoDBRdfConfiguration 
config, final MongoClient client) throws RyaDAOException {
-        MongoDBRyaDAO dao = null;
-        ConfigUtils.setIndexers(config);
-        if(client != null) {
-            dao = new MongoDBRyaDAO(config, client);
-        } else {
-            try {
-                dao = new MongoDBRyaDAO(config);
-            } catch (NumberFormatException | UnknownHostException e) {
-                throw new RyaDAOException("Unable to connect to mongo at the 
configured location.", e);
-            }
-        }
-        dao.init();
-        return dao;
-    }
-
-    private static AccumuloRyaDAO getAccumuloDAO(final 
AccumuloRdfConfiguration config) throws AccumuloException, 
AccumuloSecurityException, RyaDAOException {
-        final Connector connector = ConfigUtils.getConnector(config);
-        final AccumuloRyaDAO dao = new AccumuloRyaDAO();
-        dao.setConnector(connector);
-
-        ConfigUtils.setIndexers(config);
-        config.setDisplayQueryPlan(true);
-
-        dao.setConf(config);
-        dao.init();
-        return dao;
-    }
-
-    public static void updateAccumuloConfig(final AccumuloRdfConfiguration 
config, final String user, final String pswd, final String ryaInstance) throws 
AccumuloException, AccumuloSecurityException {
-        try {
-            final PasswordToken pswdToken = new PasswordToken(pswd);
-            final Instance accInst = ConfigUtils.getInstance(config);
-            final AccumuloRyaInstanceDetailsRepository ryaDetailsRepo = new 
AccumuloRyaInstanceDetailsRepository(accInst.getConnector(user, pswdToken), 
ryaInstance);
-            
RyaDetailsToConfiguration.addRyaDetailsToConfiguration(ryaDetailsRepo.getRyaInstanceDetails(),
 config);
-        } catch(final RyaDetailsRepositoryException e) {
-            LOG.info("Instance does not have a rya details collection, 
skipping.");
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/extras/indexing/src/main/java/org/apache/rya/accumulo/documentIndex/DocIndexIteratorUtil.java
----------------------------------------------------------------------
diff --git 
a/extras/indexing/src/main/java/org/apache/rya/accumulo/documentIndex/DocIndexIteratorUtil.java
 
b/extras/indexing/src/main/java/org/apache/rya/accumulo/documentIndex/DocIndexIteratorUtil.java
new file mode 100644
index 0000000..fefd651
--- /dev/null
+++ 
b/extras/indexing/src/main/java/org/apache/rya/accumulo/documentIndex/DocIndexIteratorUtil.java
@@ -0,0 +1,31 @@
+package mvm.rya.accumulo.documentIndex;
+
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ * 
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+
+public class DocIndexIteratorUtil {
+
+    
+    
+    public static final String DOC_ID_INDEX_DELIM = "\u001D" + "\u001E";
+    
+    
+    
+}

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