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From miha...@apache.org
Subject [03/51] [partial] incubator-rya git commit: Cannot delete temp branch, doc'd it.
Date Mon, 07 Dec 2015 12:04:33 GMT
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepository.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepository.java b/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepository.java
deleted file mode 100644
index 7003398..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepository.java
+++ /dev/null
@@ -1,53 +0,0 @@
-package mvm.rya.rdftriplestore;
-
-/*
- * 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 org.openrdf.repository.RepositoryException;
-import org.openrdf.repository.sail.SailRepository;
-import org.openrdf.repository.sail.SailRepositoryConnection;
-import org.openrdf.sail.Sail;
-import org.openrdf.sail.SailException;
-
-/**
- * Created by IntelliJ IDEA.
- * User: RoshanP
- * Date: 3/23/12
- * Time: 10:05 AM
- * To change this template use File | Settings | File Templates.
- */
-public class RyaSailRepository extends SailRepository{
-    public RyaSailRepository(Sail sail) {
-        super(sail);
-    }
-
-    @Override
-    public SailRepositoryConnection getConnection() throws RepositoryException {
-        try
-        {
-            return new RyaSailRepositoryConnection(this, this.getSail().getConnection());
-        }
-        catch(SailException e)
-        {
-            throw new RepositoryException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepositoryConnection.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepositoryConnection.java b/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepositoryConnection.java
deleted file mode 100644
index 6261b8c..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/RyaSailRepositoryConnection.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package mvm.rya.rdftriplestore;
-
-/*
- * 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.io.IOException;
-import java.io.InputStream;
-import java.io.Reader;
-
-import mvm.rya.rdftriplestore.utils.CombineContextsRdfInserter;
-
-import org.openrdf.OpenRDFUtil;
-import org.openrdf.model.Resource;
-import org.openrdf.repository.RepositoryException;
-import org.openrdf.repository.sail.SailRepository;
-import org.openrdf.repository.sail.SailRepositoryConnection;
-import org.openrdf.repository.util.RDFLoader;
-import org.openrdf.rio.RDFFormat;
-import org.openrdf.rio.RDFHandlerException;
-import org.openrdf.rio.RDFParseException;
-import org.openrdf.sail.SailConnection;
-
-/**
- * The real reason for this is so that we can combine contexts from an input stream/reader and the given contexts in the add function
- */
-public class RyaSailRepositoryConnection extends SailRepositoryConnection {
-
-    protected RyaSailRepositoryConnection(SailRepository repository, SailConnection sailConnection) {
-        super(repository, sailConnection);
-    }
-
-    @Override
-    public void add(InputStream in, String baseURI, RDFFormat dataFormat, Resource... contexts) throws IOException, RDFParseException,
-            RepositoryException {
-        OpenRDFUtil.verifyContextNotNull(contexts);
-
-        CombineContextsRdfInserter rdfInserter = new CombineContextsRdfInserter(this);
-        rdfInserter.enforceContext(contexts);
-
-        boolean localTransaction = startLocalTransaction();
-        try {
-            RDFLoader loader = new RDFLoader(getParserConfig(), getValueFactory());
-            loader.load(in, baseURI, dataFormat, rdfInserter);
-
-            conditionalCommit(localTransaction);
-        } catch (RDFHandlerException e) {
-            conditionalRollback(localTransaction);
-
-            throw ((RepositoryException) e.getCause());
-        } catch (RDFParseException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        } catch (IOException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        } catch (RuntimeException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        }
-    }
-
-    @Override
-    public void add(Reader reader, String baseURI, RDFFormat dataFormat, Resource... contexts) throws IOException, RDFParseException,
-            RepositoryException {
-        OpenRDFUtil.verifyContextNotNull(contexts);
-
-        CombineContextsRdfInserter rdfInserter = new CombineContextsRdfInserter(this);
-        rdfInserter.enforceContext(contexts);
-
-        boolean localTransaction = startLocalTransaction();
-        try {
-            RDFLoader loader = new RDFLoader(getParserConfig(), getValueFactory());
-            loader.load(reader, baseURI, dataFormat, rdfInserter);
-
-            conditionalCommit(localTransaction);
-        } catch (RDFHandlerException e) {
-            conditionalRollback(localTransaction);
-
-            throw ((RepositoryException) e.getCause());
-        } catch (RDFParseException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        } catch (IOException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        } catch (RuntimeException e) {
-            conditionalRollback(localTransaction);
-            throw e;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalBatchingIterator.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalBatchingIterator.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalBatchingIterator.java
deleted file mode 100644
index b84104a..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalBatchingIterator.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 info.aduna.iteration.CloseableIteration;
-
-import java.util.Collection;
-
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-
-public interface ExternalBatchingIterator {
-    public CloseableIteration<BindingSet, QueryEvaluationException> evaluate(Collection<BindingSet> bindingset) throws QueryEvaluationException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalMultipleBindingSetsIterator.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalMultipleBindingSetsIterator.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalMultipleBindingSetsIterator.java
deleted file mode 100644
index 16ef588..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ExternalMultipleBindingSetsIterator.java
+++ /dev/null
@@ -1,109 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.LookAheadIteration;
-
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-
-/**
- */
-public class ExternalMultipleBindingSetsIterator extends LookAheadIteration<BindingSet, QueryEvaluationException> {
-
-    private final ParallelEvaluationStrategyImpl strategy;
-    private final CloseableIteration leftIter;
-    private ExternalBatchingIterator stmtPtrn;
-    private CloseableIteration<BindingSet, QueryEvaluationException> iter;
-    //TODO: configurable
-    private int batchSize = 1000;
-
-    public ExternalMultipleBindingSetsIterator(ParallelEvaluationStrategyImpl strategy, TupleExpr leftArg, ExternalBatchingIterator stmtPattern, BindingSet bindings)
-            throws QueryEvaluationException {
-        this.strategy = strategy;
-        leftIter = strategy.evaluate(leftArg, bindings);
-        this.stmtPtrn = stmtPattern;
-        initIter();
-    }
-
-    public ExternalMultipleBindingSetsIterator(ParallelEvaluationStrategyImpl strategy, CloseableIteration leftIter, ExternalBatchingIterator stmtPattern, BindingSet bindings)
-            throws QueryEvaluationException {
-        this.strategy = strategy;
-        this.leftIter = leftIter;
-        this.stmtPtrn = stmtPattern;
-        initIter();
-    }
-
-    protected void initIter() throws QueryEvaluationException {
-        try {
-            Collection<BindingSet> sets = new ArrayList<BindingSet>();
-            int i = 0;
-            while (leftIter.hasNext()) {
-                //default to 1K for the batch size
-                if (i >= batchSize) {
-                    break;
-                }
-                sets.add((BindingSet) leftIter.next());
-                i++;
-            }
-            if (iter != null) iter.close();
-            iter = stmtPtrn.evaluate(sets);
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-
-    protected BindingSet getNextElement()
-            throws QueryEvaluationException {
-        try {
-            while (true) {
-                if (iter.hasNext()) {
-                    return iter.next();
-                }
-
-                if (leftIter.hasNext()) {
-                    initIter();
-                } else
-                    return null;
-            }
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-
-    protected void handleClose()
-            throws QueryEvaluationException {
-        try {
-            super.handleClose();
-            leftIter.close();
-            iter.close();
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/FilterRangeVisitor.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/FilterRangeVisitor.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/FilterRangeVisitor.java
deleted file mode 100644
index 24e2527..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/FilterRangeVisitor.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.RangeURI;
-import mvm.rya.api.domain.RangeValue;
-import org.openrdf.model.Value;
-import org.openrdf.model.impl.BooleanLiteralImpl;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.*;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import static mvm.rya.api.RdfCloudTripleStoreConstants.RANGE;
-
-/**
- * Class FilterTimeIndexVisitor
- * Date: Apr 11, 2011
- * Time: 10:16:15 PM
- */
-public class FilterRangeVisitor extends QueryModelVisitorBase {
-
-    private RdfCloudTripleStoreConfiguration conf;
-    private Map<Var, RangeValue> rangeValues = new HashMap<Var, RangeValue>();
-
-    public FilterRangeVisitor(RdfCloudTripleStoreConfiguration conf) {
-        this.conf = conf;
-    }
-
-    @Override
-    public void meet(Filter node) throws Exception {
-        super.meet(node);
-
-        ValueExpr arg = node.getCondition();
-        if (arg instanceof FunctionCall) {
-            FunctionCall fc = (FunctionCall) arg;
-            if (RANGE.stringValue().equals(fc.getURI())) {
-                //range(?var, start, end)
-                List<ValueExpr> valueExprs = fc.getArgs();
-                if (valueExprs.size() != 3) {
-                    throw new QueryEvaluationException("mvm:range must have 3 parameters: variable, start, end");
-                }
-                Var var = (Var) valueExprs.get(0);
-                ValueConstant startVc = (ValueConstant) valueExprs.get(1);
-                ValueConstant endVc = (ValueConstant) valueExprs.get(2);
-                Value start = startVc.getValue();
-                Value end = endVc.getValue();
-                rangeValues.put(var, new RangeValue(start, end));
-                node.setCondition(new ValueConstant(BooleanLiteralImpl.TRUE));
-            }
-        }
-    }
-
-    @Override
-    public void meet(StatementPattern node) throws Exception {
-        super.meet(node);
-
-        Var subjectVar = node.getSubjectVar();
-        RangeValue subjRange = rangeValues.get(subjectVar);
-        Var predVar = node.getPredicateVar();
-        RangeValue predRange = rangeValues.get(predVar);
-        Var objVar = node.getObjectVar();
-        RangeValue objRange = rangeValues.get(objVar);
-        if(subjRange != null) {
-            subjectVar.setValue(new RangeURI(subjRange));//Assumes no blank nodes can be ranges
-        }
-        if(predRange != null) {
-            predVar.setValue(new RangeURI(predRange));
-        }
-        if(objRange != null) {
-            objVar.setValue(objRange);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/MultipleBindingSetsIterator.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/MultipleBindingSetsIterator.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/MultipleBindingSetsIterator.java
deleted file mode 100644
index 01f3d27..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/MultipleBindingSetsIterator.java
+++ /dev/null
@@ -1,108 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.LookAheadIteration;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-
-import java.util.ArrayList;
-import java.util.Collection;
-
-/**
- */
-public class MultipleBindingSetsIterator extends LookAheadIteration<BindingSet, QueryEvaluationException> {
-
-    private final ParallelEvaluationStrategyImpl strategy;
-    private final CloseableIteration leftIter;
-    private StatementPattern stmtPtrn;
-    private CloseableIteration<BindingSet, QueryEvaluationException> iter;
-    //TODO: configurable
-    private int batchSize = 1000;
-
-    public MultipleBindingSetsIterator(ParallelEvaluationStrategyImpl strategy, TupleExpr leftArg, StatementPattern stmtPattern, BindingSet bindings)
-            throws QueryEvaluationException {
-        this.strategy = strategy;
-        leftIter = strategy.evaluate(leftArg, bindings);
-        this.stmtPtrn = stmtPattern;
-        initIter();
-    }
-
-    public MultipleBindingSetsIterator(ParallelEvaluationStrategyImpl strategy, CloseableIteration leftIter, StatementPattern stmtPattern, BindingSet bindings)
-            throws QueryEvaluationException {
-        this.strategy = strategy;
-        this.leftIter = leftIter;
-        this.stmtPtrn = stmtPattern;
-        initIter();
-    }
-
-    protected void initIter() throws QueryEvaluationException {
-        try {
-            Collection<BindingSet> sets = new ArrayList<BindingSet>();
-            int i = 0;
-            while (leftIter.hasNext()) {
-                //default to 1K for the batch size
-                if (i >= batchSize) {
-                    break;
-                }
-                sets.add((BindingSet) leftIter.next());
-                i++;
-            }
-            if (iter != null) iter.close();
-            iter = strategy.evaluate(stmtPtrn, sets);
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-
-    protected BindingSet getNextElement()
-            throws QueryEvaluationException {
-        try {
-            while (true) {
-                if (iter.hasNext()) {
-                    return iter.next();
-                }
-
-                if (leftIter.hasNext()) {
-                    initIter();
-                } else
-                    return null;
-            }
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-
-    protected void handleClose()
-            throws QueryEvaluationException {
-        try {
-            super.handleClose();
-            leftIter.close();
-            iter.close();
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
deleted file mode 100644
index 30dc966..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelEvaluationStrategyImpl.java
+++ /dev/null
@@ -1,281 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.ConvertingIteration;
-import info.aduna.iteration.EmptyIteration;
-import info.aduna.iteration.Iteration;
-import info.aduna.iteration.IteratorIteration;
-import info.aduna.iteration.LimitIteration;
-import info.aduna.iteration.OffsetIteration;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.RdfCloudTripleStoreUtils;
-import mvm.rya.api.utils.NullableStatementImpl;
-import mvm.rya.rdftriplestore.RdfCloudTripleStoreConnection;
-import mvm.rya.rdftriplestore.inference.InferenceEngine;
-import mvm.rya.rdftriplestore.inference.InferenceEngineException;
-import mvm.rya.rdftriplestore.utils.FixedStatementPattern;
-import mvm.rya.rdftriplestore.utils.TransitivePropertySP;
-
-import org.apache.log4j.Logger;
-import org.openrdf.model.Resource;
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.model.Value;
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.Dataset;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.QueryRoot;
-import org.openrdf.query.algebra.Slice;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.ValueExpr;
-import org.openrdf.query.algebra.Var;
-import org.openrdf.query.algebra.evaluation.QueryBindingSet;
-import org.openrdf.query.algebra.evaluation.ValueExprEvaluationException;
-import org.openrdf.query.algebra.evaluation.impl.EvaluationStrategyImpl;
-import org.openrdf.query.algebra.evaluation.iterator.FilterIterator;
-import org.openrdf.query.algebra.evaluation.iterator.JoinIterator;
-import org.openrdf.query.algebra.evaluation.util.QueryEvaluationUtil;
-
-import com.google.common.collect.Lists;
-
-/**
- */
-public class ParallelEvaluationStrategyImpl extends EvaluationStrategyImpl {
-    private static Logger logger = Logger.getLogger(ParallelEvaluationStrategyImpl.class);
-    
-    private int numOfThreads = 10;
-    private boolean performant = true;
-    private boolean displayQueryPlan = false;
-    private ExecutorService executorService;
-    private InferenceEngine inferenceEngine;
-
-    public ParallelEvaluationStrategyImpl(RdfCloudTripleStoreConnection.StoreTripleSource tripleSource, InferenceEngine inferenceEngine,
-                                          Dataset dataset, RdfCloudTripleStoreConfiguration conf) {
-        super(tripleSource, dataset);
-        Integer nthreads = conf.getNumThreads();
-        this.numOfThreads = (nthreads != null) ? nthreads : this.numOfThreads;
-        Boolean val = conf.isPerformant();
-        this.performant = (val != null) ? val : this.performant;
-        val = conf.isDisplayQueryPlan();
-        this.displayQueryPlan = (val != null) ? val : this.displayQueryPlan;
-        this.executorService = Executors.newFixedThreadPool(this.numOfThreads);
-        this.inferenceEngine = inferenceEngine;
-    }
-
-    @Override
-    public CloseableIteration<BindingSet, QueryEvaluationException> evaluate(Join join, BindingSet bindings) throws QueryEvaluationException {
-        if (performant) {
-            TupleExpr buffer = join.getLeftArg();
-            if (join.getRightArg() instanceof StatementPattern) {
-                TupleExpr stmtPat = join.getRightArg();
-//                if(buffer instanceof StatementPattern && !(stmtPat instanceof StatementPattern)){
-//                    buffer = stmtPat;
-//                    stmtPat = join.getLeftArg();
-//                }
-
-                return new MultipleBindingSetsIterator(this, buffer, (StatementPattern) stmtPat, bindings);
-            } else if (join.getRightArg() instanceof ExternalBatchingIterator) {
-                    TupleExpr stmtPat = join.getRightArg();
-
-                    return new ExternalMultipleBindingSetsIterator(this, buffer, (ExternalBatchingIterator) stmtPat, bindings);
-            } else if (join.getRightArg() instanceof Filter) {
-                //add performance for the filter too
-                Filter filter = (Filter) join.getRightArg();
-                TupleExpr filterChild = filter.getArg();
-                if (filterChild instanceof StatementPattern) {
-                    return new FilterIterator(filter, new MultipleBindingSetsIterator(this, buffer, (StatementPattern) filterChild, bindings), this);
-                } else if (filterChild instanceof Join) {
-                    Join filterChildJoin = (Join) filterChild;
-                    TupleExpr fcj_left = filterChildJoin.getLeftArg();
-                    TupleExpr fcj_right = filterChildJoin.getRightArg();
-                    //TODO: Should be a better way, maybe reorder the filter?
-                    //very particular case filter(join(stmtPat, stmtPat))
-                    if (fcj_left instanceof StatementPattern && fcj_right instanceof StatementPattern) {
-                        return new FilterIterator(filter, new MultipleBindingSetsIterator(this, new Join(buffer, fcj_left), (StatementPattern) fcj_right, bindings), this);
-                    }
-                }
-                //TODO: add a configuration flag for ParallelJoinIterator
-                return new JoinIterator(this, join, bindings);
-            } else {
-                //TODO: add a configuration flag for ParallelJoinIterator
-                return new JoinIterator(this, join, bindings);
-            }
-        } else {
-            return super.evaluate(join, bindings);
-        }
-    }
-
-    @Override
-    public CloseableIteration<BindingSet, QueryEvaluationException> evaluate(StatementPattern sp, BindingSet bindings) throws QueryEvaluationException {
-        //TODO: Wonder if creating a Collection here hurts performance
-        Set<BindingSet> bs = Collections.singleton(bindings);
-        return this.evaluate(sp, bs);
-    }
-
-    public CloseableIteration<BindingSet, QueryEvaluationException> evaluate(final StatementPattern sp, Collection<BindingSet> bindings)
-            throws QueryEvaluationException {
-
-        final Var subjVar = sp.getSubjectVar();
-        final Var predVar = sp.getPredicateVar();
-        final Var objVar = sp.getObjectVar();
-        final Var cntxtVar = sp.getContextVar();
-
-        List<Map.Entry<Statement, BindingSet>> stmts = new ArrayList<Map.Entry<Statement, BindingSet>>();
-
-        Iteration<? extends Map.Entry<Statement, BindingSet>, QueryEvaluationException> iter;
-        if (sp instanceof FixedStatementPattern) {
-            Collection<Map.Entry<Statement, BindingSet>> coll = Lists.newArrayList();
-            for (BindingSet binding : bindings) {
-                Value subjValue = getVarValue(subjVar, binding);
-                Value predValue = getVarValue(predVar, binding);
-                Value objValue = getVarValue(objVar, binding);
-                Resource contxtValue = (Resource) getVarValue(cntxtVar, binding);
-                for (Statement st : ((FixedStatementPattern) sp).statements) {
-                    if (!((subjValue != null && !subjValue.equals(st.getSubject())) ||
-                            (predValue != null && !predValue.equals(st.getPredicate())) ||
-                            (objValue != null && !objValue.equals(st.getObject())))) {
-                        coll.add(new RdfCloudTripleStoreUtils.CustomEntry<Statement, BindingSet>(st, binding));
-                    }
-                }
-            }
-            iter = new IteratorIteration(coll.iterator());
-        } else if (sp instanceof TransitivePropertySP &&
-                ((subjVar != null && subjVar.getValue() != null) ||
-                        (objVar != null && objVar.getValue() != null)) &&
-                sp.getPredicateVar() != null) {
-            //if this is a transitive prop ref, we need to make sure that either the subj or obj is not null
-            //TODO: Cannot handle a open ended transitive property where subj and obj are null
-            //TODO: Should one day handle filling in the subj or obj with bindings and working this
-            //TODO: a lot of assumptions, and might be a large set returned causing an OME
-            Set<Statement> sts = null;
-            try {
-                sts = inferenceEngine.findTransitiveProperty((Resource) getVarValue(subjVar),
-                        (URI) getVarValue(predVar), getVarValue(objVar), (Resource) getVarValue(cntxtVar));
-            } catch (InferenceEngineException e) {
-                throw new QueryEvaluationException(e);
-            }
-            Collection<Map.Entry<Statement, BindingSet>> coll = new ArrayList();
-            for (BindingSet binding : bindings) {
-                for (Statement st : sts) {
-                    coll.add(new RdfCloudTripleStoreUtils.CustomEntry<Statement, BindingSet>(st, binding));
-                }
-            }
-            iter = new IteratorIteration(coll.iterator());
-        } else {
-            for (BindingSet binding : bindings) {
-                Value subjValue = getVarValue(subjVar, binding);
-                Value predValue = getVarValue(predVar, binding);
-                Value objValue = getVarValue(objVar, binding);
-                Resource contxtValue = (Resource) getVarValue(cntxtVar, binding);
-                if ((subjValue != null && !(subjValue instanceof Resource)) ||
-                        (predValue != null && !(predValue instanceof URI))) {
-                    continue;
-                }
-                stmts.add(new RdfCloudTripleStoreUtils.CustomEntry<Statement, BindingSet>(
-                        new NullableStatementImpl((Resource) subjValue, (URI) predValue, objValue, contxtValue), binding));
-            }
-            if (stmts.size() == 0) {
-                return new EmptyIteration();
-            }
-
-            iter = ((RdfCloudTripleStoreConnection.StoreTripleSource) tripleSource).getStatements(stmts);
-        }
-        return new ConvertingIteration<Map.Entry<Statement, BindingSet>, BindingSet, QueryEvaluationException>(iter) {
-
-            @Override
-            protected BindingSet convert(Map.Entry<Statement, BindingSet> stbs) throws QueryEvaluationException {
-                Statement st = stbs.getKey();
-                BindingSet bs = stbs.getValue();
-                QueryBindingSet result = new QueryBindingSet(bs);
-                if (subjVar != null && !result.hasBinding(subjVar.getName())) {
-                    result.addBinding(subjVar.getName(), st.getSubject());
-                }
-                if (predVar != null && !result.hasBinding(predVar.getName())) {
-                    result.addBinding(predVar.getName(), st.getPredicate());
-                }
-                if (objVar != null && !result.hasBinding(objVar.getName())) {
-                    result.addBinding(objVar.getName(), st.getObject());
-                }
-                if (cntxtVar != null && !result.hasBinding(cntxtVar.getName()) && st.getContext() != null) {
-                    result.addBinding(cntxtVar.getName(), st.getContext());
-                }
-                return result;
-            }
-        };
-    }
-
-    @Override
-    public CloseableIteration<BindingSet, QueryEvaluationException> evaluate(TupleExpr expr, BindingSet bindings) throws QueryEvaluationException {
-        if (expr instanceof QueryRoot) {
-            if (displayQueryPlan) {
-//                System.out.println("Tables: ");
-//                System.out.println("--SPO: \t" + RdfCloudTripleStoreConstants.TBL_SPO);
-//                System.out.println("--PO: \t" + RdfCloudTripleStoreConstants.TBL_PO);
-//                System.out.println("--OSP: \t" + RdfCloudTripleStoreConstants.TBL_OSP);
-                logger.info("=================== Rya Query ===================");
-                for (String str : expr.toString().split("\\r?\\n")) {
-                    logger.info(str);
-                }
-                logger.info("================= End Rya Query =================");
-            }
-        }
-        return super.evaluate(expr, bindings);
-    }
-
-    public CloseableIteration evaluate(Slice slice, BindingSet bindings)
-            throws QueryEvaluationException {
-        CloseableIteration result = evaluate(slice.getArg(), bindings);
-        if (slice.hasOffset()) {
-            result = new OffsetIteration(result, slice.getOffset());
-        }
-        if (slice.hasLimit()) {
-            result = new LimitIteration(result, slice.getLimit());
-        }
-        return result;
-    }
-
-    protected Value getVarValue(Var var) {
-        if (var == null)
-            return null;
-        else
-            return var.getValue();
-    }
-
-    public void shutdown() {
-        executorService.shutdownNow();
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelJoinIterator.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelJoinIterator.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelJoinIterator.java
deleted file mode 100644
index 1d5c982..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ParallelJoinIterator.java
+++ /dev/null
@@ -1,139 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.LookAheadIteration;
-
-import java.util.NoSuchElementException;
-import java.util.Queue;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.QueryEvaluationException;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.evaluation.EvaluationStrategy;
-import org.openrdf.query.impl.EmptyBindingSet;
-
-/**
- */
-public class ParallelJoinIterator extends LookAheadIteration<BindingSet, QueryEvaluationException> {
-
-    public static final EmptyBindingSet EMPTY_BINDING_SET = new EmptyBindingSet();
-
-    private final EvaluationStrategy strategy;
-    private final Join join;
-    private final CloseableIteration<BindingSet, QueryEvaluationException> leftIter;
-
-    private ExecutorService executorService;
-    private Queue<ParallelIteratorWork> workQueue = new LinkedBlockingQueue<ParallelIteratorWork>();
-    private ParallelIteratorWork currentWork;
-    private int batch;
-
-    public ParallelJoinIterator(EvaluationStrategy strategy, Join join, BindingSet bindings, ExecutorService executorService, int batch)
-            throws QueryEvaluationException {
-        this.strategy = strategy;
-        this.join = join;
-        leftIter = strategy.evaluate(join.getLeftArg(), bindings);
-
-        this.executorService = executorService;
-        this.batch = batch;
-    }
-
-
-    @Override
-    protected BindingSet getNextElement() throws QueryEvaluationException {
-
-        try {
-            while (leftIter.hasNext() || !workQueue.isEmpty() || currentWork != null) {
-                if (!workQueue.isEmpty() && currentWork == null) {
-                    currentWork = workQueue.poll();
-                }
-
-                if (currentWork != null) {
-                    BindingSet bindingSet = currentWork.queue.poll();
-                    if (EMPTY_BINDING_SET.equals(bindingSet)) {
-                        currentWork = null;
-                        continue;
-                    } else if (bindingSet == null) {
-                        continue;
-                    }
-                    return bindingSet;
-                }
-
-                try {
-                    for (int i = 0; i < batch; i++) {
-                        if (leftIter.hasNext()) {
-                            ParallelIteratorWork work = new ParallelIteratorWork((BindingSet) leftIter.next(), join.getRightArg());
-                            workQueue.add(work);
-                            executorService.execute(work);
-                        } else
-                            break;
-                    }
-                } catch (NoSuchElementException ignore) {
-                }
-            }
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-        return null;
-    }
-
-    @Override
-    protected void handleClose() throws QueryEvaluationException {
-        try {
-            super.handleClose();
-            leftIter.close();
-//           rightIter.close();
-        } catch (Exception e) {
-            throw new QueryEvaluationException(e);
-        }
-    }
-
-    private class ParallelIteratorWork implements Runnable {
-
-        private BindingSet leftBindingSet;
-        private TupleExpr rightTupleExpr;
-        public LinkedBlockingQueue<BindingSet> queue = new LinkedBlockingQueue<BindingSet>();
-
-        private ParallelIteratorWork(BindingSet leftBindingSet, TupleExpr rightTupleExpr) {
-            this.leftBindingSet = leftBindingSet;
-            this.rightTupleExpr = rightTupleExpr;
-        }
-
-        @Override
-        public void run() {
-            try {
-                CloseableIteration<BindingSet, QueryEvaluationException> iter = strategy.evaluate(rightTupleExpr, leftBindingSet);
-                while (iter.hasNext()) {
-                    queue.add(iter.next());
-                }
-                queue.add(EMPTY_BINDING_SET);
-                iter.close();
-            } catch (QueryEvaluationException e) {
-                throw new RuntimeException(e);
-            }
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/PushJoinDownVisitor.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/PushJoinDownVisitor.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/PushJoinDownVisitor.java
deleted file mode 100644
index 342f98d..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/PushJoinDownVisitor.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-/**
- * Class ReorderJoinVisitor
- * Date: Apr 11, 2011
- * Time: 10:16:15 PM
- */
-public class PushJoinDownVisitor extends QueryModelVisitorBase {
-    @Override
-    public void meet(Join node) throws Exception {
-        super.meet(node);
-
-        TupleExpr leftArg = node.getLeftArg();
-        TupleExpr rightArg = node.getRightArg();
-
-        /**
-         * if join(join(1, 2), join(3,4))
-         * should be:
-         * join(join(join(1,2), 3), 4)
-         */
-        if (leftArg instanceof Join && rightArg instanceof Join) {
-            Join leftJoin = (Join) leftArg;
-            Join rightJoin = (Join) rightArg;
-            TupleExpr right_LeftArg = rightJoin.getLeftArg();
-            TupleExpr right_rightArg = rightJoin.getRightArg();
-            Join inner = new Join(leftJoin, right_LeftArg);
-            Join outer = new Join(inner, right_rightArg);
-            node.replaceWith(outer);
-        }
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinOptimizer.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinOptimizer.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinOptimizer.java
deleted file mode 100644
index 940e46e..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinOptimizer.java
+++ /dev/null
@@ -1,284 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 org.openrdf.query.BindingSet;
-import org.openrdf.query.Dataset;
-import org.openrdf.query.algebra.*;
-import org.openrdf.query.algebra.evaluation.QueryOptimizer;
-import org.openrdf.query.algebra.evaluation.impl.EvaluationStatistics;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-import org.openrdf.query.algebra.helpers.StatementPatternCollector;
-
-import java.util.*;
-
-/**
- * A query optimizer that re-orders nested Joins.
- *
- * @author Arjohn Kampman
- * @author James Leigh
- */
-public class QueryJoinOptimizer implements QueryOptimizer {
-
-    protected final EvaluationStatistics statistics;
-
-    public QueryJoinOptimizer() {
-        this(new EvaluationStatistics());
-    }
-
-    public QueryJoinOptimizer(EvaluationStatistics statistics) {
-        this.statistics = statistics;
-    }
-
-    /**
-     * Applies generally applicable optimizations: path expressions are sorted
-     * from more to less specific.
-     *
-     * @param tupleExpr
-     */
-    public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings) {
-        tupleExpr.visit(new JoinVisitor());
-    }
-
-    protected class JoinVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-        Set<String> boundVars = new HashSet<String>();
-
-        @Override
-        public void meet(LeftJoin leftJoin) {
-            leftJoin.getLeftArg().visit(this);
-
-            Set<String> origBoundVars = boundVars;
-            try {
-                boundVars = new HashSet<String>(boundVars);
-                boundVars.addAll(leftJoin.getLeftArg().getBindingNames());
-
-                leftJoin.getRightArg().visit(this);
-            } finally {
-                boundVars = origBoundVars;
-            }
-        }
-
-        @Override
-        public void meet(Join node) {
-            Set<String> origBoundVars = boundVars;
-            try {
-                boundVars = new HashSet<String>(boundVars);
-
-                // Recursively get the join arguments
-                List<TupleExpr> joinArgs = getJoinArgs(node, new ArrayList<TupleExpr>());
-
-                // Build maps of cardinalities and vars per tuple expression
-                Map<TupleExpr, Double> cardinalityMap = new HashMap<TupleExpr, Double>();
-//                Map<TupleExpr, List<Var>> varsMap = new HashMap<TupleExpr, List<Var>>();
-//                Map<Var, Double> varCardinalityMap = new HashMap<Var, Double>();
-
-                for (TupleExpr tupleExpr : joinArgs) {
-                    double cardinality = statistics.getCardinality(tupleExpr);
-//                    List<Var> statementPatternVars = getStatementPatternVars(tupleExpr);
-
-                    cardinalityMap.put(tupleExpr, cardinality);
-//                    varsMap.put(tupleExpr, statementPatternVars);
-                }
-
-                // Build map of var frequences
-//                Map<Var, Integer> varFreqMap = new HashMap<Var, Integer>();
-//                for (List<Var> varList : varsMap.values()) {
-//                    getVarFreqMap(varList, varFreqMap);
-//                }
-
-                // Reorder the (recursive) join arguments to a more optimal sequence
-                List<TupleExpr> orderedJoinArgs = new ArrayList<TupleExpr>(joinArgs.size());
-                while (!joinArgs.isEmpty()) {
-                    TupleExpr tupleExpr = selectNextTupleExpr(joinArgs, cardinalityMap
-                    );
-                    if (tupleExpr == null) {
-                        break;
-                    }
-
-                    joinArgs.remove(tupleExpr);
-                    orderedJoinArgs.add(tupleExpr);
-
-                    // Recursively optimize join arguments
-                    tupleExpr.visit(this);
-
-                    boundVars.addAll(tupleExpr.getBindingNames());
-                }
-
-                // Build new join hierarchy
-                // Note: generated hierarchy is right-recursive to help the
-                // IterativeEvaluationOptimizer to factor out the left-most join
-                // argument
-                int i = 0;
-                TupleExpr replacement = orderedJoinArgs.get(i);
-                for (i++; i < orderedJoinArgs.size(); i++) {
-                    replacement = new Join(replacement, orderedJoinArgs.get(i));
-                }
-
-                // Replace old join hierarchy
-                node.replaceWith(replacement);
-            } finally {
-                boundVars = origBoundVars;
-            }
-        }
-
-        protected <L extends List<TupleExpr>> L getJoinArgs(TupleExpr tupleExpr, L joinArgs) {
-            if (tupleExpr instanceof Join) {
-                Join join = (Join) tupleExpr;
-                getJoinArgs(join.getLeftArg(), joinArgs);
-                getJoinArgs(join.getRightArg(), joinArgs);
-            } else {
-                joinArgs.add(tupleExpr);
-            }
-
-            return joinArgs;
-        }
-
-        protected List<Var> getStatementPatternVars(TupleExpr tupleExpr) {
-            List<StatementPattern> stPatterns = StatementPatternCollector.process(tupleExpr);
-            List<Var> varList = new ArrayList<Var>(stPatterns.size() * 4);
-            for (StatementPattern sp : stPatterns) {
-                sp.getVars(varList);
-            }
-            return varList;
-        }
-
-        protected <M extends Map<Var, Integer>> M getVarFreqMap(List<Var> varList, M varFreqMap) {
-            for (Var var : varList) {
-                Integer freq = varFreqMap.get(var);
-                freq = (freq == null) ? 1 : freq + 1;
-                varFreqMap.put(var, freq);
-            }
-            return varFreqMap;
-        }
-
-        /**
-         * Selects from a list of tuple expressions the next tuple expression that
-         * should be evaluated. This method selects the tuple expression with
-         * highest number of bound variables, preferring variables that have been
-         * bound in other tuple expressions over variables with a fixed value.
-         */
-        protected TupleExpr selectNextTupleExpr(List<TupleExpr> expressions,
-                                                Map<TupleExpr, Double> cardinalityMap
-//                                                ,Map<TupleExpr, List<Var>> varsMap,
-//                                                Map<Var, Integer> varFreqMap, Set<String> boundVars
-        ) {
-            double lowestCardinality = Double.MAX_VALUE;
-            TupleExpr result = expressions.get(0);
-
-            for (TupleExpr tupleExpr : expressions) {
-                // Calculate a score for this tuple expression
-//                double cardinality = getTupleExprCardinality(tupleExpr, cardinalityMap, varsMap, varFreqMap, boundVars);
-                double cardinality = cardinalityMap.get(tupleExpr);
-//                List<Var> vars = varsMap.get(tupleExpr);
-//                List<Var> distinctUnboundVars = getUnboundVars(vars);
-//                if (distinctUnboundVars.size() >= 2) {
-//                    cardinality *= (distinctUnboundVars.size() + 1);
-//                }
-
-                if (cardinality < lowestCardinality) {
-                    // More specific path expression found
-                    lowestCardinality = cardinality;
-                    result = tupleExpr;
-                }
-            }
-
-            return result;
-        }
-
-        protected double getTupleExprCardinality(TupleExpr tupleExpr, Map<TupleExpr, Double> cardinalityMap,
-                                                 Map<TupleExpr, List<Var>> varsMap, Map<Var, Integer> varFreqMap, Set<String> boundVars) {
-            double cardinality = cardinalityMap.get(tupleExpr);
-
-            List<Var> vars = varsMap.get(tupleExpr);
-
-            // Compensate for variables that are bound earlier in the evaluation
-            List<Var> unboundVars = getUnboundVars(vars);
-            List<Var> constantVars = getConstantVars(vars);
-            int nonConstantVarCount = vars.size() - constantVars.size();
-            if (nonConstantVarCount > 0) {
-                double exp = (double) unboundVars.size() / nonConstantVarCount;
-                cardinality = Math.pow(cardinality, exp);
-            }
-
-            if (unboundVars.isEmpty()) {
-                // Prefer patterns with more bound vars
-                if (nonConstantVarCount > 0) {
-                    cardinality /= nonConstantVarCount;
-                }
-            } else {
-                // Prefer patterns that bind variables from other tuple expressions
-                int foreignVarFreq = getForeignVarFreq(unboundVars, varFreqMap);
-                if (foreignVarFreq > 0) {
-                    cardinality /= foreignVarFreq;
-                }
-            }
-
-            // Prefer patterns that bind more variables
-            List<Var> distinctUnboundVars = getUnboundVars(new
-                    HashSet<Var>(vars));
-            if (distinctUnboundVars.size() >= 2) {
-                cardinality /= distinctUnboundVars.size();
-            }
-
-            return cardinality;
-        }
-
-        protected List<Var> getConstantVars(Iterable<Var> vars) {
-            List<Var> constantVars = new ArrayList<Var>();
-
-            for (Var var : vars) {
-                if (var.hasValue()) {
-                    constantVars.add(var);
-                }
-            }
-
-            return constantVars;
-        }
-
-        protected List<Var> getUnboundVars(Iterable<Var> vars) {
-            List<Var> unboundVars = new ArrayList<Var>();
-
-            for (Var var : vars) {
-                if (!var.hasValue() && !this.boundVars.contains(var.getName())) {
-                    unboundVars.add(var);
-                }
-            }
-
-            return unboundVars;
-        }
-
-        protected int getForeignVarFreq(List<Var> ownUnboundVars, Map<Var, Integer> varFreqMap) {
-            int result = 0;
-
-            Map<Var, Integer> ownFreqMap = getVarFreqMap(ownUnboundVars, new HashMap<Var, Integer>());
-
-            for (Map.Entry<Var, Integer> entry : ownFreqMap.entrySet()) {
-                Var var = entry.getKey();
-                int ownFreq = entry.getValue();
-                result += varFreqMap.get(var) - ownFreq;
-            }
-
-            return result;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinSelectOptimizer.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinSelectOptimizer.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinSelectOptimizer.java
deleted file mode 100644
index 643446a..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/QueryJoinSelectOptimizer.java
+++ /dev/null
@@ -1,260 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.persist.joinselect.SelectivityEvalDAO;
-import mvm.rya.rdftriplestore.inference.DoNotExpandSP;
-import mvm.rya.rdftriplestore.utils.FixedStatementPattern;
-
-import org.openrdf.query.BindingSet;
-import org.openrdf.query.Dataset;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.evaluation.QueryOptimizer;
-import org.openrdf.query.algebra.evaluation.impl.EvaluationStatistics;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-public class QueryJoinSelectOptimizer implements QueryOptimizer {
-
-  private final EvaluationStatistics statistics;
-  private final SelectivityEvalDAO eval;
-  private final RdfCloudTripleStoreConfiguration config;
-
-  public QueryJoinSelectOptimizer(EvaluationStatistics statistics, SelectivityEvalDAO eval) {
-    System.out.println("Entering join optimizer!");
-    this.statistics = statistics;
-    this.eval = eval;
-    this.config = eval.getConf();
-  }
-
-  /**
-   * Applies generally applicable optimizations: path expressions are sorted from more to less specific.
-   *
-   * @param tupleExpr
-   */
-  public void optimize(TupleExpr tupleExpr, Dataset dataset, BindingSet bindings) {
-    tupleExpr.visit(new JoinVisitor());
-  }
-
-  protected class JoinVisitor extends QueryModelVisitorBase<RuntimeException> {
-
-    @Override
-    public void meet(Join node) {
-
-      try {
-        if (node.getLeftArg() instanceof FixedStatementPattern && node.getRightArg() instanceof DoNotExpandSP) {
-          return;
-        }
-
-        TupleExpr partialQuery = null;
-        List<TupleExpr> joinArgs = getJoinArgs(node, new ArrayList<TupleExpr>());
-        Map<TupleExpr,Double> cardinalityMap = new HashMap<TupleExpr,Double>();
-
-        for (TupleExpr tupleExpr : joinArgs) {
-          double cardinality = statistics.getCardinality(tupleExpr);
-          cardinalityMap.put(tupleExpr, cardinality);
-
-        }
-
-        while (!joinArgs.isEmpty()) {
-          TePairCost tpc = getBestTupleJoin(partialQuery, joinArgs);
-          List<TupleExpr> tePair = tpc.getTePair();
-          if (partialQuery == null) {
-            if (tePair.size() != 2) {
-              throw new IllegalStateException();
-            }
-            if (!(tePair.get(0) instanceof Join)) {
-              tePair.get(0).visit(this);
-            }
-            if (!(tePair.get(1) instanceof Join)) {
-              tePair.get(1).visit(this);
-            }
-            if (tePair.get(1) instanceof Join) {
-              partialQuery = new Join(tePair.get(0), ((Join) tePair.get(1)).getLeftArg());
-              partialQuery = new Join(partialQuery, ((Join) tePair.get(1)).getRightArg());
-              joinArgs.remove(tePair.get(0));
-              joinArgs.remove(tePair.get(1));
-            } else {
-              partialQuery = new Join(tePair.get(0), tePair.get(1));
-              joinArgs.remove(tePair.get(0));
-              joinArgs.remove(tePair.get(1));
-            }
-          } else {
-            if (tePair.size() != 1) {
-              throw new IllegalStateException();
-            }
-            if (!(tePair.get(0) instanceof Join)) {
-              tePair.get(0).visit(this);
-            }
-
-            if (tePair.get(0) instanceof Join) {
-              partialQuery = new Join(partialQuery, ((Join) tePair.get(0)).getLeftArg());
-              partialQuery = new Join(partialQuery, ((Join) tePair.get(0)).getRightArg());
-              joinArgs.remove(tePair.get(0));
-
-            } else {
-              partialQuery = new Join(partialQuery, tePair.get(0));
-              joinArgs.remove(tePair.get(0));
-            }
-          }
-
-        }
-
-        // Replace old join hierarchy
-        node.replaceWith(partialQuery);
-
-      } catch (Exception e) {
-        e.printStackTrace();
-      }
-    }
-
-    protected <L extends List<TupleExpr>> L getJoinArgs(TupleExpr tupleExpr, L joinArgs) {
-      if (tupleExpr instanceof Join) {
-        if (!(((Join) tupleExpr).getLeftArg() instanceof FixedStatementPattern) && !(((Join) tupleExpr).getRightArg() instanceof DoNotExpandSP)) {
-          Join join = (Join) tupleExpr;
-          getJoinArgs(join.getLeftArg(), joinArgs);
-          getJoinArgs(join.getRightArg(), joinArgs);
-        } else {
-          joinArgs.add(tupleExpr);
-        }
-      } else {
-        joinArgs.add(tupleExpr);
-      }
-
-      return joinArgs;
-    }
-
-    public TePairCost getBestTupleJoin(TupleExpr partialQuery, List<TupleExpr> teList) throws Exception {
-
-      double tempCost = 0;
-      double bestCost = Double.MAX_VALUE;
-      List<TupleExpr> bestJoinNodes = new ArrayList<TupleExpr>();
-
-      if (partialQuery == null) {
-
-        double jSelect = 0;
-        double card1 = 0;
-        double card2 = 0;
-        TupleExpr teMin1 = null;
-        TupleExpr teMin2 = null;
-        double bestCard1 = 0;
-        double bestCard2 = 0;
-
-        for (int i = 0; i < teList.size(); i++) {
-          for (int j = i + 1; j < teList.size(); j++) {
-            jSelect = eval.getJoinSelect(config, teList.get(i), teList.get(j));
-            card1 = statistics.getCardinality(teList.get(i));
-            card2 = statistics.getCardinality(teList.get(j));
-            tempCost = card1 + card2 + card1 * card2 * jSelect;
-//             System.out.println("Optimizer: TempCost is " + tempCost + " cards are " + card1 + ", " + card2 + ", selectivity is "
-//             + jSelect + ", and nodes are "
-//             + teList.get(i) + " and " + teList.get(j));
-
-            // TODO this generates a nullpointer exception if tempCost = Double.Max
-            if (bestCost > tempCost) {
-
-              teMin1 = teList.get(i);
-              teMin2 = teList.get(j);
-              bestCard1 = card1;
-              bestCard2 = card2;
-              bestCost = tempCost;
-
-              if (bestCost == 0) {
-                bestJoinNodes.add(teMin1);
-                bestJoinNodes.add(teMin2);
-                return new TePairCost(0.0, bestJoinNodes);
-              }
-            }
-          }
-        }
-
-        if (bestCard1 < bestCard2) {
-
-          bestJoinNodes.add(teMin1);
-          bestJoinNodes.add(teMin2);
-
-        } else {
-          bestJoinNodes.add(teMin2);
-          bestJoinNodes.add(teMin1);
-        }
-        //System.out.println("Optimizer: Card1 is " + card1 + ", card2 is " + card2 + ", selectivity is " + jSelect + ", and best cost is" + bestCost);
-        return new TePairCost(bestCost, bestJoinNodes);
-
-      } else {
-        double card1 = statistics.getCardinality(partialQuery);
-        TupleExpr bestTe = null;
-        double card2 = 0;
-        double select = 0;
-
-        for (TupleExpr te : teList) {
-          select = eval.getJoinSelect(config, partialQuery, te);
-          card2 = statistics.getCardinality(te);
-          tempCost = card1 + card2 + card1 * card2 * select;
-//          System.out.println("Optimizer: TempCost is " + tempCost + " cards are " + card1 + ", " + card2 + ", selectivity is "
-//                  + select + ", and nodes are "
-//                  + partialQuery + " and " + te);
-
-
-          if (bestCost > tempCost) {
-            bestTe = te;
-            bestCost = tempCost;
-          }
-
-        }
-        List<TupleExpr> teList2 = new ArrayList<TupleExpr>();
-        teList2.add(bestTe);
-        //System.out.println("Optimizer: Card1 is " + card1 + ", card2 is " + card2 + ", selectivity is " + select + ", and best cost is" + bestCost);
-        return new TePairCost(bestCost, teList2);
-      }
-
-    }
-
-    // **************************************************************************************
-    public class TePairCost {
-
-      private double cost;
-      private List<TupleExpr> tePair;
-
-      public TePairCost(double cost, List<TupleExpr> tePair) {
-        this.cost = cost;
-        this.tePair = tePair;
-
-      }
-
-      public double getCost() {
-        return cost;
-      }
-
-      public List<TupleExpr> getTePair() {
-        return tePair;
-      }
-
-    }
-
-  }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreEvaluationStatistics.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreEvaluationStatistics.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreEvaluationStatistics.java
deleted file mode 100644
index b0fa46c..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreEvaluationStatistics.java
+++ /dev/null
@@ -1,281 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 static com.google.common.base.Preconditions.checkNotNull;
-//import static RdfCloudTripleStoreUtils.getTtlValueConverter;
-
-
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.persist.RdfEvalStatsDAO;
-import mvm.rya.api.persist.RdfEvalStatsDAO.CARDINALITY_OF;
-import mvm.rya.rdftriplestore.inference.DoNotExpandSP;
-import mvm.rya.rdftriplestore.utils.FixedStatementPattern;
-
-import org.openrdf.model.Resource;
-import org.openrdf.model.Statement;
-import org.openrdf.model.URI;
-import org.openrdf.model.Value;
-import org.openrdf.model.vocabulary.RDF;
-import org.openrdf.query.algebra.BinaryTupleOperator;
-import org.openrdf.query.algebra.Filter;
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.Projection;
-import org.openrdf.query.algebra.Slice;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.UnaryTupleOperator;
-import org.openrdf.query.algebra.Var;
-import org.openrdf.query.algebra.evaluation.impl.EvaluationStatistics;
-
-/**
- * Class RdfCloudTripleStoreEvaluationStatistics
- * Date: Apr 12, 2011
- * Time: 1:31:05 PM
- */
-public class RdfCloudTripleStoreEvaluationStatistics extends EvaluationStatistics {
-
-    private RdfCloudTripleStoreConfiguration conf;
-    private RdfEvalStatsDAO rdfEvalStatsDAO;
-    protected boolean pushEmptyRdfTypeDown = true;
-    protected boolean useCompositeCardinalities = true;
-
-    public RdfCloudTripleStoreEvaluationStatistics(RdfCloudTripleStoreConfiguration conf, RdfEvalStatsDAO rdfEvalStatsDAO) {
-        checkNotNull(conf);
-        checkNotNull(rdfEvalStatsDAO);
-        try {
-            this.conf = conf;
-            this.rdfEvalStatsDAO = rdfEvalStatsDAO;
-            pushEmptyRdfTypeDown = conf.isStatsPushEmptyRdftypeDown();
-            useCompositeCardinalities = conf.isUseCompositeCardinality();
-        } catch (Exception e) {
-            throw new RuntimeException(e);
-        }
-    }
-
-    @Override
-    public double getCardinality(TupleExpr expr) {
-        if (expr instanceof Filter) {
-            Filter f = (Filter) expr;
-            // filters must make sets smaller
-            return super.getCardinality(f.getArg()) / 10;
-        }
-        return super.getCardinality(expr);
-    }
-
-    @Override
-    protected CardinalityCalculator createCardinalityCalculator() {
-        return new RdfCloudTripleStoreCardinalityCalculator(this);
-    }
-
-    public RdfEvalStatsDAO getRdfEvalStatsDAO() {
-        return rdfEvalStatsDAO;
-    }
-
-    public void setRdfEvalStatsDAO(RdfEvalStatsDAO rdfEvalStatsDAO) {
-        this.rdfEvalStatsDAO = rdfEvalStatsDAO;
-    }
-
-    public class RdfCloudTripleStoreCardinalityCalculator extends CardinalityCalculator {
-        private RdfCloudTripleStoreEvaluationStatistics statistics;
-        protected Map<Var, Collection<Statement>> fspMap;
-
-        public RdfCloudTripleStoreCardinalityCalculator(RdfCloudTripleStoreEvaluationStatistics statistics) {
-            this.statistics = statistics;
-        }
-        
- 
-        @Override
-        protected double getCardinality(StatementPattern sp) {
-            Var subjectVar = sp.getSubjectVar();
-            Resource subj = (Resource) getConstantValue(subjectVar);
-            Var predicateVar = sp.getPredicateVar();
-            URI pred = (URI) getConstantValue(predicateVar);
-            Var objectVar = sp.getObjectVar();
-            Value obj = getConstantValue(objectVar);
-            Resource context = (Resource) getConstantValue(sp.getContextVar());
-
-            // set rdf type to be a max value (as long as the object/subject aren't specified) to 
-                if (pred != null) {
-                    if (statistics.pushEmptyRdfTypeDown && RDF.TYPE.equals(pred) && subj == null && obj == null) {
-                        return Double.MAX_VALUE;
-                    }
-                }
-
-            // FixedStatementPattern indicates that this is when backward chaining reasoning is being used
-            if (sp instanceof FixedStatementPattern) {
-                //no query here
-                FixedStatementPattern fsp = (FixedStatementPattern) sp;
-                //TODO: assume that only the subject is open ended here
-                Var fspSubjectVar = fsp.getSubjectVar();
-                if (fspSubjectVar != null && fspSubjectVar.getValue() == null) {
-                    if (fspMap == null) {
-                        fspMap = new HashMap<Var, Collection<Statement>>();
-                    }
-                    fspMap.put(fspSubjectVar, fsp.statements);
-                }
-                return fsp.statements.size();
-            }
-
-            /**
-             * Use the output of the FixedStatementPattern to determine more information
-             */
-            if (fspMap != null && sp instanceof DoNotExpandSP) {
-                //TODO: Might be a better way than 3 map pulls
-                RdfEvalStatsDAO.CARDINALITY_OF cardinality_of = null;
-                Collection<Statement> statements = null;
-                // TODO unsure of how to incorporate additional cardinalities here
-                if (objectVar != null && objectVar.getValue() == null) {
-                    statements = fspMap.get(objectVar);
-                    cardinality_of = RdfEvalStatsDAO.CARDINALITY_OF.OBJECT;
-                }
-                if (statements == null && predicateVar != null && predicateVar.getValue() == null) {
-                    statements = fspMap.get(predicateVar);
-                    cardinality_of = RdfEvalStatsDAO.CARDINALITY_OF.PREDICATE;
-                }
-                if (statements == null && subjectVar != null && subjectVar.getValue() == null) {
-                    statements = fspMap.get(subjectVar);
-                    cardinality_of = RdfEvalStatsDAO.CARDINALITY_OF.SUBJECT;
-                }
-                if (statements != null) {
-                    double fspCard = 0;
-                    for (Statement statement : statements) {
-                    	List<Value> values = new ArrayList<Value>();
-                    	values.add(statement.getSubject());
-                    	fspCard  += rdfEvalStatsDAO.getCardinality(conf, cardinality_of, values, context);
-                    }
-                    return fspCard;
-                }
-            }
-
-            /**
-             * We put full triple scans before rdf:type because more often than not
-             * the triple scan is being joined with something else that is better than
-             * asking the full rdf:type of everything.
-             */
-            double cardinality = Double.MAX_VALUE - 1;
-            try {
-                if (subj != null) {
-                	List<Value> values = new ArrayList<Value>();
-                	CARDINALITY_OF card = RdfEvalStatsDAO.CARDINALITY_OF.SUBJECT;
-            		values.add(subj);
-            		if (useCompositeCardinalities){
-                   	    if (pred != null){
-                    		values.add(pred);
-                    		card = RdfEvalStatsDAO.CARDINALITY_OF.SUBJECTPREDICATE;
-                    	}
-                   	    else if (obj != null){
-                    		values.add(obj);
-                    		card = RdfEvalStatsDAO.CARDINALITY_OF.SUBJECTOBJECT;
-                   	    }
-            		}
-                	double evalCard = evalCard = rdfEvalStatsDAO.getCardinality(conf, card, values, context);
-                	// the cardinality will be -1 if there was no value found (if the index does not exist)
-                    if (evalCard >= 0) {
-                        cardinality = Math.min(cardinality, evalCard);
-                    } else {
-                        cardinality = 1;
-                    }
-                }
-                else if (pred != null) {
-                	List<Value> values = new ArrayList<Value>();
-                	CARDINALITY_OF card = RdfEvalStatsDAO.CARDINALITY_OF.PREDICATE;
-            		values.add(pred);
-            		if (useCompositeCardinalities){
-                   	    if (obj != null){
-                    		values.add(obj);
-                    		card = RdfEvalStatsDAO.CARDINALITY_OF.PREDICATEOBJECT;
-                   	    }
-            		}
-                	double evalCard = evalCard = rdfEvalStatsDAO.getCardinality(conf, card, values, context);
-                    if (evalCard >= 0) {
-                        cardinality = Math.min(cardinality, evalCard);
-                    } else {
-                        cardinality = 1;
-                    }
-                }
-                else if (obj != null) {
-                	List<Value> values = new ArrayList<Value>();
-            		values.add(obj);
-                    double evalCard = rdfEvalStatsDAO.getCardinality(conf, RdfEvalStatsDAO.CARDINALITY_OF.OBJECT, values, context);
-                    if (evalCard >= 0) {
-                        cardinality = Math.min(cardinality, evalCard);
-                    } else {
-                        cardinality = 1;
-                    }
-                }
-            } catch (Exception e) {
-                throw new RuntimeException(e);
-            }
-
-            return cardinality;
-        }
-
-        @Override
-        protected void meetUnaryTupleOperator(UnaryTupleOperator node) {
-            if (node instanceof Projection) {
-                cardinality += -1.0;
-            }
-            super.meetUnaryTupleOperator(node);
-        }
-
-        @Override
-        protected void meetBinaryTupleOperator(BinaryTupleOperator node) {
-            node.getLeftArg().visit(this);
-            double leftArgCost = cardinality;
-            node.getRightArg().visit(this);
-            cardinality += leftArgCost;
-        }
-        
-        // TODO Is this sufficient for add capability of slice node?
-        @Override
-        public void meet(Slice node) {
-            cardinality = node.getLimit();
-        }
-        
-
-        @Override
-        public void meet(Join node) {
-            node.getLeftArg().visit(this);
-            double leftArgCost = cardinality;
-            node.getRightArg().visit(this);
-            if (leftArgCost > cardinality) {
-                cardinality = leftArgCost;    //TODO: Is this ok?
-            }
-        }
-
-        protected Value getConstantValue(Var var) {
-            if (var != null)
-                return var.getValue();
-            else
-                return null;
-        }
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreSelectivityEvaluationStatistics.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreSelectivityEvaluationStatistics.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreSelectivityEvaluationStatistics.java
deleted file mode 100644
index 7c88640..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/RdfCloudTripleStoreSelectivityEvaluationStatistics.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 static com.google.common.base.Preconditions.checkNotNull;
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.persist.RdfEvalStatsDAO;
-import mvm.rya.api.persist.joinselect.SelectivityEvalDAO;
-import mvm.rya.rdftriplestore.inference.DoNotExpandSP;
-import mvm.rya.rdftriplestore.utils.FixedStatementPattern;
-
-import org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.StatementPattern;
-
-public class RdfCloudTripleStoreSelectivityEvaluationStatistics extends RdfCloudTripleStoreEvaluationStatistics {
-
-  // allows access to join selectivity and extending RdfCloudTripleStoreEvaluationStatistics allows for use of prospector
-  private SelectivityEvalDAO selectEvalStatsDAO; // TODO redundancy here as RdfCloudTripleStoreEvalStats object contains
-                                                 // RdfEvalStatsDAO object
-
-  protected double filterCard;
-  RdfCloudTripleStoreConfiguration config; // TODO redundancy here as RdfCloudTripleStoreEvalStats object contains conf as well
-
-  public RdfCloudTripleStoreSelectivityEvaluationStatistics(RdfCloudTripleStoreConfiguration conf,
-      RdfEvalStatsDAO<RdfCloudTripleStoreConfiguration> prospector, SelectivityEvalDAO selectEvalStatsDAO) {
-
-    super(conf, prospector);
-    checkNotNull(selectEvalStatsDAO);
-
-    try {
-      this.selectEvalStatsDAO = selectEvalStatsDAO;
-      this.config = conf; // TODO fix this!
-    } catch (Exception e) {
-      throw new RuntimeException(e);
-    }
-  }
-
-  @Override
-  protected CardinalityCalculator createCardinalityCalculator() {
-    try {
-      return new SelectivityCardinalityCalculator(this);
-    } catch (Exception e) {
-      System.out.println(e);
-      throw new RuntimeException(e);
-    }
-  }
-
-  public class SelectivityCardinalityCalculator extends RdfCloudTripleStoreCardinalityCalculator {
-
-    public SelectivityCardinalityCalculator(RdfCloudTripleStoreSelectivityEvaluationStatistics statistics) {
-      super(statistics);
-    }
-
-    @Override
-    public void meet(Join node) {
-      node.getLeftArg().visit(this);
-      double leftArgCost = cardinality;
-      // System.out.println("Left cardinality is " + cardinality);
-      node.getRightArg().visit(this);
-
-      if (node.getLeftArg() instanceof FixedStatementPattern && node.getRightArg() instanceof DoNotExpandSP) {
-        return;
-      }
-
-      try {
-        double selectivity = selectEvalStatsDAO.getJoinSelect(config, node.getLeftArg(), node.getRightArg());
-//        System.out.println("CardCalc: left cost of " + node.getLeftArg() + " is " + leftArgCost + " right cost of "
-//        + node.getRightArg() + " is " + cardinality);
-//         System.out.println("Right cardinality is " + cardinality);
-        cardinality += leftArgCost + leftArgCost * cardinality * selectivity;
-//        System.out.println("CardCalc: Cardinality is " + cardinality);
-//        System.out.println("CardCalc: Selectivity is " + selectivity);
-        // System.out.println("Join cardinality is " + cardinality);
-
-      } catch (Exception e) {
-        e.printStackTrace();
-      }
-
-    }
-    
-    
-    
-    
-        @Override
-        public double getCardinality(StatementPattern node) {
-
-            cardinality = super.getCardinality(node);
-
-            // If sp contains all variables or is EmptyRDFtype, assign
-            // cardinality
-            // equal to table size
-            if (cardinality == Double.MAX_VALUE || cardinality == Double.MAX_VALUE - 1) {
-                try {
-                    cardinality = selectEvalStatsDAO.getTableSize(config);
-                } catch (Exception e) {
-                    // TODO Auto-generated catch block
-                    e.printStackTrace();
-                }
-            }
-
-            return cardinality;
-        }
-    
-    
-    
-
-  }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ReorderJoinVisitor.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ReorderJoinVisitor.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ReorderJoinVisitor.java
deleted file mode 100644
index f825921..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/ReorderJoinVisitor.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 org.openrdf.query.algebra.Join;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-/**
- * Class ReorderJoinVisitor
- * Date: Apr 11, 2011
- * Time: 10:16:15 PM
- */
-public class ReorderJoinVisitor extends QueryModelVisitorBase {
-    @Override
-    public void meet(Join node) throws Exception {
-        super.meet(node);
-        
-        TupleExpr leftArg = node.getLeftArg();
-        TupleExpr rightArg = node.getRightArg();
-
-        /**
-         * if join(stmtPattern1, join(stmtPattern2, anything)
-         * Should be
-         * join(join(stmtPattern1, stmtPattern2), anything)
-         */
-        if (leftArg instanceof StatementPattern && rightArg instanceof Join) {
-            Join rightJoin = (Join) rightArg;
-            //find the stmtPattern in the right side
-            TupleExpr right_LeftArg = rightJoin.getLeftArg();
-            TupleExpr right_rightArg = rightJoin.getRightArg();
-            if (right_LeftArg instanceof StatementPattern || right_rightArg instanceof StatementPattern) {
-                StatementPattern stmtPattern = null;
-                TupleExpr anything = null;
-                if (right_LeftArg instanceof StatementPattern) {
-                    stmtPattern = (StatementPattern) right_LeftArg;
-                    anything = right_rightArg;
-                } else {
-                    stmtPattern = (StatementPattern) right_rightArg;
-                    anything = right_LeftArg;
-                }
-
-                Join inner = new Join(leftArg, stmtPattern);
-                Join outer = new Join(inner, anything);
-                node.replaceWith(outer);
-            }
-        }
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/5a03ef61/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/SeparateFilterJoinsVisitor.java
----------------------------------------------------------------------
diff --git a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/SeparateFilterJoinsVisitor.java b/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/SeparateFilterJoinsVisitor.java
deleted file mode 100644
index 002b804..0000000
--- a/sail/src/main/java/mvm/rya/rdftriplestore/evaluation/SeparateFilterJoinsVisitor.java
+++ /dev/null
@@ -1,55 +0,0 @@
-package mvm.rya.rdftriplestore.evaluation;
-
-/*
- * 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 org.openrdf.query.algebra.*;
-import org.openrdf.query.algebra.helpers.QueryModelVisitorBase;
-
-/**
- * TODO: This might be a very bad thing. It may force all AND and not allow ORs?. Depends on how they do the bindings.
- * Class SeparateFilterJoinsVisitor
- * Date: Apr 11, 2011
- * Time: 10:16:15 PM
- */
-public class SeparateFilterJoinsVisitor extends QueryModelVisitorBase {
-    @Override
-    public void meet(Filter node) throws Exception {
-        super.meet(node);
-
-        ValueExpr condition = node.getCondition();
-        TupleExpr arg = node.getArg();
-        if (!(arg instanceof Join)) {
-            return;
-        }
-
-        Join join = (Join) arg;
-        TupleExpr leftArg = join.getLeftArg();
-        TupleExpr rightArg = join.getRightArg();
-
-        if (leftArg instanceof StatementPattern && rightArg instanceof StatementPattern) {
-            Filter left = new Filter(leftArg, condition);
-            Filter right = new Filter(rightArg, condition);
-            node.replaceWith(new Join(left, right));
-        }
-
-    }
-}



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