http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/instance/RyaDetailsUpdater.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/instance/RyaDetailsUpdater.java 
b/common/rya.api/src/main/java/mvm/rya/api/instance/RyaDetailsUpdater.java
deleted file mode 100644
index 9d5dae7..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/instance/RyaDetailsUpdater.java
+++ /dev/null
@@ -1,124 +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.api.instance;
-
-import static java.util.Objects.requireNonNull;
-
-import javax.annotation.ParametersAreNonnullByDefault;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import mvm.rya.api.instance.RyaDetailsRepository.ConcurrentUpdateException;
-import mvm.rya.api.instance.RyaDetailsRepository.RyaDetailsRepositoryException;
-import 
mvm.rya.api.instance.RyaDetailsUpdater.RyaDetailsMutator.CouldNotApplyMutationException;
-
-/**
- * A utility that will attempt to commit a change to a Rya instance's details
- * until it either takes or the mutation can no longer be applied. This can
- * can be used in place of boilerplate code that handles the concurrent nature
- * of details updates.
- */
-@ParametersAreNonnullByDefault
-public class RyaDetailsUpdater {
-    private static final Logger log = 
LoggerFactory.getLogger(RyaDetailsUpdater.class);
-
-    /**
-     * Applies a mutation to a an instance of {@link RyaDetails}.
-     */
-    @ParametersAreNonnullByDefault
-    public static interface RyaDetailsMutator {
-
-        /**
-         * Applies a mutation to a {@link RyaDetails} object.
-         *
-         * @param originalDetails - The {@link RyaDetails} that were just 
fetched
-         *   from the {@link RyaDetailsRepository}.
-         * @return The updated details.
-         * @throws CouldNotApplyMutationException The mutation could not be 
applied
-         *   to the supplied {@link RyaDetails}. This can be used to break out 
of
-         *   the update loop when the details are in a state the mutation can 
not
-         *   be applied to.
-         */
-        public RyaDetails mutate(RyaDetails originalDetails) throws 
CouldNotApplyMutationException;
-
-        /**
-         * Indicates a mutation could not be applied to an instance of {@link 
RyaDetails}.
-         */
-        public static class CouldNotApplyMutationException extends Exception {
-            private static final long serialVersionUID = 1L;
-
-            /**
-             * Constructs a new exception with the specified detail message.  
The
-             * cause is not initialized, and may subsequently be initialized by
-             * a call to {@link #initCause(Throwable)}.
-             *
-             * @param   message   the detail message. The detail message is 
saved for
-             *          later retrieval by the {@link #getMessage()} method.
-             */
-            public CouldNotApplyMutationException(final String message) {
-                super(message);
-            }
-        }
-    }
-
-    private final RyaDetailsRepository repo;
-
-    /**
-     * Constructs an instance of {@link RyaDetailsUpdater}.
-     *
-     * @param repo - The repository that this updater will commit changes to. 
(not null)
-     */
-    public RyaDetailsUpdater(final RyaDetailsRepository repo) {
-        this.repo = requireNonNull(repo);
-    }
-
-    /**
-     * Updates an instance of {@link RyaDetails} by fetching the details from
-     * the {@link RyaDetailsRepository} that was supplied at construction time,
-     * applying the {@link RyaDetailsMutator} to them, and them committing the
-     * change. If the update failed because of a concurrent update problem, 
then
-     * it will try again. The updater will continue to do this until the 
changes
-     * take or another exception type is thrown.
-     *
-     * @param mutator - The mutator that will be used to apply a chagne to the
-     *   repository's {@link RyaDetails}.
-     * @throws RyaDetailsRepositoryException A repository side error caused
-     *   the update to fail. This could be a communications problem with the
-     *   store repository, uninitialized, etc.
-     * @throws CouldNotApplyMutationException An application side error caused
-     *   the update to fail. This is thrown by the mutator when the details
-     *   would be in an illegal state if the mutation were to be applied.
-     */
-    public void update(final RyaDetailsMutator mutator) throws 
RyaDetailsRepositoryException, CouldNotApplyMutationException {
-        requireNonNull(mutator);
-
-        boolean updated = false;
-        while(!updated) {
-            try {
-                final RyaDetails original = repo.getRyaInstanceDetails();
-                final RyaDetails mutated = mutator.mutate(original);
-                repo.update(original, mutated);
-                updated = true;
-            } catch(final ConcurrentUpdateException e) {
-                log.debug("Failed to update the details because another 
application changed them. Trying again.", e);
-            }
-        }
-    }
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/layout/TableLayoutStrategy.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/layout/TableLayoutStrategy.java 
b/common/rya.api/src/main/java/mvm/rya/api/layout/TableLayoutStrategy.java
deleted file mode 100644
index 61732d3..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/layout/TableLayoutStrategy.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package mvm.rya.api.layout;
-
-/*
- * 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.
- */
-
-
-
-/**
- * Created by IntelliJ IDEA.
- * Date: 4/25/12
- * Time: 12:20 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface TableLayoutStrategy {
-    
-    public String getSpo();
-    public String getPo();
-    public String getOsp();
-    public String getNs();
-    public String getEval();
-    public String getProspects();
-    public String getSelectivity();
-    
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/layout/TablePrefixLayoutStrategy.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/layout/TablePrefixLayoutStrategy.java
 
b/common/rya.api/src/main/java/mvm/rya/api/layout/TablePrefixLayoutStrategy.java
deleted file mode 100644
index 0e995ab..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/layout/TablePrefixLayoutStrategy.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package mvm.rya.api.layout;
-
-/*
- * 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.RdfCloudTripleStoreConstants;
-
-/**
- * Created by IntelliJ IDEA.
- * Date: 4/25/12
- * Time: 12:20 PM
- * To change this template use File | Settings | File Templates.
- */
-public class TablePrefixLayoutStrategy implements TableLayoutStrategy{
-    private String tablePrefix = RdfCloudTripleStoreConstants.TBL_PRFX_DEF;
-
-    public TablePrefixLayoutStrategy() {
-    }
-
-    public TablePrefixLayoutStrategy(String tablePrefix) {
-        this.tablePrefix = tablePrefix;
-    }
-
-    @Override
-    public String getSpo() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_SPO_SUFFIX;
-    }
-
-    @Override
-    public String getPo() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_PO_SUFFIX;
-    }
-
-    @Override
-    public String getOsp() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_OSP_SUFFIX;
-    }
-
-    @Override
-    public String getNs() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_NS_SUFFIX;
-    }
-
-    @Override
-    public String getEval() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_EVAL_SUFFIX;
-    }
-
-    @Override
-    public String getProspects() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_STATS_SUFFIX;
-    }
-    
-    @Override
-    public String getSelectivity() {
-        return tablePrefix + RdfCloudTripleStoreConstants.TBL_SEL_SUFFIX;
-    }
-
-    
-    public String getTablePrefix() {
-        return tablePrefix;
-    }
-
-    public void setTablePrefix(String tablePrefix) {
-        this.tablePrefix = tablePrefix;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RdfDAOException.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/RdfDAOException.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RdfDAOException.java
deleted file mode 100644
index 54444d4..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RdfDAOException.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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.
- */
-
-
-
-/**
- * Class RdfDAOException
- * Date: Feb 28, 2012
- * Time: 3:39:36 PM
- */
-public class RdfDAOException extends RuntimeException {
-    public RdfDAOException() {
-    }
-
-    public RdfDAOException(String s) {
-        super(s);
-    }
-
-    public RdfDAOException(String s, Throwable throwable) {
-        super(s, throwable);
-    }
-
-    public RdfDAOException(Throwable throwable) {
-        super(throwable);
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RdfEvalStatsDAO.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/RdfEvalStatsDAO.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RdfEvalStatsDAO.java
deleted file mode 100644
index 020464b..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RdfEvalStatsDAO.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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.List;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-
-import org.openrdf.model.Resource;
-import org.openrdf.model.Value;
-
-/**
- * Class RdfEvalStatsDAO
- * Date: Feb 28, 2012
- * Time: 4:17:05 PM
- */
-public interface RdfEvalStatsDAO<C extends RdfCloudTripleStoreConfiguration> {
-    public enum CARDINALITY_OF {
-        SUBJECT, PREDICATE, OBJECT, SUBJECTPREDICATE, SUBJECTOBJECT, 
PREDICATEOBJECT
-    }
-
-    public void init() throws RdfDAOException;
-
-    public boolean isInitialized() throws RdfDAOException;
-
-    public void destroy() throws RdfDAOException;
-
-    public double getCardinality(C conf, CARDINALITY_OF card, List<Value> val) 
throws RdfDAOException;
-       public double getCardinality(C conf, CARDINALITY_OF card, List<Value> 
val, Resource context) throws RdfDAOException;
- 
-    public void setConf(C conf);
-
-    public C getConf();
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RyaConfigured.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaConfigured.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RyaConfigured.java
deleted file mode 100644
index 00c246e..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaConfigured.java
+++ /dev/null
@@ -1,35 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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;
-
-/**
- * Date: 7/17/12
- * Time: 8:24 AM
- */
-public interface RyaConfigured<C extends RdfCloudTripleStoreConfiguration> {
-
-    public void setConf(C conf);
-
-    public C getConf();
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAO.java
----------------------------------------------------------------------
diff --git a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAO.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAO.java
deleted file mode 100644
index e326f7d..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAO.java
+++ /dev/null
@@ -1,126 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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.Iterator;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.domain.RyaURI;
-import mvm.rya.api.persist.query.RyaQueryEngine;
-
-/**
- * Provides the access layer to the Rya triple store.
- *
- * Date: Feb 28, 2012
- * Time: 3:30:14 PM
- */
-public interface RyaDAO<C extends RdfCloudTripleStoreConfiguration> extends 
RyaConfigured<C> {
-
-    /**
-     * Initialize the RyaDAO. Should only be called once, otherwise, if 
already initialized, it will
-     * throw an exception.
-     *
-     * @throws RyaDAOException
-     */
-    public void init() throws RyaDAOException;
-
-    /**
-     *
-     * @return true if the store is already initiailized
-     * @throws RyaDAOException
-     */
-    public boolean isInitialized() throws RyaDAOException;
-
-    /**
-     * Shutdown the store. To reinitialize, call the init() method.
-     *
-     * @throws RyaDAOException
-     */
-    public void destroy() throws RyaDAOException;
-
-    /**
-     * Add and commit a single RyaStatement
-     *
-     * @param statement
-     * @throws RyaDAOException
-     */
-    public void add(RyaStatement statement) throws RyaDAOException;
-
-    /**
-     * Add and commit a collection of RyaStatements
-     *
-     * @param statement
-     * @throws RyaDAOException
-     */
-    public void add(Iterator<RyaStatement> statement) throws RyaDAOException;
-
-    /**
-     * Delete a RyaStatement. The Configuration should provide the auths to 
perform the delete
-     *
-     * @param statement
-     * @param conf
-     * @throws RyaDAOException
-     */
-    public void delete(RyaStatement statement, C conf) throws RyaDAOException;
-
-    /**
-     * Drop a set of Graphs. The Configuration should provide the auths to 
perform the delete
-     *
-     * @param conf
-     * @throws RyaDAOException
-     */
-    public void dropGraph(C conf, RyaURI... graphs) throws RyaDAOException; 
-
-    /**
-     * Delete a collection of RyaStatements.
-     *
-     * @param statements
-     * @param conf
-     * @throws RyaDAOException
-     */
-    public void delete(Iterator<RyaStatement> statements, C conf) throws 
RyaDAOException;
-
-    /**
-     * Get the version of the store.
-     *
-     * @return
-     * @throws RyaDAOException
-     */
-    public String getVersion() throws RyaDAOException;
-
-    /**
-     * Get the Rya query engine
-     * @return
-     */
-    public RyaQueryEngine<C> getQueryEngine();
-
-    /**
-     * Get the Rya Namespace Manager
-     * @return
-     */
-    public RyaNamespaceManager<C> getNamespaceManager();
-
-    public void purge(RdfCloudTripleStoreConfiguration configuration);
-
-    public void dropAndDestroy() throws RyaDAOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAOException.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAOException.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAOException.java
deleted file mode 100644
index 2322119..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaDAOException.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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.
- */
-
-
-
-/**
- * Date: 7/17/12
- * Time: 8:20 AM
- */
-public class RyaDAOException extends Exception {
-    public RyaDAOException() {
-    }
-
-    public RyaDAOException(String s) {
-        super(s);
-    }
-
-    public RyaDAOException(String s, Throwable throwable) {
-        super(s, throwable);
-    }
-
-    public RyaDAOException(Throwable throwable) {
-        super(throwable);
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/RyaNamespaceManager.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaNamespaceManager.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/RyaNamespaceManager.java
deleted file mode 100644
index 77cd4bd..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/RyaNamespaceManager.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package mvm.rya.api.persist;
-
-/*
- * 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 mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import org.openrdf.model.Namespace;
-
-/**
- * Date: 7/17/12
- * Time: 8:23 AM
- */
-public interface RyaNamespaceManager<C extends 
RdfCloudTripleStoreConfiguration> extends RyaConfigured<C> {
-
-    public void addNamespace(String pfx, String namespace) throws 
RyaDAOException;
-
-    public String getNamespace(String pfx) throws RyaDAOException;
-
-    public void removeNamespace(String pfx) throws RyaDAOException;
-
-    public CloseableIteration<? extends Namespace, RyaDAOException> 
iterateNamespace() throws RyaDAOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/index/RyaSecondaryIndexer.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/index/RyaSecondaryIndexer.java
 
b/common/rya.api/src/main/java/mvm/rya/api/persist/index/RyaSecondaryIndexer.java
deleted file mode 100644
index 4047670..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/persist/index/RyaSecondaryIndexer.java
+++ /dev/null
@@ -1,63 +0,0 @@
-package mvm.rya.api.persist.index;
-
-/*
- * 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.Closeable;
-import java.io.Flushable;
-import java.io.IOException;
-import java.util.Collection;
-import java.util.Set;
-
-import org.apache.hadoop.conf.Configurable;
-import org.openrdf.model.URI;
-
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.domain.RyaURI;
-
-public interface RyaSecondaryIndexer extends Closeable, Flushable, 
Configurable {
-
-    /**
-     * Returns the table name if the implementation supports it.
-     * Note that some indexers use multiple tables, this only returns one.
-     * TODO recommend that we deprecate this method because it's a leaky 
interface. 
-     * @return table name as a string.
-     */
-    public String getTableName(); 
-
-    public void storeStatements(Collection<RyaStatement> statements) throws 
IOException;
-
-    public void storeStatement(RyaStatement statement) throws IOException;
-
-    public void deleteStatement(RyaStatement stmt) throws IOException;
-
-    public void dropGraph(RyaURI... graphs);
-
-    /**
-     * @return the set of predicates indexed by the indexer.
-     */
-    public abstract Set<URI> getIndexablePredicates();
-
-    @Override
-    public abstract void flush() throws IOException;
-
-    @Override
-    public abstract void close() throws IOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/joinselect/SelectivityEvalDAO.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/joinselect/SelectivityEvalDAO.java
 
b/common/rya.api/src/main/java/mvm/rya/api/persist/joinselect/SelectivityEvalDAO.java
deleted file mode 100644
index 28f797b..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/persist/joinselect/SelectivityEvalDAO.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package mvm.rya.api.persist.joinselect;
-
-/*
- * 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.persist.RdfEvalStatsDAO;
-import org.openrdf.query.algebra.StatementPattern;
-import org.openrdf.query.algebra.TupleExpr;
-
-public interface SelectivityEvalDAO<C extends 
RdfCloudTripleStoreConfiguration> extends RdfEvalStatsDAO<C> {
-
-  public double getJoinSelect(C conf, TupleExpr te1, TupleExpr te2) throws 
Exception;
-
-  public long getCardinality(C conf, StatementPattern sp) throws Exception;
-  
-  public int getTableSize(C conf) throws Exception;
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/BatchRyaQuery.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/BatchRyaQuery.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/BatchRyaQuery.java
deleted file mode 100644
index 113ce51..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/BatchRyaQuery.java
+++ /dev/null
@@ -1,115 +0,0 @@
-package mvm.rya.api.persist.query;
-
-/*
- * 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 com.google.common.base.Preconditions;
-import com.google.common.collect.Iterables;
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.RyaStatement;
-
-/**
- * Query domain object contains the query to run as a {@link 
mvm.rya.api.domain.RyaStatement} and options for running the query
- */
-public class BatchRyaQuery extends RyaQueryOptions {
-
-    //queries
-    private Iterable<RyaStatement> queries;
-
-    //maximum number of ranges before we use a batchScanner
-    private int maxRanges = 2;
-
-    public BatchRyaQuery(Iterable<RyaStatement> queries) {
-        Preconditions.checkNotNull(queries, "RyaStatement queries cannot be 
null");
-        this.queries = queries;
-    }
-
-    public static RyaBatchQueryBuilder builder(Iterable<RyaStatement> queries) 
{
-        return new RyaBatchQueryBuilder(queries);
-    }
-
-    public static class RyaBatchQueryBuilder extends 
RyaOptionsBuilder<RyaBatchQueryBuilder> {
-        private BatchRyaQuery ryaQuery;
-
-        public RyaBatchQueryBuilder(Iterable<RyaStatement> queries) {
-            this(new BatchRyaQuery(queries));
-        }
-
-        public RyaBatchQueryBuilder(BatchRyaQuery query) {
-            super(query);
-            this.ryaQuery = query;
-        }
-
-        public RyaBatchQueryBuilder setMaxRanges(int maxRanges) {
-            ryaQuery.setMaxRanges(maxRanges);
-            return this;
-        }
-
-        public BatchRyaQuery build() {
-            return ryaQuery;
-        }
-    }
-
-    public Iterable<RyaStatement> getQueries() {
-        return queries;
-    }
-
-    public void setQueries(Iterable<RyaStatement> queries) {
-        this.queries = queries;
-    }
-
-    public int getMaxRanges() {
-        return maxRanges;
-    }
-
-    public void setMaxRanges(int maxRanges) {
-        this.maxRanges = maxRanges;
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
-        if (!super.equals(o)) return false;
-
-        BatchRyaQuery that = (BatchRyaQuery) o;
-
-        if (queries != null ? !queries.equals(that.queries) : that.queries != 
null) return false;
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = super.hashCode();
-        result = 31 * result + (queries != null ? queries.hashCode() : 0);
-        return result;
-    }
-
-    @Override
-    public String toString() {
-        return "BatchRyaQuery{" +
-                "queries=" + Iterables.toString(queries) +
-                "options={" + super.toString() +
-                '}' +
-                '}';
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQuery.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQuery.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQuery.java
deleted file mode 100644
index 5235989..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQuery.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package mvm.rya.api.persist.query;
-
-/*
- * 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 com.google.common.base.Preconditions;
-import mvm.rya.api.domain.RyaStatement;
-
-/**
- * Query domain object contains the query to run as a {@link RyaStatement} and 
options for running the query
- */
-public class RyaQuery extends RyaQueryOptions {
-
-    //query
-    private RyaStatement query;
-
-    public RyaQuery(RyaStatement query) {
-        Preconditions.checkNotNull(query, "RyaStatement query cannot be null");
-        this.query = query;
-    }
-
-    public static RyaQueryBuilder builder(RyaStatement query) {
-        return new RyaQueryBuilder(query);
-    }
-
-    public static class RyaQueryBuilder extends 
RyaOptionsBuilder<RyaQueryBuilder> {
-        private RyaQuery ryaQuery;
-
-        public RyaQueryBuilder(RyaStatement query) {
-            this(new RyaQuery(query));
-        }
-
-        public RyaQueryBuilder(RyaQuery query) {
-            super(query);
-            this.ryaQuery = query;
-        }
-
-        public RyaQuery build() {
-            return ryaQuery;
-        }
-    }
-
-    public RyaStatement getQuery() {
-        return query;
-    }
-
-    public void setQuery(RyaStatement query) {
-        this.query = query;
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
-        if (!super.equals(o)) return false;
-
-        RyaQuery ryaQuery = (RyaQuery) o;
-
-        if (query != null ? !query.equals(ryaQuery.query) : ryaQuery.query != 
null) return false;
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = super.hashCode();
-        result = 31 * result + (query != null ? query.hashCode() : 0);
-        return result;
-    }
-
-    @Override
-    public String toString() {
-        return "RyaQuery{" +
-                "query=" + query +
-                "options={" + super.toString() +
-                '}' +
-                '}';
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryEngine.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryEngine.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryEngine.java
deleted file mode 100644
index 7454eea..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryEngine.java
+++ /dev/null
@@ -1,96 +0,0 @@
-package mvm.rya.api.persist.query;
-
-/*
- * 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 java.util.Map;
-
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.persist.RyaConfigured;
-import mvm.rya.api.persist.RyaDAOException;
-
-import org.calrissian.mango.collect.CloseableIterable;
-import org.openrdf.query.BindingSet;
-
-/**
- * Rya Query Engine to perform queries against the Rya triple store.
- * <p/>
- * Date: 7/17/12
- * Time: 8:25 AM
- */
-public interface RyaQueryEngine<C extends RdfCloudTripleStoreConfiguration> 
extends RyaConfigured<C> {
-
-    /**
-     * Query the Rya store using the RyaStatement. The Configuration object 
provides information such as auths, ttl, etc
-     *
-     * @param stmt
-     * @param conf
-     * @return
-     * @throws RyaDAOException
-     * @deprecated
-     */
-    public CloseableIteration<RyaStatement, RyaDAOException> 
query(RyaStatement stmt, C conf) throws RyaDAOException;
-
-    /**
-     * Batch query
-     *
-     * @param stmts
-     * @param conf
-     * @return
-     * @throws RyaDAOException
-     */
-    public CloseableIteration<? extends Map.Entry<RyaStatement, BindingSet>, 
RyaDAOException>
-    queryWithBindingSet(Collection<Map.Entry<RyaStatement, BindingSet>> stmts, 
C conf) throws RyaDAOException;
-
-    /**
-     * Performs intersection joins.
-     *
-     * @param stmts
-     * @param conf
-     * @return
-     * @throws RyaDAOException
-     * @deprecated
-     */
-    public CloseableIteration<RyaStatement, RyaDAOException> 
batchQuery(Collection<RyaStatement> stmts, C conf) throws RyaDAOException;
-
-    /**
-     * Query with a {@link} RyaQuery. A single query that will return a {@link 
CloseableIterable} of RyaStatements
-     *
-     * @param ryaQuery
-     * @return
-     * @throws RyaDAOException
-     */
-    public CloseableIterable<RyaStatement> query(RyaQuery ryaQuery) throws 
RyaDAOException;
-
-    /**
-     * Run a batch rya query
-     *
-     * @param batchRyaQuery
-     * @return
-     * @throws RyaDAOException
-     */
-    public CloseableIterable<RyaStatement> query(BatchRyaQuery batchRyaQuery) 
throws RyaDAOException;
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryOptions.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryOptions.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryOptions.java
deleted file mode 100644
index c77796e..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/RyaQueryOptions.java
+++ /dev/null
@@ -1,246 +0,0 @@
-package mvm.rya.api.persist.query;
-
-/*
- * 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 org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.Arrays;
-
-/**
- */
-public class RyaQueryOptions {
-    private static final Logger logger = 
LoggerFactory.getLogger(RyaQueryOptions.class);
-    //options
-    protected String[] auths;
-    protected Long ttl;
-    protected Long currentTime;
-    protected Long maxResults;
-    protected Integer numQueryThreads = 4;
-    protected Integer batchSize = 1000;
-    protected String regexSubject;
-    protected String regexPredicate;
-    protected String regexObject;
-    protected RdfCloudTripleStoreConfiguration conf;
-
-    public static class RyaOptionsBuilder<T extends RyaOptionsBuilder> {
-        private RyaQueryOptions options;
-
-        public RyaOptionsBuilder(RyaQueryOptions query) {
-            this.options = query;
-        }
-
-        public T load(RdfCloudTripleStoreConfiguration conf) {
-               options.setConf(conf);
-            return (T) this.setAuths(conf.getAuths())
-                    .setBatchSize(conf.getBatchSize())
-                    .setCurrentTime(conf.getStartTime())
-                    .setMaxResults(conf.getLimit())
-                    .setNumQueryThreads(conf.getNumThreads())
-                    .setRegexObject(conf.getRegexObject())
-                    .setRegexPredicate(conf.getRegexPredicate())
-                    .setRegexSubject(conf.getRegexSubject())
-                    .setTtl(conf.getTtl());
-        }
-
-        public T setAuths(String[] auths) {
-            options.setAuths(auths);
-            return (T) this;
-        }
-
-        public T setRegexObject(String regexObject) {
-            options.setRegexObject(regexObject);
-            return (T) this;
-        }
-
-        public T setRegexPredicate(String regexPredicate) {
-            options.setRegexPredicate(regexPredicate);
-            return (T) this;
-        }
-
-        public T setRegexSubject(String regexSubject) {
-            options.setRegexSubject(regexSubject);
-            return (T) this;
-        }
-
-        public T setBatchSize(Integer batchSize) {
-            options.setBatchSize(batchSize);
-            return (T) this;
-        }
-
-        public T setNumQueryThreads(Integer numQueryThreads) {
-            options.setNumQueryThreads(numQueryThreads);
-            return (T) this;
-        }
-
-        public T setMaxResults(Long maxResults) {
-            options.setMaxResults(maxResults);
-            return (T) this;
-        }
-
-        public T setCurrentTime(Long currentTime) {
-            options.setCurrentTime(currentTime);
-            return (T) this;
-        }
-
-        public T setTtl(Long ttl) {
-            options.setTtl(ttl);
-            return (T) this;
-        }
-    }
-
-    public RdfCloudTripleStoreConfiguration getConf() {
-       return conf;
-    }
-
-    public void setConf(RdfCloudTripleStoreConfiguration conf) {
-       this.conf = conf;
-    }
-
-    public Long getTtl() {
-        return ttl;
-    }
-
-    public void setTtl(Long ttl) {
-        this.ttl = ttl;
-    }
-
-    public Long getCurrentTime() {
-        return currentTime;
-    }
-
-    public void setCurrentTime(Long currentTime) {
-        this.currentTime = currentTime;
-    }
-
-    public Integer getNumQueryThreads() {
-        return numQueryThreads;
-    }
-
-    public void setNumQueryThreads(Integer numQueryThreads) {
-        this.numQueryThreads = numQueryThreads;
-    }
-
-    public Long getMaxResults() {
-        return maxResults;
-    }
-
-    public void setMaxResults(Long maxResults) {
-        this.maxResults = maxResults;
-    }
-
-    public Integer getBatchSize() {
-        return batchSize;
-    }
-
-    public void setBatchSize(Integer batchSize) {
-        this.batchSize = batchSize;
-    }
-
-    public String getRegexSubject() {
-        return regexSubject;
-    }
-
-    public void setRegexSubject(String regexSubject) {
-        this.regexSubject = regexSubject;
-    }
-
-    public String getRegexPredicate() {
-        return regexPredicate;
-    }
-
-    public void setRegexPredicate(String regexPredicate) {
-        this.regexPredicate = regexPredicate;
-    }
-
-    public String getRegexObject() {
-        return regexObject;
-    }
-
-    public void setRegexObject(String regexObject) {
-        this.regexObject = regexObject;
-    }
-
-    public String[] getAuths() {
-        return auths;
-    }
-
-    public void setAuths(String[] auths) {
-        if (auths == null) {
-            this.auths = new String[0];
-        } else {
-            this.auths = auths.clone();
-        }
-    }
-
-    @Override
-    public String toString() {
-        return "RyaQueryOptions{" +
-                "auths=" + (auths == null ? null : Arrays.asList(auths)) +
-                ", ttl=" + ttl +
-                ", currentTime=" + currentTime +
-                ", maxResults=" + maxResults +
-                ", numQueryThreads=" + numQueryThreads +
-                ", batchSize=" + batchSize +
-                ", regexSubject='" + regexSubject + '\'' +
-                ", regexPredicate='" + regexPredicate + '\'' +
-                ", regexObject='" + regexObject + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
-
-        RyaQueryOptions that = (RyaQueryOptions) o;
-
-        if (!Arrays.equals(auths, that.auths)) return false;
-        if (batchSize != null ? !batchSize.equals(that.batchSize) : 
that.batchSize != null) return false;
-        if (currentTime != null ? !currentTime.equals(that.currentTime) : 
that.currentTime != null) return false;
-        if (maxResults != null ? !maxResults.equals(that.maxResults) : 
that.maxResults != null) return false;
-        if (numQueryThreads != null ? 
!numQueryThreads.equals(that.numQueryThreads) : that.numQueryThreads != null)
-            return false;
-        if (regexObject != null ? !regexObject.equals(that.regexObject) : 
that.regexObject != null) return false;
-        if (regexPredicate != null ? 
!regexPredicate.equals(that.regexPredicate) : that.regexPredicate != null)
-            return false;
-        if (regexSubject != null ? !regexSubject.equals(that.regexSubject) : 
that.regexSubject != null) return false;
-        if (ttl != null ? !ttl.equals(that.ttl) : that.ttl != null) return 
false;
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = auths != null ? Arrays.hashCode(auths) : 0;
-        result = 31 * result + (ttl != null ? ttl.hashCode() : 0);
-        result = 31 * result + (currentTime != null ? currentTime.hashCode() : 
0);
-        result = 31 * result + (maxResults != null ? maxResults.hashCode() : 
0);
-        result = 31 * result + (numQueryThreads != null ? 
numQueryThreads.hashCode() : 0);
-        result = 31 * result + (batchSize != null ? batchSize.hashCode() : 0);
-        result = 31 * result + (regexSubject != null ? regexSubject.hashCode() 
: 0);
-        result = 31 * result + (regexPredicate != null ? 
regexPredicate.hashCode() : 0);
-        result = 31 * result + (regexObject != null ? regexObject.hashCode() : 
0);
-        return result;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/HashJoin.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/HashJoin.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/HashJoin.java
deleted file mode 100644
index 286ea7a..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/HashJoin.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package mvm.rya.api.persist.query.join;
-
-/*
- * 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 mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.RdfCloudTripleStoreUtils;
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.domain.RyaType;
-import mvm.rya.api.domain.RyaURI;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.api.persist.query.RyaQueryEngine;
-import mvm.rya.api.resolver.RyaContext;
-import mvm.rya.api.utils.EnumerationWrapper;
-
-import java.util.Enumeration;
-import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
-
-/**
- * Use HashTable to do a HashJoin.
- * <p/>
- * TODO: Somehow make a more streaming way of doing this hash join. This will 
not support large sets.
- * Date: 7/26/12
- * Time: 8:58 AM
- */
-public class HashJoin<C extends RdfCloudTripleStoreConfiguration> implements 
Join<C> {
-
-    private RyaContext ryaContext = RyaContext.getInstance();
-    private RyaQueryEngine ryaQueryEngine;
-
-    public HashJoin() {
-    }
-
-    public HashJoin(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-
-    @Override
-    public CloseableIteration<RyaStatement, RyaDAOException> join(C conf, 
RyaURI... preds) throws RyaDAOException {
-        ConcurrentHashMap<Map.Entry<RyaURI, RyaType>, Integer> ht = new 
ConcurrentHashMap<Map.Entry<RyaURI, RyaType>, Integer>();
-        int count = 0;
-        boolean first = true;
-        for (RyaURI pred : preds) {
-            count++;
-            //query
-            CloseableIteration<RyaStatement, RyaDAOException> results = 
ryaQueryEngine.query(new RyaStatement(null, pred, null), null);
-            //add to hashtable
-            while (results.hasNext()) {
-                RyaStatement next = results.next();
-                RyaURI subject = next.getSubject();
-                RyaType object = next.getObject();
-                Map.Entry<RyaURI, RyaType> entry = new 
RdfCloudTripleStoreUtils.CustomEntry<RyaURI, RyaType>(subject, object);
-                if (!first) {
-                    if (!ht.containsKey(entry)) {
-                        continue; //not in join
-                    }
-                }
-                ht.put(entry, count);
-            }
-            //remove from hashtable values that are under count
-            if (first) {
-                first = false;
-            } else {
-                for (Map.Entry<Map.Entry<RyaURI, RyaType>, Integer> entry : 
ht.entrySet()) {
-                    if (entry.getValue() < count) {
-                        ht.remove(entry.getKey());
-                    }
-                }
-            }
-        }
-        final Enumeration<Map.Entry<RyaURI, RyaType>> keys = ht.keys();
-        return new CloseableIteration<RyaStatement, RyaDAOException>() {
-            @Override
-            public void close() throws RyaDAOException {
-
-            }
-
-            @Override
-            public boolean hasNext() throws RyaDAOException {
-                return keys.hasMoreElements();
-            }
-
-            @Override
-            public RyaStatement next() throws RyaDAOException {
-                Map.Entry<RyaURI, RyaType> subjObj = keys.nextElement();
-                return new RyaStatement(subjObj.getKey(), null, 
subjObj.getValue());
-            }
-
-            @Override
-            public void remove() throws RyaDAOException {
-                keys.nextElement();
-            }
-        };
-    }
-
-    @Override
-    public CloseableIteration<RyaURI, RyaDAOException> join(C conf, 
Map.Entry<RyaURI, RyaType>... predObjs) throws RyaDAOException {
-        ConcurrentHashMap<RyaURI, Integer> ht = new ConcurrentHashMap<RyaURI, 
Integer>();
-        int count = 0;
-        boolean first = true;
-        for (Map.Entry<RyaURI, RyaType> predObj : predObjs) {
-            count++;
-            RyaURI pred = predObj.getKey();
-            RyaType obj = predObj.getValue();
-            //query
-            CloseableIteration<RyaStatement, RyaDAOException> results = 
ryaQueryEngine.query(new RyaStatement(null, pred, obj), null);
-            //add to hashtable
-            while (results.hasNext()) {
-                RyaURI subject = results.next().getSubject();
-                if (!first) {
-                    if (!ht.containsKey(subject)) {
-                        continue; //not in join
-                    }
-                }
-                ht.put(subject, count);
-            }
-            //remove from hashtable values that are under count
-            if (first) {
-                first = false;
-            } else {
-                for (Map.Entry<RyaURI, Integer> entry : ht.entrySet()) {
-                    if (entry.getValue() < count) {
-                        ht.remove(entry.getKey());
-                    }
-                }
-            }
-        }
-        return new EnumerationWrapper<RyaURI, RyaDAOException>(ht.keys());
-    }
-
-    public RyaQueryEngine getRyaQueryEngine() {
-        return ryaQueryEngine;
-    }
-
-    public void setRyaQueryEngine(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/IterativeJoin.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/IterativeJoin.java
 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/IterativeJoin.java
deleted file mode 100644
index 3cb48a5..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/IterativeJoin.java
+++ /dev/null
@@ -1,233 +0,0 @@
-package mvm.rya.api.persist.query.join;
-
-/*
- * 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 com.google.common.base.Preconditions;
-import info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.ConvertingIteration;
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.RdfCloudTripleStoreUtils;
-import mvm.rya.api.domain.*;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.api.persist.query.RyaQueryEngine;
-import mvm.rya.api.resolver.RyaContext;
-import org.openrdf.query.BindingSet;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Map;
-
-/**
- * Date: 7/24/12
- * Time: 8:52 AM
- */
-public class IterativeJoin<C extends RdfCloudTripleStoreConfiguration> 
implements Join<C> {
-
-    private RyaContext ryaContext = RyaContext.getInstance();
-    private RyaQueryEngine ryaQueryEngine;
-
-    public IterativeJoin() {
-    }
-
-    public IterativeJoin(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-
-    /**
-     * Return all statements that have input predicates. Predicates must not 
be null or ranges
-     *
-     * @param preds
-     * @return
-     */
-    @Override
-    public CloseableIteration<RyaStatement, RyaDAOException> join(C conf, 
RyaURI... preds)
-            throws RyaDAOException {
-        Preconditions.checkNotNull(preds);
-        Preconditions.checkArgument(preds.length > 1, "Must join 2 or more");
-        //TODO: Reorder predObjs based on statistics
-
-        CloseableIteration<RyaStatement, RyaDAOException> iter = null;
-        for (RyaURI pred : preds) {
-            if (iter == null) {
-                iter = ryaQueryEngine.query(new RyaStatement(null, pred, 
null), null);
-            } else {
-                iter = join(iter, pred);
-            }
-        }
-
-        return iter;
-    }
-
-    /**
-     * Return all subjects that have the predicate objects associated. 
Predicate and objects must be not null or ranges
-     * to ensure sorting
-     *
-     * @param predObjs
-     * @return
-     * @throws mvm.rya.api.persist.RyaDAOException
-     *
-     */
-    @Override
-    public CloseableIteration<RyaURI, RyaDAOException> join(C conf, 
Map.Entry<RyaURI, RyaType>... predObjs)
-            throws RyaDAOException {
-        Preconditions.checkNotNull(predObjs);
-        Preconditions.checkArgument(predObjs.length > 1, "Must join 2 or 
more");
-
-        //TODO: Reorder predObjs based on statistics
-        CloseableIteration<RyaStatement, RyaDAOException> first = null;
-        CloseableIteration<RyaURI, RyaDAOException> iter = null;
-        for (Map.Entry<RyaURI, RyaType> entry : predObjs) {
-            if (first == null) {
-                first = ryaQueryEngine.query(new RyaStatement(null, 
entry.getKey(), entry.getValue()), null);
-            } else if (iter == null) {
-                iter = join(new ConvertingIteration<RyaStatement, RyaURI, 
RyaDAOException>(first) {
-
-                    @Override
-                    protected RyaURI convert(RyaStatement statement) throws 
RyaDAOException {
-                        return statement.getSubject();
-                    }
-                }, entry);
-            } else {
-                iter = join(iter, entry);
-            }
-        }
-
-        return iter;
-    }
-
-    protected CloseableIteration<RyaURI, RyaDAOException> join(final 
CloseableIteration<RyaURI, RyaDAOException> iteration,
-                                                               final 
Map.Entry<RyaURI, RyaType> predObj) {
-        //TODO: configure batch
-        //TODO: batch = 1, does not work
-        final int batch = 100;
-        return new CloseableIteration<RyaURI, RyaDAOException>() {
-
-            private CloseableIteration<Map.Entry<RyaStatement, BindingSet>, 
RyaDAOException> query;
-
-            @Override
-            public void close() throws RyaDAOException {
-                iteration.close();
-                if (query != null) {
-                    query.close();
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws RyaDAOException {
-                return !(query == null || !query.hasNext()) || batchNext();
-            }
-
-            @Override
-            public RyaURI next() throws RyaDAOException {
-                if (query == null || !query.hasNext()) {
-                    if (!batchNext()) return null;
-                }
-                if (query != null && query.hasNext()) {
-                    return query.next().getKey().getSubject();
-                } else {
-                    return null;
-                }
-            }
-
-            private boolean batchNext() throws RyaDAOException {
-                if (!iteration.hasNext()) {
-                    return false;
-                }
-                Collection<Map.Entry<RyaStatement, BindingSet>> batchedResults 
= new ArrayList<Map.Entry<RyaStatement, BindingSet>>();
-                for (int i = 0; i < batch && iteration.hasNext(); i++) {
-                    batchedResults.add(new 
RdfCloudTripleStoreUtils.CustomEntry<RyaStatement, BindingSet>(
-                            new RyaStatement(iteration.next(), 
predObj.getKey(), predObj.getValue()), null));
-                }
-                query = ryaQueryEngine.queryWithBindingSet(batchedResults, 
null);
-                return query.hasNext();
-            }
-
-            @Override
-            public void remove() throws RyaDAOException {
-                this.next();
-            }
-        };
-    }
-
-    protected CloseableIteration<RyaStatement, RyaDAOException> join(
-            final CloseableIteration<RyaStatement, RyaDAOException> iteration, 
final RyaURI pred) {
-        //TODO: configure batch
-        //TODO: batch = 1, does not work
-        final int batch = 100;
-        return new CloseableIteration<RyaStatement, RyaDAOException>() {
-
-            private CloseableIteration<Map.Entry<RyaStatement, BindingSet>, 
RyaDAOException> query;
-
-            @Override
-            public void close() throws RyaDAOException {
-                iteration.close();
-                if (query != null) {
-                    query.close();
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws RyaDAOException {
-                return !(query == null || !query.hasNext()) || batchNext();
-            }
-
-            @Override
-            public RyaStatement next() throws RyaDAOException {
-                if (query == null || !query.hasNext()) {
-                    if (!batchNext()) return null;
-                }
-                if (query != null && query.hasNext()) {
-                    return query.next().getKey();
-                } else {
-                    return null;
-                }
-            }
-
-            private boolean batchNext() throws RyaDAOException {
-                if (!iteration.hasNext()) {
-                    return false;
-                }
-                Collection<Map.Entry<RyaStatement, BindingSet>> batchedResults 
= new ArrayList<Map.Entry<RyaStatement, BindingSet>>();
-                for (int i = 0; i < batch && iteration.hasNext(); i++) {
-                    RyaStatement next = iteration.next();
-                    batchedResults.add(new 
RdfCloudTripleStoreUtils.CustomEntry<RyaStatement, BindingSet>(
-                            new RyaStatement(next.getSubject(), pred, 
next.getObject()), null));
-                }
-                query = ryaQueryEngine.queryWithBindingSet(batchedResults, 
null);
-                return query.hasNext();
-            }
-
-            @Override
-            public void remove() throws RyaDAOException {
-                this.next();
-            }
-        };
-    }
-
-    public RyaQueryEngine getRyaQueryEngine() {
-        return ryaQueryEngine;
-    }
-
-    public void setRyaQueryEngine(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/Join.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/Join.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/Join.java
deleted file mode 100644
index 775af53..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/Join.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package mvm.rya.api.persist.query.join;
-
-/*
- * 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 mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.domain.RyaType;
-import mvm.rya.api.domain.RyaURI;
-import mvm.rya.api.persist.RyaDAOException;
-
-import java.util.Map;
-
-/**
- * Date: 7/24/12
- * Time: 4:28 PM
- */
-public interface Join<C extends RdfCloudTripleStoreConfiguration> {
-
-    CloseableIteration<RyaStatement, RyaDAOException> join(C conf, RyaURI... 
preds)
-            throws RyaDAOException;
-
-    CloseableIteration<RyaURI, RyaDAOException> join(C conf, Map.Entry<RyaURI, 
RyaType>... predObjs)
-                    throws RyaDAOException;
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/MergeJoin.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/MergeJoin.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/MergeJoin.java
deleted file mode 100644
index 1dfcbf1..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/query/join/MergeJoin.java
+++ /dev/null
@@ -1,244 +0,0 @@
-package mvm.rya.api.persist.query.join;
-
-/*
- * 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 com.google.common.base.Preconditions;
-import info.aduna.iteration.CloseableIteration;
-import info.aduna.iteration.EmptyIteration;
-import mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.domain.*;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.api.persist.query.RyaQueryEngine;
-import mvm.rya.api.resolver.RyaContext;
-import mvm.rya.api.utils.PeekingCloseableIteration;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Date: 7/24/12
- * Time: 8:52 AM
- */
-public class MergeJoin<C extends RdfCloudTripleStoreConfiguration> implements 
Join<C> {
-
-    private RyaContext ryaContext = RyaContext.getInstance();
-    private RyaQueryEngine ryaQueryEngine;
-
-    public MergeJoin() {
-    }
-
-    public MergeJoin(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-
-    /**
-     * Return all statements that have input predicates. Predicates must not 
be null or ranges
-     *
-     * @param preds
-     * @return
-     */
-    @Override
-    public CloseableIteration<RyaStatement, RyaDAOException> join(C conf, 
RyaURI... preds)
-            throws RyaDAOException {
-        Preconditions.checkNotNull(preds);
-        Preconditions.checkArgument(preds.length > 1, "Must join 2 or more");
-        //TODO: Reorder predObjs based on statistics
-        final List<CloseableIteration<RyaStatement, RyaDAOException>> iters = 
new ArrayList<CloseableIteration<RyaStatement, RyaDAOException>>();
-        for (RyaURI predicate : preds) {
-            Preconditions.checkArgument(predicate != null && !(predicate 
instanceof RyaRange));
-
-            CloseableIteration<RyaStatement, RyaDAOException> iter = 
ryaQueryEngine.query(new RyaStatement(null, predicate, null), conf);
-            iters.add(iter);
-        }
-        Preconditions.checkArgument(iters.size() > 1, "Must join 2 or more");
-
-        final CloseableIteration<RyaStatement, RyaDAOException> first = 
iters.remove(0);
-
-        //perform merge operation
-
-        return new CloseableIteration<RyaStatement, RyaDAOException>() {
-
-            private RyaStatement first_stmt;
-            private RyaType first_obj;
-
-            @Override
-            public void close() throws RyaDAOException {
-                for (CloseableIteration<RyaStatement, RyaDAOException> iter : 
iters) {
-                    iter.close();
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws RyaDAOException {
-                return first_stmt != null || check();
-            }
-
-            @Override
-            public RyaStatement next() throws RyaDAOException {
-                if (first_stmt != null) {
-                    RyaStatement temp = first_stmt;
-                    first_stmt = null;
-                    return temp;
-                }
-                if (check()) {
-                    RyaStatement temp = first_stmt;
-                    first_stmt = null;
-                    return temp;
-                }
-                return null;
-            }
-
-            @Override
-            public void remove() throws RyaDAOException {
-                this.next();
-            }
-
-            protected boolean check() throws RyaDAOException {
-                if (!first.hasNext()) return false;
-                first_stmt = first.next();
-                first_obj = first_stmt.getObject();
-                for (CloseableIteration<RyaStatement, RyaDAOException> iter : 
iters) {
-                    if (!iter.hasNext()) return false; //no more left to join
-                    RyaType iter_obj = iter.next().getObject();
-                    while (first_obj.compareTo(iter_obj) < 0) {
-                        if (!first.hasNext()) return false;
-                        first_obj = first.next().getObject();
-                    }
-                    while (first_obj.compareTo(iter_obj) > 0) {
-                        if (!iter.hasNext()) return false;
-                        iter_obj = iter.next().getObject();
-                    }
-                }
-                return true;
-            }
-        };
-    }
-
-    /**
-     * Return all subjects that have the predicate objects associated. 
Predicate and objects must be not null or ranges
-     * to ensure sorting
-     *
-     * @param predObjs
-     * @return
-     * @throws RyaDAOException
-     */
-    @Override
-    public CloseableIteration<RyaURI, RyaDAOException> join(C conf, 
Map.Entry<RyaURI, RyaType>... predObjs)
-            throws RyaDAOException {
-        Preconditions.checkNotNull(predObjs);
-        Preconditions.checkArgument(predObjs.length > 1, "Must join 2 or 
more");
-
-        //TODO: Reorder predObjs based on statistics
-        final List<CloseableIteration<RyaStatement, RyaDAOException>> iters = 
new ArrayList<CloseableIteration<RyaStatement, RyaDAOException>>();
-        RyaURI earliest_subject = null;
-        for (Map.Entry<RyaURI, RyaType> predObj : predObjs) {
-            RyaURI predicate = predObj.getKey();
-            RyaType object = predObj.getValue();
-            Preconditions.checkArgument(predicate != null && !(predicate 
instanceof RyaRange));
-            Preconditions.checkArgument(object != null && !(object instanceof 
RyaRange));
-
-            PeekingCloseableIteration<RyaStatement, RyaDAOException> iter = 
null;
-            if (earliest_subject == null) {
-                iter = new PeekingCloseableIteration<RyaStatement, 
RyaDAOException>(
-                        ryaQueryEngine.query(new RyaStatement(null, predicate, 
object), conf));
-            } else {
-                iter = new PeekingCloseableIteration<RyaStatement, 
RyaDAOException>(
-                        ryaQueryEngine.query(new RyaStatement(new 
RyaURIRange(earliest_subject, RyaURIRange.LAST_URI), predicate, object), conf));
-            }
-            if (!iter.hasNext()) {
-                return new EmptyIteration<RyaURI, RyaDAOException>();
-            }
-            //setting up range to make performant query
-            earliest_subject = iter.peek().getSubject();
-            iters.add(iter);
-        }
-        Preconditions.checkArgument(iters.size() > 1, "Must join 2 or more");
-
-        final CloseableIteration<RyaStatement, RyaDAOException> first = 
iters.remove(0);
-
-        //perform merge operation
-
-        return new CloseableIteration<RyaURI, RyaDAOException>() {
-
-            private RyaURI first_subj;
-
-            @Override
-            public void close() throws RyaDAOException {
-                for (CloseableIteration<RyaStatement, RyaDAOException> iter : 
iters) {
-                    iter.close();
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws RyaDAOException {
-                return first_subj != null || check();
-            }
-
-            @Override
-            public RyaURI next() throws RyaDAOException {
-                if (first_subj != null) {
-                    RyaURI temp = first_subj;
-                    first_subj = null;
-                    return temp;
-                }
-                if (check()) {
-                    RyaURI temp = first_subj;
-                    first_subj = null;
-                    return temp;
-                }
-                return null;
-            }
-
-            @Override
-            public void remove() throws RyaDAOException {
-                this.next();
-            }
-
-            protected boolean check() throws RyaDAOException {
-                if (!first.hasNext()) return false;
-                first_subj = first.next().getSubject();
-                for (CloseableIteration<RyaStatement, RyaDAOException> iter : 
iters) {
-                    if (!iter.hasNext()) return false; //no more left to join
-                    RyaURI iter_subj = iter.next().getSubject();
-                    while (first_subj.compareTo(iter_subj) < 0) {
-                        if (!first.hasNext()) return false;
-                        first_subj = first.next().getSubject();
-                    }
-                    while (first_subj.compareTo(iter_subj) > 0) {
-                        if (!iter.hasNext()) return false;
-                        iter_subj = iter.next().getSubject();
-                    }
-                }
-                return true;
-            }
-        };
-    }
-
-    public RyaQueryEngine getRyaQueryEngine() {
-        return ryaQueryEngine;
-    }
-
-    public void setRyaQueryEngine(RyaQueryEngine ryaQueryEngine) {
-        this.ryaQueryEngine = ryaQueryEngine;
-    }
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/persist/utils/RyaDAOHelper.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/persist/utils/RyaDAOHelper.java 
b/common/rya.api/src/main/java/mvm/rya/api/persist/utils/RyaDAOHelper.java
deleted file mode 100644
index 81f42b4..0000000
--- a/common/rya.api/src/main/java/mvm/rya/api/persist/utils/RyaDAOHelper.java
+++ /dev/null
@@ -1,176 +0,0 @@
-package mvm.rya.api.persist.utils;
-
-/*
- * 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 mvm.rya.api.RdfCloudTripleStoreConfiguration;
-import mvm.rya.api.RdfCloudTripleStoreUtils;
-import mvm.rya.api.domain.RyaStatement;
-import mvm.rya.api.persist.RyaDAO;
-import mvm.rya.api.persist.RyaDAOException;
-import mvm.rya.api.resolver.RdfToRyaConversions;
-import mvm.rya.api.resolver.RyaToRdfConversions;
-import mvm.rya.api.utils.NullableStatementImpl;
-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.QueryEvaluationException;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Map;
-import java.util.NoSuchElementException;
-
-/**
- * Date: 7/20/12
- * Time: 10:36 AM
- */
-public class RyaDAOHelper {
-
-    public static CloseableIteration<Statement, QueryEvaluationException> 
query(RyaDAO ryaDAO, Resource subject, URI predicate, Value object, 
RdfCloudTripleStoreConfiguration conf, Resource... contexts) throws 
QueryEvaluationException {
-        return query(ryaDAO, new NullableStatementImpl(subject, predicate, 
object, contexts), conf);
-    }
-
-    public static CloseableIteration<Statement, QueryEvaluationException> 
query(RyaDAO ryaDAO, Statement stmt, RdfCloudTripleStoreConfiguration conf) 
throws QueryEvaluationException {
-        final CloseableIteration<RyaStatement, RyaDAOException> query;
-        try {
-            query = 
ryaDAO.getQueryEngine().query(RdfToRyaConversions.convertStatement(stmt),
-                    conf);
-        } catch (RyaDAOException e) {
-            throw new QueryEvaluationException(e);
-        }
-        //TODO: only support one context for now
-        return new CloseableIteration<Statement, QueryEvaluationException>() { 
  //TODO: Create a new class struct for this
-
-            private boolean isClosed = false;
-            @Override
-            public void close() throws QueryEvaluationException {
-                try {
-                    isClosed = true;
-                    query.close();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws QueryEvaluationException {
-                try {
-                    return query.hasNext();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public Statement next() throws QueryEvaluationException {
-                if (!hasNext() || isClosed) {
-                    throw new NoSuchElementException();
-                }
-
-                try {
-                    RyaStatement next = query.next();
-                    if (next == null) {
-                        return null;
-                    }
-                    return RyaToRdfConversions.convertStatement(next);
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public void remove() throws QueryEvaluationException {
-                try {
-                    query.remove();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-        };
-    }
-
-    public static CloseableIteration<? extends Map.Entry<Statement, 
BindingSet>, QueryEvaluationException> query(RyaDAO ryaDAO, 
Collection<Map.Entry<Statement, BindingSet>> statements, 
RdfCloudTripleStoreConfiguration conf) throws QueryEvaluationException {
-        Collection<Map.Entry<RyaStatement, BindingSet>> ryaStatements = new 
ArrayList<Map.Entry<RyaStatement, BindingSet>>(statements.size());
-        for (Map.Entry<Statement, BindingSet> entry : statements) {
-            ryaStatements.add(new 
RdfCloudTripleStoreUtils.CustomEntry<RyaStatement, BindingSet>
-                    (RdfToRyaConversions.convertStatement(entry.getKey()), 
entry.getValue()));
-        }
-        final CloseableIteration<? extends Map.Entry<RyaStatement, 
BindingSet>, RyaDAOException> query;
-        try {
-            query = ryaDAO.getQueryEngine().queryWithBindingSet(ryaStatements, 
conf);
-        } catch (RyaDAOException e) {
-            throw new QueryEvaluationException(e);
-        }
-        return new CloseableIteration<Map.Entry<Statement, BindingSet>, 
QueryEvaluationException>() {   //TODO: Create a new class struct for this
-            private boolean isClosed = false;
-
-            @Override
-            public void close() throws QueryEvaluationException {
-                isClosed = true;
-                try {
-                    query.close();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public boolean hasNext() throws QueryEvaluationException {
-                try {
-                    return query.hasNext();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public Map.Entry<Statement, BindingSet> next() throws 
QueryEvaluationException {
-                if (!hasNext() || isClosed) {
-                    throw new NoSuchElementException();
-                }
-                try {
-
-                    Map.Entry<RyaStatement, BindingSet> next = query.next();
-                    if (next == null) {
-                        return null;
-                    }
-                    return new RdfCloudTripleStoreUtils.CustomEntry<Statement, 
BindingSet>(RyaToRdfConversions.convertStatement(next.getKey()), 
next.getValue());
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-
-            @Override
-            public void remove() throws QueryEvaluationException {
-                try {
-                    query.remove();
-                } catch (RyaDAOException e) {
-                    throw new QueryEvaluationException(e);
-                }
-            }
-        };
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/44a2dcf0/common/rya.api/src/main/java/mvm/rya/api/query/strategy/AbstractTriplePatternStrategy.java
----------------------------------------------------------------------
diff --git 
a/common/rya.api/src/main/java/mvm/rya/api/query/strategy/AbstractTriplePatternStrategy.java
 
b/common/rya.api/src/main/java/mvm/rya/api/query/strategy/AbstractTriplePatternStrategy.java
deleted file mode 100644
index 5171feb..0000000
--- 
a/common/rya.api/src/main/java/mvm/rya/api/query/strategy/AbstractTriplePatternStrategy.java
+++ /dev/null
@@ -1,93 +0,0 @@
-package mvm.rya.api.query.strategy;
-
-/*
- * 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 com.google.common.base.Preconditions;
-import mvm.rya.api.RdfCloudTripleStoreConstants;
-import mvm.rya.api.resolver.RyaContext;
-import mvm.rya.api.resolver.triple.TripleRowRegex;
-
-import static mvm.rya.api.RdfCloudTripleStoreConstants.DELIM;
-import static mvm.rya.api.RdfCloudTripleStoreConstants.TYPE_DELIM;
-
-/**
- * Date: 7/14/12
- * Time: 8:06 AM
- */
-public abstract class AbstractTriplePatternStrategy implements 
TriplePatternStrategy {
-    public static final String ALL_REGEX = "([\\s\\S]*)";
-
-    public abstract RdfCloudTripleStoreConstants.TABLE_LAYOUT getLayout();
-
-    @Override
-    public TripleRowRegex buildRegex(String subject, String predicate, String 
object, String context, byte[] objectTypeInfo) {
-        RdfCloudTripleStoreConstants.TABLE_LAYOUT table_layout = getLayout();
-        Preconditions.checkNotNull(table_layout);
-        if (subject == null && predicate == null && object == null && context 
== null && objectTypeInfo == null) {
-            return null; //no regex
-        }
-        StringBuilder sb = new StringBuilder();
-        String first = subject;
-        String second = predicate;
-        String third = object;
-        if (table_layout == RdfCloudTripleStoreConstants.TABLE_LAYOUT.PO) {
-            first = predicate;
-            second = object;
-            third = subject;
-        } else if (table_layout == 
RdfCloudTripleStoreConstants.TABLE_LAYOUT.OSP) {
-            first = object;
-            second = subject;
-            third = predicate;
-        }
-
-        if (first != null) {
-            sb.append(first);
-        } else {
-            sb.append(ALL_REGEX);
-        }
-        sb.append(DELIM);
-
-        if (second != null) {
-            sb.append(second);
-        } else {
-            sb.append(ALL_REGEX);
-        }
-        sb.append(DELIM);
-
-        if (third != null) {
-            sb.append(third);
-            if (objectTypeInfo == null) {
-                sb.append(TYPE_DELIM);
-                sb.append(ALL_REGEX);
-            }else {
-                sb.append(new String(objectTypeInfo));
-            }
-        }else {
-            sb.append(ALL_REGEX);
-            if (objectTypeInfo != null) {
-                sb.append(new String(objectTypeInfo));
-            }
-        }
-
-        return new TripleRowRegex(sb.toString(), (context != null) ? (context 
+ ALL_REGEX) : null, null);
-    }
-}


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