Moved Neighborhood into algo package for public visibility

Author: tgsmith61591

README.md

@@ -9,7 +9,7 @@ A Java-based set of __classification__ clustering algorithms. Built under JDK 1.
 
 ___
 ### Installation:
-__Clust4j 1.0.0 prerelease is now available under [releases](https://github.com/tgsmith61591/clust4j/releases) (jar included)__. To build the bleeding edge, use the included gradle wrapper:
+__Clust4j 1.1.6 prerelease is now available under [releases](https://github.com/tgsmith61591/clust4j/releases). To build the bleeding edge, use the included gradle wrapper:
 
 ```bash
 git clone https://github.com/tgsmith61591/clust4j.git

build.gradle

@@ -5,7 +5,7 @@ apply plugin: 'jacoco'
 sourceCompatibility = 1.7
 targetCompatibility = 1.7
 archivesBaseName = 'clust4j'
-version = '1.1.5-SNAPSHOT'
+version = '1.1.6-SNAPSHOT'
 
 
 

src/main/java/com/clust4j/algo/AbstractClusterer.java

@@ -13,6 +13,7 @@
  *    See the License for the specific language governing permissions and
  *    limitations under the License.
  *******************************************************************************/
+
 package com.clust4j.algo;
 
 import java.text.NumberFormat;
@@ -124,7 +125,7 @@ protected AbstractClusterer(AbstractClusterer caller) {
 	 * @param planner
 	 */
 	protected AbstractClusterer(AbstractClusterer caller, BaseClustererParameters planner) {
-		this.dist_metric= null == planner ? caller.dist_metric : planner.getSep();
+		this.dist_metric= null == planner ? caller.dist_metric : planner.getMetric();
 		this.verbose 	= null == planner ? false : planner.getVerbose(); // if another caller, default to false
 		this.modelKey 	= UUID.randomUUID();
 		this.random_state 		= null == planner ? caller.random_state : planner.getSeed();
@@ -138,7 +139,7 @@ protected AbstractClusterer(AbstractClusterer caller, BaseClustererParameters pl
 
 	protected AbstractClusterer(AbstractRealMatrix data, BaseClustererParameters planner, boolean as_is) {
 
-		this.dist_metric = planner.getSep();
+		this.dist_metric = planner.getMetric();
 		this.verbose = planner.getVerbose();
 		this.modelKey = UUID.randomUUID();
 		this.random_state = planner.getSeed();

src/main/java/com/clust4j/algo/AbstractDBSCAN.java

@@ -43,9 +43,12 @@ abstract public static class AbstractDBSCANPlanner<T extends AbstractDBSCAN>
 			extends BaseClustererParameters 
 			implements UnsupervisedClassifierParameters<T> {
 		private static final long serialVersionUID = 765572960123009344L;
+		protected int minPts = DEF_MIN_PTS;
 
 		abstract public AbstractDBSCANPlanner<T> setMinPts(final int minPts);
-		abstract public int getMinPts();
+		final public int getMinPts() { 
+			return minPts; 
+		}
 	}
 
 	public int getMinPts() {

src/main/java/com/clust4j/algo/AffinityPropagationParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;

src/main/java/com/clust4j/algo/BaseClustererParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;
@@ -36,7 +52,7 @@ abstract public class BaseClustererParameters
 	abstract public BaseClustererParameters setForceParallel(final boolean b);
 
 	final public FeatureNormalization getNormalizer() { return norm; }
-	final public GeometricallySeparable getSep() 	{ return metric; }
+	final public GeometricallySeparable getMetric() { return metric; }
 	final public boolean getParallel() 				{ return parallel; }
 	final public boolean getScale()					{ return scale; }
 	final public Random getSeed() 					{ return seed; }

src/main/java/com/clust4j/algo/BaseNeighborsModel.java

@@ -18,7 +18,7 @@
 import org.apache.commons.math3.linear.AbstractRealMatrix;
 
 import com.clust4j.GlobalState;
-import com.clust4j.algo.NearestNeighborHeapSearch.Neighborhood;
+import com.clust4j.algo.Neighborhood;
 import com.clust4j.except.ModelNotFitException;
 import com.clust4j.metrics.pairwise.DistanceMetric;
 import com.clust4j.metrics.pairwise.GeometricallySeparable;

src/main/java/com/clust4j/algo/BoruvkaAlgorithm.java

@@ -18,7 +18,7 @@
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.util.FastMath;
 
-import com.clust4j.algo.NearestNeighborHeapSearch.Neighborhood;
+import com.clust4j.algo.Neighborhood;
 import com.clust4j.algo.NearestNeighborHeapSearch.NodeData;
 import com.clust4j.log.LogTimer;
 import com.clust4j.log.Loggable;

src/main/java/com/clust4j/algo/CentroidClustererParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import org.apache.commons.math3.linear.AbstractRealMatrix;

src/main/java/com/clust4j/algo/DBSCANParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;
@@ -17,7 +33,6 @@ final public class DBSCANParameters extends AbstractDBSCANPlanner<DBSCAN> {
 	private static final long serialVersionUID = -5285244186285768512L;
 
 	private double eps = DBSCAN.DEF_EPS;
-	private int minPts = DBSCAN.DEF_MIN_PTS;
 
 
 	public DBSCANParameters() { }
@@ -46,11 +61,6 @@ public DBSCANParameters copy() {
 	public double getEps() {
 		return eps;
 	}
-
-	@Override
-	public int getMinPts() {
-		return minPts;
-	}
 
 	public DBSCANParameters setEps(final double eps) {
 		this.eps = eps;

src/main/java/com/clust4j/algo/HDBSCAN.java

@@ -31,7 +31,7 @@
 
 import com.clust4j.GlobalState;
 import com.clust4j.utils.QuadTup;
-import com.clust4j.algo.NearestNeighborHeapSearch.Neighborhood;
+import com.clust4j.algo.Neighborhood;
 import com.clust4j.except.ModelNotFitException;
 import com.clust4j.log.LogTimer;
 import com.clust4j.log.Loggable;

src/main/java/com/clust4j/algo/HDBSCANParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;
@@ -17,7 +33,6 @@
 final public class HDBSCANParameters extends AbstractDBSCANPlanner<HDBSCAN> {
 	private static final long serialVersionUID = 7197585563308908685L;
 
-	private int minPts = HDBSCAN.DEF_MIN_PTS;
 	private HDBSCAN_Algorithm algo = HDBSCAN.DEF_ALGO;
 	private double alpha = HDBSCAN.DEF_ALPHA;
 	private boolean approxMinSpanTree = HDBSCAN.DEF_APPROX_MIN_SPAN;
@@ -52,11 +67,6 @@ public HDBSCANParameters copy() {
 			.setNormalizer(norm)
 			.setForceParallel(parallel);
 	}
-
-	@Override
-	public int getMinPts() {
-		return minPts;
-	}
 
 	public HDBSCAN_Algorithm getAlgo() {
 		return this.algo;

src/main/java/com/clust4j/algo/HierarchicalAgglomerativeParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;

src/main/java/com/clust4j/algo/KMeansParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;

src/main/java/com/clust4j/algo/KMedoidsParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;

src/main/java/com/clust4j/algo/MeanShift.java

@@ -30,7 +30,7 @@
 import org.apache.commons.math3.util.FastMath;
 
 import com.clust4j.algo.NearestNeighborsParameters;
-import com.clust4j.algo.NearestNeighborHeapSearch.Neighborhood;
+import com.clust4j.algo.Neighborhood;
 import com.clust4j.algo.RadiusNeighborsParameters;
 import com.clust4j.except.IllegalClusterStateException;
 import com.clust4j.except.ModelNotFitException;

src/main/java/com/clust4j/algo/MeanShiftParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;

src/main/java/com/clust4j/algo/NearestCentroidParameters.java

@@ -1,3 +1,19 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed 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 com.clust4j.algo;
 
 import java.util.Random;