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Commit 1526e3f5 authored by Alexander David Hellwig's avatar Alexander David Hellwig
Browse files

Move clust4j from helpers to com package

parent 490694c8
Pipeline #95861 passed with stages
in 13 minutes and 52 seconds
......@@ -14,22 +14,22 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import java.util.concurrent.RejectedExecutionException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.optimize.BrentDownhillOptimizer;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.optimize.OptimizableCaller;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import com.clust4j.optimize.BrentDownhillOptimizer;
import com.clust4j.optimize.OptimizableCaller;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.exception.NotStrictlyPositiveException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.util.FastMath;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.ParallelChunkingTask;
import com.clust4j.algo.ParallelChunkingTask;
public class BoxCoxTransformer extends Transformer {
private static final long serialVersionUID = -5397818601304593058L;
......
......@@ -14,11 +14,11 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
......
......@@ -14,11 +14,11 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
......
......@@ -14,11 +14,11 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
......
......@@ -14,12 +14,12 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.EntryPair;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.EntryPair;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.BlockRealMatrix;
......
......@@ -13,15 +13,15 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.Clust4j;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.DeepCloneable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.SynchronicityLock;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.TableFormatter;
import com.clust4j.utils.DeepCloneable;
import com.clust4j.utils.SynchronicityLock;
import com.clust4j.utils.TableFormatter;
import com.clust4j.Clust4j;
import org.apache.commons.math3.linear.RealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.BaseModel;
import com.clust4j.algo.BaseModel;
public abstract class PreProcessor extends Clust4j implements DeepCloneable {
private static final long serialVersionUID = -312158525538380532L;
......
......@@ -14,11 +14,11 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
......
......@@ -14,11 +14,11 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.ModelNotFitException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.ModelNotFitException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
......
......@@ -14,7 +14,7 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import org.apache.commons.math3.linear.RealMatrix;
......
......@@ -14,10 +14,10 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
......
......@@ -14,7 +14,7 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess;
package com.clust4j.algo.preprocess;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
......
......@@ -13,19 +13,19 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
import java.util.Random;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.NaNException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.sample.Bootstrapper;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.NaNException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import com.clust4j.log.Log;
import com.clust4j.sample.Bootstrapper;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import com.clust4j.log.LogTimer;
/**
* The BootstrapImputation class will impute {@link Double#NaN}<tt>s</tt>
......
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
public enum CentralTendencyMethod implements java.io.Serializable {
MEAN,
......
......@@ -14,18 +14,18 @@
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
import java.util.Random;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.NamedEntity;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.AbstractClusterer;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.PreProcessor;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.NaNException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Loggable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import com.clust4j.except.NaNException;
import com.clust4j.utils.MatUtils;
import com.clust4j.NamedEntity;
import com.clust4j.algo.AbstractClusterer;
import com.clust4j.algo.preprocess.PreProcessor;
import com.clust4j.log.Log;
import com.clust4j.log.LogTimer;
import com.clust4j.log.Loggable;
/**
* {@link AbstractClusterer} algorithms are not capable of robustly handling
......
......@@ -13,16 +13,16 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
import java.util.Random;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import com.clust4j.utils.MatUtils;
import com.clust4j.log.Log;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import com.clust4j.log.LogTimer;
/**
* Imputes the missing values in a matrix with the column means.
......
......@@ -13,17 +13,17 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
import java.util.Random;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import com.clust4j.log.Log;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import com.clust4j.log.LogTimer;
/**
* Imputes the missing values in a matrix with the column medians.
......
......@@ -13,24 +13,24 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.preprocess.impute;
package com.clust4j.algo.preprocess.impute;
import java.util.ArrayList;
import java.util.Random;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.NaNException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.metrics.pairwise.Distance;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.metrics.pairwise.GeometricallySeparable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.NaNException;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import com.clust4j.log.Log;
import com.clust4j.metrics.pairwise.Distance;
import com.clust4j.metrics.pairwise.GeometricallySeparable;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.BaseNeighborsModel;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.NearestNeighbors;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.NearestNeighborsParameters;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import com.clust4j.algo.BaseNeighborsModel;
import com.clust4j.algo.NearestNeighbors;
import com.clust4j.algo.NearestNeighborsParameters;
import com.clust4j.log.LogTimer;
public class NearestNeighborImputation extends MatrixImputation {
private static final long serialVersionUID = -2717555601058365204L;
......
......@@ -13,7 +13,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.data;
package com.clust4j.data;
abstract class BreastCancerLoader {
final static DataSet load() {
......
......@@ -13,7 +13,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.data;
package com.clust4j.data;
import java.io.File;
import java.io.IOException;
......@@ -23,20 +23,20 @@ import java.util.Arrays;
import java.util.concurrent.RecursiveTask;
import java.util.concurrent.RejectedExecutionException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.Clust4j;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.GlobalState;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.except.MatrixParseException;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Log;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Loggable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.ArrayFormatter;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.DeepCloneable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.except.MatrixParseException;
import com.clust4j.utils.ArrayFormatter;
import com.clust4j.utils.DeepCloneable;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.VecUtils;
import com.clust4j.Clust4j;
import com.clust4j.GlobalState;
import com.clust4j.log.Log;
import com.clust4j.log.Loggable;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.util.FastMath;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.algo.ParallelChunkingTask;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.LogTimer;
import com.clust4j.algo.ParallelChunkingTask;
import com.clust4j.log.LogTimer;
/**
......
......@@ -13,7 +13,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*******************************************************************************/
package de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.data;
package com.clust4j.data;
import java.io.BufferedWriter;
import java.io.File;
......@@ -23,16 +23,16 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.Clust4j;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.log.Loggable;
import com.clust4j.Clust4j;
import com.clust4j.log.Loggable;
import org.apache.commons.math3.exception.DimensionMismatchException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.DeepCloneable;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatUtils;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.MatrixFormatter;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.TableFormatter;
import de.monticore.lang.monticar.generator.middleware.helpers.AffinityPropagationHelper.clust4j.utils.VecUtils;
import com.clust4j.utils.DeepCloneable;
import com.clust4j.utils.MatUtils;
import com.clust4j.utils.MatrixFormatter;
import com.clust4j.utils.TableFormatter;
import com.clust4j.utils.VecUtils;
/**
* A lightweight dataset wrapper that stores information on
......
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