Laboratoire ICAR » Plateforme TXM

<?xml version="1.0" encoding="UTF-8"?>

<projectDescription>

	<name>org.txm.statsengine.r.core</name>

	<comment></comment>

	<projects>

	</projects>

	<buildSpec>

		<buildCommand>

			<name>org.eclipse.jdt.core.javabuilder</name>

			<arguments>

			</arguments>

		</buildCommand>

		<buildCommand>

			<name>org.eclipse.pde.ManifestBuilder</name>

			<arguments>

			</arguments>

		</buildCommand>

		<buildCommand>

			<name>org.eclipse.pde.SchemaBuilder</name>

			<arguments>

			</arguments>

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	<natures>

		<nature>org.eclipse.pde.PluginNature</nature>

		<nature>org.eclipse.jdt.core.javanature</nature>

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// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.data;

import org.txm.statsengine.core.StatException;

import org.txm.statsengine.r.core.RWorkspaceException;

// TODO: Auto-generated Javadoc

/**

 * The Interface ContingencyTable.

 * 

 * @author sloiseau

 */

public interface ContingencyTable extends Matrix {

	/**

	 * Gets the row margin.

	 * 

	 * @return the row margin

	 * 

	 * @throws RWorkspaceException

	 *             the r workspace exception

	 */

	public Vector getRowMarginsVector() throws StatException;

	/**

	 * Gets the col margin.

	 * 

	 * @return the col margin

	 * 

	 * @throws RWorkspaceException

	 *             the r workspace exception

	 */

	public Vector getColMarginsVector() throws StatException;

	/**

	 * Gets the col margin.

	 * 

	 * @return the col margin

	 * 

	 * @throws RWorkspaceException

	 *             the r workspace exception

	 */

	public int[] getColMargins() throws Exception;

	/**

	 * Gets the col margin.

	 * 

	 * @return the col margin

	 * 

	 * @throws RWorkspaceException

	 *             the r workspace exception

	 */

	public int[] getRowMargins() throws Exception;

	/**

	 * Gets the total.

	 * 

	 * @return the total

	 * 

	 * @throws RWorkspaceException

	 *             the r workspace exception

	 */

	public int getTotal() throws RWorkspaceException;

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.data;

import org.txm.core.results.ITXMResult;

// TODO: Auto-generated Javadoc

/**

 * The root of all other data structures.

 * 

 * @author sloiseau

 */

public interface QuantitativeDataStructure extends ITXMResult {

	/**

	 * The symbol is a the name of the data structure in a wrapped statistical

	 * engine.

	 * 

	 * @return the symbol of this data structure.

	 */

	public String getSymbol();

}

<html>

<body>

<p>Definition of quantitative data structures for representing corpus.</p>

</body>

</html>

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.data;

import java.util.List;

import org.txm.statsengine.core.StatException;

// TODO: Auto-generated Javadoc

/**

 * The interface Vector.

 * 

 * @author sloiseau

 */

public interface Vector extends QuantitativeDataStructure {

	/**

	 * Get the sub-vector given index.

	 * 

	 * @param index

	 *            0-based index.

	 * 

	 * @return a new vector, copy to the selected values (modif ication to the

	 *         vector returned does not modif y the vector).

	 * 

	 * @throws StatException

	 *             if anything goes wrong.

	 */

	public Vector get(int[] index) throws StatException;

	/**

	 * Convert the vector to a java array of <code>int</code>, if possible.

	 * 

	 * @return a java array of <code>int</code>.

	 * 

	 * @throws StatException

	 *             if anything goes wrong, ni particular if this Vector cannot

	 *             be converted into <code>int</code>.

	 */

	public int[] asIntArray() throws StatException;

	/**

	 * Convert the vector to a java array of <code>double</code>, if possible.

	 * 

	 * @return a java array of <code>double</code>.

	 * 

	 * @throws StatException

	 *             if anything goes wrong, ni particular if this Vector cannot

	 *             be converted into <code>double</code>.

	 */

	public double[] asDoubleArray() throws StatException;

	/**

	 * Convert the vector to a java array of <code>String</code>, if possible.

	 * 

	 * @return a java array of <code>String</code>.

	 * 

	 * @throws StatException

	 *             if anything goes wrong, ni particular if this Vector cannot

	 *             be converted into <code>String</code>.

	 */

	public String[] asStringsArray() throws StatException;

	/**

	 * Get the length of the vector.

	 * 

	 * @return the length.

	 * 

	 * @throws StatException

	 *             if anything goes wrong.

	 */

	public int getLength() throws StatException;

	/**

	 * Removes the.

	 *

	 * @param col the col

	 * @return true, if successful

	 */

	public boolean remove(int col);

	/**

	 * Sets the string.

	 *

	 * @param i the i

	 * @param value the value

	 */

	public void setString(int i, String value);

	/**

	 * Sets the int.

	 *

	 * @param i the i

	 * @param value the value

	 */

	public void setInt(int i, int value);

	/**

	 * Sets the double.

	 *

	 * @param i the i

	 * @param value the value

	 */

	public void setDouble(int i, double value);

	/**

	 * Sort.

	 *

	 * @param reverse the reverse

	 */

	public void sort(Boolean reverse);

	/**

	 * Sets the order.

	 *

	 * @param neworder the neworder

	 * @param reverse the reverse

	 */

	public void setOrder(List<Integer> neworder, Boolean reverse);

	/**

	 * Cut.

	 *

	 * @param nlines the nlines

	 */

	public void cut(int nlines);

	// public String get(int i);

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.data;

import org.txm.statsengine.core.StatException;

// TODO: Auto-generated Javadoc

/**

 * The Interface Matrix, root of all other matrix-like structure.

 * 

 * @author sloiseau

 */

public interface Matrix extends QuantitativeDataStructure {

	/**

	 * Get the value at the specif ied cell.

	 *

	 * @param row 0-based row index

	 * @param col 0-based column index

	 * @return the value as a <code>double</code>

	 * @throws StatException the stat exception

	 */

	public double get(int row, int col) throws StatException;

	/**

	 * The number of rows in the contingency table.

	 * 

	 * @return the number of raw

	 */

	public abstract int getNRows();

	/**

	 * Exchange 2 columns in the lexical table

	 * @param c1 1..N+1

	 * @param c2 1..N+1

	 */

	public abstract void exchangeColumns(int c1, int c2);

	/**

	 * The number of columns in the contingency table.

	 * 

	 * @return the number of columns

	 */

	public abstract int getNColumns();

	/**

	 * Get the row names or null if no row names.

	 * 

	 * Row names are available if the

	 *

	 * @return the row names

	 * {@link #Matrix(DoubleMatrix2D, String[], String[], Header)} constructor

	 * has been used for this object.

	 */

	public abstract Vector getRowNames();

	/**

	 * Get the col names or null if no col names.

	 * 

	 * Col names are available if the

	 *

	 * @return the col names

	 * {@link #Matrix(DoubleMatrix2D, String[], String[], Header)} constructor

	 * has been used for this object.

	 */

	public abstract Vector getColNames();

	/**

	 * Gets a row vector as a Vector object.

	 *

	 * @param index 0-based row index.

	 * @return the row

	 * @throws StatException the stat exception

	 */

	public abstract Vector getRow(int index) throws StatException;

	/**

	 * Gets a column vector as a Vector object.

	 *

	 * @param index 0-based index column index.

	 * @return the row

	 * @throws StatException the stat exception

	 */

	public abstract Vector getCol(int index) throws StatException;

	/**

	 * Gets a column vector as a Vector object.

	 *

	 * @param column the column name

	 * @return the column vector

	 * @throws StatException the stat exception

	 */

	public abstract Vector getCol(String column) throws StatException;

	/**

	 * Gets a row vector as a Vector object.

	 *

	 * @param row the row name

	 * @return the row vector

	 * @throws StatException the stat exception

	 */

	public abstract Vector getRow(String row) throws StatException;

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core;

// TODO: Auto-generated Javadoc

/**

 * General exception in statistical computing, the super class of all exceptions

 * related to statistical computing.

 * 

 * @author sloiseau

 * 

 */

public class StatException extends Exception {

	/** The Constant serialVersionUID. */

	private static final long serialVersionUID = 7220819361950262761L;

	/**

	 * Instantiates a new stat exception.

	 */

	public StatException() {

		super();

		// TODO Auto-generated constructor stub

	}

	/**

	 * Instantiates a new stat exception.

	 *

	 * @param message the message

	 * @param cause the cause

	 */

	public StatException(String message, Throwable cause) {

		super(message, cause);

		// TODO Auto-generated constructor stub

	}

	/**

	 * Instantiates a new stat exception.

	 *

	 * @param message the message

	 */

	public StatException(String message) {

		super(message);

		// TODO Auto-generated constructor stub

	}

	/**

	 * Instantiates a new stat exception.

	 *

	 * @param cause the cause

	 */

	public StatException(Throwable cause) {

		super(cause);

		// TODO Auto-generated constructor stub

	}

}

<html>

<body>

<p>Root package of all statistical and numeric computing functions of the toolbox.</p>

</body>

</html>

<html>

<body>

<p>Utility functions for dealing with array (vectorizing, indexing, checking consistency...).</p>

</body>

</html>

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.utils;

import java.util.HashMap;

import java.util.Map;

import org.txm.core.messages.TXMCoreMessages;

// TODO: Auto-generated Javadoc

/**

 * Utilities for managing index of vector.

 * 

 * @author sloiseau

 * 

 */

public final class ArrayIndex {

	/**

	 * Convert an array of zero-based index to an array of one-base index, that

	 * is, add <code>1</code> to all elements.

	 * 

	 * This method check every index (see exception thrown).

	 *

	 * @param zero_based the zero based index.

	 * @param length the number of elements that can be indexed.

	 * @return the one base index.

	 */

	public static final int[] zeroToOneBasedIndex(int[] zero_based, int length) {

		if (zero_based == null || zero_based.length == 0) {

			throw new IllegalArgumentException(TXMCoreMessages.ArrayIndex_0);

		}

		int[] one_based = new int[zero_based.length];

		for (int i = 0; i < zero_based.length; i++) {

			if (zero_based[i] < 0 || zero_based[i] >= length) {

				throw new IllegalArgumentException(TXMCoreMessages.ArrayIndex_1);

			}

			one_based[i] = zero_based[i] + 1;

		}

		return one_based;

	}

	/**

	 * Zero to one based index.

	 *

	 * @param zero_based the zero_based

	 * @return the int

	 */

	public static final int zeroToOneBasedIndex(int zero_based) {

		return zero_based + 1;

	}

	/**

	 * Get the index (0-based) of the element of subvector into vector. Return

	 * <code>-1</code> when no element in vector correspond to the element in

	 * subvector.

	 *

	 * @param vector the vector

	 * @param subvector the subvector

	 * @return the index

	 */

	public static int[] getIndex(String[] vector, String[] subvector) {

		int[] result = new int[subvector.length];

		Map<String, Integer> index = new HashMap<String, Integer>();

		for (int i = 0; i < subvector.length; i++) {

			index.put(subvector[i], i);

			result[i] = -1;

		}

		for (int i = 0; i < vector.length; i++) {

			if (index.containsKey(vector[i])) {

				result[index.get(vector[i])] = i;

			}

		}

		return result;

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.utils;

import java.util.Arrays;

// TODO: Auto-generated Javadoc

/**

 * Utility methods for testing for equality of arrays.

 * 

 * @author sloiseau

 * 

 */

public final class ArrayEquals {

	/**

	 * Test for equality of both array. For consistency with Arrays.equals

	 * contract, the two arrays are equals if both are <code>null</code>.

	 *

	 * @param array1 the array1

	 * @param array2 the array2

	 * @return <code>true</code> if (1) both arrays are <code>null</code> or if

	 * (2) both arrays have the same length and contain pair of arrays

	 * equals to each other according to

	 * {@link Arrays#equals(int[], int[])}.

	 */

	public static final boolean deepEquals(int[][] array1, int[][] array2) {

		if (array1 == null && array2 == null)

			return true;

		if (array1 == null || array2 == null)

			return false;

		if (array1.length != array2.length)

			return false;

		for (int i = 0; i < array2.length; i++) {

			if (!Arrays.equals(array1[i], array2[i]))

				return false;

		}

		return true;

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.utils;

import org.txm.core.messages.TXMCoreMessages;

// TODO: Auto-generated Javadoc

/**

 * Static methods for dealing vectorization of Arrays.

 * 

 * @author sloiseau

 * 

 */

public final class VectorizeArray {

	/**

	 * Convert a <code>double * double</code> array in a <code>double</code>

	 * array. Each inner array of the argument is added one after the other into

	 * the result array.

	 * 

	 * <pre>

	 * [

	 * [1, 2, 3],

	 * [4, 5, 6]

	 * ]

	 * </pre>

	 * 

	 * result in :

	 * 

	 * <pre>

	 * [1, 2, 3, 4, 5, 6]

	 * </pre>

	 * 

	 * that is, "row first".

	 *

	 * @param matrix a <code>double * double</code> array where all inner arrays

	 * have the same length.

	 * @return an array of <code>double</code> produced by vectorization of the

	 * matrix.

	 */

	public final static double[] vectorizeByInner(double[][] matrix) {

		if (matrix == null || matrix.length == 0) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_0);

		}

		int inner_length = matrix[0].length;

		if (inner_length < 1) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_1);

		}

		double[] vector = new double[matrix.length * matrix[0].length];

		for (int i = 0; i < matrix.length; i++) {

			if (matrix[i] == null) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_10);

			}

			if (inner_length != matrix[i].length) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_3);

			}

			System.arraycopy(matrix[i], 0, vector, i * inner_length,

					inner_length);

		}

		return vector;

	}

	/**

	 * Convert a <code>int * int</code> array in a <code>double</code> array.

	 * Each inner array of the argument is added one after the other into the

	 * result array.

	 * 

	 * <pre>

	 * [

	 * [1, 2, 3],

	 * [4, 5, 6]

	 * ]

	 * </pre>

	 * 

	 * result in :

	 * 

	 * <pre>

	 * [1, 2, 3, 4, 5, 6]

	 * </pre>

	 * 

	 * that is, "row first".

	 *

	 * @param matrix a <code>int * int</code> array where all inner arrays have the

	 * same length.

	 * @return an array of <code>int</code> produced by vectorization of the

	 * matrix.

	 */

	public final static int[] vectorizeByInner(int[][] matrix) {

		if (matrix == null || matrix.length == 0) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_4);

		}

		int inner_length = matrix[0].length;

		if (inner_length < 1) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_5);

		}

		int[] vector = new int[matrix.length * matrix[0].length];

		for (int i = 0; i < matrix.length; i++) {

			if (matrix[i] == null) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_10);

			}

			if (inner_length != matrix[i].length) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_7);

			}

			System.arraycopy(matrix[i], 0, vector, i * inner_length,

					inner_length);

		}

		return vector;

	}

	/**

	 * Convert a <code>double * double</code> array in a <code>double</code>

	 * array. The elements of the input array are assembled in the output array

	 * so that elements of same index in the outer array are consecutive. So :

	 * 

	 * <pre>

	 * [

	 * [1, 2, 3],

	 * [4, 5, 6]

	 * ]

	 * </pre>

	 * 

	 * result in :

	 * 

	 * <pre>

	 * [1, 4, 2, 5, 3, 6]

	 * </pre>

	 * 

	 * that is, "column first".

	 *

	 * @param matrix a <code>double * double</code> array where all inner arrays

	 * have the same length.

	 * @return an array of <code>double</code> produced by vectorization of the

	 * matrix.

	 */

	public final static double[] vectorizeByOuter(double[][] matrix) {

		if (matrix == null || matrix.length == 0) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_8);

		}

		int inner_length = matrix[0].length;

		int outer_length = matrix.length;

		if (inner_length < 1) {

			throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_9);

		}

		double[] vector = new double[matrix.length * matrix[0].length];

		for (int i = 0; i < matrix.length; i++) {

			if (matrix[i] == null) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_10);

			}

			if (inner_length != matrix[i].length) {

				throw new IllegalArgumentException(TXMCoreMessages.VectorizeArray_11);

			}

			for (int j = 0; j < matrix[i].length; j++) {

				vector[(j * outer_length) + i] = matrix[i][j];

			}

		}

		return vector;

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.utils;

import java.util.Arrays;

// TODO: Auto-generated Javadoc

/**

 * Various utilities method for printing arrays.

 * 

 * @author sloiseau

 * 

 */

public final class PrintArray {

	/**

	 * Double array.

	 *

	 * @param matrix the matrix

	 * @return the string

	 */

	public final static String doubleArray(double[][] matrix) {

		// DoubleMatrix2D m = new SparseDoubleMatrix2D(matrix);

		// return m.toString();

		StringBuffer sb = new StringBuffer();

		for (int i = 0; i < matrix.length; i++) {

			sb.append(Arrays.toString(matrix[i]));

		}

		return sb.toString();

	}

	/**

	 * Int array.

	 *

	 * @param matrix the matrix

	 * @return the string

	 */

	public final static String intArray(int[][] matrix) {

		double[][] doublematrix = new double[matrix.length][matrix[0].length];

		for (int i = 0; i < matrix.length; i++) {

			for (int j = 0; j < doublematrix[i].length; j++) {

				doublematrix[i][j] = matrix[i][j];

			}

		}

		return doubleArray(doublematrix);

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2013-05-06 17:38:43 +0200 (lun., 06 mai 2013) $

// $LastChangedRevision: 2386 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.core.utils;

// TODO: Auto-generated Javadoc

/**

 * Various utility methods for checking consistency of matrix as java array of

 * arrays.

 * 

 * @author sloiseau

 * 

 */

public final class CheckArray {

	/**

	 * Check if an array is not null (or 0-length), does not include null inner

	 * array (or 0 length), and if all inner arrays have the same length.

	 *

	 * @param array the array

	 * @return <code>true</code> if the condition are satisfied,

	 * <code>false</code> otherwise.

	 */

	public final static boolean checkMatrixRepresentation(int[][] array) {

		// same code as in #checkMatrixRepresentation(double[][])

		if (array == null)

			return false;

		int length = array.length;

		if (length < 1)

			return false;

		if (array[0] == null)

			return false;

		int firstElementLength = array[0].length;

		if (firstElementLength == 0)

			return false;

		for (int i = 0; i < array.length; i++) {

			if (array[i] == null)

				return false;

			if (array[i].length != firstElementLength)

				return false;

		}

		return true;

	}

	/**

	 * Check if an array is not null (or 0-length), does not include null inner

	 * array (or 0 length), and if all inner arrays have the same length.

	 *

	 * @param array the array

	 * @return <code>true</code> if the condition are satisfied,

	 * <code>false</code> otherwise.

	 */

	public final static boolean checkMatrixRepresentation(double[][] array) {

		// same code as in #checkMatrixRepresentation(int[][])

		if (array == null)

			return false;

		int length = array.length;

		if (length < 1)

			return false;

		if (array[0] == null)

			return false;

		int firstElementLength = array[0].length;

		if (firstElementLength == 0)

			return false;

		for (int i = 0; i < array.length; i++) {

			if (array[i] == null)

				return false;

			if (array[i].length != firstElementLength)

				return false;

		}

		return true;

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate:$

// $LastChangedRevision:$

// $LastChangedBy:$ 

//

package org.txm.statsengine.r.core;

import org.txm.Toolbox;

import org.txm.Watcher;

// TODO: Auto-generated Javadoc

/**

 * The Class RserveWatcher.

 */

//FIXME: not used ?

public class RserveWatcher extends Watcher	{

	/**

	 * Instantiates a new rserve watcher.

	 */

	public RserveWatcher()

	{

		this.processname = "RSERVE"; //$NON-NLS-1$

	}

	/* (non-Javadoc)

	 * @see org.txm.Watcher#check()

	 */

	@Override

	protected boolean check() {

		RWorkspace rw;

		try {

			rw = RWorkspace.getRWorkspaceInstance();

		} catch (RWorkspaceException e1) {

			System.out.println("Rserve watcher encounter an error: "+e1); //$NON-NLS-1$

			return false;

		}

		if (rw == null)

		{

			return false;

		}

		else

		{

			try {

				rw.eval("print(\"test\")"); //$NON-NLS-1$

			} catch (Exception e) {

				System.out.println("Rserve watcher encounter an error: "+e); //$NON-NLS-1$

				return false;

			}

		}

		return true;

	}

	/* (non-Javadoc)

	 * @see org.txm.Watcher#restart()

	 */

	@Override

	protected boolean restart() {

		return Toolbox.restartStatEngine(true);

	}

}

// Copyright © 2010-2013 ENS de Lyon.

// Copyright © 2007-2010 ENS de Lyon, CNRS, INRP, University of

// Lyon 2, University of Franche-Comté, University of Nice

// Sophia Antipolis, University of Paris 3.

// 

// The TXM platform is free software: you can redistribute it

// and/or modify it under the terms of the GNU General Public

// License as published by the Free Software Foundation,

// either version 2 of the License, or (at your option) any

// later version.

// 

// The TXM platform is distributed in the hope that it will be

// useful, but WITHOUT ANY WARRANTY; without even the implied

// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR

// PURPOSE. See the GNU General Public License for more

// details.

// 

// You should have received a copy of the GNU General

// Public License along with the TXM platform. If not, see

// http://www.gnu.org/licenses.

// 

// 

// 

// $LastChangedDate: 2015-06-15 15:29:16 +0200 (Mon, 15 Jun 2015) $

// $LastChangedRevision: 2989 $

// $LastChangedBy: mdecorde $ 

//

package org.txm.statsengine.r.core;

import java.io.File;

import org.rosuda.REngine.Rserve.RConnection;

import org.txm.statsengine.r.core.messages.RCoreMessages;

import org.txm.utils.OSDetector;

import org.txm.utils.StreamHog;

import org.txm.utils.logger.Log;

// TODO: Auto-generated Javadoc

/**

 * Helper class that consumes output of a process. In addition, it filter output

 * of the REG command on Windows to look for InstallPath registry entry which

 * specif ies the location of R.

 * 

 * @author RServe library

 */

/**

 * simple class that start Rserve locally if it's not running already - see

 * mainly <code>checkLocalRserve</code> method. It spits out quite some

 * debugging outout of the console, so feel free to modif y it for your

 * application if desired.

 * <p>

 * <i>Important:</i> All applications should shutdown every Rserve that they

 * started! Never leave Rserve running if you started it after your application

 * quits since it may pose a security risk. Inform the user if you started an

 * Rserve instance.

 */

public class StartRserve {

	/** shortcut to <code>launchRserve(cmd, "--no-save --slave", "--no-save --slave", false)</code>. */

	public static Process Rserveprocess;

	/**

	 * Launch rserve.

	 *

	 * @param cmd the cmd

	 * @param options 

	 * @return true, if successful

	 */

	protected static boolean launchRserve(String cmd, int port, boolean debug, String rArgs, String rServeArgs) {

		if (new File(cmd).exists() && !new File(cmd).isDirectory()

				&& new File(cmd).canExecute())

			return launchRserve(cmd,

					"--no-save --slave --encoding utf8 "+rArgs, "--RS-encoding utf8 --no-save --slave --encoding utf8 "+rServeArgs, port, debug); //$NON-NLS-1$ //$NON-NLS-2$

		return false;

	}

	/**

	 * attempt to start Rserve. Note: parameters are <b>not</b> quoted, so avoid

	 * using any quotes in arguments

	 *

	 * @param cmd command necessary to start R

	 * @param rargs arguments are are to be passed to R

	 * @param rsrvargs arguments to be passed to Rserve

	 * @param debug the debug

	 * @return <code>true</code> if Rserve is running or was successfully

	 * started, <code>false</code> otherwise.

	 */

	protected static boolean launchRserve(String cmd, String rargs,

			String rsrvargs, int port, boolean debug) {

		//System.out.println("LAUNCH R SERVER "+cmd+" "+port+" "+debug);

		try {

			String[] cmdline = null;

			// FIXME: don't forget to remove this Window dedicated code if we manage to use http_proxy command line argument

			boolean isWindows = false;

			// Windows OS

			if (OSDetector.isFamilyWindows()) {

				isWindows = true; /* Windows startup */

				// TODO: old tests for setting proxy in R

				//Windows : set --internet2 option to manage proxy if any

//				// set Proxy configuration using Eclipse RCP stored values

//				String proxy_conf = "";

//				ProxyConf conf = new ProxyConf(RWorkspace.getRWorkspaceInstance());

//				if (conf.mustSetProxyConfiguration()) {

//					proxy_conf = "http_proxy="+conf.getHttpProxyUrl();

//					rsrvargs += " "+proxy_conf; // add the http_proxy parameter

//					Log.info("Run Rserve with proxy configuration: "+proxy_conf);

//				}

				cmdline = new String[] {

						cmd,

						rargs, 

						"-e", //$NON-NLS-1$

						"library(Rserve);Rserve(" //$NON-NLS-1$ 

						+ (debug ? "TRUE" : "FALSE")  //$NON-NLS-1$ //$NON-NLS-2$

						+ ",port=" + port + "" //$NON-NLS-1$ //$NON-NLS-2$

						+ ",args='" //$NON-NLS-1$

						+ rsrvargs + "')\" " //$NON-NLS-1$

				};	

			}

			// Mac, Linux

			else {

				cmdline = new String[] {

						"/bin/sh", //$NON-NLS-1$

						"-c", //$NON-NLS-1$

						"echo 'library(Rserve);Rserve(" //$NON-NLS-1$

						+ (debug ? "TRUE" : "FALSE") //$NON-NLS-1$ //$NON-NLS-2$

						+ ",port="+port+"" //$NON-NLS-1$ //$NON-NLS-2$

						+ ",args=\"" + rsrvargs //$NON-NLS-1$

						+ "\")'|" + cmd //$NON-NLS-1$ 

						+ " " + rargs }; //$NON-NLS-1$

			}

//			ProcessBuilder builder = new ProcessBuilder(cmdline);

//			Rserveprocess = builder.start();

			Runtime runtime = Runtime.getRuntime();

			Rserveprocess = runtime.exec(cmdline);

			//Log.info(Messages.StartRserve_0+Arrays.toString(cmdline));

			StreamHog errStream = new StreamHog(Rserveprocess.getErrorStream(), debug);

			StreamHog inStream = new StreamHog(Rserveprocess.getInputStream(), debug);

			RWorkspace.getRWorkspaceInstance().registerLogger(errStream, inStream);

			if (!debug && !isWindows)

				Rserveprocess.waitFor();

			// System.out.println("call terminated, let us try to connect ...");