/ - Diff - Plateforme TXM - Forge du Centre Blaise Pascal

     	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
     	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
     	<classpathentry kind="src" path="src"/>
     	<classpathentry exported="true" kind="lib" path="lib/colt-1.2.0.jar"/>
     	<classpathentry exported="true" kind="lib" path="lib/REngine.jar"/>
     	<classpathentry exported="true" kind="lib" path="lib/RserveEngine.jar"/>
     	<classpathentry kind="output" path="bin"/>
     </classpath>

     Bundle-Name: R Statistics Engine Core
     Bundle-SymbolicName: org.txm.statsengine.r.core;singleton:=true
     Bundle-Version: 1.0.0.qualifier
     Require-Bundle: org.txm.core;bundle-version="0.7.0",
      org.eclipse.core.runtime,
      org.txm.utils;bundle-version="1.0.0"
     Require-Bundle: org.txm.libs.colt;bundle-version="1.0.0";visibility:=reexport,
      org.txm.libs.rserve;bundle-version="0.0.0";visibility:=reexport,
      org.txm.statsengine.core;bundle-version="1.0.0";visibility:=reexport,
      org.txm.core;bundle-version="0.7.0",
      org.eclipse.core.runtime
     Bundle-RequiredExecutionEnvironment: JavaSE-1.6
     Bundle-ActivationPolicy: lazy
     Export-Package: cern.clhep,
      cern.colt,
      cern.colt.bitvector,
      cern.colt.buffer,
      cern.colt.function,
      cern.colt.list,
      cern.colt.list.adapter,
      cern.colt.map,
      cern.colt.matrix,
      cern.colt.matrix.bench,
      cern.colt.matrix.doublealgo,
      cern.colt.matrix.impl,
      cern.colt.matrix.linalg,
      cern.colt.matrix.objectalgo,
      cern.jet.math,
      cern.jet.random,
      cern.jet.random.engine,
      cern.jet.random.sampling,
      cern.jet.stat,
      cern.jet.stat.quantile,
      corejava,
      hep.aida,
      hep.aida.bin,
      hep.aida.ref,
      org.rosuda.REngine,
      org.rosuda.REngine.Rserve,
      org.rosuda.REngine.Rserve.protocol,
      org.txm.statsengine.core,
      org.txm.statsengine.core.data,
      org.txm.statsengine.core.utils,
      org.txm.statsengine.r.core,
     Export-Package: org.txm.statsengine.r.core,
      org.txm.statsengine.r.core.data,
      org.txm.statsengine.r.core.exceptions,
      org.txm.statsengine.r.core.messages,
      org.txm.statsengine.r.core.preferences,
      org.txm.statsengine.r.core.rcolt
     Bundle-ClassPath: REngine.jar,
      RserveEngine.jar,
      .,
      colt-1.2.0.jar
     Bundle-Vendor: Textometrie.org

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core;
     import org.txm.statsengine.core.StatException;
     // TODO: Auto-generated Javadoc
     /**
      * Super-class of all exception related to the R engine.
+     *
      * @author sloiseau
      */
     public class RWorkspaceException extends StatException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 1630828823146927953L;
     	/**
     	 * Instantiates a new r workspace exception.
     	 */
     	public RWorkspaceException() {
     		super();
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RWorkspaceException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RWorkspaceException(String arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RWorkspaceException(Throwable arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core;
     import org.txm.statsengine.r.core.messages.RCoreMessages;
     // TODO: Auto-generated Javadoc
     /**
      * An exception indicating an error during the evaluation of an expression by
      * the R engine.
+     *
      * @author sloiseau
      */
     public class RException extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = -3459835604570896478L;
     	/**
     	 * Instantiates a new r exception.
     	 */
     	public RException() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param msg the msg
     	 */
     	public RException(String msg) {
     		super(msg);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param expr the expr
     	 * @param msg the msg
     	 */
     	public RException(String expr, String msg) {
     		super(RCoreMessages.RException_0 + msg + RCoreMessages.RException_1 + RCoreMessages.RException_2 + expr);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RException(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core;
     // TODO: Auto-generated Javadoc
     /**
      * The Class RServeException.
      */
     public class RServeException extends RException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 1L;
     	/**
     	 * Instantiates a new r serve exception.
     	 */
     	public RServeException() {
     		super();
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RServeException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RServeException(String arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RServeException(Throwable arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
+    }

     import org.rosuda.REngine.REngineException;
     import org.rosuda.REngine.Rserve.RConnection;
     import org.rosuda.REngine.Rserve.RserveException;
     import org.txm.core.messages.TXMCoreMessages;
     import org.txm.statsengine.core.StatException;
     import org.txm.statsengine.core.data.QuantitativeDataStructure;
     import org.txm.statsengine.core.messages.StatsEngineCoreMessages;
     import org.txm.statsengine.core.utils.VectorizeArray;
     import org.txm.statsengine.r.core.data.RObjectAlreadyExist;
     import org.txm.statsengine.r.core.exceptions.RException;
     import org.txm.statsengine.r.core.exceptions.RObjectAlreadyExist;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import org.txm.statsengine.r.core.messages.RCoreMessages;
     import org.txm.statsengine.r.core.rcolt.RColt;
     import org.txm.utils.OSDetector;
     import org.txm.utils.StreamHog;
     import org.txm.utils.SystemProxyDetector;
     import org.txm.utils.logger.Log;
     import org.txm.utils.network.SystemProxyDetector;
     import cern.colt.list.DoubleArrayList;
     import cern.colt.list.IntArrayList;
-...
     		if (isRServerOk) {
     			Log.finest("RSERVE_ACTIVATED"); //$NON-NLS-1$
     			System.out.println(TXMCoreMessages.CONNECTED_TO_STATS_MODULE);
     			System.out.println(RCoreMessages.CONNECTED_TO_STATS_MODULE);
     			RserveProcess = StartRserve.Rserveprocess;
+    		}
     		return isRServerOk;
-...
     				arguments_as_string[i] = "NULL"; //$NON-NLS-1$
     			} else {
     				if (!containsVariable(arguments[i].getSymbol())) {
     					throw new RWorkspaceException(TXMCoreMessages.REQUESTED_OBJECT
     							+ arguments[i].getSymbol()
     							+ TXMCoreMessages.NOT_FOUND_IN_R);
     					throw new RWorkspaceException(NLS.bind(RCoreMessages.REQUESTED_OBJECT_NOT_FOUND_IN_R, arguments[i].getSymbol()));
+    				}
     				arguments_as_string[i] = arguments[i].getSymbol();
+    			}
-...
     	public int[][] evalToInt2D(String exp) throws RWorkspaceException {
     		int[][] res = null;
     		try {
     			int[] dims = eval(TXMCoreMessages.MatrixImpl_2+exp+")").asIntegers(); //$NON-NLS-2$
     			int[] dims = eval(StatsEngineCoreMessages.MatrixImpl_2+exp+")").asIntegers(); //$NON-NLS-2$
     			int ncol = dims[1];
     			int nrow = dims[0];
     			int[] tmp = eval("c("+exp+")").asIntegers(); //$NON-NLS-1$ //$NON-NLS-2$
-...
     		try {
     			return list.asList().at(item_name);
     		} catch (REXPMismatchException e) {
     			throw new RWorkspaceException(TXMCoreMessages.ERROR_EXTRACT_ITEM
     			throw new RWorkspaceException(RCoreMessages.ERROR_EXTRACT_ITEM
     					+ e.getMessage());
+    		}
+    	}

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.exceptions;
     import org.txm.statsengine.core.StatException;
     // TODO: Auto-generated Javadoc
     /**
      * Super-class of all exception related to the R engine.
+     *
      * @author sloiseau
      */
     public class RWorkspaceException extends StatException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 1630828823146927953L;
     	/**
     	 * Instantiates a new r workspace exception.
     	 */
     	public RWorkspaceException() {
     		super();
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RWorkspaceException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RWorkspaceException(String arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r workspace exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RWorkspaceException(Throwable arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.exceptions;
     import org.txm.statsengine.r.core.messages.RCoreMessages;
     // TODO: Auto-generated Javadoc
     /**
      * An exception indicating an error during the evaluation of an expression by
      * the R engine.
+     *
      * @author sloiseau
      */
     public class RException extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = -3459835604570896478L;
     	/**
     	 * Instantiates a new r exception.
     	 */
     	public RException() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param msg the msg
     	 */
     	public RException(String msg) {
     		super(msg);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param expr the expr
     	 * @param msg the msg
     	 */
     	public RException(String expr, String msg) {
     		super(RCoreMessages.RException_0 + msg + RCoreMessages.RException_1 + RCoreMessages.RException_2 + expr);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RException(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.exceptions;
     // TODO: Auto-generated Javadoc
     /**
      * Exception thrown if a symbol without corresponding object in the R workspace
      * is used.
+     *
      * @author sloiseau
      */
     public class RObjectDoesNotExist extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = -1344530765750521820L;
     	/**
     	 * Instantiates a new r object does not exist.
     	 */
     	public RObjectDoesNotExist() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RObjectDoesNotExist(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectDoesNotExist(String arg0) {
     		super(arg0);
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectDoesNotExist(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.exceptions;
     // TODO: Auto-generated Javadoc
     /**
      * The Class RServeException.
      */
     public class RServeException extends RException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 1L;
     	/**
     	 * Instantiates a new r serve exception.
     	 */
     	public RServeException() {
     		super();
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RServeException(String arg0, Throwable arg1) {
     		super(arg0, arg1);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RServeException(String arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
     	/**
     	 * Instantiates a new r serve exception.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RServeException(Throwable arg0) {
     		super(arg0);
     		// TODO Auto-generated constructor stub
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.exceptions;
     // TODO: Auto-generated Javadoc
     /**
      * When one try to create an object with a symbol already existing in the
      * workspace.
+     *
      * @author sloiseau
      */
     public class RObjectAlreadyExist extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 3386015668080138287L;
     	/**
     	 * Instantiates a new r object already exist.
     	 */
     	public RObjectAlreadyExist() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RObjectAlreadyExist(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectAlreadyExist(String arg0) {
     		super(arg0);
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectAlreadyExist(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     import org.eclipse.core.runtime.preferences.DefaultScope;
     import org.osgi.framework.FrameworkUtil;
     import org.osgi.service.prefs.Preferences;
     import org.txm.utils.preferences.TXMPreferences;
     import org.txm.core.preferences.TXMPreferences;
     /**
      * Default preferences initializer.

     //
     package org.txm.statsengine.r.core;
     import org.txm.Toolbox;
     import org.txm.Watcher;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import org.txm.utils.Watcher;
     // TODO: Auto-generated Javadoc
     /**

     import java.io.IOException;
     import org.txm.core.preferences.TXMPreferences;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import org.txm.statsengine.r.core.messages.RCoreMessages;
     import org.txm.statsengine.r.core.preferences.RPreferences;
     import org.txm.utils.OSDetector;
     import org.txm.utils.logger.Log;
     import org.txm.utils.preferences.TXMPreferences;
     /**
      * R statistics engine. Contains methods to start, stop, kill, etc. the R and RServe process.

     import java.io.FileWriter;
     import java.io.IOException;
     import org.eclipse.core.runtime.Platform;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import org.txm.utils.OSDetector;

     package org.txm.statsengine.r.core.messages;
     import org.eclipse.osgi.util.NLS;
     import org.txm.core.messages.TXMCoreMessages;
     import org.txm.utils.messages.Utf8NLS;
     public class RCoreMessages extends NLS {
-...
     	public static String RSERVE_PATH_NOT_SET_ERROR;
     	public static String RSERVE_PATH_SET_ERROR;
     	public static String CONNECTED_TO_STATS_MODULE;
     	public static String CHAR_VECTOR_ADDED_TO_WORKSPACE;
     	public static String CONNECTION_OK;
     	public static String ERROR_EXTRACT_ITEM;
     	public static String REQUESTED_OBJECT_NOT_FOUND_IN_R;
     	// FIXME: unused keys
-...
     	static {
     		// initialize resource bundle
     		TXMCoreMessages.initializeMessages(BUNDLE_NAME, RCoreMessages.class);
     		Utf8NLS.initializeMessages(BUNDLE_NAME, RCoreMessages.class);
+    	}
     	private RCoreMessages() {

     StartRserve_3  = Rserve already running on port
     StartRserve_4  = try R path : 'R'
     StartRserve_6  = try R path :
     CHAR_VECTOR_ADDED_TO_WORKSPACE = Vector "{1}" ({0,number,integer} "character") has been transmited to the Statistics Engine.
     CONNECTED_TO_STATS_MODULE = connected.
     CONNECTION_OK = Connected to the Statistics Engine.
     ERROR_EXTRACT_ITEM = ** Error extracting list item:
     REQUESTED_OBJECT_NOT_FOUND_IN_R = The requested object ({0}) was not found in the R workspace.

     StartRserve_3  = Rserve déja démarré sur le port
     StartRserve_4  = Essai du chemin de R : 'R'
     StartRserve_6  = Essai du chemin de R :
     CHAR_VECTOR_ADDED_TO_WORKSPACE = Le vecteur "{1}" ({0,number,integer} valeurs "character") a été transmis au Moteur Statistique.
     CONNECTED_TO_STATS_MODULE = connecté.
     CONNECTION_OK = Connexion au Moteur Statistique établie.
     ERROR_EXTRACT_ITEM = ** Erreur lors de l'extraction de la liste d'items : \
     REQUESTED_OBJECT_NOT_FOUND_IN_R = L'objet demandé ({0}) n'a pas été trouvé dans l'espace de travail R.

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.data;
     import org.txm.statsengine.r.core.RWorkspaceException;
     // TODO: Auto-generated Javadoc
     /**
      * Exception thrown if a symbol without corresponding object in the R workspace
      * is used.
+     *
      * @author sloiseau
      */
     public class RObjectDoesNotExist extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = -1344530765750521820L;
     	/**
     	 * Instantiates a new r object does not exist.
     	 */
     	public RObjectDoesNotExist() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RObjectDoesNotExist(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectDoesNotExist(String arg0) {
     		super(arg0);
+    	}
     	/**
     	 * Instantiates a new r object does not exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectDoesNotExist(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     // 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 (Mon, 06 May 2013) $
     // $LastChangedRevision: 2386 $
     // $LastChangedBy: mdecorde $
     //
     package org.txm.statsengine.r.core.data;
     import org.txm.statsengine.r.core.RWorkspaceException;
     // TODO: Auto-generated Javadoc
     /**
      * When one try to create an object with a symbol already existing in the
      * workspace.
+     *
      * @author sloiseau
      */
     public class RObjectAlreadyExist extends RWorkspaceException {
     	/** The Constant serialVersionUID. */
     	private static final long serialVersionUID = 3386015668080138287L;
     	/**
     	 * Instantiates a new r object already exist.
     	 */
     	public RObjectAlreadyExist() {
     		super();
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 * @param arg1 the arg1
     	 */
     	public RObjectAlreadyExist(String arg0, Throwable arg1) {
     		super(arg0, arg1);
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectAlreadyExist(String arg0) {
     		super(arg0);
+    	}
     	/**
     	 * Instantiates a new r object already exist.
+    	 *
     	 * @param arg0 the arg0
     	 */
     	public RObjectAlreadyExist(Throwable arg0) {
     		super(arg0);
+    	}
+    }

     import org.txm.statsengine.core.StatException;
     import org.txm.statsengine.core.data.Vector;
     import org.txm.statsengine.core.utils.ArrayIndex;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     // TODO: Auto-generated Javadoc
     /**

     import org.rosuda.REngine.REXP;
     import org.rosuda.REngine.REXPMismatchException;
     import org.txm.core.messages.TXMCoreMessages;
     import org.txm.statsengine.core.StatException;
     import org.txm.statsengine.core.data.Matrix;
     import org.txm.statsengine.core.data.Vector;
     import org.txm.statsengine.core.messages.StatsEngineCoreMessages;
     import org.txm.statsengine.core.utils.ArrayIndex;
     import org.txm.statsengine.r.core.RException;
     import org.txm.statsengine.r.core.RWorkspace;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.r.core.exceptions.RException;
     import org.txm.statsengine.r.core.exceptions.RObjectDoesNotExist;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import org.txm.statsengine.r.core.messages.RCoreMessages;
     import org.txm.utils.CharsetDetector;
     import org.txm.utils.OSDetector;
-...
     		this(matrix);
     		if (rowNames == null) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_4);
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_4);
+    		}
     		//		if (rowNames.length != nrow) {
     		//			throw new IllegalArgumentException(Messages.MatrixImpl_5);
-...
     		rw.assignRowNamesToMatrix(symbol, new VectorImpl(rowNames).getSymbol());
     		if (columnNames == null) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_6);
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_6);
+    		}
     		//		if (columnNames.length != ncol) {
     		//			throw new IllegalArgumentException(Messages.MatrixImpl_7
-...
     		this(matrix);
     		if (lineNames == null) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_4);
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_4);
+    		}
     		//		if (lineNames.length != nrow) {
     		//			throw new IllegalArgumentException(Messages.MatrixImpl_5);
-...
     		rw.assignRowNamesToMatrix(symbol, new VectorImpl(lineNames).getSymbol());
     		if (partNames == null) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_6);
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_6);
+    		}
     		//		if (partNames.length != ncol) {
     		//			throw new IllegalArgumentException(Messages.MatrixImpl_7
-...
     	protected MatrixImpl(String symbol) throws RWorkspaceException {
     		super(symbol);
     		if (!rw.containsVariable(symbol)) {
     			throw new RObjectDoesNotExist(TXMCoreMessages.MatrixImpl_0 + symbol
     					+ TXMCoreMessages.MatrixImpl_1);
     			throw new RObjectDoesNotExist(StatsEngineCoreMessages.MatrixImpl_0 + symbol
     					+ StatsEngineCoreMessages.MatrixImpl_1);
+    		}
     		REXP res = rw.eval("dim(" + symbol + ")"); //$NON-NLS-2$ //$NON-NLS-1$
     		int[] dim = null;
-...
     				throw new RWorkspaceException(e);
+    			}
     		} else if (r.isNull()) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_19);
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_19);
     		} else {
     			// System.out.println("row: " + row);
     			// System.out.println("col: " + col);
     			// System.out.println("nrow: " + nrow);
     			// System.out.println("ncol: " + ncol);
     			// System.out.println(rw.eval("print(" + getSymbol() + ");"));
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_20
     					+ r.getAttribute(TXMCoreMessages.MatrixImpl_21));
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_20
     					+ r.getAttribute(StatsEngineCoreMessages.MatrixImpl_21));
+    		}
+    	}
-...
     		int ncol = this.getNColumns();
     		if (index < 0 || index >= ncol) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_28 + index
     					+ TXMCoreMessages.MatrixImpl_29 + ncol + ")"); //$NON-NLS-1$
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_28 + index
     					+ StatsEngineCoreMessages.MatrixImpl_29 + ncol + ")"); //$NON-NLS-1$
+    		}
     		String colName = createSymbole(Vector.class);
     		rw.voidEval(colName + "<- " + symbol + "[ ," + (index + 1) + "];"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-...
     	@Override
     	public int getNColumns() {
     		try {
     			return RWorkspace.getRWorkspaceInstance().eval(TXMCoreMessages.MatrixImpl_2+symbol+")[2]").asInteger(); //$NON-NLS-2$
     			return RWorkspace.getRWorkspaceInstance().eval(StatsEngineCoreMessages.MatrixImpl_2+symbol+")[2]").asInteger(); //$NON-NLS-2$
     		} catch (Exception e) {
     			System.out.println("Matrix: failed to get nrow: "+e); //$NON-NLS-1$
+    		}
-...
     	@Override
     	public int getNRows() {
     		try {
     			return RWorkspace.getRWorkspaceInstance().eval(TXMCoreMessages.MatrixImpl_2+symbol+")[1]").asInteger(); //$NON-NLS-2$
     			return RWorkspace.getRWorkspaceInstance().eval(StatsEngineCoreMessages.MatrixImpl_2+symbol+")[1]").asInteger(); //$NON-NLS-2$
     		} catch (Exception e) {
     			System.out.println(TXMCoreMessages.MatrixImpl_67+e);
     			System.out.println(StatsEngineCoreMessages.MatrixImpl_67+e);
+    		}
     		return 0;
+    	}
-...
     	public Vector getRow(int index) throws RException, RWorkspaceException {
     		int nrow = getNRows();
     		if (index < 0 || index >= nrow) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_22 + index
     					+ TXMCoreMessages.MatrixImpl_23 + nrow + ")"); //$NON-NLS-1$
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_22 + index
     					+ StatsEngineCoreMessages.MatrixImpl_23 + nrow + ")"); //$NON-NLS-1$
+    		}
     		String rowName = createSymbole(Vector.class);
     		rw.voidEval(rowName + "<- " + symbol + "[" + (index + 1) + ", ];"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
-...
     		int linesize = rw.eval("dim(tmpmat)[1]").asInteger(); //$NON-NLS-1$
     		int ncol = this.getNColumns();
     		if (colsize != ncol) {
     			System.out.println(TXMCoreMessages.MatrixImpl_73+ncol+" imported="+colsize); //$NON-NLS-2$
     			System.out.println(StatsEngineCoreMessages.MatrixImpl_73+ncol+" imported="+colsize); //$NON-NLS-2$
     			return false;
+    		}
-...
     				try {
     					rowNames = getRowNames().asStringsArray();
     				} catch (StatException e) {
     					System.out.println(TXMCoreMessages.MatrixImpl_79);
     					System.out.println(StatsEngineCoreMessages.MatrixImpl_79);
     					org.txm.utils.logger.Log.printStackTrace(e);
     					return;
+    				}
-...
     			try {
     				rowNames = getRowNames().asStringsArray();
     			} catch (StatException e) {
     				System.out.println(TXMCoreMessages.MatrixImpl_79);
     				System.out.println(StatsEngineCoreMessages.MatrixImpl_79);
     				org.txm.utils.logger.Log.printStackTrace(e);
     				return;
+    			}
     			String lastRowName = rowNames[last];
     			System.out.println("table<-matrix(table[c(-"+idx+"),],nrow=1,dimnames = list(rownames="+lastRowName+",colnames(table)))"); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
     		} else {
     			System.out.println(TXMCoreMessages.MatrixImpl_88);
     			System.out.println(StatsEngineCoreMessages.MatrixImpl_88);
+    		}
+    	}
-...
     		int nrow = this.getNRows();
     		int ncol = this.getNColumns();
     		if (row < 0 || row >= nrow) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_10 + row
     					+ TXMCoreMessages.MatrixImpl_11 + nrow + ")"); //$NON-NLS-1$
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_10 + row
     					+ StatsEngineCoreMessages.MatrixImpl_11 + nrow + ")"); //$NON-NLS-1$
+    		}
     		if (col < 0 || col >= ncol) {
     			throw new IllegalArgumentException(TXMCoreMessages.MatrixImpl_13 + col
     					+ TXMCoreMessages.MatrixImpl_14 + ncol + ")"); //$NON-NLS-1$
     			throw new IllegalArgumentException(StatsEngineCoreMessages.MatrixImpl_13 + col
     					+ StatsEngineCoreMessages.MatrixImpl_14 + ncol + ")"); //$NON-NLS-1$
+    		}
     		// appel à R
     		try {

     import org.txm.statsengine.core.StatException;
     import org.txm.statsengine.core.data.ContingencyTable;
     import org.txm.statsengine.core.data.Vector;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import cern.colt.matrix.DoubleMatrix2D;

     package org.txm.statsengine.r.core.data;
     import org.rosuda.REngine.REXP;
     import org.txm.core.messages.TXMCoreMessages;
     import org.txm.core.results.TXMResult;
     import org.txm.statsengine.core.data.QuantitativeDataStructure;
     import org.txm.statsengine.core.data.Vector;
     import org.txm.statsengine.core.messages.StatsEngineCoreMessages;
     import org.txm.statsengine.r.core.RWorkspace;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.r.core.exceptions.RObjectDoesNotExist;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     // TODO: Auto-generated Javadoc
     /**
-...
     	protected void removeFromRWorkspace() throws RWorkspaceException {
     		if (!rw.containsVariable(symbol)) {
     			throw new RObjectDoesNotExist(
     					TXMCoreMessages.QuantitativeDataStructureImpl_2);
     					StatsEngineCoreMessages.QuantitativeDataStructureImpl_2);
+    		}
     		rw.voidEval("rm(" + symbol + ")"); //$NON-NLS-1$ //$NON-NLS-2$
+    	}

     //
     package org.txm.statsengine.r.core.data;
     import org.txm.core.messages.TXMCoreMessages;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.core.messages.StatsEngineCoreMessages;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     // TODO: Auto-generated Javadoc
     /**
-...
     	 * @throws RWorkspaceException the r workspace exception
     	 */
     	public Factor(String values) throws RWorkspaceException {
     		throw new UnsupportedOperationException(TXMCoreMessages.Factor_0);
     		throw new UnsupportedOperationException(StatsEngineCoreMessages.Factor_0);
+    	}
     	/**
-...
     	 * @return the levels
     	 */
     	public String[] getLevels() {
     		throw new UnsupportedOperationException(TXMCoreMessages.Factor_0);
     		throw new UnsupportedOperationException(StatsEngineCoreMessages.Factor_0);
+    	}
     	@Override

     //
     package org.txm.statsengine.r.core.data;
     import org.txm.statsengine.r.core.RWorkspaceException;
     import org.txm.statsengine.r.core.exceptions.RWorkspaceException;
     import cern.colt.matrix.DoubleMatrix2D;

     source.. = src/
     output.. = bin/
     bin.includes = META-INF/,\
                    .,\
                    lib/colt-1.2.0.jar,\
                    plugin.xml,\
                    lib/RserveEngine.jar,\
                    lib/REngine.jar
                    plugin.xml

Laboratoire ICAR » Plateforme TXM

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