Laboratoire ICAR » Plateforme TXM

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Manifest-Version: 1.0

Bundle-ManifestVersion: 2

Bundle-Name: org.txm.querycooccurrence.rcp

Bundle-SymbolicName: org.txm.querycooccurrence.rcp;singleton:=true

Bundle-Version: 1.0.0.qualifier

Bundle-Activator: listcooccurrences.Activator

Require-Bundle: org.eclipse.ui,

 org.eclipse.core.runtime,

 org.eclipse.core.expressions;bundle-version="3.4.500",

 org.txm.rcp;bundle-version="0.7.8",

 org.txm.core;bundle-version="0.7.0",

 org.txm.queryindex.rcp;bundle-version="1.0.0",

 org.txm.ca.core,

 org.txm.statsengine.r.core,

 org.txm.lexicaltable.core,

 org.txm.statsengine.core,

 org.txm.statsengine.r.rcp

Bundle-RequiredExecutionEnvironment: JavaSE-1.6

Bundle-ActivationPolicy: lazy

Export-Package: org.txm.functions.coocmatrix

Bundle-Vendor: Textometrie.org

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

<projectDescription>

	<name>QueryCooccurrencesRCP</name>

	<comment></comment>

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package org.txm.functions.coocmatrix;

import java.io.File;

import java.util.ArrayList;

import org.eclipse.core.runtime.IAdaptable;

import org.eclipse.jface.resource.ImageDescriptor;

import org.eclipse.ui.model.IWorkbenchAdapter;

import org.txm.ca.core.functions.CA;

import org.txm.ca.core.functions.ICAComputable;

import org.txm.core.results.TXMResult;

import org.txm.functions.ProgressWatcher;

import org.txm.lexicaltable.core.functions.LexicalTable;

import org.txm.lexicaltable.core.statsengine.r.data.LexicalTableImpl;

import org.txm.rcp.IImageKeys;

import org.txm.searchengine.cqp.clientExceptions.CqiClientException;

import org.txm.searchengine.cqp.corpus.Corpus;

import org.txm.searchengine.cqp.corpus.Partition;

import org.txm.searchengine.cqp.corpus.Property;

import org.txm.searchengine.cqp.corpus.QueryResult;

import org.txm.searchengine.cqp.corpus.query.Query;

import org.txm.statsengine.core.StatException;

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

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

import org.txm.utils.logger.Log;

public class QueryAutoCooccurrence extends TXMResult implements ICAComputable, IAdaptable {

	protected Corpus corpus;

	protected int[][] coocs;

	protected ArrayList<Query> queries;

	protected ArrayList<String> names;

	protected int dist;

	protected String struct = "";

	protected String symbol;

	protected static int noCoocMatrix = 1;

	protected static String prefixR = "CoocMatrix";

	protected int nNodes = 0;

	protected int nEdges = 0;

	protected int minCooc;

	protected boolean oriented = false;

	public QueryAutoCooccurrence(Corpus corpus, ArrayList<Query> queries, 

			ArrayList<String> names, int dist, int minCooc, String struct, boolean oriented, ProgressWatcher monitor) throws CqiClientException, RWorkspaceException {

		this.queries = queries;

		this.names = names;

		this.corpus = corpus;

		this.dist = dist;

		this.minCooc = minCooc;

		this.oriented = oriented;

		if (struct != null)

			this.struct = "within "+struct; 

		else

			this.struct = "within text";

		nNodes = queries.size();

		coocs = new int[queries.size()][queries.size()];

		if (monitor != null) monitor.beginTask("Querying cooccurrences...", nNodes);

		for (int i = 0 ; i < queries.size() ; i++) {

			int j = i;

			if (oriented) j = 0; // if the graph is not oriented, we don't need to evaluate all queries

			for (; j < queries.size() ; j++) {

				if (monitor != null) monitor.worked(1);

				String query = null;

				if (oriented)

					query = "("+queries.get(i)+"[]{0,"+dist+"}"+queries.get(j)+") "+this.struct;

				else

					query = "("+queries.get(i)+"[]{0,"+dist+"}"+queries.get(j)+")|("+queries.get(j)+"[]{0,"+dist+"}"+queries.get(i)+") "+this.struct;

				Log.info("ListCooc: query "+query);

				QueryResult result = corpus.query(new Query(query), "tmp", false);

				coocs[i][j] = result.getNMatch();

				if (coocs[i][j] >= minCooc) {

					nEdges++;

				} else {

					coocs[i][j] = 0;

				}

				result.drop();

			}

		}

		if (!oriented) //// if the graph is not oriented, copy upper triangle values to lower triangle values

			for (int i = 0 ; i < queries.size() ; i++) {

				for (int j = i ; j < queries.size() ; j++) {

					coocs[j][i] = coocs[i][j];

				}

			}

		if (monitor != null) monitor.done();

	}

	public String getName() {

		return corpus.getName()+ " d="+dist+ " min="+minCooc;

	}

	public Corpus getParent() {

		return corpus;

	}

	public String getSymbol() {

		return symbol;

	}

	public int getNNodes() {

		return nNodes;

	}

	public int getNEdges() {

		return nEdges;

	}

	private void sendToR() throws RWorkspaceException {

		if (symbol != null) return;

		this.symbol = prefixR+(QueryCooccurrence.noCoocMatrix ++);

		RWorkspace rw = RWorkspace.getRWorkspaceInstance();

		rw.eval("rm("+symbol+")");

		rw.addMatrixToWorkspace(symbol, coocs);

		rw.addVectorToWorkspace("cooclabels", names.toArray(new String[names.size()]));

		rw.eval("rownames("+symbol+") <- cooclabels");

		rw.eval("colnames("+symbol+") <- cooclabels");

	}

	public LexicalTable toLexicalTable() throws RWorkspaceException, CqiClientException {

		sendToR();

		RWorkspace rw = RWorkspace.getRWorkspaceInstance();

		rw.eval("LT<-"+this.getSymbol());

		rw.eval("LT<-LT[rowSums(LT) != 0, ]");

		rw.eval("LT<-LT[, colSums(LT) != 0]");

		rw.eval(this.getSymbol()+"LT<-LT");

		rw.eval("rm(LT)");

		LexicalTable table = new LexicalTable(corpus, corpus.getProperty("word"), new LexicalTableImpl(this.getSymbol()+"LT"));

		return table;

	}

	public boolean toGraphml(File outfile) throws RWorkspaceException {

		RWorkspace rw = null;

		try {

			rw = RWorkspace.getRWorkspaceInstance();

			rw.eval("library(\"igraph\")");

			Log.info("Package 'igraph' installed. Now running CoocMatrix");

		} catch (Exception e) {

			Log.printStackTrace(e);

			Log.warning("The 'igraph' package is not installed: "+e);

			boolean install = true;

			if (install) {

				Log.warning("Installing 'igraph'");

				try {

					rw.eval("install.packages(\"igraph\", dependencies=TRUE, repos=\"http://cran.rstudio.com\");");

				} catch(Exception e2) {

					Log.severe("Could not install the 'igraph' package");

					Log.printStackTrace(e2);

					return false;

				}

			} else {

				System.out.println("Operation canceled by user");

				return false;

			}

		}

		sendToR();

		outfile.delete();

		String orientationMode = "undirected";

		//if (oriented) orientationMode = "directed";

		rw.eval("library(igraph)");

		rw.eval("g <- graph.adjacency("+symbol+", weighted=T, mode = \""+orientationMode+"\", diag=FALSE)"); // create graph from matrix

		rw.eval("V(g)$label <- V(g)$name"); // copy names in labels

		//rw.eval("g <- set.vertex.attribute(g, \"label\", colnames("+symbol+"))");

		//rw.eval("g <- set.vertex.attribute(g, \"color\", value=colors)");

		String path = outfile.getAbsolutePath();//.replaceAll("\\\\", "\\\\")

		path = path.replace('\\', '/');

		rw.eval("write.graph(g, \""+path+"\", format = 'graphml')");

		return outfile.exists();

	}

	public Corpus getCorpus() {

		return corpus;

	}

	public int[][] getCoocs() {

		return coocs;

	}

	public ArrayList<Query> getQueries() {

		return queries;

	}

	public java.util.ArrayList<String> getNames() {

		return names;

	}

	public int getDist() {

		return dist;

	}

	public void printCoocs() {

		for (int i = 0 ; i < queries.size() ; i++) {

			System.out.print(names.get(i));

			for (int j = 0 ; j < queries.size() ; j++) {

				System.out.print("\t"+coocs[i][j]);

			}

			System.out.println();

		}

	}

	@Override

	public void clean() {

		// TODO Auto-generated method stub

	}

	public boolean toTxt(File outfile, String encoding, String colseparator,

			String txtseparator) throws Exception {

		return toGraphml(outfile);

	}

	public String toString() {

		return getName();

	}

	@Override

	public CA toCA() throws StatException, CqiClientException {

		Corpus corpus = this.getCorpus();

		Property analysisProperty = null;

		try {

			analysisProperty = this.getCorpus().getProperty("word"); //$NON-NLS-1$

		} catch (CqiClientException e) {

			// TODO Auto-generated catch block

			org.txm.utils.logger.Log.printStackTrace(e);

		}

		LexicalTable table = this.toLexicalTable();

		int fmin = table.getFmin();

		CA ca = new CA(table);

		ca.setPartition(null);

		ca.setCorpus(corpus);

		ca.setFMin(fmin);

		ca.setAnalysisProperty(analysisProperty);

		return ca;

	}

	@Override

	public Partition getPartition() {

		return null;

	}

	@Override

	public boolean delete() {

		return corpus.removeResult(this);

	}

	/** The WordCloud adapter. */

	private static IWorkbenchAdapter coocMatrixAdapter = new IWorkbenchAdapter() {

		@Override

		public Object[] getChildren(Object o) {

			return new Object[0];

		}

		@Override

		public ImageDescriptor getImageDescriptor(Object object) {

			return IImageKeys.getImageDescriptor(IImageKeys.COOCMATRIX);

		}

		@Override

		public String getLabel(Object o) {

			return ((QueryAutoCooccurrence) o).getName();

		}

		@Override

		public Object getParent(Object o) {

			if (((QueryAutoCooccurrence) o).getPartition() != null) {

				return ((QueryAutoCooccurrence) o).getPartition();

			} else {

				return ((QueryAutoCooccurrence) o).getCorpus();

			}

		}

	};

	@Override

	public Object getAdapter(Class adapter) {

		return coocMatrixAdapter;

	}

	@Override

	public String getSimpleName() {

		return "QueryCooccurrence";

	}

	@Override

	public String getDetails() {

		return queries.toString();

	}

}

<html>

<body>

<p>Cooccurrence Matrix</p>

</body>

</html>

package org.txm.functions.coocmatrix;

import java.io.File;

import java.util.ArrayList;

import org.eclipse.core.runtime.IAdaptable;

import org.eclipse.jface.resource.ImageDescriptor;

import org.eclipse.ui.model.IWorkbenchAdapter;

import org.txm.ca.core.functions.CA;

import org.txm.ca.core.functions.ICAComputable;

import org.txm.core.results.TXMResult;

import org.txm.lexicaltable.core.functions.LexicalTable;

import org.txm.lexicaltable.core.statsengine.r.data.LexicalTableImpl;

import org.txm.rcp.IImageKeys;

import org.txm.searchengine.cqp.clientExceptions.CqiClientException;

import org.txm.searchengine.cqp.corpus.Corpus;

import org.txm.searchengine.cqp.corpus.Partition;

import org.txm.searchengine.cqp.corpus.Property;

import org.txm.searchengine.cqp.corpus.QueryResult;

import org.txm.searchengine.cqp.corpus.query.Query;

import org.txm.statsengine.core.StatException;

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

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

import org.txm.utils.logger.Log;

public class QueryCooccurrence extends TXMResult implements ICAComputable, IAdaptable {

	protected Corpus corpus;

	protected int[][] coocs;

	protected ArrayList<Query> queries1;

	protected ArrayList<String> names1;

	protected ArrayList<Query> queries2;

	protected ArrayList<String> names2;

	protected int dist;

	protected String struct = "";

	protected String symbol;

	protected static int noCoocMatrix = 1;

	protected static String prefixR = "CoocMatrix";

	protected int nNodes = 0;

	protected int nEdges = 0;

	protected int minCooc;

	public QueryCooccurrence(Corpus corpus, 

			ArrayList<Query> queries1, ArrayList<String> names1, 

			ArrayList<Query> queries2, ArrayList<String> names2, 

			int dist, int minCooc, String struct) throws CqiClientException, RWorkspaceException {

		this.queries1 = queries1;

		this.names1 = names1;

		this.queries2 = queries2;

		this.names2 = names2;

		this.corpus = corpus;

		this.dist = dist;

		this.minCooc = minCooc;

		if (struct != null)

			this.struct = "within "+struct; 

		else

			this.struct = "within text";

		nNodes = queries1.size();

		coocs = new int[queries1.size()][queries2.size()];

		for (int i = 0 ; i < queries1.size() ; i++) {

			//if (oriented) j = 0; // if the graph is not oriented, we don't need to evaluate all queries

			for (int j = 0 ; j < queries2.size() ; j++) {

				String query = "("+queries1.get(i)+"[]{0,"+dist+"}"+queries2.get(j)+")|("+queries2.get(j)+"[]{0,"+dist+"}"+queries1.get(i)+") "+this.struct;

				Log.info("ListCooc: query "+query);

				QueryResult result = corpus.query(new Query(query), "tmp", false);

				coocs[i][j] = result.getNMatch();

				if (coocs[i][j] >= minCooc) {

					nEdges++;

				} else {

					coocs[i][j] = 0;

				}

				result.drop();

			}

		}

	}

	public String getName() {

		return corpus.getName()+ " d="+dist+ " min="+minCooc;

	}

	public Corpus getParent() {

		return corpus;

	}

	public String getSymbol() {

		return symbol;

	}

	public int getNNodes() {

		return nNodes;

	}

	public int getNEdges() {

		return nEdges;

	}

	public LexicalTable toLexicalTable() throws RWorkspaceException, CqiClientException {

		sendToR();

		RWorkspace rw = RWorkspace.getRWorkspaceInstance();

		rw.eval("LT<-"+this.getSymbol());

		rw.eval("LT<-LT[rowSums(LT) != 0, ]");

		rw.eval("LT<-LT[, colSums(LT) != 0]");

		rw.eval(this.getSymbol()+"LT<-LT");

		rw.eval("rm(LT)");

		LexicalTable table = new LexicalTable(corpus, corpus.getProperty("word"), new LexicalTableImpl(this.getSymbol()+"LT"));

		return table;

	}

	private void sendToR() throws RWorkspaceException {

		if (symbol != null) return;

		this.symbol = prefixR+(QueryCooccurrence.noCoocMatrix ++);

		RWorkspace rw = RWorkspace.getRWorkspaceInstance();

		rw.eval("rm("+symbol+")");

		rw.addMatrixToWorkspace(symbol, coocs);

		rw.addVectorToWorkspace("cooclabels", names1.toArray(new String[names1.size()]));

		rw.eval("rownames("+symbol+") <- cooclabels");

		rw.eval("colnames("+symbol+") <- cooclabels");

	}

	public Corpus getCorpus() {

		return corpus;

	}

	public int[][] getCoocs() {

		return coocs;

	}

	public ArrayList<Query> getQueries() {

		return queries1;

	}

	public java.util.ArrayList<String> getNames() {

		return names1;

	}

	public int getDist() {

		return dist;

	}

	public void printCoocs() {

		for (int i = 0 ; i < queries1.size() ; i++) {

			System.out.print(names1.get(i));

			for (int j = 0 ; j < queries1.size() ; j++) {

				System.out.print("\t"+coocs[i][j]);

			}

			System.out.println();

		}

	}

	@Override

	public void clean() {

		// TODO Auto-generated method stub

	}

	public boolean toTxt(File outfile, String encoding, String colseparator,

			String txtseparator) throws Exception {

		return false;

	}

	public String toString() {

		return getName();

	}

	@Override

	public CA toCA() throws StatException, CqiClientException {

		Corpus corpus = this.getCorpus();

		Property analysisProperty = null;

		try {

			analysisProperty = this.getCorpus().getProperty("word"); //$NON-NLS-1$

		} catch (CqiClientException e) {

			// TODO Auto-generated catch block

			org.txm.utils.logger.Log.printStackTrace(e);

		}

		LexicalTable table = this.toLexicalTable();

		int fmin = table.getFmin();

		CA ca = new CA(table);

		ca.setPartition(null);

		ca.setCorpus(corpus);

		ca.setFMin(fmin);

		ca.setAnalysisProperty(analysisProperty);

		return ca;

	}

	@Override

	public Partition getPartition() {

		return null;

	}

	@Override

	public boolean delete() {

		return corpus.removeResult(this);

	}

	public String[] getExportTXTExtensions() {

		return new String[]{"*.txt"};

	}

	/** The WordCloud adapter. */

	private static IWorkbenchAdapter coocMatrixAdapter = new IWorkbenchAdapter() {

		@Override

		public Object[] getChildren(Object o) {

			return new Object[0];

		}

		@Override

		public ImageDescriptor getImageDescriptor(Object object) {

			return IImageKeys.getImageDescriptor(IImageKeys.COOCMATRIX);

		}

		@Override

		public String getLabel(Object o) {

			return ((QueryCooccurrence) o).getName();

		}

		@Override

		public Object getParent(Object o) {

			if (((QueryCooccurrence) o).getPartition() != null) {

				return ((QueryCooccurrence) o).getPartition();

			} else {

				return ((QueryCooccurrence) o).getCorpus();

			}

		}

	};

	@Override

	public Object getAdapter(Class adapter) {

		return coocMatrixAdapter;

	}

	@Override

	public String getSimpleName() {

		return "QueryCooccurrence";

	}

	@Override

	public String getDetails() {

		return queries1.toString()+ " "+queries2.toString();

	}

}

// 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.rcpapplication.commands.function;

import java.io.File;

import java.util.ArrayList;

import org.eclipse.core.commands.AbstractHandler;

import org.eclipse.core.commands.ExecutionEvent;

import org.eclipse.core.commands.ExecutionException;

import org.eclipse.core.runtime.IProgressMonitor;

import org.eclipse.core.runtime.IStatus;

import org.eclipse.core.runtime.Status;

import org.eclipse.jface.dialogs.Dialog;

import org.eclipse.jface.viewers.IStructuredSelection;

import org.eclipse.jface.window.Window;

import org.eclipse.swt.SWT;

import org.eclipse.swt.events.SelectionEvent;

import org.eclipse.swt.events.SelectionListener;

import org.eclipse.swt.graphics.GC;

import org.eclipse.swt.layout.GridData;

import org.eclipse.swt.layout.GridLayout;

import org.eclipse.swt.widgets.Button;

import org.eclipse.swt.widgets.Composite;

import org.eclipse.swt.widgets.Control;

import org.eclipse.swt.widgets.FileDialog;

import org.eclipse.swt.widgets.Label;

import org.eclipse.swt.widgets.Shell;

import org.eclipse.swt.widgets.Spinner;

import org.eclipse.ui.handlers.HandlerUtil;

import org.txm.functions.coocmatrix.QueryAutoCooccurrence;

import org.txm.functions.queryindex.QueryIndex;

import org.txm.functions.queryindex.QueryIndexLine;

import org.txm.rcp.JobsTimer;

import org.txm.rcp.Messages;

import org.txm.rcp.utils.JobHandler;

import org.txm.rcp.views.QueriesView;

import org.txm.rcp.views.corpora.CorporaView;

import org.txm.searchengine.cqp.CQPEngine;

import org.txm.searchengine.cqp.clientExceptions.CqiClientException;

import org.txm.searchengine.cqp.corpus.Corpus;

import org.txm.searchengine.cqp.corpus.StructuralUnit;

import org.txm.searchengine.cqp.corpus.query.Query;

import org.txm.stat.utils.ConsoleProgressBar;

import org.txm.statsengine.r.rcp.views.RVariablesView;

//import org.txm.functions.queryindex.*;

import org.txm.utils.logger.Log;

/**

 * if the selection is a corpus, open an empty Cooc editor if the selection is a

 * concordance, open a Cooc editor already computed @ author mdecorde.

 */

public class ComputeQueryAutoCooccurrence extends AbstractHandler {

	float reqtime = 0.5f;

	/* (non-Javadoc)

	 * @see org.eclipse.core.commands.AbstractHandler#execute(org.eclipse.core.commands.ExecutionEvent)

	 */

	@Override

	public Object execute(ExecutionEvent event) throws ExecutionException {

		IStructuredSelection selection = (IStructuredSelection) HandlerUtil.getCurrentSelection(event);

		final Object element = selection.getFirstElement();

		final Shell shell = HandlerUtil.getActiveWorkbenchWindowChecked(event)

				.getShell();

		JobHandler jobhandler = new JobHandler("Computing cooccurrences matrix") {

			@Override

			protected IStatus run(IProgressMonitor monitor) {

				this.runInit(monitor);

				try {

					JobsTimer.start();

					if (!(element instanceof QueryIndex)) {

						System.out.println(Messages.ComputeCooccurrences_1+ element);

						return Status.CANCEL_STATUS;

					}

					QueryIndex qi = ((QueryIndex)element);

					Corpus corpus = qi.getCorpus();

					final CoocMatrixDialog dialog = new ComputeQueryAutoCooccurrence.CoocMatrixDialog(shell, corpus);

					syncExec(new Runnable() {

						@Override

						public void run() {

							dialog.open();

						}

					});

					if (dialog.getReturnCode() != Window.OK) System.out.println("Canceled");

					this.acquireSemaphore();

					final QueryAutoCooccurrence cooc = computeCooc(shell, corpus, (QueryIndex)element, dialog);

					this.releaseSemaphore();

					if (cooc == null) return null;

					corpus.addResult(cooc);

					System.out.println(Messages.ComputeCoocMatrix_0+cooc.getSymbol());

					syncExec(new Runnable() {

						@Override

						public void run() {

							CorporaView.refresh();

							CorporaView.expand(cooc.getCorpus());

							QueriesView.refresh();

							RVariablesView.refresh();

						}

					});

				} catch (ThreadDeath td) { 

					return Status.CANCEL_STATUS;

				} catch (Exception e) {

					Log.printStackTrace(e);

					try { System.out.println(Messages.LastCQPError+CQPEngine.getCqiClient().getLastCQPError());

					} catch (Exception e1) { e1.printStackTrace(); }

				} finally {

					monitor.done();

					JobsTimer.stopAndPrint();

				}

				return Status.OK_STATUS;

			}

		};

		jobhandler.startJob();

		return null;

	}

	private QueryAutoCooccurrence computeCooc(Shell shell, Corpus corpus, QueryIndex element, CoocMatrixDialog dialog) {

		ArrayList<Query> queries = new ArrayList<Query>();

		ArrayList<String> names = new ArrayList<String>();

		String struct = dialog.getStruct();

		int dist = dialog.getDist();

		int min = dialog.getMin();

		File outfile = dialog.getOutFile();

		boolean oriented = dialog.getOriented();

		for (QueryIndexLine line : element.getLines()) {

			queries.add(line.getQuery());

			names.add(line.getName());

		}

		System.out.println(Messages.ProgressionDialog_8+queries);

		System.out.println(Messages.MergeCols_5+names);

		QueryAutoCooccurrence cooc = null;

		try {

			int nqueries = (queries.size()*queries.size()/2);

			System.out.println("Number of queries: "+nqueries);

			System.out.println("Estimated time: "+(nqueries*reqtime/1000)+" secs");

			cooc = new QueryAutoCooccurrence(corpus, queries, names, dist, min, struct, oriented, new ConsoleProgressBar(nqueries));

			System.out.println(Messages.ComputeCoocMatrix_1+cooc.getNNodes());

			System.out.println(Messages.ComputeCoocMatrix_2+cooc.getNEdges());

			System.out.println(Messages.ComputeCoocMatrix_3+dist);

			if (outfile != null) {

				cooc.toGraphml(outfile);

				System.out.println(Messages.ComputeCoocMatrix_4+outfile);

			}

		} catch (Exception e) {

			Log.printStackTrace(e);

			try { System.out.println(Messages.LastCQPError+CQPEngine.getCqiClient().getLastCQPError());

			} catch (Exception e1) { e1.printStackTrace(); }

		}

		return cooc;

	}

	public class CoocMatrixDialog extends Dialog {

		Corpus corpus;

		org.eclipse.swt.widgets.List propsCombo;

		Spinner distSpinner;

		Spinner minSpinner;

		Label outfileLabel;

		File outfile;

		int dist;

		int min;

		String struct;

		private boolean oriented;

		private Button orientedButton;

		public CoocMatrixDialog(Shell parentShell, Corpus corpus) {

			super(parentShell);

			this.setShellStyle(this.getShellStyle() | SWT.RESIZE);

			this.corpus = corpus;

		}

		public boolean getOriented() {

			return oriented;

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.window.Window#configureShell(org.eclipse.swt.widgets.Shell)

		 */

		@Override

		protected void configureShell(Shell newShell) {

			super.configureShell(newShell);

			newShell.setText(Messages.ComputeCoocMatrix_7);

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.dialogs.Dialog#createDialogArea(org.eclipse.swt.widgets.Composite)

		 */

		@Override

		protected Control createDialogArea(Composite parent) {

			Composite composite = parent; //new Composite(parent, SWT.NONE);

			// TODO : we just put a composite into another composite. Everything

			// should be directly put into parent

			GridLayout layout = new GridLayout(2, false);

			composite.setLayout(layout);

			Label anaPropLabel = new Label(composite, SWT.NONE);

			anaPropLabel.setText(Messages.ParaBrowserEditor_5);

			anaPropLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER, false, false));

			propsCombo = new org.eclipse.swt.widgets.List(composite, SWT.READ_ONLY);

			GridData gdata = new GridData(GridData.FILL, GridData.FILL, true, false);

			propsCombo.setLayoutData(gdata);

			GC gc = new GC(propsCombo);

			gc.setFont(this.propsCombo.getFont());

			gdata.heightHint = gc.getFontMetrics().getHeight() * 5;

			gc.dispose();

			propsCombo.add("");

			try {

				for (StructuralUnit p : corpus.getStructuralUnits()) {

					if (!("text".equals(p.getName()) ||  //$NON-NLS-1$

							"txmcorpus".equals(p.getName()))) //$NON-NLS-1$

						propsCombo.add(p.getName());

				}

			} catch (CqiClientException e) {

				Log.printStackTrace(e);

				return parent;

			}

			Label distLabel = new Label(composite, SWT.NONE);

			distLabel.setText(Messages.ComputeCoocMatrix_10);

			distLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			distSpinner = new Spinner(composite, SWT.BORDER);

			distSpinner.setMinimum(0);

			distSpinner.setMaximum(1000);

			distSpinner.setSelection(10);

			Label minLabel = new Label(composite, SWT.NONE);

			minLabel.setText(Messages.ComputeCoocMatrix_11);

			minLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			minSpinner = new Spinner(composite, SWT.BORDER);

			minSpinner.setMinimum(1);

			minSpinner.setMaximum(1000);

			minSpinner.setSelection(20);

			Label orientedLabel = new Label(composite, SWT.NONE);

			orientedLabel.setText("Oriented");

			orientedLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			orientedButton = new Button(composite, SWT.CHECK);

			orientedButton.setSelection(false);

			outfileLabel = new Label(composite, SWT.NONE);

			outfileLabel.setText(Messages.ComputeCoocMatrix_12);

			outfileLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			Button outfileButton = new Button(composite, SWT.PUSH);

			outfileButton.setText(Messages.ComputeCoocMatrix_13);

			outfileButton.addSelectionListener(new SelectionListener() {

				@Override

				public void widgetSelected(SelectionEvent e) {

					FileDialog dialog = new FileDialog(e.display.getActiveShell(), SWT.SAVE);

					String extensions[] = {"*.graphml"}; //$NON-NLS-1$

					dialog.setFilterExtensions(extensions);

					String path = dialog.open();

					if (path != null) {

						outfile = new File(path);

						if (!(outfile.getName().toLowerCase().endsWith(".graphml"))) { //$NON-NLS-1$

							outfile = new File(path+".graphml"); //$NON-NLS-1$

						}

						outfileLabel.setText(outfile.getAbsolutePath());

					}

				}

				@Override

				public void widgetDefaultSelected(SelectionEvent e) { }

			});

			return parent;

		}

		public File getOutFile() {

			return outfile;

		}

		public int getDist() {

			return dist;

		}

		public int getMin() {

			return min;

		}

		public String getStruct() {

			return struct;

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.dialogs.Dialog#okPressed()

		 */

		@Override

		protected void okPressed() {

			dist = distSpinner.getSelection();

			min = minSpinner.getSelection();

			struct = null;

			oriented = orientedButton.getSelection();

			for (int i : propsCombo.getSelectionIndices()) {

				String sname = propsCombo.getItem(i);

				if (sname != null && sname.length() > 0) {

					struct = sname;

					break;

				}

			}

			super.okPressed();

		}

	}

}

// 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.rcpapplication.commands.function;

import java.io.BufferedReader;

import java.io.File;

import java.io.FileInputStream;

import java.io.IOException;

import java.io.InputStreamReader;

import java.util.ArrayList;

import org.eclipse.core.commands.AbstractHandler;

import org.eclipse.core.commands.ExecutionEvent;

import org.eclipse.core.commands.ExecutionException;

import org.eclipse.core.runtime.IProgressMonitor;

import org.eclipse.core.runtime.IStatus;

import org.eclipse.core.runtime.Status;

import org.eclipse.jface.dialogs.Dialog;

import org.eclipse.jface.viewers.IStructuredSelection;

import org.eclipse.jface.window.Window;

import org.eclipse.swt.SWT;

import org.eclipse.swt.events.SelectionEvent;

import org.eclipse.swt.events.SelectionListener;

import org.eclipse.swt.graphics.GC;

import org.eclipse.swt.layout.GridData;

import org.eclipse.swt.layout.GridLayout;

import org.eclipse.swt.widgets.Button;

import org.eclipse.swt.widgets.Composite;

import org.eclipse.swt.widgets.Control;

import org.eclipse.swt.widgets.FileDialog;

import org.eclipse.swt.widgets.Label;

import org.eclipse.swt.widgets.Shell;

import org.eclipse.swt.widgets.Spinner;

import org.eclipse.ui.handlers.HandlerUtil;

import org.txm.functions.coocmatrix.QueryCooccurrence;

//import org.txm.functions.queryindex.*;

import org.txm.rcp.JobsTimer;

import org.txm.rcp.Messages;

import org.txm.rcp.utils.JobHandler;

import org.txm.rcp.views.QueriesView;

import org.txm.rcp.views.corpora.CorporaView;

import org.txm.searchengine.cqp.CQPEngine;

import org.txm.searchengine.cqp.clientExceptions.CqiClientException;

import org.txm.searchengine.cqp.corpus.Corpus;

import org.txm.searchengine.cqp.corpus.StructuralUnit;

import org.txm.searchengine.cqp.corpus.query.Query;

import org.txm.statsengine.r.rcp.views.RVariablesView;

import org.txm.utils.logger.Log;

// TODO: Auto-generated Javadoc

/**

 * if the selection is a corpus, open an empty Cooc editor if the selection is a

 * concordance, open a Cooc editor already computed @ author mdecorde.

 */

public class ComputeQueryCooccurrence extends AbstractHandler {

	float reqtime = 0.5f;

	/* (non-Javadoc)

	 * @see org.eclipse.core.commands.AbstractHandler#execute(org.eclipse.core.commands.ExecutionEvent)

	 */

	@Override

	public Object execute(ExecutionEvent event) throws ExecutionException {

		IStructuredSelection selection = (IStructuredSelection) HandlerUtil.getCurrentSelection(event);

		final Object element = selection.getFirstElement();

		final Shell shell = HandlerUtil.getActiveWorkbenchWindowChecked(event)

				.getShell();

		JobHandler jobhandler = new JobHandler("Computing cooccurrences matrix") {

			@Override

			protected IStatus run(IProgressMonitor monitor) {

				this.runInit(monitor);

				try {

					JobsTimer.start();

					if (!(element instanceof Corpus)) {

						System.out.println(Messages.ComputeCooccurrences_1+ element);

						return Status.CANCEL_STATUS;

					}

					Corpus corpus = ((Corpus)element);

					final CoocMatrixDialog dialog = new ComputeQueryCooccurrence.CoocMatrixDialog(shell, corpus);

					syncExec(new Runnable() {

						@Override

						public void run() {

							dialog.open();

						}

					});

					if (dialog.getReturnCode() != Window.OK) System.out.println("Canceled");

					this.acquireSemaphore();

					final QueryCooccurrence cooc = computeCooc(shell, corpus, dialog);

					this.releaseSemaphore();

					if (cooc == null) return null;

					corpus.addResult(cooc);

					System.out.println(Messages.ComputeCoocMatrix_0+cooc.getSymbol());

					syncExec(new Runnable() {

						@Override

						public void run() {

							CorporaView.refresh();

							CorporaView.expand(cooc.getCorpus());

							QueriesView.refresh();

							RVariablesView.refresh();

						}

					});

				} catch (ThreadDeath td) { 

					return Status.CANCEL_STATUS;

				} catch (Exception e) {

					Log.printStackTrace(e);

					try { System.out.println(Messages.LastCQPError+CQPEngine.getCqiClient().getLastCQPError());

					} catch (Exception e1) { e1.printStackTrace(); }

				} finally {

					monitor.done();

					JobsTimer.stopAndPrint();

				}

				return Status.OK_STATUS;

			}

		};

		jobhandler.startJob();

		return null;

	}

	private QueryCooccurrence computeCooc(Shell shell, Corpus corpus, CoocMatrixDialog dialog) throws IOException {

		ArrayList<Query> queries1 = new ArrayList<Query>();

		ArrayList<String> names1 = new ArrayList<String>();

		ArrayList<Query> queries2 = new ArrayList<Query>();

		ArrayList<String> names2 = new ArrayList<String>();

		String struct = dialog.getStruct();

		int dist = dialog.getDist();

		int min = dialog.getMin();

		getQueriesAndNames(dialog.getQueryFile1(), queries1, names1);

		getQueriesAndNames(dialog.getQueryFile2(), queries2, names2);

		System.out.println(Messages.ProgressionDialog_8+queries1);

		System.out.println(Messages.MergeCols_5+names1);

		QueryCooccurrence cooc = null;

		try {

			int nqueries = (queries1.size()*queries2.size());

			System.out.println("Number of queries: "+nqueries);

			System.out.println("Estimated time: "+(nqueries*reqtime/1000)+" secs");

			cooc = new QueryCooccurrence(corpus, queries1, names1, queries2, names2, dist, min, struct);

			System.out.println(Messages.ComputeCoocMatrix_1+cooc.getNNodes());

			System.out.println(Messages.ComputeCoocMatrix_2+cooc.getNEdges());

			System.out.println(Messages.ComputeCoocMatrix_3+dist);

		} catch (Exception e) {

			// TODO Auto-generated catch block

			Log.printStackTrace(e);

			try { System.out.println(Messages.LastCQPError+CQPEngine.getCqiClient().getLastCQPError());

			} catch (Exception e1) { e1.printStackTrace(); }

		}

		return cooc;

	}

	private void getQueriesAndNames(File propFile, ArrayList<Query> queries,

			ArrayList<String> names) throws IOException {

		BufferedReader reader = new BufferedReader(new InputStreamReader(

				new FileInputStream(propFile), "UTF-8")); //$NON-NLS-1$

		String line = reader.readLine();

		while (line != null) {

			String[] split = line.split("=", 2); //$NON-NLS-1$

			if (split.length == 2) {

				queries.add(new Query(split[1]));

				names.add(split[0]);

			}

			line = reader.readLine();

		}

		reader.close();

	}

	public class CoocMatrixDialog extends Dialog {

		Corpus corpus;

		org.eclipse.swt.widgets.List propsCombo;

		Spinner distSpinner;

		Spinner minSpinner;

		Label queriesFile1Label;

		Label queriesFile2Label;

		File queriesFile1;

		File queriesFile2;

		int dist;

		int min;

		String struct;

		private boolean oriented;

		private Button orientedButton;

		public CoocMatrixDialog(Shell parentShell, Corpus corpus) {

			super(parentShell);

			this.setShellStyle(this.getShellStyle() | SWT.RESIZE);

			this.corpus = corpus;

		}

		public boolean getOriented() {

			return oriented;

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.window.Window#configureShell(org.eclipse.swt.widgets.Shell)

		 */

		@Override

		protected void configureShell(Shell newShell) {

			super.configureShell(newShell);

			newShell.setText(Messages.ComputeCoocMatrix_7);

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.dialogs.Dialog#createDialogArea(org.eclipse.swt.widgets.Composite)

		 */

		@Override

		protected Control createDialogArea(Composite parent) {

			Composite composite = parent; //new Composite(parent, SWT.NONE);

			// TODO : we just put a composite into another composite. Everything

			// should be directly put into parent

			GridLayout layout = new GridLayout(2, false);

			composite.setLayout(layout);

			Label anaPropLabel = new Label(composite, SWT.NONE);

			anaPropLabel.setText(Messages.ParaBrowserEditor_5);

			anaPropLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER, false, false));

			propsCombo = new org.eclipse.swt.widgets.List(composite, SWT.READ_ONLY);

			GridData gdata = new GridData(GridData.FILL, GridData.FILL, true, false);

			propsCombo.setLayoutData(gdata);

			GC gc = new GC(propsCombo);

			gc.setFont(this.propsCombo.getFont());

			gdata.heightHint = gc.getFontMetrics().getHeight() * 5;

			gc.dispose();

			propsCombo.add("");

			try {

				for (StructuralUnit p : corpus.getStructuralUnits()) {

					if (!("text".equals(p.getName()) ||  //$NON-NLS-1$

							"txmcorpus".equals(p.getName()))) //$NON-NLS-1$

						propsCombo.add(p.getName());

				}

			} catch (CqiClientException e) {

				Log.printStackTrace(e);

				return parent;

			}

			Label distLabel = new Label(composite, SWT.NONE);

			distLabel.setText(Messages.ComputeCoocMatrix_10);

			distLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			distSpinner = new Spinner(composite, SWT.BORDER);

			distSpinner.setMinimum(0);

			distSpinner.setMaximum(1000);

			distSpinner.setSelection(10);

			Label minLabel = new Label(composite, SWT.NONE);

			minLabel.setText(Messages.ComputeCoocMatrix_11);

			minLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			minSpinner = new Spinner(composite, SWT.BORDER);

			minSpinner.setMinimum(1);

			minSpinner.setMaximum(1000);

			minSpinner.setSelection(20);

			Label orientedLabel = new Label(composite, SWT.NONE);

			orientedLabel.setText("Oriented");

			orientedLabel.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			orientedButton = new Button(composite, SWT.CHECK);

			orientedButton.setSelection(false);

			queriesFile1Label = new Label(composite, SWT.NONE);

			queriesFile1Label.setText("Query file 1");

			queriesFile1Label.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			Button queriesFile1Button = new Button(composite, SWT.PUSH);

			queriesFile1Button.setText("Select...");

			queriesFile1Button.addSelectionListener(new SelectionListener() {

				@Override

				public void widgetSelected(SelectionEvent e) {

					FileDialog dialog = new FileDialog(e.display.getActiveShell(), SWT.OPEN);

					String extensions[] = {"*.properties"}; //$NON-NLS-1$

					dialog.setFilterExtensions(extensions);

					String path = dialog.open();

					if (path != null) {

						queriesFile1 = new File(path);

						queriesFile1Label.setText(queriesFile1.getAbsolutePath());

					}

				}

				@Override

				public void widgetDefaultSelected(SelectionEvent e) { }

			});

			queriesFile2Label = new Label(composite, SWT.NONE);

			queriesFile2Label.setText("Query file 2");

			queriesFile2Label.setLayoutData(new GridData(GridData.END, GridData.CENTER,

					false, false));

			Button queriesFile2Button = new Button(composite, SWT.PUSH);

			queriesFile2Button.setText("Select...");

			queriesFile2Button.addSelectionListener(new SelectionListener() {

				@Override

				public void widgetSelected(SelectionEvent e) {

					FileDialog dialog = new FileDialog(e.display.getActiveShell(), SWT.OPEN);

					String extensions[] = {"*.properties"}; //$NON-NLS-1$

					dialog.setFilterExtensions(extensions);

					String path = dialog.open();

					if (path != null) {

						queriesFile2 = new File(path);

						queriesFile2Label.setText(queriesFile2.getAbsolutePath());

					}

				}

				@Override

				public void widgetDefaultSelected(SelectionEvent e) { }

			});

			return parent;

		}

		public File getQueryFile1() {

			return queriesFile1;

		}

		public File getQueryFile2() {

			return queriesFile2;

		}

		public int getDist() {

			return dist;

		}

		public int getMin() {

			return min;

		}

		public String getStruct() {

			return struct;

		}

		/* (non-Javadoc)

		 * @see org.eclipse.jface.dialogs.Dialog#okPressed()

		 */

		@Override

		protected void okPressed() {

			dist = distSpinner.getSelection();

			min = minSpinner.getSelection();

			struct = null;

			oriented = orientedButton.getSelection();

			for (int i : propsCombo.getSelectionIndices()) {

				String sname = propsCombo.getItem(i);

				if (sname != null && sname.length() > 0) {

					struct = sname;

					break;

				}

			}

			super.okPressed();

		}

	}

}

package org.txm.links.coocmatrix;

import org.txm.ca.core.functions.CA;

import org.txm.functions.coocmatrix.QueryCooccurrence;

import org.txm.lexicaltable.core.functions.LexicalTable;

import org.txm.searchengine.cqp.clientExceptions.CqiClientException;

import org.txm.searchengine.cqp.corpus.Corpus;

import org.txm.searchengine.cqp.corpus.Property;

import org.txm.statsengine.core.StatException;

public class toCA {

	/**

	 * Instantiates a new cA.

	 *

	 * @param lexicaltable the lexicaltable

	 * @throws StatException the stat exception

	 * @throws CqiClientException 

	 */

	public static CA link(QueryCooccurrence coocs) throws StatException, CqiClientException {

		Corpus corpus = coocs.getCorpus();

		Property analysisProperty = null;

		try {

			analysisProperty = coocs.getCorpus().getProperty("word"); //$NON-NLS-1$

		} catch (CqiClientException e) {

			// TODO Auto-generated catch block

			org.txm.utils.logger.Log.printStackTrace(e);

		}

		LexicalTable table = coocs.toLexicalTable();

		int fmin = table.getFmin();

		CA ca = new CA(table);

		ca.setPartition(null);

		ca.setCorpus(corpus);

		ca.setFMin(fmin);

		ca.setAnalysisProperty(analysisProperty);