Laboratoire ICAR » Plateforme TXM

	 * if not try to launch it.

	 *

	 * @param pathToRExecutable the path to r executable

	 * @param rServeArgs

	 * @return true if Rserve is launched

	 * @throws RWorkspaceException the r workspace exception

	 * Launch rserve.

	 *

	 * @param cmd the cmd

	 * @return true, if successful

	 */

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

	 * checks whether Rserve is running and if that's not the case it attempts

	 * to start it using the defaults for the platform where it is run on. This

	 * method is meant to be set-and-forget and cover most default setups. For

	 * 

	 * @param rServeArgs

	 * @param rargs

import org.kohsuke.args4j.spi.Setter;

/**

 * This setter adds a new entry to a Map.

 * The value which is passed is split into the Map-key and Map-value by a "=".

 * </p>

 */

@SuppressWarnings("rawtypes")

 *

 * <p>

 * This annotation can be placed on a field of type T or the method

 * modified can be anything, but if it's not public, your application

 * needs to run in a security context that allows args4j to access

 * the field/method (see {@link AccessibleObject#setAccessible(boolean)}.

package org.kohsuke.args4j.spi;

/**

 * 

 * @author Jan Materne

 */

 * Exactly one of the attributes 'field' or 'method' must be set.

 * The 'handler' value specifies a full qualified class name.

 *

 * 

 * <pre>

 * <args>

		this.setDirty();

	}

	protected boolean __compute(TXMProgressMonitor monitor) {

		monitor.setTask("Computing balance with metadata propertyName = " + this.structuralUnitProperty + ", structural unit = " + this.structuralUnit.getName() + " and groupByTexts = " + this.countTexts); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

	/**

	 * Creates the output.

	 *

	 * @return true, if successful

	 * @throws XMLStreamException

	 * @throws IOException

	 */

	private boolean createOutput(File f) throws XMLStreamException, IOException {

		if (writer != null) { // process from a file

			writer.close();

		}

	/**

	 * Creates the output.

	 *

	 * @return true, if successful

	 */

	private boolean createOutput(File f, String encoding) {

	/**

	 * Instantiates a new workspace.

	 *

	 * @throws CoreException 

	 */

	private Workspace() throws CoreException {

	/**

	 * Creates a new editor.

	 * 

	 * @param chartEditorInput

	 */

	protected ChartEditor(ChartEditorInput chartEditorInput) {

	/**

	 * Creates a new chart component.

	 * 

	 * @return

	 */

	protected abstract IChartComponent _createChartComponent();

	/**

	 * Creates a charts engine with the specified name, description and output format.

	 * 

	 * @param description

	 * @param outputFormat

	 */

	/**

	 * Populates the chart creators from loaded extensions according to the specified chars engine name.

	 * 

	 */

	protected void registerChartCreatorExtensions(Class<? extends ChartsEngine> chartsEngineClass) {

	/**

	 */

	public final static String RENDERING_COLORS_MODE = "colors_mode"; //$NON-NLS-1$

	/**

	 * The chart object.

	 * TODO: MD: this is problematic, the chart object should allow us to edit the chart. In the case of the R charts, the File has not the same value as the JFC Chart (which can be edited)

	 */

	protected Object chart;

	/**

	 * The chart type;

	 */

	@Parameter(key = ChartsEnginePreferences.CHART_TYPE, type = Parameter.RENDERING)

	protected String chartType;

	}

	/**

	 * @param itemsCount

	 * @return the created palette

	 */

	public static final String RENDERING = "rendering"; //$NON-NLS-1$

	/**

	 */

	public static final String METHOD = "method"; //$NON-NLS-1$

	protected String metric;

	/**

	 */

	@Parameter(key = AHCPreferences.METHOD)

	protected String method;

	 * @return true if success

	 */

	// FIXME: SJ: to extract to future exporter extension

	public boolean _toTxt(File outfile, String encoding, String colsep, String txtsep) {

		boolean ret = true;

		acquireSemaphore();

	/**

	 * Gets the cluster tree heights.

	 * 

	 */

	public double[] getClusterTreeHeights() {

		if (this.clusterHeights == null) {

	/**

	 * Gets the cluster tree merges.

	 * 

	 */

	public double[][] getClusterTreeMerges() {

		if (this.clusterMerges == null) {

	 * notifyDispose

	 * notifyDoSave

	 * 

	 * @throws SecurityException

	 */

	protected void notifyExtensions(final String step) {

import org.eclipse.ui.IEditorInput;

import org.eclipse.ui.IPersistableElement;

/**

 * This is a root implementation for other abstract implementation of tab type (.

 *

 * @author sloiseau

 */

@SuppressWarnings("rawtypes") //$NON-NLS-1$

	/**

	 * dont manage SearchEngine state

	 * 

	 * @param job

	 * @param monitor

	 * @return the loaded projects

	/**

	 * dont manage SearchEngine state

	 * 

	 * @param job

	 * @param monitor

	 * @param replace if true replace existing corpus

	 * @return the loaded projects

	 */

	protected static ArrayList<Project> loadBinaryCorpusFromCorporaDirectory(List<File> corporaFiles, JobHandler job, IProgressMonitor monitor, boolean replace, String sourceName) {

	/**

	 * Creates the advanced query field.

	 *

	 */

	private void createAdvancedQueryField() {

	/**

	 * Adds the query field.

	 *

	 */

	private QueryWidget addQueryField() {

	 * @param property the property

	 * @param freq the freq

	 * @param ids the ids

	 */

	protected void init(TXMResult corpus, Property property, int[] freq, int[] ids) {

		if (freq.length != ids.length) {

	/**

	 * As r matrix.

	 *

	 * TODO MD: finalize a export to R mechanism (maybe linked to the export engines to be implemented 

	 *

	 * @return the string

	/**

	 * As r matrix.

	 *

	 * TODO MD: finalize a export to R mechanism (maybe linked to the export engines to be implemented

	 *

	 * @return the string

/**

 * A logger whose messages are translated unsing a {@link Localizer}.

 * 

 * @author sloiseau

 */

@Deprecated

		super(parametersNodePath);

	}

	public boolean canCompute() {

		return criterii.size() > 0;

	}

	public boolean __compute(TXMProgressMonitor monitor) throws Exception {

		StringBuilder buffer = new StringBuilder();

	 * @throws StatException the stat exception

	 * @throws IOException 

	 */

	public boolean _toTxt(File outfile, String encoding, String colseparator, String txtseparator) throws StatException, IOException {

		OutputStreamWriter writer;

	 *

	 * @param symbol the symbol

	 * @param specIndex the spec index (as double[row][column])

	 */

	protected void init(String symbol, double[][] specIndex) throws Exception {

	 * 

	 * @param name

	 * @param functions 

	 * @throws Exception

	 */

	protected Dictionary(String name, HSQLFunctions functions) throws Exception {

	 * @return

	 * @throws IOException

	 */

	public boolean _toTxt(File outfile, String encoding, String colseparator, String txtseparator) throws IOException {

		// NK: writer declared as class attribute to perform a clean if the operation is interrupted

	}

	/**

	 *

	 * @param registryfile the registry file to patch

	 * @param targetcorpus the aligned corpus

	}

	/**

	 *

	 * @param registryfile the registry file to patch

	 * @param oldname the oldname

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

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

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

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

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

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

	 * Gives the lexicon size of an attribute.

	 *

	 * @param attribute the attribute

	 * @throws IOException Signals that an I/O exception has occurred.

	 * @throws UnexpectedAnswerException Signals that the data read on the socket is unexpected

	 * @throws CqiServerError Signals that the cqi server raised an error

	 */

	@Override

	public abstract int lexiconSize(String attribute) throws IOException, UnexpectedAnswerException, CqiServerError;

	public abstract int[] cpos2Alg(String attribute, int[] cpos) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 * out of range.

	 *

	 * @param attribute the attribute

	public abstract int[] id2Cpos(String attribute, int id) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 * occurs; the returned list is sorted as a whole, not per token id.

	 *

	 * @param attribute the attribute

	public abstract int[] idList2Cpos(String attribute, int[] ids) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 *

	 * @param attribute the attribute

	 * @param regex the regex

	public abstract int[] regex2Id(String attribute, String regex) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	/**

	 * Retrieves start and end corpus positions of an alignement region in the

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	public abstract boolean subCorpusHasField(String subcorpus, byte field) throws IOException, UnexpectedAnswerException, CqiServerError;

	/**

	 * 

	 * @param subcorpus

	 *            the subcorpus

			UnexpectedAnswerException, CqiServerError;

	/**

	 * pairs are sorted by frequency desc.

	 * 

	 * @param subcorpus

			UnexpectedAnswerException, CqiServerError;

	/**

	 * 

	 * @param subcorpus

	 *            the subcorpus

	/**

	 * Write a string on the socket.

	 * 

	 * 

	 * @throws IOException

	 *             Signals that an I/O exception has occurred.

	/**

	 * Write a string array on the socket.

	 * 

	 * 

	 * @throws IOException

	 *             Signals that an I/O exception has occurred.

	 */

		int length = strings.length;

		this.streamToServer.writeInt(length);

		for (int i = 0; i < length; i++)

	 */

	@Override

	public synchronized boolean connect(String username, String password) throws UnexpectedAnswerException, IOException, CqiServerError {

		this.username = username;

		this.password = password;

	 * 

	 * @return true, if successful

	 * 

	 */

	@Override

	public synchronized boolean disconnect() throws UnexpectedAnswerException, CqiServerError, IOException {

	String lastError;

	@Override

	public synchronized String getLastError() {

			return lastError;

		}

		return CQPSearchEngineCoreMessages.noError;

	/**

	 * Drop a corpus.

	 * 

	 * @throws IOException 

	 */

	@Override

	 * Gives the lexicon size of an attribute.

	 *

	 * @param attribute the attribute

	 * @throws IOException Signals that an I/O exception has occurred.

	 * @throws UnexpectedAnswerException Signals that the data read on the socket is unexpected

	 * @throws CqiServerError Signals that the cqi server raised an error

	 */

	@Override

	public synchronized int lexiconSize(String attribute) throws IOException, UnexpectedAnswerException, CqiServerError {

	}

	/**

	 * out of range.

	 *

	 * @param attribute the attribute

	}

	/**

	 * out of range.

	 *

	 * @param attribute the attribute

	}

	/**

	 * occurs; the returned list is sorted as a whole, not per token id.

	 *

	 * @param attribute the attribute

	}

	/**

	 * list may be empty (size 0);.

	 *

	 * @param attribute the attribute

	}

	/**

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	}

	/**

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	}

	/**

	 * 

	 * @param subcorpus

	 *            the subcorpus

	}

	/**

	 * pairs are sorted by frequency desc.

	 * 

	 * @param subcorpus

	}

	/**

	 * 

	 * @param subcorpus

	 *            the subcorpus

	 * Gives the lexicon size of an attribute.

	 *

	 * @param attribute the attribute

	 * @throws IOException Signals that an I/O exception has occurred.

	 * @throws UnexpectedAnswerException Signals that the data read on the socket is unexpected

	 * @throws CqiServerError Signals that the cqi server raised an error

	 */

	public int lexiconSize(String attribute) throws IOException, UnexpectedAnswerException, CqiServerError;

	public int[] cpos2Alg(String attribute, int[] cpos) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 * out of range.

	 *

	 * @param attribute the attribute

	public int[] id2Cpos(String attribute, int id) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 * occurs; the returned list is sorted as a whole, not per token id.

	 *

	 * @param attribute the attribute

	public int[] idList2Cpos(String attribute, int[] ids) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 * list may be empty (size 0).

	 *

	 * @param attribute the attribute

	public int[] regex2Id(String attribute, String regex) throws UnexpectedAnswerException, IOException, CqiServerError;

	/**

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	/**

	 * Retrieves start and end corpus positions of an alignement region in the

	 *

	 * @param attribute the attribute

	 * @param struc the struc

	public boolean subCorpusHasField(String subcorpus, byte field) throws IOException, UnexpectedAnswerException, CqiServerError;

	/**

	 * 

	 * @param subcorpus

	 *            the subcorpus

	 * @param field CQI_CONST_FIELD_MATCH, CQI_CONST_FIELD_MATCHEND or CQI_CONST_FIELD_TARGET

	 * 

	 * @return the values

	 * 

	/**

	 * Drops a subcorpus.

	 * 

	 * 

	 * @throws IOException

	 *             Signals that an I/O exception has occurred.

	UnexpectedAnswerException, CqiServerError;

	/**

	 * pairs are sorted by frequency desc.

	 * 

	 * 

	 * @return the int[][]

	 * 

			UnexpectedAnswerException, CqiServerError;

	/**

	 * 

	 * 

	 * @return the int[]

	 * 

	 * @param corpus the corpus

	 * @param property the property

	 * @param freq the freq

	 */

	protected void init(TXMResult corpus, WordProperty property, int[] freq, int[] ids) {

		if (freq.length != ids.length) {

	 * 

	 * The partition has as many parts as the size of the list of value. The ith

	 * part is composed by all the structure <code>structure</code> such as

	 * 

	 * @throws Exception

	 */

	/**

	 * Run a query on all the parts of this partition.

	 * 

	 * 

	 * 

	 */

	public List<QueryResult> query(CQLQuery query, String name) throws CqiClientException {

		Log.finest(TXMCoreMessages.bind(TXMCoreMessages.queryingPartitionP0, this.getUserName()));

		List<Part> parts = getParts();

		List<QueryResult> results = new ArrayList<>(parts.size());

	 * 

	 * Not intended to be used directly.

	 *

	 *             {@link CQPCorpus#createSubcorpus(CQLQuery, String)}

	 */

	@Override

	 *

	 * @param pID the cqp id

	 * @param name the name

	 * @param query the query

	 * @throws InvalidCqpIdException the invalid cqp id exception

	 *             {@link CQPCorpus#createSubcorpus(CQLQuery, String)}

	 */

	protected void setParameters(String pID, String name, CQLQuery query) throws InvalidCqpIdException {

		this.pID = pID;

		this.pQuery = query;

		this.setUserName(name);

	 * @param queryResult

	 */

	public void setParameters(String cqpId, String name, QueryResult queryResult) {

		this.pID = cqpId;

		this.setUserName(name);

		this.pQuery = queryResult.getQuery();

	/**

	 * Builds the tree content.

	 *

	 */

	protected void buildTreeContent()

	{

	 * Instantiates a new lexical table impl.

	 *

	 * @param matrix the matrix

	 * @param formNames the form names

	 * @param partNames the part names

	 * @throws RWorkspaceException the r workspace exception

	 * Creates the lexical table.

	 *

	 * @param indexes the vocabularies

	 * @return the lexical table

	 * @throws RWorkspaceException the r workspace exception

	 */

	/**

	 * protected on purpose. See {@link #getInstance()}.

	 *

	 * @throws RWorkspaceException the r workspace exception

	 */

		this.workspace = workspace;

	}