r3350 - in isis-fish/branches/3.3.1/src/main: java/fr/ifremer/isisfish java/fr/ifremer/isisfish/mexico/xml java/fr/ifremer/isisfish/simulator/launcher java/fr/ifremer/isisfish/simulator/sensitivity java/fr/ifremer/isisfish/simulator/sensitivity/domain java/fr/ifremer/isisfish/ui/sensitivity java/fr/ifremer/isisfish/ui/simulator resources/i18n - Isis-fish-commits

6 Jun 2011

Author: jcouteau
Date: 2011-06-06 15:12:08 +0000 (Mon, 06 Jun 2011)
New Revision: 3350

Log:
- Remove autocomplete
- Clean factors and domains and everything that comes with it
- Clean some code



Modified:
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/IsisFish.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityCalculator.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/EquationContinuousDomain.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/MatrixContinuousDomain.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EquationContinuousPanelUI.jaxx
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java
   isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java
   isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_en_GB.properties
   isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_fr_FR.properties

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/IsisFish.java
===================================================================

--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/IsisFish.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/IsisFish.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -36,7 +36,6 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.text.SimpleDateFormat;
-import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
@@ -53,11 +52,6 @@
 import org.apache.commons.beanutils.ConvertUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.fife.rsta.ac.LanguageSupport;
-import org.fife.rsta.ac.LanguageSupportFactory;
-import org.fife.rsta.ac.java.JarInfo;
-import org.fife.rsta.ac.java.JavaLanguageSupport;
-import org.fife.ui.rsyntaxtextarea.SyntaxConstants;
 import org.nuiton.i18n.I18n;
 import org.nuiton.i18n.init.ClassPathI18nInitializer;
 import org.nuiton.math.matrix.DoubleBigVector;
@@ -86,7 +80,6 @@
 import fr.ifremer.isisfish.types.TimeUnit;
 import fr.ifremer.isisfish.ui.WelcomeUI;
 import fr.ifremer.isisfish.ui.util.ErrorHelper;
-import fr.ifremer.isisfish.util.CompileHelper;
 import fr.ifremer.isisfish.util.ConverterUtil;
 import fr.ifremer.isisfish.util.DateConverter;
 import fr.ifremer.isisfish.util.MonthConverter;
@@ -206,7 +199,7 @@
                     filesToMigrate.putAll(FileUtil.grep("org\\.codelutin\\.", folder, ".*\\.java", "ISO-8859-1"));
                 }
     
-                if (filesToMigrate != null && !filesToMigrate.isEmpty()) {
+                if (!filesToMigrate.isEmpty()) {
     
                     // yes by defaut (for tests)
                     // but ask user if UI launch
@@ -383,12 +376,11 @@
      * @return true if user confirm question
      */
     protected static boolean ask(Object msg) {
-        boolean result = true;
         int value = JOptionPane.showConfirmDialog(null, msg);
         if (value == JOptionPane.CANCEL_OPTION) {
             quit();
         }
-        result = value == JOptionPane.YES_OPTION;
+        boolean result = value == JOptionPane.YES_OPTION;
         return result;
     }
 
@@ -508,7 +500,7 @@
                 // il est possiblement obligatoire de ne plus etre sur le trunk, ou
                 // de migrer sur un autre tag
 
-                List<File> filesInClonflict = null;
+                List<File> filesInClonflict;
                 
                 // si on est sur une branche, on est en developpement, on ne fait donc rien
                 if (vcs.getTag().startsWith("branches")) {
@@ -703,44 +695,5 @@
         // par defaut on utilise des doubles pour les matrices
         MatrixFactory.setDefaultVectorClass(DoubleBigVector.class);
     }
-
-    /**
-     * Ajout les bons jar et sources au support de language
-     * de rSyntaxTextArea pour avoir un meilleur support.
-     * 
-     * Doit être fait avant l'instanciation de l'editor rSyntaxTextArea.
-     * 
-     * @param config config
-     */
-    protected static void initRSyntaxJavaSupport(IsisConfig config) {
-        // TODO: This API will change!  It will be easier to do per-editor
-        // changes to the build path.
-        LanguageSupportFactory lsf = LanguageSupportFactory.get();
-        LanguageSupport support = lsf.getSupportFor(SyntaxConstants.SYNTAX_STYLE_JAVA);
-        JavaLanguageSupport jls = (JavaLanguageSupport)support;
-        try {
-            // system JRE
-            jls.getJarManager().addJar(null);
-
-            // ajout des scripts utilisateur dans le lots
-            JarInfo ji = new JarInfo(config.getCompileDirectory());
-            ji.setSourceLocation(config.getDatabaseDirectory());
-            jls.getJarManager().addJar(ji);
-
-            // Ajout des jars
-            String paths = CompileHelper.getClassPathAsString(Collections.EMPTY_LIST);
-            for (String path : paths.split(File.pathSeparator)) {
-                File filePath = new File(path);
-                if (filePath.isFile()) { // bug avec les directory
-                    JarInfo ji2 = new JarInfo(filePath);
-                    jls.getJarManager().addJar(ji2);
-                }
-            }
-        } catch (Exception ex) {
-            if (log.isWarnEnabled()) {
-                log.warn("Can't install Java support", ex);
-            }
-        }
-    }
     
 } // IsisFish

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/DomXMLParser.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -57,6 +57,33 @@
  */
 public class DomXMLParser {
 
+    public static final String DISCRETE = "discrete";
+    public static final String ENUMERATION = "enumeration";
+    public static final String DOMAIN = "domain";
+    public static final String FIXED = "fixed";
+    public static final String VALUE = "value";
+    public static final String RULE = "rule";
+    public static final String RULES = "rules";
+    public static final String VERSION = "version";
+    public static final String NAME = "name";
+    public static final String TYPE = "type";
+    public static final String PROPERTY = "property";
+    public static final String TARGET = "target";
+    public static final String CONTINUOUS = "continuous";
+    public static final String MATRIXCONTINUOUS = "matrixcontinuous";
+    public static final String COEFFICIENT = "coefficient";
+    public static final String EQUATIONCONTINUOUS = "equationcontinuous";
+    public static final String EQUATION = "equation";
+    public static final String VARIABLE = "variable";
+    public static final String PERCENTAGE = "percentage";
+    public static final String REFERENCE = "reference";
+    public static final String RANGE = "range";
+    public static final String MIN = "min";
+    public static final String MAX = "max";
+    public static final String CARDINALITY = "cardinality";
+    public static final String INTEGER = "integer";
+    public static final String MX = "mx";
+
     /**
      * Parse element root node as Design plan.
      * 
@@ -69,7 +96,7 @@
         DesignPlan plan = new DesignPlan();
 
         // could return "2" or null
-        String version = rootElement.attributeValue("version");
+        String version = rootElement.attributeValue(VERSION);
 
         List<Element> factorGroupElements = rootElement.selectNodes("child::factors");
         FactorGroup factorGroup = null;
@@ -91,11 +118,8 @@
      * 
      * @param fgElement factor group element (>factors<)
      * @param topiaContext context
-     * @param mixed {@code true} if create factor group need to be mixed
      * @return factor group
-     * 
-     * @see FactorGroup#isMixed()
-     * 
+     *
      * @deprecated since 3.4.0.0, this parsing method parse experimentalDesign
      *      in version "0" or "null" version, don't remove for
      *      data reading purpose, but could be removed in a future version
@@ -103,7 +127,7 @@
     @Deprecated
     protected static FactorGroup parseFactorGroup(Element fgElement, TopiaContext topiaContext) {
 
-        String factorGroupName = fgElement.attributeValue("name");
+        String factorGroupName = fgElement.attributeValue(NAME);
         FactorGroup factorGroup = new FactorGroup(factorGroupName);
 
         // sub factor group
@@ -117,43 +141,43 @@
         List<Element> factorElements = fgElement.selectNodes("child::factor");
 
         for (Element factorElement : factorElements) {
-            String type = factorElement.attributeValue("type");
-            String name = factorElement.attributeValue("name");
-            String property = factorElement.attributeValue("property");
-            String path = factorElement.element("target").getText().trim();
+            String type = factorElement.attributeValue(TYPE);
+            String name = factorElement.attributeValue(NAME);
+            String property = factorElement.attributeValue(PROPERTY);
+            String path = factorElement.element(TARGET).getText().trim();
 
             // double
             if ("real".equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
                 // tous les domaines continues
-                if (property.endsWith("continuous")) {
+                if (property.endsWith(CONTINUOUS)) {
 
                     ContinuousDomain domain;
-                    if(property.equals("matrixcontinuous")) {
+                    if(property.equals(MATRIXCONTINUOUS)) {
                         // matrix specific
                         // <coefficient operator="-" value="0.799"/>
                         MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
-                        Element coefficientElement = fixedElement.element("coefficient");
-                        mdomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue("value")));
+                        Element coefficientElement = fixedElement.element(COEFFICIENT);
+                        mdomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue(VALUE)));
                         
                         // <mx name="test1" step="0">...
-                        Element matrixElement = fixedElement.element("mx");
+                        Element matrixElement = fixedElement.element(MX);
                         MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
-                        mdomain.setMatrix(matrix);
+                        mdomain.setReferenceValue(matrix);
 
                         domain = mdomain;
                     }
-                    else if (property.equals("equationcontinuous")) {
+                    else if (property.equals(EQUATIONCONTINUOUS)) {
                         // equation specific
                         EquationContinuousDomain edomain = new EquationContinuousDomain();
-                        Element coefficientElement = fixedElement.element("coefficient");
-                        edomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue("value")));
+                        Element coefficientElement = fixedElement.element(COEFFICIENT);
+                        edomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue(VALUE)));
                         
-                        Element equationElement = fixedElement.element("equation");
-                        edomain.setReferenceValue(Double.valueOf(equationElement.attributeValue("reference")));
-                        edomain.setVariableName(equationElement.attributeValue("variable"));
+                        Element equationElement = fixedElement.element(EQUATION);
+                        edomain.setReferenceValue(Double.valueOf(equationElement.attributeValue(REFERENCE)));
+                        edomain.setVariableName(equationElement.attributeValue(VARIABLE));
 
                         domain = edomain;
                     }
@@ -161,67 +185,67 @@
                         // continous domain
                         domain = new ContinuousDomain();
 
-                        Element percentageElement = fixedElement.element("percentage");
+                        Element percentageElement = fixedElement.element(PERCENTAGE);
                         if (percentageElement != null) {
-                            domain.setCoefficient(Double.valueOf(percentageElement.attributeValue("coefficient")));
-                            domain.setReferenceValue(Double.valueOf(percentageElement.attributeValue("reference")));
+                            domain.setCoefficient(Double.valueOf(percentageElement.attributeValue(COEFFICIENT)));
+                            domain.setReferenceValue(Double.valueOf(percentageElement.attributeValue(REFERENCE)));
                         }
                         else {
                             // <range max="1.0" min="0.0"/>
-                            Element rangeElement = fixedElement.element("range");
-                            domain.setMinBound(Double.valueOf(rangeElement.attributeValue("min")));
-                            domain.setMaxBound(Double.valueOf(rangeElement.attributeValue("max")));
+                            Element rangeElement = fixedElement.element(RANGE);
+                            domain.setMinBound(Double.valueOf(rangeElement.attributeValue(MIN)));
+                            domain.setMaxBound(Double.valueOf(rangeElement.attributeValue(MAX)));
                         }
                     }
 
-                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue(CARDINALITY)));
 
                     factor.setDomain(domain);
-                } else if ("discrete".equals(property)) {
+                } else if (DISCRETE.equals(property)) {
                     DiscreteDomain domain = new DiscreteDomain();
                     List<Element> valueElements = fixedElement.element(
-                            "enumeration").elements("value");
+                            ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        domain.getValues().put(Integer.valueOf(label),
+                        domain.getValues().put(label,
                                 Double.valueOf(valueElement.getTextTrim()));
                         ++label;
                     }
                     factor.setDomain(domain);
                 }
                 factorGroup.addFactor(factor);
-            } else if ("integer".equals(type)) {
+            } else if (INTEGER.equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
-                if ("continuous".equals(property)) {
-                    ContinuousDomain domain = null;
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
+                if (CONTINUOUS.equals(property)) {
+                    ContinuousDomain domain;
 
-                    if(property.equals("matrixcontinuous")) {
+                    if(property.equals(MATRIXCONTINUOUS)) {
                         // matrix specific
                         MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
 
-                        Element coefficientElement = fixedElement.element("coefficient");
-                        mdomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue("value")));
+                        Element coefficientElement = fixedElement.element(COEFFICIENT);
+                        mdomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue(VALUE)));
 
                         // matrix specific
-                        Element matrixElement = fixedElement.element("mx");
+                        Element matrixElement = fixedElement.element(MX);
                         MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
-                        mdomain.setMatrix(matrix);
+                        mdomain.setReferenceValue(matrix);
 
                         domain = mdomain;
                     }
-                    else if (property.equals("equationcontinuous")) {
+                    else if (property.equals(EQUATIONCONTINUOUS)) {
                         // equation specific
                         
                         EquationContinuousDomain edomain = new EquationContinuousDomain();
                         
-                        Element coefficientElement = fixedElement.element("coefficient");
-                        edomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue("value")));
+                        Element coefficientElement = fixedElement.element(COEFFICIENT);
+                        edomain.setCoefficient(Double.valueOf(coefficientElement.attributeValue(VALUE)));
                         
-                        Element equationElement = fixedElement.element("equation");
-                        edomain.setReferenceValue(Double.valueOf(equationElement.attributeValue("reference")));
-                        edomain.setVariableName(equationElement.attributeValue("variable"));
+                        Element equationElement = fixedElement.element(EQUATION);
+                        edomain.setReferenceValue(Double.valueOf(equationElement.attributeValue(REFERENCE)));
+                        edomain.setVariableName(equationElement.attributeValue(VARIABLE));
 
                         domain = edomain;
                     }
@@ -229,48 +253,48 @@
                         // continous domain
                         domain = new ContinuousDomain();
                         
-                        Element percentageElement = fixedElement.element("percentage");
+                        Element percentageElement = fixedElement.element(PERCENTAGE);
                         if (percentageElement != null) {
-                            domain.setCoefficient(Double.valueOf(percentageElement.attributeValue("coefficient")));
-                            domain.setReferenceValue(Double.valueOf(percentageElement.attributeValue("reference")));
+                            domain.setCoefficient(Double.valueOf(percentageElement.attributeValue(COEFFICIENT)));
+                            domain.setReferenceValue(Double.valueOf(percentageElement.attributeValue(REFERENCE)));
                         }
                         else {
                             // <range max="1" min="3"/>
-                            Element rangeElement = fixedElement.element("range");
-                            domain.setMinBound(Integer.valueOf(rangeElement.attributeValue("min")));
-                            domain.setMaxBound(Integer.valueOf(rangeElement.attributeValue("max")));
+                            Element rangeElement = fixedElement.element(RANGE);
+                            domain.setMinBound(Integer.valueOf(rangeElement.attributeValue(MIN)));
+                            domain.setMaxBound(Integer.valueOf(rangeElement.attributeValue(MAX)));
                         }
                         
                     }
 
-                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue(CARDINALITY)));
 
                     factor.setDomain(domain);
-                } else if ("discrete".equals(property)) {
+                } else if (DISCRETE.equals(property)) {
                     DiscreteDomain domain = new DiscreteDomain();
                     List<Element> valueElements = fixedElement.element(
-                            "enumeration").elements("value");
+                            ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        domain.getValues().put(Integer.valueOf(label),
+                        domain.getValues().put(label,
                                 Integer.valueOf(valueElement.getTextTrim()));
                         ++label;
                     }
                     factor.setDomain(domain);
                 }
                 factorGroup.addFactor(factor);
-            } else if ("rule".equals(type)) {
+            } else if (RULE.equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
-                if ("discrete".equals(property)) {
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
+                if (DISCRETE.equals(property)) {
                     RuleDiscreteDomain domain = new RuleDiscreteDomain();
-                    List<Element> valueElements = fixedElement.element("enumeration").elements("value");
+                    List<Element> valueElements = fixedElement.element(ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        Element rulesElement = valueElement.element("rules");
+                        Element rulesElement = valueElement.element(RULES);
                         List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext);
-                        domain.getValues().put(Integer.valueOf(label), rulesValue);
+                        domain.getValues().put(label, rulesValue);
                         ++label;
                     }
                     factor.setDomain(domain);
@@ -290,14 +314,11 @@
      * 
      * @param fgElement factor group element (>factors<)
      * @param topiaContext context
-     * @param mixed {@code true} if create factor group need to be mixed
      * @return factor group
-     * 
-     * @see FactorGroup#isMixed()
      */
     protected static FactorGroup parseFactorGroupV2(Element fgElement, TopiaContext topiaContext) {
 
-        String factorGroupName = fgElement.attributeValue("name");
+        String factorGroupName = fgElement.attributeValue(NAME);
         FactorGroup factorGroup = new FactorGroup(factorGroupName);
 
         // sub factor group
@@ -311,58 +332,58 @@
         List<Element> factorElements = fgElement.selectNodes("child::factor");
 
         for (Element factorElement : factorElements) {
-            String type = factorElement.attributeValue("type");
-            String name = factorElement.attributeValue("name");
-            String property = factorElement.attributeValue("property");
-            String path = factorElement.element("target").getText().trim();
+            String type = factorElement.attributeValue(TYPE);
+            String name = factorElement.attributeValue(NAME);
+            String property = factorElement.attributeValue(PROPERTY);
+            String path = factorElement.element(TARGET).getText().trim();
 
             // double
             if ("real".equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
                 // tous les domaines continues
-                if (property.endsWith("continuous")) {
+                if (property.endsWith(CONTINUOUS)) {
 
                     ContinuousDomain domain;
-                    if(property.equals("matrixcontinuous")) {
+                    if(property.equals(MATRIXCONTINUOUS)) {
                         
                         MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
-                        Element referenceElement = fixedElement.element("reference");
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
                             // matrix specific
                             // <coefficient operator="-" value="0.799"/>
-                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             // <mx name="test1" step="0">...
-                            Element matrixElement = referenceElement.element("mx");
+                            Element matrixElement = referenceElement.element(MX);
                             MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
-                            mdomain.setMatrix(matrix);
+                            mdomain.setReferenceValue(matrix);
                         }
                         else {
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
-                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element("mx"), topiaContext);
-                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element("mx"), topiaContext);
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
+                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element(MX), topiaContext);
+                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element(MX), topiaContext);
                             mdomain.setMinBound(minMatrix);
                             mdomain.setMaxBound(maxMatrix);
                         }
 
                         domain = mdomain;
                     }
-                    else if (property.equals("equationcontinuous")) {
+                    else if (property.equals(EQUATIONCONTINUOUS)) {
                         // equation specific
                         EquationContinuousDomain edomain = new EquationContinuousDomain();
-                        edomain.setVariableName(fixedElement.attributeValue("variable"));
-                        Element referenceElement = fixedElement.element("reference");
+                        edomain.setVariableName(fixedElement.attributeValue(VARIABLE));
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
-                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             edomain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
                         }
                         else {
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
                             edomain.setMinBound(Double.valueOf(minElement.getTextTrim()));
                             edomain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
                         }
@@ -373,82 +394,82 @@
                         // continous domain
                         domain = new ContinuousDomain();
 
-                        Element referenceElement = fixedElement.element("reference");
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
-                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             domain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
                         }
                         else {
                             // <range max="1.0" min="0.0"/>
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
                             domain.setMinBound(Double.valueOf(minElement.getTextTrim()));
                             domain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
                         }
                     }
 
-                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue(CARDINALITY)));
 
                     factor.setDomain(domain);
-                } else if ("discrete".equals(property)) {
+                } else if (DISCRETE.equals(property)) {
                     DiscreteDomain domain = new DiscreteDomain();
                     List<Element> valueElements = fixedElement.element(
-                            "enumeration").elements("value");
+                            ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        domain.getValues().put(Integer.valueOf(label),
+                        domain.getValues().put(label,
                                 Double.valueOf(valueElement.getTextTrim()));
                         ++label;
                     }
                     factor.setDomain(domain);
                 }
                 factorGroup.addFactor(factor);
-            } else if ("integer".equals(type)) {
+            } else if (INTEGER.equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
-                if ("continuous".equals(property)) {
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
+                if (CONTINUOUS.equals(property)) {
                     ContinuousDomain domain = null;
 
-                    if(property.equals("matrixcontinuous")) {
+                    if(property.equals(MATRIXCONTINUOUS)) {
                         
                         MatrixContinuousDomain mdomain = new MatrixContinuousDomain();
-                        Element referenceElement = fixedElement.element("reference");
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
                             // matrix specific
                             // <coefficient operator="-" value="0.799"/>
-                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            mdomain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             // <mx name="test1" step="0">...
-                            Element matrixElement = referenceElement.element("mx");
+                            Element matrixElement = referenceElement.element(MX);
                             MatrixND matrix = MexicoHelper.getMatrixFromXml(matrixElement, topiaContext);
-                            mdomain.setMatrix(matrix);
+                            mdomain.setReferenceValue(matrix);
                         }
                         else {
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
-                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element("mx"), topiaContext);
-                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element("mx"), topiaContext);
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
+                            MatrixND minMatrix = MexicoHelper.getMatrixFromXml(minElement.element(MX), topiaContext);
+                            MatrixND maxMatrix = MexicoHelper.getMatrixFromXml(maxElement.element(MX), topiaContext);
                             mdomain.setMinBound(minMatrix);
                             mdomain.setMaxBound(maxMatrix);
                         }
 
                         domain = mdomain;
                     }
-                    else if (property.equals("equationcontinuous")) {
+                    else if (property.equals(EQUATIONCONTINUOUS)) {
                         // equation specific
                         EquationContinuousDomain edomain = new EquationContinuousDomain();
-                        edomain.setVariableName(fixedElement.attributeValue("variable"));
-                        Element referenceElement = fixedElement.element("reference");
+                        edomain.setVariableName(fixedElement.attributeValue(VARIABLE));
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
-                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            edomain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             edomain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
                         }
                         else {
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
                             edomain.setMinBound(Double.valueOf(minElement.getTextTrim()));
                             edomain.setMaxBound(Double.valueOf(maxElement.getTextTrim()));
                         }
@@ -459,65 +480,65 @@
                         // continous domain
                         domain = new ContinuousDomain();
 
-                        Element referenceElement = fixedElement.element("reference");
+                        Element referenceElement = fixedElement.element(REFERENCE);
                         if (referenceElement != null) {
-                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue("coefficient")));
+                            domain.setCoefficient(Double.valueOf(referenceElement.attributeValue(COEFFICIENT)));
                             domain.setReferenceValue(Double.valueOf(referenceElement.getTextTrim()));
                         }
                         else {
                             // <range max="1.0" min="0.0"/>
-                            Element rangeElement = fixedElement.element("range");
-                            Element minElement = rangeElement.element("min");
-                            Element maxElement = rangeElement.element("max");
+                            Element rangeElement = fixedElement.element(RANGE);
+                            Element minElement = rangeElement.element(MIN);
+                            Element maxElement = rangeElement.element(MAX);
                             domain.setMinBound(Integer.valueOf(minElement.getTextTrim()));
                             domain.setMaxBound(Integer.valueOf(maxElement.getTextTrim()));
                         }
                     }
 
-                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue("cardinality")));
+                    domain.setCardinality(Integer.valueOf(fixedElement.attributeValue(CARDINALITY)));
 
                     factor.setDomain(domain);
-                } else if ("discrete".equals(property)) {
+                } else if (DISCRETE.equals(property)) {
                     DiscreteDomain domain = new DiscreteDomain();
                     List<Element> valueElements = fixedElement.element(
-                            "enumeration").elements("value");
+                            ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        domain.getValues().put(Integer.valueOf(label),
+                        domain.getValues().put(label,
                                 Integer.valueOf(valueElement.getTextTrim()));
                         ++label;
                     }
                     factor.setDomain(domain);
                 }
                 factorGroup.addFactor(factor);
-            } else if ("rule".equals(type)) {
+            } else if (RULE.equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
-                if ("discrete".equals(property)) {
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
+                if (DISCRETE.equals(property)) {
                     RuleDiscreteDomain domain = new RuleDiscreteDomain();
-                    List<Element> valueElements = fixedElement.element("enumeration").elements("value");
+                    List<Element> valueElements = fixedElement.element(ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
-                        Element rulesElement = valueElement.element("rules");
+                        Element rulesElement = valueElement.element(RULES);
                         List<Rule> rulesValue = MexicoHelper.getRulesFromXml(rulesElement, topiaContext);
-                        domain.getValues().put(Integer.valueOf(label), rulesValue);
+                        domain.getValues().put(label, rulesValue);
                         ++label;
                     }
                     factor.setDomain(domain);
                 }
                 factorGroup.addFactor(factor);
-            } else if ("equation".equals(type)) {
+            } else if (EQUATION.equals(type)) {
                 Factor factor = new Factor(name);
                 factor.setPath(path);
-                Element fixedElement = factorElement.element("domain").element("fixed");
-                if ("discrete".equals(property)) {
+                Element fixedElement = factorElement.element(DOMAIN).element(FIXED);
+                if (DISCRETE.equals(property)) {
                     EquationDiscreteDomain domain = new EquationDiscreteDomain();
-                    List<Element> valueElements = fixedElement.element("enumeration").elements("value");
+                    List<Element> valueElements = fixedElement.element(ENUMERATION).elements(VALUE);
                     int label = 0;
                     for (Element valueElement : valueElements) {
                         String content = StringEscapeUtils.unescapeXml(valueElement.getText());
-                        domain.getValues().put(Integer.valueOf(label), content);
+                        domain.getValues().put(label, content);
                         ++label;
                     }
                     factor.setDomain(domain);

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/EquationContinuousDomainXMLVisitor.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -50,7 +50,11 @@
 
         EquationContinuousDomain eDomain = (EquationContinuousDomain)domain;
         // this version add variable name
-        xmlBuffer.append(" cardinality=\"" + eDomain.getCardinality() + "\" variable=\"" + eDomain.getVariableName()+ "\">");
+        xmlBuffer.append(" cardinality=\"")
+                 .append(eDomain.getCardinality())
+                 .append("\" variable=\"")
+                 .append(eDomain.getVariableName())
+                 .append("\">");
 
         appendDomain(eDomain);
     }
@@ -65,15 +69,21 @@
 
         // facteur continue pourcentage
         if (domain.getCoefficient() != null || domain.getReferenceValue() != null) {
-            xmlBuffer.append("<reference coefficient=\"" + eDomain.getCoefficient() + "\">");
+            xmlBuffer.append("<reference coefficient=\"")
+                     .append(eDomain.getCoefficient())
+                     .append( "\">");
             xmlBuffer.append(eDomain.getReferenceValue());
             xmlBuffer.append("</reference>");
         }
         else {
             // facteur continue min/max
             xmlBuffer.append("<range>");
-            xmlBuffer.append("<min>" + domain.getOriginalMinBound() + "</min>");
-            xmlBuffer.append("<max>" + domain.getOriginalMaxBound() + "</max>");
+            xmlBuffer.append("<min>")
+                     .append(domain.getMinBound())
+                     .append("</min>");
+            xmlBuffer.append("<max>")
+                     .append(domain.getMaxBound())
+                     .append("</max>");
             xmlBuffer.append("</range>");
         }
     }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/FactorXMLVisitor.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -54,34 +54,28 @@
     @Override
     public void start(Factor factor) {
         xmlBuffer.append("<factor");
-        xmlBuffer.append(" name=\"" + factor.getName() + "\"");
+        xmlBuffer.append(" name=\"").append(factor.getName()).append("\"");
         Object referenceValueForType = null;
         // property attribute
-        if (factor.getDomain() instanceof MatrixContinuousDomain) {
-            xmlBuffer.append(" property=\"matrixcontinuous\"");
-            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
-            if (referenceValueForType == null) {
-                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
+
+        Domain domain = factor.getDomain();
+
+        if (domain instanceof ContinuousDomain) {
+            if (domain instanceof MatrixContinuousDomain) {
+                xmlBuffer.append(" property=\"matrixcontinuous\"");
+            } else if (domain instanceof EquationContinuousDomain) {
+                xmlBuffer.append(" property=\"equationcontinuous\"");
+            } else {
+                xmlBuffer.append(" property=\"continuous\"");
             }
-        }
-        else if (factor.getDomain() instanceof EquationContinuousDomain) {
-            xmlBuffer.append(" property=\"equationcontinuous\"");
-            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
+            referenceValueForType = ((ContinuousDomain) domain).getReferenceValue();
             if (referenceValueForType == null) {
-                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
+                referenceValueForType = ((ContinuousDomain) domain).getMinBound();
             }
-        }
-        else if (factor.getDomain() instanceof ContinuousDomain) {
-            xmlBuffer.append(" property=\"continuous\"");
-            referenceValueForType = ((ContinuousDomain)factor.getDomain()).getReferenceValue();
-            if (referenceValueForType == null) {
-                referenceValueForType = ((ContinuousDomain)factor.getDomain()).getOriginalMinBound();
-            }
-        }
-        else if (factor.getDomain() instanceof DiscreteDomain) {
+        } else if (domain instanceof DiscreteDomain) {
             xmlBuffer.append(" property=\"discrete\"");
-            Object firstKey = ((DiscreteDomain)factor.getDomain()).getValues().firstKey();
-            referenceValueForType = ((DiscreteDomain)factor.getDomain()).getValues().get(firstKey);
+            Object firstKey = ((DiscreteDomain) domain).getValues().firstKey();
+            referenceValueForType = ((DiscreteDomain) domain).getValues().get(firstKey);
         }
         // type attribute
         if (referenceValueForType instanceof Double || referenceValueForType instanceof Float
@@ -91,15 +85,15 @@
         else if (referenceValueForType instanceof Integer) {
             xmlBuffer.append(" type=\"integer\"");
         }
-        else if (factor.getDomain() instanceof RuleDiscreteDomain) {
+        else if (domain instanceof RuleDiscreteDomain) {
             xmlBuffer.append(" type=\"rule\"");
         }
-        else if (factor.getDomain() instanceof EquationDiscreteDomain) {
+        else if (domain instanceof EquationDiscreteDomain) {
             xmlBuffer.append(" type=\"equation\"");
         }
         xmlBuffer.append(">");
         // target element
-        xmlBuffer.append("<target>" + factor.getPath() + "</target>");
+        xmlBuffer.append("<target>").append(factor.getPath()).append("</target>");
         // value element
         /* TODO value should be only in simulation export,
         not in design plan export

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/mexico/xml/MatrixContinuousDomainXMLVisitor.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -51,16 +51,22 @@
         MatrixContinuousDomain mDomain = (MatrixContinuousDomain)domain;
 
         // facteur continue pourcentage
-        if (domain.getCoefficient() != null || domain.getReferenceValue() != null) {
-            xmlBuffer.append("<reference coefficient=\"" + mDomain.getCoefficient() + "\">");
-            xmlBuffer.append(MexicoHelper.getMatrixAsXML(mDomain.getMatrix()));
+        if (domain.isPercentageType()) {
+            xmlBuffer.append("<reference coefficient=\"")
+                     .append(mDomain.getCoefficient())
+                     .append("\">");
+            xmlBuffer.append(MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getReferenceValue()));
             xmlBuffer.append("</reference>");
         }
         else {
             // facteur continue min/max
             xmlBuffer.append("<range>");
-            xmlBuffer.append("<min>" + MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getOriginalMaxBound()) + "</min>");
-            xmlBuffer.append("<max>" + MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getOriginalMaxBound()) + "</max>");
+            xmlBuffer.append("<min>")
+                     .append(MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getMinBound()))
+                     .append("</min>");
+            xmlBuffer.append("<max>")
+                     .append(MexicoHelper.getMatrixAsXML((MatrixND)mDomain.getMaxBound()))
+                     .append("</max>");
             xmlBuffer.append("</range>");
         }
     }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/launcher/SimulationService.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -94,7 +94,7 @@
 
 /**
  * Cette classe est responsable de conservation de toutes les simulations faites
- * ou a faire. Pour ajouter une nouvelle simulation on appelle la methode
+ * ou a faire. Pour ajouter une nouvelle simulation on appelle une des méthodes
  * {@link #submit}.
  * <p>
  * Cette classe sert aussi de modele pour le moniteur de queue
@@ -268,7 +268,8 @@
 
     /**
      * Ajoute le job au job en cours previent s'il n'etait pas deja present
-     * les listener {@link SimulationServiceListener#simulationStart}.
+     * les listeners
+     * {@link SimulationServiceListener#simulationStart(SimulationService, SimulationJob)}.
      * @param job
      */
     protected synchronized void fireStartEvent(SimulationJob job) {
@@ -285,8 +286,8 @@
      * Supprime le job de la liste des jobs en cours et l'ajoute le job si
      * besoin a la liste des jobs faits (s'il y a une erreur ou qu'il ne sagit
      * pas d'une simulation lancer par un plan d'analyse).
-     * Les listener sont prevenu par la methode
-     * {@link SimulationServiceListener#simulationStop}.
+     * Les listener sont prevenu par la méthode
+     * {@link SimulationServiceListener#simulationStop(SimulationService, SimulationJob)}.
      * @param job
      */
     protected synchronized void fireStopEvent(SimulationJob job) {
@@ -445,9 +446,6 @@
             SensitivityScenarios sensitivityScenarios = sensitivitycalculator
                     .compute(designPlan, masterExportDirectory);
 
-            // close context opened for nominal values
-            context.closeContext();
-
             // ajout des parametres de simulation
             localParameters.setSensitivityCalculator(sensitivitycalculator);
             localParameters.setNumberOfSensitivitySimulation(sensitivityScenarios.getScenarios().size());
@@ -585,7 +583,7 @@
      * 
      * @param beanUtils beanUtils converter
      * @param buffer buffer to fill
-     * @param level call level used to avoid variables name collision
+     * @param counter call counter used to avoid variables name collision
      * @param factors factor list to manage
      */
     protected void generatePreScript(ConvertUtilsBean beanUtils, StringBuffer buffer, Counter counter, Collection<Factor> factors) {

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/AbstractSensitivityCalculator.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -36,22 +36,17 @@
 import javax.swing.JScrollPane;
 import javax.swing.JTextPane;
 
-import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.nuiton.j2r.REngine;
 import org.nuiton.j2r.RException;
 import org.nuiton.j2r.RProxy;
-import org.nuiton.topia.TopiaContext;
-import org.nuiton.topia.persistence.TopiaEntity;
 import org.nuiton.util.FileUtil;
 
 import fr.ifremer.isisfish.datastore.SimulationStorage;
 import fr.ifremer.isisfish.export.SensitivityExport;
 import fr.ifremer.isisfish.simulator.sensitivity.domain.ContinuousDomain;
 import fr.ifremer.isisfish.simulator.sensitivity.domain.DiscreteDomain;
-import fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain;
-import fr.ifremer.isisfish.simulator.sensitivity.domain.MatrixContinuousDomain;
 
 public abstract class AbstractSensitivityCalculator implements
         SensitivityCalculator {
@@ -59,19 +54,6 @@
     /** to use log facility, just put in your code: log.info("..."); */
     private static Log log = LogFactory
             .getLog(AbstractSensitivityCalculator.class);
-
-    /** Topia context used for discrete domain nominal value compute. */
-    protected TopiaContext context;
-
-    /**
-     * Set topia context on current region to nominal value compute.
-     * 
-     * @param context context
-     */
-    @Override
-    public void setTopiaContext(TopiaContext context) {
-        this.context = context;
-    }
     
     /**
      * Method to create the isis.factors dataframe in R.
@@ -81,7 +63,7 @@
      * destination RData file. The RData file will be named directory.RData and
      * saved in the directory parent.
      * 
-     * @throws SensitivityException
+     * @throws SensitivityException if an error occur while talking to R
      */
     public void setIsisFactorsR(DesignPlan plan, File outputdirectory)
             throws SensitivityException {
@@ -119,58 +101,25 @@
             //Factor names
             factorNames += "\"" + factor.getName() + "\"";
 
-            if (factor.getDomain() instanceof MatrixContinuousDomain) {
+            if (factor.getDomain() instanceof ContinuousDomain) {
                 //Continu values, binf values, bsup values and discrete factors attributes
 
-                nominalValues += getNominalValue(factor);
+                nominalValues += factor.getNominalValue();
 
                 //Continu values
                 continuValues += "TRUE";
 
                 //Binf values
 
-                binfValues += ((MatrixContinuousDomain) factor.getDomain())
-                        .getRealMinBound();
-
-                //Bsup values
-                bsupValues += ((MatrixContinuousDomain) factor.getDomain())
-                        .getRealMaxBound();
-
-            } else if (factor.getDomain() instanceof EquationContinuousDomain) {
-                //Continu values, binf values, bsup values and discrete factors attributes
-
-                nominalValues += ((EquationContinuousDomain) factor.getDomain())
-                        .getReferenceValue();
-
-                //Continu values
-                continuValues += "TRUE";
-
-                //Binf values
-                binfValues += ((EquationContinuousDomain) factor.getDomain())
-                        .getValueForIdentifier(0.0);
-
-                //Bsup values
-                bsupValues += ((EquationContinuousDomain) factor.getDomain())
-                        .getValueForIdentifier(1.0);
-            } else if (factor.getDomain() instanceof ContinuousDomain) {
-                //Continu values, binf values, bsup values and discrete factors attributes
-
-                nominalValues += getNominalValue(factor);
-
-                //Continu values
-                continuValues += "TRUE";
-
-                //Binf values
-
                 binfValues += ((ContinuousDomain) factor.getDomain())
-                        .getMinBound();
+                        .getCalculatorMinBound();
 
                 //Bsup values
                 bsupValues += ((ContinuousDomain) factor.getDomain())
-                        .getMaxBound();
+                        .getCalculatorMaxBound();
 
             } else {
-                nominalValues += getNominalValue(factor);
+                nominalValues += factor.getNominalValue();
 
                 //Continu values
                 continuValues += "FALSE";
@@ -245,33 +194,6 @@
 
     }
 
-    protected String getNominalValue(Factor factor) {
-        String result = null;
-
-        Domain domain = factor.getDomain();
-        if (domain instanceof MatrixContinuousDomain) {
-            result = "1.0";
-        }
-        else {
-            String path = factor.getPath();
-            String topiaId = path.substring(0, path.lastIndexOf("#"));
-            String propertyName=path.substring(path.lastIndexOf("#") + 1);
-
-            try {
-                TopiaEntity entity = context.findByTopiaId(topiaId);
-                result = BeanUtils.getProperty(entity, propertyName);
-            } catch (Exception ex) {
-                if (log.isErrorEnabled()) {
-                    log.error("An error occurred while trying to get nominal value", ex);
-                }
-            }
-        }
-        if (log.isDebugEnabled()) {
-            log.debug("Nominal value :" + result);
-        }
-        return result;
-    }
-
     protected String editRInstruction(String rCall){
         JLabel label = new JLabel(
                     "Modifier le code R envoyé si vous le souhaitez");

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/Factor.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -75,6 +75,11 @@
     protected Domain domain;
 
     /**
+     * Value that this factor got in the database
+     */
+    protected Object nominalValue;
+
+    /**
      * Factor value.
      */
     protected Object value;
@@ -201,6 +206,15 @@
         this.path = path;
     }
 
+    public Object getNominalValue() {
+        return nominalValue;
+    }
+
+    public void setNominalValue(Object nominalValue) {
+        this.nominalValue = nominalValue;
+    }
+
+
     /**
      * Accept a new visitor.
      * 
@@ -218,7 +232,7 @@
     @Override
     public Object clone() {
 
-        Factor f = null;
+        Factor f;
         try {
             f = (Factor)super.clone();
 

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityCalculator.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityCalculator.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/SensitivityCalculator.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -28,8 +28,6 @@
 import java.io.File;
 import java.util.List;
 
-import org.nuiton.topia.TopiaContext;
-
 import fr.ifremer.isisfish.datastore.SimulationStorage;
 
 /**
@@ -46,13 +44,6 @@
 public interface SensitivityCalculator {
 
     /**
-     * Set topia context on current region to nominal value compute.
-     * 
-     * @param context context
-     */
-    void setTopiaContext(TopiaContext context);
-
-    /**
      * Return calculator description.
      * 
      * @return calculator description

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/ContinuousDomain.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -27,17 +27,25 @@
 
 import fr.ifremer.isisfish.simulator.sensitivity.Domain;
 import fr.ifremer.isisfish.simulator.sensitivity.visitor.DomainVisitor;
+import org.nuiton.math.matrix.MapFunction;
+import org.nuiton.math.matrix.MatrixND;
 
 /**
- * Tous les domaines continues sont de deux formes (min/max ou pourcentage).
+ *
+ * All the continuous domains can be of 2 different types (min/max or
+ * percentage).
+ *
+ * A min/max domain can take 2 values : {@link #minBound} and {@link #maxBound}.
+ * A percentage domain got 2 values {@link #coefficient} and
+ * {@link #referenceValue} that are the basis to calculate the {@link #minBound}
+ * and {@link #maxBound} values.
+ *
+ * A continuous domain also got a cardinality, either filled in by the user or
+ * the sensitivity method if it manages it.
+ *
+ * To do sensitivity calculations, you MUST use {@link #getCalculatorMinBound()},
+ * {@link #getCalculatorMaxBound()}.
  * 
- * Un domaine min/max a deux valeurs : {@link #minBound} et {@link #maxBound}.
- * Un domaine pourcentage a deux autres valeurs {@link #coefficient} et
- * {@link #referenceValue}.
- * 
- * Un domain continue a également une cardialité, soit renseigné directement
- * par l'utilisateur, soit par la methode d'AS (si elle le gere).
- * 
  * @author chatellier
  * @version $Revision: 1.0 $
  * 
@@ -64,6 +72,9 @@
     /** Cardinality */
     protected int cardinality;
 
+    /** Flag to know the type of the domain **/
+    protected boolean percentageType;
+
     /**
      * Empty constructor.
      */
@@ -82,52 +93,85 @@
         this.minBound = minBound;
         this.maxBound = maxBound;
     }
+
+    public boolean isPercentageType() {
+        return percentageType;
+    }
+
+    public void setPercentageType(boolean percentageType) {
+        this.percentageType = percentageType;
+    }
     
     /**
-     * Return minBound to use for sensitivity. This method can be overridden
-     * and can return another value than {@link #minBound}.
+     * Return the minimum bound of the domain. Do not use this value for
+     * sensitivity calculation, prefer using {@link #getCalculatorMinBound}.
      * 
-     * @return the minBound
+     * @return the minimum bound
      */
     public Object getMinBound() {
-        return getOriginalMinBound();
+        if (isPercentageType()) {
+            MatrixND temp = ((MatrixND) getReferenceValue()).copy();
+
+            // since 3.4.0.0, operator is always *
+            temp.map(new MapFunction() {
+                public double apply(double val) {
+                    return (val + ((val * coefficient) * ((2 * getCalculatorMinBound() - 1))));
+                }
+            });
+            return temp;
+        } else {
+            return minBound;
+        }
     }
     
     /**
-     * Return original domain min bound.
+     * Return the minimum bound for sensitivity calculators. It always returns 0.
      * 
-     * @return the minBound
+     * @return the minimum bound for sensitivity analysis.
      */
-    public final Object getOriginalMinBound() {
-        return minBound;
+    public double getCalculatorMinBound() {
+        return 0;
     }
 
     /**
-     * Set min value.
+     * Set the minimum bound of the domain.
      * 
-     * @param minBound the minBound to set
+     * @param minBound the minimum bound.
      */
     public void setMinBound(Object minBound) {
         this.minBound = minBound;
     }
 
     /**
-     * Return maxBound to use for sensitivity. This method can be overridden
-     * and can return another value than {@link #maxBound}.
+     * Return the maximum bound of the domain. Do not use this value for
+     * sensitivity calculation, prefer using {@link #getCalculatorMaxBound}.
      * 
-     * @return the maxBound
+     * @return the maximum bound
      */
     public Object getMaxBound() {
-        return getOriginalMaxBound();
+        if (isPercentageType()) {
+            MatrixND temp = ((MatrixND) getReferenceValue()).copy();
+
+            // since 3.4.0.0, operator is always *
+            temp.map(new MapFunction() {
+                public double apply(double val) {
+                    return (val + ((val * coefficient) *
+                            ((2 * getCalculatorMaxBound() - 1))));
+                }
+            });
+            return temp;
+        } else {
+            return maxBound;
+        }
     }
     
     /**
-     * Return original domain max bound.
+     * Return the minimum bound for sensitivity calculators. It always returns 1.
      * 
-     * @return the maxBound
+     * @return the maximum bound for sensitivity analysis.
      */
-    public final Object getOriginalMaxBound() {
-        return maxBound;
+    public double getCalculatorMaxBound() {
+        return 1;
     }
 
     /**
@@ -178,17 +222,18 @@
 
     /**
      * {@inheritDoc}.
-     * 
-     * In continuous domain, just return identifier
      */
     public Object getValueForIdentifier(Object identifier) {
-        return identifier;
+        // since 3.4.0.0, operator is always *
+        Double result = ((Double)referenceValue + (((Double)referenceValue * coefficient)
+                * ((2 * (Double)identifier - 1))));
+        return result;
     }
 
     /**
      * Accept a new visitor.
      * 
-     * @param visitor
+     * @param visitor the visitor
      */
     public void accept(DomainVisitor visitor) {
         visitor.start(this);
@@ -207,7 +252,7 @@
     /**
      * Set cardinality
      * 
-     * @param cardinality
+     * @param cardinality the domain cardinality
      */
     public void setCardinality(int cardinality) {
         this.cardinality = cardinality;
@@ -215,7 +260,7 @@
     
     @Override
     public ContinuousDomain clone() {
-        ContinuousDomain cloned = null;
+        ContinuousDomain cloned;
         try {
             cloned = (ContinuousDomain)super.clone();
         } catch (CloneNotSupportedException e) {

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/EquationContinuousDomain.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/EquationContinuousDomain.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/EquationContinuousDomain.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -43,13 +43,6 @@
 
     /** Variable name (must be java valid identifier) */
     protected String variableName;
-    
-    /**
-     * Value used to create the factor.
-     * 
-     * Only used by sensitivity analysis scripts.
-     */
-    protected Double value;
 
     /**
      * Get variable name.
@@ -69,74 +62,13 @@
         this.variableName = variableName;
     }
     
-    /**
-     * {@inheritDoc}.
-     * 
-     * In equation continuous domain, always return 0
-     */
     @Override
-    public Object getMinBound() {
-        return 0.0;
-    }
-
-    /**
-     * {@inheritDoc}.
-     * 
-     * In equation continuous domain, always return 1
-     */
-    @Override
-    public Object getMaxBound() {
-        return 1.0;
-    }
-
-    @Override
-    public Object getValueForIdentifier(Object identifier) {
-        return getValueForIdentifier((Double)identifier);
-    }
-
-    /**
-     * In equation continuous domain, value appear in continuous domain values
-     * only. Here : return identifier.
-     * 
-     * @param identifier identifier
-     * @return ?
-     */
-    public Double getValueForIdentifier(Double identifier) {
-        
-        this.value = identifier;
-
-        Double doubleReference = (Double)referenceValue;
-        // since 3.4.0.0, operator is always *
-        Double result = ((Double) (doubleReference + ((doubleReference * coefficient) * ((2 * value - 1)))));
-        return result;
-    }
-
-    /**
-     * Get value used to create the equation.
-     * 
-     * @return the value
-     */
-    public Double getValue() {
-        return this.value;
-    }
-
-    /**
-     * Set value used to create the equation.
-     * 
-     * @param value the value to set
-     */
-    public void setValue(Double value) {
-        this.value = value;
-    }
-    
-    @Override
     public EquationContinuousDomain clone() {
         EquationContinuousDomain cloned = (EquationContinuousDomain)super.clone();
         cloned.setCardinality(this.cardinality);
         cloned.setMaxBound(this.maxBound);
         cloned.setMinBound(this.minBound);
         cloned.setCoefficient(this.coefficient);
-        cloned.setValue(this.value);
         cloned.setReferenceValue(this.referenceValue);
         cloned.setVariableName(this.variableName);
         return cloned;
@@ -146,7 +78,7 @@
     public String toString() {
         String result = "variableName=" + variableName +
                 " coefficient=" + coefficient + " referenceValue=" + referenceValue +
-                " value=" + value;
+                " min=" + minBound + "max=" + maxBound;
         return result;
     }
 }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/MatrixContinuousDomain.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/MatrixContinuousDomain.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/simulator/sensitivity/domain/MatrixContinuousDomain.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -41,52 +41,7 @@
     /** serialVersionUID. */
     private static final long serialVersionUID = -2037768174807839046L;
 
-    /**
-     * Value used to create the matrix
-     * 
-     * Only used by sensitivity analysis scripts.
-     */
-    protected double value;
-
-    /**
-     * Get matrix.
-     * 
-     * @return the matrix
-     */
-    public MatrixND getMatrix() {
-        return (MatrixND)referenceValue;
-    }
-
-    /**
-     * Set matrix.
-     * 
-     * @param matrix the matrix to set
-     */
-    public void setMatrix(MatrixND matrix) {
-        this.referenceValue = matrix;
-    }
-
-    /**
-     * {@inheritDoc}.
-     * 
-     * In matrix continuous domain, always return 0.0
-     */
     @Override
-    public Object getMinBound() {
-        return 0.0;
-    }
-
-    /**
-     * {@inheritDoc}.
-     * 
-     * In matrix continuous domain, always return 1.0
-     */
-    @Override
-    public Object getMaxBound() {
-        return 1.0;
-    }
-
-    @Override
     public Object getValueForIdentifier(Object identifier) {
         return getValueForIdentifier((Double)identifier);
     }
@@ -97,38 +52,18 @@
      * @param identifier identifier
      * @return a new computed matrix
      */
-    public MatrixND getValueForIdentifier(Double identifier) {
+    public MatrixND getValueForIdentifier(final Double identifier) {
+        MatrixND temp = ((MatrixND)getReferenceValue()).copy();
         
-        this.value = (Double)identifier;
-        MatrixND temp = getMatrix().copy();
-        
         // since 3.4.0.0, operator is always *
         temp.map(new MapFunction() {
             public double apply(double val) {
-                return (val + ((val * coefficient) * ((2 * value - 1))));
+                return (val + ((val * coefficient) * ((2 * identifier - 1))));
             }
         });
         return temp;
     }
 
-    /**
-     * Get value used to create the matrix.
-     * 
-     * @return the value
-     */
-    public Double getValue() {
-        return this.value;
-    }
-
-    /**
-     * Set value used to create the matrix.
-     * 
-     * @param value the value to set
-     */
-    public void setValue(Double value) {
-        this.value = value;
-    }
-
     @Override
     public MatrixContinuousDomain clone() {
         MatrixContinuousDomain cloned = (MatrixContinuousDomain)super.clone();
@@ -136,27 +71,46 @@
     }
 
     /**
-     * Get the minimum bound of the coefficient used to create the matrix. As
-     * the {@link #getMinBound()} for use in R always return 0.
+     * {@inheritDoc}
      * 
-     * @return the real minimum bound
+     * @return the minimum bound
      */
-    public Double getRealMinBound() {
-        // since 3.4.0.0, operator is always *
-        Double result = (1.0 + ((1.0 * coefficient) * ((2 * 0.0 - 1))));
-        return result;
+    public Object getMinBound() {
+
+        if (minBound == null) {
+            MatrixND temp = ((MatrixND) getReferenceValue()).copy();
+
+            // since 3.4.0.0, operator is always *
+            temp.map(new MapFunction() {
+                public double apply(double val) {
+                    return (val + ((val * coefficient) * ((2 * getCalculatorMinBound() - 1))));
+                }
+            });
+            return temp;
+        } else {
+            return minBound;
+        }
     }
 
     /**
-     * Get the maximal bound of the coefficient used to create the matrix. As
-     * the {@link #getMaxBound()} for use in R always return 1.
+     * {@inheritDoc}
      * 
-     * @return the real maximum bound
+     * @return the maximum bound
      */
-    public Double getRealMaxBound() {
-        // since 3.4.0.0, operator is always *
-        Double result = (1.0 + ((1.0 * coefficient) * ((2 * 1.0 - 1))));
-        return result;
-        
+    public Object getMaxBound() {
+
+        if (maxBound == null) {
+            MatrixND temp = ((MatrixND) getReferenceValue()).copy();
+
+            // since 3.4.0.0, operator is always *
+            temp.map(new MapFunction() {
+                public double apply(double val) {
+                    return (val + ((val * coefficient) * ((2 * getCalculatorMaxBound() - 1))));
+                }
+            });
+            return temp;
+        } else {
+            return maxBound;
+        }
     }
 }

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EquationContinuousPanelUI.jaxx
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EquationContinuousPanelUI.jaxx	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/EquationContinuousPanelUI.jaxx	2011-06-06 15:12:08 UTC (rev 3350)
@@ -32,15 +32,15 @@
     java.util.List
     java.util.regex.Matcher
     java.util.regex.Pattern
-	javax.swing.table.AbstractTableModel
-	javax.swing.table.DefaultTableModel
+	  javax.swing.table.AbstractTableModel
+	  javax.swing.table.DefaultTableModel
     javax.swing.table.TableCellEditor
     javax.swing.table.TableModel
     javax.swing.JComboBox
     javax.swing.DefaultCellEditor
     javax.swing.event.CellEditorListener
-	fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain
-	org.apache.commons.lang.StringUtils
+	  fr.ifremer.isisfish.simulator.sensitivity.domain.EquationContinuousDomain
+	  org.apache.commons.lang.StringUtils
     </import>
 
     <String id='text' javaBean='null'/>
@@ -138,13 +138,13 @@
         } else {
             referenceValueField.setText("");
         }
-        if (selectedDomain.getOriginalMinBound() != null) {
-            minBoundField.setText(selectedDomain.getOriginalMinBound().toString());
+        if (selectedDomain.getMinBound() != null) {
+            minBoundField.setText(selectedDomain.getMinBound().toString());
         } else {
             minBoundField.setText("");
         }
-        if (selectedDomain.getOriginalMaxBound() != null) {
-            maxBoundField.setText(selectedDomain.getOriginalMaxBound().toString());
+        if (selectedDomain.getMaxBound() != null) {
+            maxBoundField.setText(selectedDomain.getMaxBound().toString());
         } else {
             maxBoundField.setText("");
         }
@@ -171,7 +171,7 @@
                 valid = false;
             }
             else if (domain.getCoefficient() == null) {
-                valid = domain.getOriginalMinBound() != null && domain.getOriginalMaxBound() != null;
+                valid = domain.getMinBound() != null && domain.getMaxBound() != null;
             }
             else {
                 valid = domain.getReferenceValue() != null;

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/sensitivity/SensitivityInputHandler.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -618,7 +618,7 @@
      * @return component copy
      */
     public ContinuousPanelContainerUI getContinuousPanel(Object value, TopiaEntityContextable bean, String property) {
-        ContinuousPanelContainerUI result = null;
+        ContinuousPanelContainerUI result;
 
         if (value instanceof RangeOfValues) {
             RangeOfValues rangeOfValues = (RangeOfValues)value;
@@ -627,11 +627,7 @@
             String min = "0";
             String max = "0";
             if (values.matches("^\\ *[0-9]*\\ *\\-\\ *[0-9]*\\ *$")) {
-                int first = 0;
-                if (values.startsWith("-")) {
-                    first = 1;
-                }
-                first = values.indexOf("-");
+                int first = values.indexOf("-");
                 if (first != -1) {
                     min = values.substring(0, first);
                     max = values.substring(first + 1);
@@ -728,8 +724,8 @@
             else {
                 // factor numerique continue (min/max)
                 // pas d'erreur sur 2 fois domain.getMinBound()
-                MatrixND matrixMin = (MatrixND)domain.getOriginalMinBound();
-                MatrixND matrixMax = (MatrixND)domain.getOriginalMaxBound();
+                MatrixND matrixMin = (MatrixND)domain.getMinBound();
+                MatrixND matrixMax = (MatrixND)domain.getMaxBound();
                 continuousPanel.initExisting(
                     matrixMin.clone(),
                     matrixMax.clone(),
@@ -752,10 +748,11 @@
             else {
                 // factor numerique continue (min/max)
                 // pas d'erreur sur 2 fois domain.getMinBound()
+                // on initialise avec minBound comme valeur de référence.
                 continuousPanel.initExisting(
-                    String.valueOf(domain.getOriginalMinBound()),
-                    String.valueOf(domain.getOriginalMaxBound()),
-                    String.valueOf(domain.getOriginalMinBound()),
+                    String.valueOf(domain.getMinBound()),
+                    String.valueOf(domain.getMaxBound()),
+                    String.valueOf(domain.getMinBound()),
                     "");
             }
             result = continuousPanel;
@@ -769,8 +766,8 @@
      * 
      * @param factorWizardUI context for context value (RegionStorage)
      * @param value type to get editor
-     * @param factorPath for equation
-     * @param context for equation
+     * @param factor
+     * @param domain
      * @return component
      */
     protected JComponent getEditorWithValue(FactorWizardUI factorWizardUI, Factor factor, Domain domain, Object value) {
@@ -991,7 +988,7 @@
             try {
                 EquationContinuousPanelUI equationPanel = (EquationContinuousPanelUI) panel;
 
-                TopiaEntityContextable bean = (TopiaEntityContextable)equationPanel.getBean();
+                TopiaEntityContextable bean = equationPanel.getBean();
                 TopiaContext topiaContext = bean.getTopiaContext();
 
                 String property = equationPanel.getBeanProperty();

Modified: isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java
===================================================================
--- isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/java/fr/ifremer/isisfish/ui/simulator/SimulAction.java	2011-06-06 15:12:08 UTC (rev 3350)
@@ -997,7 +997,7 @@
             MatrixND referenceValue, Double coef, boolean exist) {
         Factor f = new Factor(name);
         MatrixContinuousDomain domain = new MatrixContinuousDomain();
-        domain.setMatrix(referenceValue);
+        domain.setReferenceValue(referenceValue);
         domain.setCoefficient(coef);
         f.setComment(comment);
         f.setDomain(domain);
@@ -1304,7 +1304,7 @@
                 selectedFactor.setPath(factorName);
                 MatrixContinuousDomain factorDomain = new MatrixContinuousDomain();
                 MatrixND populationEffectives = getSimulationParameter().getNumberOf(population);
-                factorDomain.setMatrix(populationEffectives.copy());
+                factorDomain.setReferenceValue(populationEffectives.copy());
                 factorDomain.setCoefficient(0.0);
                 selectedFactor.setDomain(factorDomain);
             }

Modified: isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_en_GB.properties
===================================================================
--- isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_en_GB.properties	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_en_GB.properties	2011-06-06 15:12:08 UTC (rev 3350)
@@ -141,6 +141,8 @@
 isisfish.config.category.misc.description=Miscealenous
 isisfish.config.category.officialvcs=Official VCS
 isisfish.config.category.officialvcs.description=Official VCS repository
+isisfish.config.category.versioning=
+isisfish.config.category.versioning.description=
 isisfish.config.database.lockmode.description=Database lock mode
 isisfish.config.main.compileDirectory.description=Script compilation directory
 isisfish.config.main.configFileName.description=Configuration filename
@@ -200,9 +202,12 @@
 isisfish.config.vcs.hostName.description=Official VCS host name
 isisfish.config.vcs.localCommunityDatabasePath.description=Community VCS local storage directory
 isisfish.config.vcs.localDatabasePath.description=Official VCS local storage directory
+isisfish.config.vcs.noPassPhrase.description=
+isisfish.config.vcs.passphrase.description=
 isisfish.config.vcs.protocol.description=Official VCS protocol
 isisfish.config.vcs.remotePath.description=Official VCS remote path
 isisfish.config.vcs.type.description=Official VCS type
+isisfish.config.vcs.useSshConnexion.description=
 isisfish.config.vcs.userName.description=Official VCS user name
 isisfish.config.vcs.userPassword.description=Official VCS password
 isisfish.date.toString=%1$s %2$s

Modified: isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_fr_FR.properties
===================================================================
--- isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_fr_FR.properties	2011-06-06 14:14:32 UTC (rev 3349)
+++ isis-fish/branches/3.3.1/src/main/resources/i18n/isis-fish_fr_FR.properties	2011-06-06 15:12:08 UTC (rev 3350)
@@ -141,6 +141,8 @@
 isisfish.config.category.misc.description=Divers
 isisfish.config.category.officialvcs=VCS Officiel
 isisfish.config.category.officialvcs.description=Dépôt contenant les scripts officiels
+isisfish.config.category.versioning=
+isisfish.config.category.versioning.description=
 isisfish.config.database.lockmode.description=Méthode de vérouillage à utiliser pour la base de données
 isisfish.config.main.compileDirectory.description=le répertoire où sont compilés les scripts
 isisfish.config.main.configFileName.description=le fichier de configuration à utiliser
@@ -200,9 +202,12 @@
 isisfish.config.vcs.hostName.description=le nom du serveur vcs à utiliser
 isisfish.config.vcs.localCommunityDatabasePath.description=Dossier de stockage local du dépôt communauté
 isisfish.config.vcs.localDatabasePath.description=Dossier de stockage local du dépôt officiel
+isisfish.config.vcs.noPassPhrase.description=
+isisfish.config.vcs.passphrase.description=
 isisfish.config.vcs.protocol.description=le protocol pour acceder au serveur vcs
 isisfish.config.vcs.remotePath.description=le chemin jusqu'au parent du module de données sur le serveur vcs
 isisfish.config.vcs.type.description=le type de communication vcs utilisé
+isisfish.config.vcs.useSshConnexion.description=
 isisfish.config.vcs.userName.description=le login de l'utilisateur sur le serveur vcs
 isisfish.config.vcs.userPassword.description=le mot de passe de l'utilsateur sur le serveur vcs
 isisfish.date.toString=%1$s %2$s

    

jcouteau＠users.labs.libre-entreprise.org

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