Commit a6332c99 authored by pfreon's avatar pfreon
Browse files

Changes in system files

Some of these changes are automated
parent 41fef001
......@@ -19,7 +19,7 @@ is divided into following sections:
- cleanup
-->
<project xmlns:if="ant:if" xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" xmlns:unless="ant:unless" basedir=".." default="default" name="Climprod5-impl">
<project xmlns:if="ant:if" xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" xmlns:unless="ant:unless" basedir=".." default="default" name="Climprod6-impl">
<fail message="Please build using Ant 1.8.0 or higher.">
<condition>
<not>
......@@ -119,7 +119,43 @@ is divided into following sections:
<property name="module.name" value=""/>
</target>
<target depends="-pre-init,-init-private,-init-user,-init-project,-init-macrodef-property,-init-modules-supported" name="-do-init">
<property name="platform.java" value="${java.home}/bin/java"/>
<j2seproject1:property name="platform.home" value="platforms.${platform.active}.home"/>
<j2seproject1:property name="platform.bootcp" value="platforms.${platform.active}.bootclasspath"/>
<j2seproject1:property name="platform.compiler" value="platforms.${platform.active}.compile"/>
<j2seproject1:property name="platform.javac.tmp" value="platforms.${platform.active}.javac"/>
<condition property="platform.javac" value="${platform.home}/bin/javac">
<equals arg1="${platform.javac.tmp}" arg2="$${platforms.${platform.active}.javac}"/>
</condition>
<property name="platform.javac" value="${platform.javac.tmp}"/>
<j2seproject1:property name="platform.java.tmp" value="platforms.${platform.active}.java"/>
<condition property="platform.java" value="${platform.home}/bin/java">
<equals arg1="${platform.java.tmp}" arg2="$${platforms.${platform.active}.java}"/>
</condition>
<property name="platform.java" value="${platform.java.tmp}"/>
<j2seproject1:property name="platform.javadoc.tmp" value="platforms.${platform.active}.javadoc"/>
<condition property="platform.javadoc" value="${platform.home}/bin/javadoc">
<equals arg1="${platform.javadoc.tmp}" arg2="$${platforms.${platform.active}.javadoc}"/>
</condition>
<property name="platform.javadoc" value="${platform.javadoc.tmp}"/>
<condition property="platform.invalid" value="true">
<or>
<contains string="${platform.javac}" substring="$${platforms."/>
<contains string="${platform.java}" substring="$${platforms."/>
<contains string="${platform.javadoc}" substring="$${platforms."/>
</or>
</condition>
<fail unless="platform.home">Must set platform.home</fail>
<fail unless="platform.bootcp">Must set platform.bootcp</fail>
<fail unless="platform.java">Must set platform.java</fail>
<fail unless="platform.javac">Must set platform.javac</fail>
<fail if="platform.invalid">
The J2SE Platform is not correctly set up.
Your active platform is: ${platform.active}, but the corresponding property "platforms.${platform.active}.home" is not found in the project's properties files.
Either open the project in the IDE and setup the Platform with the same name or add it manually.
For example like this:
ant -Duser.properties.file=&lt;path_to_property_file&gt; jar (where you put the property "platforms.${platform.active}.home" in a .properties file)
or ant -Dplatforms.${platform.active}.home=&lt;path_to_JDK_home&gt; jar (where no properties file is used)
</fail>
<available file="${manifest.file}" property="manifest.available"/>
<condition property="splashscreen.available">
<and>
......@@ -240,20 +276,6 @@ is divided into following sections:
<condition else="" property="javac.profile.cmd.line.arg" value="-profile ${javac.profile}">
<isset property="profile.available"/>
</condition>
<condition else="false" property="jdkBug6558476">
<and>
<matches pattern="1\.[56]" string="${java.specification.version}"/>
<not>
<os family="unix"/>
</not>
</and>
</condition>
<condition else="false" property="javac.fork">
<or>
<istrue value="${jdkBug6558476}"/>
<istrue value="${javac.external.vm}"/>
</or>
</condition>
<property name="jar.index" value="false"/>
<property name="jar.index.metainf" value="${jar.index}"/>
<property name="copylibs.rebase" value="true"/>
......@@ -340,7 +362,7 @@ is divided into following sections:
</path>
</resourcecount>
</condition>
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<src>
<dirset dir="@{gensrcdir}" erroronmissingdir="false">
<include name="*"/>
......@@ -391,7 +413,7 @@ is divided into following sections:
<property location="${build.dir}/empty" name="empty.dir"/>
<mkdir dir="${empty.dir}"/>
<mkdir dir="@{apgeneratedsrcdir}"/>
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<src>
<dirset dir="@{gensrcdir}" erroronmissingdir="false">
<include name="*"/>
......@@ -433,7 +455,7 @@ is divided into following sections:
<sequential>
<property location="${build.dir}/empty" name="empty.dir"/>
<mkdir dir="${empty.dir}"/>
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
<src>
<dirset dir="@{gensrcdir}" erroronmissingdir="false">
<include name="*"/>
......@@ -512,7 +534,7 @@ is divided into following sections:
<element name="customizePrototype" optional="true"/>
<sequential>
<property name="junit.forkmode" value="perTest"/>
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
<syspropertyset>
<propertyref prefix="test-sys-prop."/>
<mapper from="test-sys-prop.*" to="*" type="glob"/>
......@@ -540,7 +562,7 @@ is divided into following sections:
<element name="customizePrototype" optional="true"/>
<sequential>
<property name="junit.forkmode" value="perTest"/>
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
<junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
<syspropertyset>
<propertyref prefix="test-sys-prop."/>
<mapper from="test-sys-prop.*" to="*" type="glob"/>
......@@ -609,7 +631,7 @@ is divided into following sections:
</condition>
<union id="test.set"/>
<taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
<testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="Climprod5" testname="TestNG tests" workingDir="${work.dir}">
<testng classfilesetref="test.set" failureProperty="tests.failed" jvm="${platform.java}" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="Climprod6" testname="TestNG tests" workingDir="${work.dir}">
<xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
<propertyset>
<propertyref prefix="test-sys-prop."/>
......@@ -706,7 +728,7 @@ is divided into following sections:
<condition else="-testclass @{testClass}" property="test.class.or.method" value="-methods @{testClass}.@{testMethod}">
<isset property="test.method"/>
</condition>
<condition else="-suitename Climprod5 -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
<condition else="-suitename Climprod6 -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
<matches pattern=".*\.xml" string="@{testClass}"/>
</condition>
<delete dir="${build.test.results.dir}" quiet="true"/>
......@@ -840,6 +862,9 @@ is divided into following sections:
<classpath>
<path path="@{classpath}"/>
</classpath>
<bootclasspath>
<path path="${platform.bootcp}"/>
</bootclasspath>
</nbjpdastart>
</sequential>
</macrodef>
......@@ -889,7 +914,7 @@ is divided into following sections:
<attribute default="jvm" name="jvm"/>
<element name="customize" optional="true"/>
<sequential>
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" module="@{modulename}">
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}" module="@{modulename}">
<classpath>
<path path="@{classpath}"/>
</classpath>
......@@ -923,7 +948,7 @@ is divided into following sections:
<attribute default="jvm" name="jvm"/>
<element name="customize" optional="true"/>
<sequential>
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
<classpath>
<path path="@{classpath}"/>
</classpath>
......@@ -955,7 +980,7 @@ is divided into following sections:
<attribute default="jvm" name="jvm"/>
<element name="customize" optional="true"/>
<sequential>
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
<java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
<jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
<jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
<redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
......@@ -1047,7 +1072,7 @@ is divided into following sections:
<delete file="${built-jar.properties}" quiet="true"/>
</target>
<target if="already.built.jar.${basedir}" name="-warn-already-built-jar">
<echo level="warn" message="Cycle detected: Climprod5 was already built"/>
<echo level="warn" message="Cycle detected: Climprod6 was already built"/>
</target>
<target depends="init,-deps-jar-init" name="deps-jar" unless="no.deps">
<mkdir dir="${build.dir}"/>
......@@ -1189,7 +1214,7 @@ is divided into following sections:
<j2seproject3:copylibs manifest="${tmp.manifest.file}"/>
<echo level="info">To run this application from the command line without Ant, try:</echo>
<property location="${dist.jar}" name="dist.jar.resolved"/>
<echo level="info">java -jar "${dist.jar.resolved}"</echo>
<echo level="info">${platform.java} -jar "${dist.jar.resolved}"</echo>
</target>
<target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen,-check-do-mkdist" if="do.archive" name="-do-jar-jar" unless="do.mkdist">
<j2seproject1:jar manifest="${tmp.manifest.file}"/>
......@@ -1291,8 +1316,8 @@ is divided into following sections:
<isset property="main.class.available"/>
</and>
</condition>
<property name="platform.jlink" value="${jdk.home}/bin/jlink"/>
<property name="jlink.systemmodules.internal" value="${jdk.home}/jmods"/>
<property name="platform.jlink" value="${platform.home}/bin/jlink"/>
<property name="jlink.systemmodules.internal" value="${platform.home}/jmods"/>
<exec executable="${platform.jlink}">
<arg value="--module-path"/>
<arg path="${jlink.systemmodules.internal}:${run.modulepath}:${dist.jar}"/>
......@@ -1485,16 +1510,19 @@ is divided into following sections:
</not>
</and>
</condition>
<exec executable="${platform.java}" failonerror="false" outputproperty="platform.version.output">
<arg value="-version"/>
</exec>
<condition else="" property="bug5101868workaround" value="*.java">
<matches pattern="1\.[56](\..*)?" string="${java.version}"/>
<matches multiline="true" pattern="1\.[56](\..*)?" string="${platform.version.output}"/>
</condition>
<condition else="" property="javadoc.html5.cmd.line.arg" value="-html5">
<and>
<isset property="javadoc.html5"/>
<available file="${jdk.home}${file.separator}lib${file.separator}jrt-fs.jar"/>
<available file="${platform.home}${file.separator}lib${file.separator}jrt-fs.jar"/>
</and>
</condition>
<javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
<javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" executable="${platform.javadoc}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
<classpath>
<path path="${javac.classpath}"/>
</classpath>
......@@ -1713,7 +1741,7 @@ is divided into following sections:
<delete file="${built-clean.properties}" quiet="true"/>
</target>
<target if="already.built.clean.${basedir}" name="-warn-already-built-clean">
<echo level="warn" message="Cycle detected: Climprod5 was already built"/>
<echo level="warn" message="Cycle detected: Climprod6 was already built"/>
</target>
<target depends="init,-deps-clean-init" name="deps-clean" unless="no.deps">
<mkdir dir="${build.dir}"/>
......
......@@ -3,6 +3,6 @@ build.xml.script.CRC32=09205104
build.xml.stylesheet.CRC32=f85dc8f2@1.94.0.48
# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
nbproject/build-impl.xml.data.CRC32=957ba411
nbproject/build-impl.xml.script.CRC32=1eaa2199
nbproject/build-impl.xml.data.CRC32=f4df99d6
nbproject/build-impl.xml.script.CRC32=637ee443
nbproject/build-impl.xml.stylesheet.CRC32=f89f7d21@1.94.0.48
......@@ -4,15 +4,14 @@
<editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/2" lastBookmarkId="0"/>
<open-files xmlns="http://www.netbeans.org/ns/projectui-open-files/2">
<group>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Data.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Cadre_Plot.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/CadreMain.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/nbproject/build-impl.xml</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Modele.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Cadre_Modele.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Stat1.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Validation.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/TexteRegles.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/Cadre_Question.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/UtilCadre.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/org/apache/commons/math3/optim/nonlinear/vector/jacobian/AbstractLeastSquaresOptimizer.java</file>
<file>file:/E:/CLIMPROD_Git2/climprod/src/fr/ird/climprod/QuestionReponse.java</file>
</group>
</open-files>
</project-private>
# Declaration of directories etc. Right place to modify climprod5 into climprodxx (5 occurrences). Comment 2020.
annotation.processing.enabled=true
annotation.processing.enabled.in.editor=false
annotation.processing.processors.list=
annotation.processing.run.all.processors=true
annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
application.title=Climprod5
application.title=Climprod6
application.vendor=pverley
build.classes.dir=${build.dir}/classes
build.classes.excludes=**/*.java,**/*.form
......@@ -27,7 +28,7 @@ debug.test.modulepath=\
${run.test.modulepath}
# This directory is removed when the project is cleaned:
dist.dir=dist
dist.jar=${dist.dir}/Climprod5.jar
dist.jar=${dist.dir}/Climprod6.jar
dist.javadoc.dir=${dist.dir}/javadoc
endorsed.classpath=
excludes=
......@@ -65,12 +66,12 @@ javadoc.use=true
javadoc.version=false
javadoc.windowtitle=
jlink.launcher=false
jlink.launcher.name=Climprod5
jlink.launcher.name=Climprod6
main.class=fr.ird.climprod.Main
manifest.file=manifest.mf
meta.inf.dir=${src.dir}/META-INF
mkdist.disabled=false
platform.active=default_platform
platform.active=JDK_1.7
run.classpath=\
${javac.classpath}:\
${build.classes.dir}
......
......@@ -3,7 +3,8 @@
<type>org.netbeans.modules.java.j2seproject</type>
<configuration>
<data xmlns="http://www.netbeans.org/ns/j2se-project/3">
<name>Climprod5</name>
<name>Climprod6</name>
<explicit-platform explicit-source-supported="true"/>
<source-roots>
<root id="src.dir"/>
</source-roots>
......
......@@ -22,6 +22,7 @@ public class TexteRegles {
private static int Flag_Modele_Lineaire_deja_recherche;
private static int Flag_Modele_Exponentiel_deja_recherche;
private static int Flag_Modele_General_deja_recherche=0;
private static int param_m_generalise;
private static String scriptEnCours;
private static String[] itemEnCours;
private static String commentaireEnCours="";
......@@ -158,7 +159,6 @@ public static boolean isTrue(){
double[] ext=Stat1.Extremas(effort);
temp=((ext[1]-ext[0])/ext[0]);
result = temp<1.0d; // Avant <0.4d. Modif. 2020.
System.out.println("Règle 47 ext[1] = " + ext[1] + " ext[0] = " + ext[0] + " temp = " + temp + " result= " + result);
if(!result)
commentaireEnCours="The range of fishing effort variation of your data set is " + (temp);
break;
......@@ -173,7 +173,6 @@ public static boolean isTrue(){
break;
case 46:
result = (Global.stock_unique!=1 && Global.metapopulation!=1); // Changement de nom variable. Modif. 2020
//System.out.println("Dans TexteRegles.java ligne 169 case 46, result = " + result);
if(!result){
commentaireEnCours="Metapopulations are special cases that difficult the application of any kind of population dynamics model. \nAccording to the level connectivity between sub-stocks, modelization might be borderline or not recommended as you will see \nafter answering the next question.";
}
......@@ -189,7 +188,6 @@ public static boolean isTrue(){
break;
case 35:
result = (Global.under_and_over_exploited!=1);// Avant Global.under_and_over_exploited!=1 && Global.under_and_optimaly==1). Modif 2020.
//System.out.println("Dans TexteRegles.java ligne 182, case 35, result = " + result);
break;
case 49:
result = (Global.under_and_optimaly!=1); // Avant (Global.under_and_over_exploited!=1 && Global.under_and_optimaly!=1). Modif 2020.
......@@ -314,8 +312,8 @@ public static boolean isTrue(){
}
break;
case 23:
Global.relationCPU_E=RechercheModele.general; //Tjrs vrai
Flag_Modele_General_deja_recherche=1;
Global.relationCPU_E=RechercheModele.general;
Flag_Modele_General_deja_recherche=1;
result=true;
break;
case 24:
......@@ -351,51 +349,87 @@ public static boolean isTrue(){
case 51:
//Global.val_param[2]=2;
//System.out.println("Flag_Modele_Lineaire_deja_recherche = " + Flag_Modele_Lineaire_deja_recherche +" Global.relationCPU_E = " + Global.relationCPU_E);
result = (Flag_Modele_Lineaire_deja_recherche!=1 && Global.relationCPU_E==RechercheModele.general && Global.coeff_determination>0.4 && Global.val_param[2]<2.2d && Global.val_param[2]>1.8d);
if (Global.effort_preponderant==1) param_m_generalise = 2;
else param_m_generalise = 3;
result = (Flag_Modele_Lineaire_deja_recherche!=1 && Global.relationCPU_E==RechercheModele.general && Global.coeff_determination>0.4 && Global.val_param[param_m_generalise]<2.2d && Global.val_param[param_m_generalise]>1.8d);
if (result)
{
Global.relationCPU_E=RechercheModele.lineaire;
R2limite=true;
R2limite=true; // Pas utilisé? Commentaire 2020.
}
System.out.println("Dans TexteRegle Global.val_param[2]: " + Global.val_param[2] + " commentaireEnCours: " + commentaireEnCours);
commentaireEnCours="Coefficient c (m in the Pella and Tomlinson notation) value is :" + Global.val_param[2];
break;
case 52:
result = (Flag_Modele_Exponentiel_deja_recherche!=1 && Global.relationCPU_E==RechercheModele.general && Global.coeff_determination>0.4 && Global.pessimiste!=1 && Global.val_param[2]<1.2d && Global.val_param[2]>0.8d);
if (Global.effort_preponderant==1) param_m_generalise = 2;
else param_m_generalise = 3;
result = (Flag_Modele_Exponentiel_deja_recherche!=1 && Global.relationCPU_E==RechercheModele.general && Global.coeff_determination>0.4 && Global.pessimiste!=1 && Global.val_param[param_m_generalise]<1.2d && Global.val_param[param_m_generalise]>0.8d);
if (result)
{
Global.relationCPU_E=RechercheModele.exponentiel;
R2limite=true;
R2limite=true; // Pas utilisé? Commentaire 2020.
}
commentaireEnCours="Coefficient c (m in the Pella and Tomlinson notation) value is :" + Global.val_param[2];
break;
case 53:
// Pour cas modèle simple influence Environnement (V) > Effort (E)
result=(Global.coeff_determination<0.4);
if(result)
{
commentaireEnCours="The coefficient of determination of the model " + RechercheModele.getEquation()+ " is " +nf.format(Global.coeff_determination)+"\n";
commentaireEnCours=commentaireEnCours+ "From the current rule this model is not convenient.";
commentaireEnCours=commentaireEnCours+"\n There is no available empirical model CPUE = f(V) appropriate to your case in CLIMPROD.\n";
commentaireEnCours=commentaireEnCours+"\n Please make sure that your answer to the question 'Is the influence of fishing effort on CPUE more important than the environmental influence?' \nwas the correct one";
}
break;
case 54:
//Global.coeff_determination=0.3;
// Pour cas modèle simple influence Effort (E) > Environnement (V)
result=(Global.coeff_determination<0.4);
if(result)
{
commentaireEnCours="The coefficient of determination of the model " + RechercheModele.getEquation()+ " is " +nf.format(Global.coeff_determination)+"\n";
commentaireEnCours=commentaireEnCours+ "From the current rule this model is not convenient.";
commentaireEnCours=commentaireEnCours+"\n There is no available model fully appropriate to your case";
commentaireEnCours=commentaireEnCours+"\n There is no available conventional model CPUE = f(E) appropriate to your case in CLIMPROD.";
commentaireEnCours=commentaireEnCours+"\n Please make sure that your answer to the question 'Is the influence of fishing effort on CPUE more important than the environmental influence?' \nwas the correct one";
}
//result=(Global.typeModele == RechercheModele.mixte) ;
break;
// commentaireEnCours="The value of coefficient of determination is " + Global.coeff_determination;
// if(result) commentaireEnCours=commentaireEnCours+"/n There is no available model fully appropriate to your case";
case 55:
result=(Global.acceptable_graphs!=1);
if(result)
commentaireEnCours="From the current rule the model " + RechercheModele.getEquation()+ " is not validated";
break;
case 56:
result=(Flag_Modele_Exponentiel_deja_recherche==1);
break;
case 57:
result=(Global.linear_relationship!=1);
if(result)
{
commentaireEnCours="There is no available empirical model CPUE = f(E,V) fully appropriate to your case in CLIMPROD\n";
commentaireEnCours=commentaireEnCours+"because you declared that the stock may present large fluctuations in CPUE when overexploited,\n";
commentaireEnCours=commentaireEnCours+"and that the relationship CPUE residuals = f(V) is not linear. In this particular case, the ideal model\n";
commentaireEnCours=commentaireEnCours+"CPUE = f(E,V) should be an exponential additive model with more that four parameters. This option\n";
commentaireEnCours=commentaireEnCours+"is not considered in CLIMPROD in order to avoid over-parameterized models.\n\n";
commentaireEnCours=commentaireEnCours+"Please make sure that your answer to the question 'May the stock present large fluctuations in CPUE when overexploited?'\n";
commentaireEnCours=commentaireEnCours+"was the correct one. If so, you can try to fit a model CPUE = f(E,V) where the the effect of fishing effort (E)\n";
commentaireEnCours=commentaireEnCours+"is linear which would provide a pessimistic response of the stock to overexploitation.\n";
}
break;
case 58:
result=(((Global.numero_modele > 5) || (Global.numero_modele < 2)) && (Global.numero_modele != 20)); // Exclusion modèles CPUE=f(V) et modèle exponentiel additif
if(!result)
{
commentaireEnCours="There is no possibility of drawing MSY and MS-E graphs for the selected model\n";
}
break;
/* case 56:
result = (Global.relationCPU_E==RechercheModele.general && Global.coeff_determination>0.4);
Flag_Modele_General_deja_recherche=1;
// commentaireEnCours="Oui le modèle est généralisé";
break;
case 56:
case 57:
result = true;
//System.out.println("Global.CadreJackniffePlots = " + Global.CadreJackniffePlots);
if (Global.CadreJackniffePlots == null)
{
Cadre_Plot dlg;
......@@ -406,22 +440,23 @@ public static boolean isTrue(){
}
else {Global.CadreJackniffePlots.setVisible(true);}
break;
case 57:
case 58:
result = false;
break;
*/
case 4:
result = (Global.effort_preponderant==1 && Global.cpue_sous_sur_production!=1 && Global.coeff_determination>0.7);
if(result)
commentaireEnCours="From the current rule the model " + RechercheModele.getEquation()+ " is convenient.";
break;
case 5:
result = (Global.effort_preponderant==1 && Global.cpue_sous_sur_production==1 && Global.relationCPU_E==6 && Global.coeff_determination>0.7);
result = (Global.effort_preponderant==1 && Global.environmental_influence.equals("abundance") && Global.cpue_sous_sur_production==1 && Global.relationCPU_E==6 && Global.coeff_determination>0.7);
if(result)
{
commentaireEnCours="From the current rule the model " + RechercheModele.getEquation()+ " is convenient.";
}
else
//System.out.println("Global.effort_preponderant= "+Global.effort_preponderant+ " Global.cpue_sous_sur_production= "+Global.cpue_sous_sur_production +" Global.relationCPU_E= "+ Global.relationCPU_E+" Global.coeff_determination= "+Global.coeff_determination);
commentaireEnCours="The model is not convenient because R2 = "+ Global.coeff_determination + " .\nYou may still generate a report.";
break;
case 6:
......@@ -448,11 +483,21 @@ public static boolean isTrue(){
result=(Global.test_jackknife==false);
System.out.println("La valeur de test_jackknife est "+Global.test_jackknife);
if(result){
commentaireEnCours="The Student's test on jackknife is not acceptable.\nAt least one of the regression coefficients is not significant as you can see in the jackknife plots.\nFrom the current rule the model " + RechercheModele.getEquation()+ " is not validated";
commentaireEnCours="The Student's test on jackknife is not acceptable.\nAt least one of the regression coefficients is not significant as you can see in the jackknife plots.\nFrom the current rule the model " + RechercheModele.getEquation()+ " is not validated";
if (Global.CadreJackniffePlots == null)
{
Cadre_Plot dlg;
dlg = new Cadre_Plot(Global.jackknifePlot);
dlg.setTitle("Climprod: Jackknife plots");
dlg.setVisible(true);
Global.CadreJackniffePlots = dlg;
}
else {Global.CadreJackniffePlots.setVisible(true);}
break;
}
else
commentaireEnCours="The Student's test on jackknife regression coefficients is acceptable";
commentaireEnCours=commentaireEnCours+"\n\nDue to usual autocorrelation in time series and non independance between CPUE and E, conventional statistics are usually provide too optimistic results";
commentaireEnCours=commentaireEnCours+"\n\nDue to usual autocorrelation in time series and non independance between CPUE and E, \nconventional statistics are usually provide too optimistic results";
break;
case 1:
result=( Global.coeff_determination_instable!=1);
......@@ -474,14 +519,13 @@ public static boolean isTrue(){
if(result)
commentaireEnCours="From the current rule the model " + RechercheModele.getEquation()+ " is validated";
break;
case 32:
case 32: // Pas appelé dans arbre décisions. A éliminer??? Commentaire 2020.
result= (Global.environmental_influence.equals(Global.influenceEnv[2]));
break;
}
//System.out.println("Le commentaire du numEnCours " + numEnCours + "dans TexteRegles.java ligne 466) est: " + commentaireEnCours + "result = " + result);
if (result && commentaireEnCours.equals(""))
{ commentaireEnCours=(String)htComment.get(Integer.toString(numEnCours));
//System.out.println("Le commentaire est (dans TexteRegles.java ligne 468) " + commentaireEnCours);
System.out.println("On teste la règle (dans TexteRegles.java ligne 469) " + numEnCours + " elle est "+ result );
}
return result;
......
......@@ -16,90 +16,89 @@
15;16;16;50;1;effort_increasing;Constantly increasing effort?; increasf.hlp ;
16;17;17;40;1;independance;Are the two variables dependent?; independ.hlp ;;;;;;;;;;;
17;18;18;-1;1;nb_classes_exploitees;Number of significantly exploited year-classes; nbclass.hlp ;1;2;3;4;5;6;7;8;>8;;;
18;19;57;-1;1;effort_preponderant;Is the influence of fishing effort on CPUE more important than the environmental influence?; fishmore.hlp ;;;;;;;;;;;
18;19;56;-1;1;effort_preponderant;Is the influence of fishing effort on CPUE more important than the environmental influence?; fishmore.hlp ;;;;;;;;;;;
19;20;-1;48;1;decreasing_relationship;Does this plot appear to be decreasing?; decreas.hlp ;;;;;;;;;;;
20;40;21;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
21;40;22;18;1;pessimiste;Do you have any (additional) reason to expect a highly unstable behaviour or a collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
22;40;23;19;1;stock_deja_effondre;Did the stock already collapse or did it exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
20;39;21;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
21;39;22;18;1;pessimiste;Do you have any (additional) reason to expect a highly unstable behaviour or a collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
22;39;23;19;1;stock_deja_effondre;Did the stock already collapse or did it exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
23;24;24;-1;1;lifespan;What is the life span of the species?; lifespan.hlp ;1;2;3;4;5;6;7;8;9;10;>10
24;26;26;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
26;27;27;-1;1;reserves_naturelles;Are there natural protected areas for the stock or constantly inacessible adult biomass?; protect.hlp ;;;;;;;;;;;
27;28;28;-1;1;premiere_reproduction_avant_recrutement;Are there one or several non negligible spawnings before recruitment?; firstspa.hlp ;;;;;;;;;;;
28;29;29;-1;1;fecondite_faible;Is the fecundity of the species very low (sharks mammals etc.)?; fecundit.hlp ;;;;;;;;;;;;;;;;;;;;;
29;30;30;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; pueunsta.hlp ;;;;;;;;;;;
30;42;31;10;1;;;;;;;;;;;;;;
31;42;32;11;1;;;;;;;;;;;;;;
32;42;33;12;1;;;;;;
33;42;34;13;1;;;;;;
34;42;35;14;1;;;;;;
35;42;36;16;1;;;;;;
36;40;37;20;1;;;;;;
37;40;38;22;1;;;;;;
38;40;39;21;1;;;;;;
39;44;44;23;1;;;;;;
40;41;46;24;2;;;;;;
41;102;43;51;2;;;;;;
42;43;46;25;2;;;;;;
43;102;102;52;2;;;;;;
44;102;45;51;2;;;;;;
45;102;103;52;2;;;;;;
46;97;47;6;2;;;;;;
47;48;49;-1;1;environmental_influence;Does the environment influence:; Influenc.hlp ;abundance;catchability;both
48;51;49;-1;1;cpue_sous_sur_production;May the stock present large fluctuations in CPUE when overexploited?; additif.hlp ;;;;;;;;;;;;
49;52;50;17;1;linear_relationship;Does this plot look linear; linear.hlp ;;;;;;;;;;;;
50;52;52;-1;1;monotonic_relationship;Does this plot look monotonic?; monotoni.hlp ;;;;;;;;;;;;
51;52;105;-1;1;linear_relationship;Does this plot look linear?; linear.hlp ;;;;;;;;;;;;
52;53;53;-1;1;recruitment_age;Age at recruitment; Agerec.hlp ;1;2;3;4;5;6;7;8;9;10;>10;
53;54;54;-1;1;begin_influence_period;Age at the begining of environmental influence; begin.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
54;55;55;-1;1;end_influence_period;Age at the end of environmental influence; end.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
55;97;56;4;2;;;;;;;;;;;;;;;
56;97;-1;5;2;;;;;;;;;;;;;;;
57;58;58;-1;1;recruitment_age;Age at recruitment; Agerec.hlp ;1;2;3;4;5;6;7;8;9;10;>10;
58;59;59;-1;1;begin_influence_period;Age at the begining of environmental influence; begin.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
59;60;60;-1;1;end_influence_period;Age at the end of environmental influence; end.hlp ;0;1;2;3;4;5;6;7;8;9;10;>10
60;62;61;-1;1;linear_relationship;Does_this_plot_look_linear?; linear.hlp ;;;;;;;;;;;;
61;63;64;-1;1;monotonic_relationship;Does this plot look monotonic?; monotoni.hlp ;;;;;;;;;;;;
62;65;63;26;1;;;;;;;;;;;;;;;
63;65;64;28;1;;;;;;;;;;;;;;;
64;65;65;29;1;;;;;;;;;;;;;;
65;97;66;9;2;;;;;;;;;;;;;;
66;-1;67;53;2;;;;;;;;;;;;;;
67;68;69;-1;1;environmental_influence;Does the environment influence:; Influenc.hlp ;abundance;catchability;both;;;;;;;;
68;69;69;-1;1;cpue_sous_sur_production;May the stock present large fluctuations in CPUE when overexploited?; additif.hlp;;;;;;;;;;;
69;89;70;17;1;obviously;Does this plot look obviously linear?; obvious.hlp ;;;;;;;;;;;
70;89;71;18;1;pessimiste;Do you have any (additional) reason to expect highly unstable behaviour or collapse of the stock?; pessimis.hlp ;;;;;;;;;;;
71;89;72;19;1;stock_deja_effondre;Did the stock already collapse or exhibit drastic decrease(s) in catches?; collapse.hlp ;;;;;;;;;;;
72;73;73;-1;1;lifespan;What is the life span of the species?; lifespan.hlp ;1;2;3;4;5;6;7;8;9;10;>10
73;74;74;-1;1;rapport_vie_exploitee_inferieur_deux;Is the ratio (lifespan/number of exploited year-classes) lower than 2?; ratio.hlp ;;;;;;;;;;;
74;75;75;-1;1;stock_divise;Is the single stock subdivided into various geographical sub-stocks (all must be exploited by the fleet)?; stockdiv.hlp ;;;;;;;;;;;
75;76;76;-1;1;reserves_naturelles;Are there natural protected areas for the stock or constantly inacessible adult biomass?; protect.hlp ;;;;;;;;;;;
76;77;77;-1;1;premiere_reproduction_avant_recrutement;Are there one or several non negligible spawnings before recruitment?; firstspa.hlp ;;;;;;;;;;;
77;78;78;-1;1;fecondite_faible;Is the fecundity of the species very low (sharks mammals etc.)?; fecundit.hlp ;;;;;;;;;;;;;;;;;;;;;
78;79;79;-1;1;cpue_unstable;Is there a strong instability in the cpue time series?; unstabil.hlp ;;;;;;;;;;;
79;91;80;10;1;;;;;;;;;;;;;;
80;91;81;11;1
81;91;82;12;1
82;91;83;13;1
83;91;84;14;1
84;91;85;16;1
85;89;86;20;1
86;89;87;22;1
87;89;88;21;1
88;93;93;23;1
89;90;95;24;2
90;92;92;51;2
91;92;95;25;2
92;95;95;52;2
93;97;94;51;2
94;95;95;52;2
95;97;96;7;2
96;97;-2;8;2;;;;
97;98;-3;0;3;good_results;Is this an acceptable model?; acceptab.hlp ;
98;99;-3;15;3;trend_residuals;Are there a good fit and no trend or strong autocorrelation in residuals?; fitresid.hlp ;
99;104;100;2;3;;;;