From ad365ec9f0f0e8d2af5a9fe93719259d46cfa7c7 Mon Sep 17 00:00:00 2001
From: Dumoulin Nicolas <nicolas.dumoulin@irstea.fr>
Date: Fri, 19 May 2017 15:43:46 +0200
Subject: [PATCH] cleanup
---
.classpath | 20 --
.gitignore | 4 +
.project | 23 --
.settings/org.eclipse.core.resources.prefs | 3 -
.settings/org.eclipse.jdt.core.prefs | 12 -
.settings/org.eclipse.m2e.core.prefs | 4 -
.svn/entries | 1 -
.svn/format | 1 -
...94c1ec2a3f8e6e40f608f76cc2f526e6d.svn-base | 23 --
...290f30b92993711930f524170969c88c5.svn-base | 3 -
...73b6dfe70254123aa3ffeca6975f6207e.svn-base | 205 -------------
...ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base | 140 ---------
...6af4cd4e5d2a986c7688a6eeefa80191b.svn-base | 23 --
...3bad9b10658390d20fdac65c5e656b1c2.svn-base | 126 --------
...f6b4154efd48681b889b1f6c996506960.svn-base | 118 --------
...0b994318fc090429771a6dc7470cba503.svn-base | 87 ------
...8ef110c51c396b85a6352a4fbcd7fe475.svn-base | 85 ------
...b69b47a6e335d0724cc20ee1263fb9c07.svn-base | 12 -
...29a2404bf1299b4ffdaaa53bbeaaf1591.svn-base | 29 --
...ec18773650423aab6f3c0ede28f5c6a02.svn-base | 72 -----
...19a22963124aef81d1ab465f8512aca66.svn-base | 279 ------------------
...a45e00f89e1d164f1b101181624fed021.svn-base | 43 ---
...c847f6c3cf61cb64ffad3d915ee1a67e2.svn-base | 22 --
...76936d0f6f255b7510fbe974add550c00.svn-base | 142 ---------
...199c4d28b30319d02f8fcffbc62beb770.svn-base | 12 -
...05b3ef9fe5bbc8f128e4ce7e50d26e601.svn-base | 66 -----
...9a82458ac8c31e81ade3dec2acef32c2f.svn-base | 23 --
...d2816e4a86c9e30d6bae6c34bec25bcaf.svn-base | 118 --------
...40b92b7ffb0b4e12474e6e08d0a9871a3.svn-base | 80 -----
...89898442d011ad0dad23fc8a4dec8d7b7.svn-base | 58 ----
...c20f0afbc186e26cb897f085366a789e9.svn-base | 69 -----
...1c325d37ebc17baafd40c0386b5d09df1.svn-base | 4 -
...e6c80c4ba1df383b332984d83c507d474.svn-base | 80 -----
...38346e9008f73c721f76668cee1c0f01e.svn-base | 95 ------
...70bb5c18ee3c407f189a2451ff6e0e186.svn-base | 3 -
...2023625e3c8ba6ccdbd4a5982933751d8.svn-base | 23 --
...ebd097b94487ff2b13441cbe94a9509f6.svn-base | 76 -----
...457800c0961dac1151087ae25753ac0ab.svn-base | 20 --
...dacf2a350183ab3df355b7f4bb5163568.svn-base | 45 ---
...91319c64e6bb16de9ec68d1f39bd923a3.svn-base | 45 ---
...ac6f2338d6acaf267057c979e724ebe64.svn-base | 138 ---------
...d7e12cadaf53b18520d4255b15150f25e.svn-base | 72 -----
...96e179b6763c9a7ef5402ccfe04a5f1f0.svn-base | 38 ---
...ff87cde0595b5024f67733ea8122261cc.svn-base | 25 --
...90ac859b9e02cbe2e020a68f4d40e9a3a.svn-base | 81 -----
...f18ff816ab9386ae70b586063bbee403f.svn-base | 76 -----
...a424c79ff067bd6ecf4e09a73442bb497.svn-base | 76 -----
...16469a5b5605c3038ce6a7f0d1175b55c.svn-base | 54 ----
.svn/wc.db | Bin 66560 -> 0 bytes
49 files changed, 4 insertions(+), 2850 deletions(-)
delete mode 100644 .classpath
delete mode 100644 .project
delete mode 100644 .settings/org.eclipse.core.resources.prefs
delete mode 100644 .settings/org.eclipse.jdt.core.prefs
delete mode 100644 .settings/org.eclipse.m2e.core.prefs
delete mode 100644 .svn/entries
delete mode 100644 .svn/format
delete mode 100644 .svn/pristine/02/02ba1c394c1ec2a3f8e6e40f608f76cc2f526e6d.svn-base
delete mode 100644 .svn/pristine/03/0364424290f30b92993711930f524170969c88c5.svn-base
delete mode 100644 .svn/pristine/09/09a593e73b6dfe70254123aa3ffeca6975f6207e.svn-base
delete mode 100644 .svn/pristine/0f/0fb6877ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base
delete mode 100644 .svn/pristine/16/165a0396af4cd4e5d2a986c7688a6eeefa80191b.svn-base
delete mode 100644 .svn/pristine/1b/1b6713d3bad9b10658390d20fdac65c5e656b1c2.svn-base
delete mode 100644 .svn/pristine/27/2708e0bf6b4154efd48681b889b1f6c996506960.svn-base
delete mode 100644 .svn/pristine/29/29012f70b994318fc090429771a6dc7470cba503.svn-base
delete mode 100644 .svn/pristine/2c/2c1d6d58ef110c51c396b85a6352a4fbcd7fe475.svn-base
delete mode 100644 .svn/pristine/34/347ffdcb69b47a6e335d0724cc20ee1263fb9c07.svn-base
delete mode 100644 .svn/pristine/36/361c5a629a2404bf1299b4ffdaaa53bbeaaf1591.svn-base
delete mode 100644 .svn/pristine/43/432db9fec18773650423aab6f3c0ede28f5c6a02.svn-base
delete mode 100644 .svn/pristine/46/46e8ddb19a22963124aef81d1ab465f8512aca66.svn-base
delete mode 100644 .svn/pristine/5c/5c0fa9fa45e00f89e1d164f1b101181624fed021.svn-base
delete mode 100644 .svn/pristine/5d/5d8750dc847f6c3cf61cb64ffad3d915ee1a67e2.svn-base
delete mode 100644 .svn/pristine/69/69ae76376936d0f6f255b7510fbe974add550c00.svn-base
delete mode 100644 .svn/pristine/6a/6ab0a26199c4d28b30319d02f8fcffbc62beb770.svn-base
delete mode 100644 .svn/pristine/83/839d12205b3ef9fe5bbc8f128e4ce7e50d26e601.svn-base
delete mode 100644 .svn/pristine/88/88234ca9a82458ac8c31e81ade3dec2acef32c2f.svn-base
delete mode 100644 .svn/pristine/89/890cd70d2816e4a86c9e30d6bae6c34bec25bcaf.svn-base
delete mode 100644 .svn/pristine/96/960e25840b92b7ffb0b4e12474e6e08d0a9871a3.svn-base
delete mode 100644 .svn/pristine/97/9712c4489898442d011ad0dad23fc8a4dec8d7b7.svn-base
delete mode 100644 .svn/pristine/9c/9c52379c20f0afbc186e26cb897f085366a789e9.svn-base
delete mode 100644 .svn/pristine/a1/a112be21c325d37ebc17baafd40c0386b5d09df1.svn-base
delete mode 100644 .svn/pristine/a1/a1445bee6c80c4ba1df383b332984d83c507d474.svn-base
delete mode 100644 .svn/pristine/a1/a1c6e6d38346e9008f73c721f76668cee1c0f01e.svn-base
delete mode 100644 .svn/pristine/a4/a480ba770bb5c18ee3c407f189a2451ff6e0e186.svn-base
delete mode 100644 .svn/pristine/ad/adfb7cb2023625e3c8ba6ccdbd4a5982933751d8.svn-base
delete mode 100644 .svn/pristine/c0/c0cd8a1ebd097b94487ff2b13441cbe94a9509f6.svn-base
delete mode 100644 .svn/pristine/ce/ce816ea457800c0961dac1151087ae25753ac0ab.svn-base
delete mode 100644 .svn/pristine/d1/d10271adacf2a350183ab3df355b7f4bb5163568.svn-base
delete mode 100644 .svn/pristine/d4/d4a815491319c64e6bb16de9ec68d1f39bd923a3.svn-base
delete mode 100644 .svn/pristine/d6/d6dad07ac6f2338d6acaf267057c979e724ebe64.svn-base
delete mode 100644 .svn/pristine/e1/e1d718cd7e12cadaf53b18520d4255b15150f25e.svn-base
delete mode 100644 .svn/pristine/e3/e3327ad96e179b6763c9a7ef5402ccfe04a5f1f0.svn-base
delete mode 100644 .svn/pristine/e5/e506a5bff87cde0595b5024f67733ea8122261cc.svn-base
delete mode 100644 .svn/pristine/ea/eaba64b90ac859b9e02cbe2e020a68f4d40e9a3a.svn-base
delete mode 100644 .svn/pristine/f0/f0ab6cdf18ff816ab9386ae70b586063bbee403f.svn-base
delete mode 100644 .svn/pristine/f3/f3b8f77a424c79ff067bd6ecf4e09a73442bb497.svn-base
delete mode 100644 .svn/pristine/f5/f55c8c416469a5b5605c3038ce6a7f0d1175b55c.svn-base
delete mode 100644 .svn/wc.db
diff --git a/.classpath b/.classpath
deleted file mode 100644
index dbf82ad..0000000
--- a/.classpath
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/.gitignore b/.gitignore
index e69de29..beef00d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1,4 @@
+.classpath
+.project
+.settings
+target
diff --git a/.project b/.project
deleted file mode 100644
index a8f3d17..0000000
--- a/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>SturioSaintSeurin</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
-</projectDescription>
diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs
deleted file mode 100644
index b083d7b..0000000
--- a/.settings/org.eclipse.core.resources.prefs
+++ /dev/null
@@ -1,3 +0,0 @@
-eclipse.preferences.version=1
-encoding/<project>=ISO-8859-15
-encoding/src=ISO-8859-15
diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644
index 6428c68..0000000
--- a/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,12 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.6
diff --git a/.settings/org.eclipse.m2e.core.prefs b/.settings/org.eclipse.m2e.core.prefs
deleted file mode 100644
index 14b697b..0000000
--- a/.settings/org.eclipse.m2e.core.prefs
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/.svn/entries b/.svn/entries
deleted file mode 100644
index 48082f7..0000000
--- a/.svn/entries
+++ /dev/null
@@ -1 +0,0 @@
-12
diff --git a/.svn/format b/.svn/format
deleted file mode 100644
index 48082f7..0000000
--- a/.svn/format
+++ /dev/null
@@ -1 +0,0 @@
-12
diff --git a/.svn/pristine/02/02ba1c394c1ec2a3f8e6e40f608f76cc2f526e6d.svn-base b/.svn/pristine/02/02ba1c394c1ec2a3f8e6e40f608f76cc2f526e6d.svn-base
deleted file mode 100644
index a8f3d17..0000000
--- a/.svn/pristine/02/02ba1c394c1ec2a3f8e6e40f608f76cc2f526e6d.svn-base
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>SturioSaintSeurin</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
-</projectDescription>
diff --git a/.svn/pristine/03/0364424290f30b92993711930f524170969c88c5.svn-base b/.svn/pristine/03/0364424290f30b92993711930f524170969c88c5.svn-base
deleted file mode 100644
index b083d7b..0000000
--- a/.svn/pristine/03/0364424290f30b92993711930f524170969c88c5.svn-base
+++ /dev/null
@@ -1,3 +0,0 @@
-eclipse.preferences.version=1
-encoding/<project>=ISO-8859-15
-encoding/src=ISO-8859-15
diff --git a/.svn/pristine/09/09a593e73b6dfe70254123aa3ffeca6975f6207e.svn-base b/.svn/pristine/09/09a593e73b6dfe70254123aa3ffeca6975f6207e.svn-base
deleted file mode 100644
index 6defe9b..0000000
--- a/.svn/pristine/09/09a593e73b6dfe70254123aa3ffeca6975f6207e.svn-base
+++ /dev/null
@@ -1,205 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.TreeMap;
-
-
-
-import species.Sturgeon.Gender;
-import species.Sturgeon.Status;
-import environment.Station;
-import fr.cemagref.observation.kernel.Observable;
-import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class SturgeonGroup extends AquaNismsGroup<Sturgeon, Station> {
-
- private transient Map<String, List<Sturgeon>> batches;
- private transient List<Integer> femaleSpawnerNbHistory;
- private transient List<Double> larvaeProductionHistory;
- private transient double annualLarvaeProduction;
-
- @Override
- public void initTransientParameters(Pilot pilot) throws IllegalArgumentException,
- IllegalAccessException, InvocationTargetException {
- // TODO Auto-generated method stub
- super.initTransientParameters(pilot);
- batches = new TreeMap<String, List<Sturgeon>>();
-
- femaleSpawnerNbHistory = new LinkedList<Integer>();
- larvaeProductionHistory = new LinkedList<Double>();
-
- }
-
- @Override
- public void addAquaNism(Sturgeon fish) {
- super.addAquaNism(fish);
-
- if(batches.containsKey(fish.getBatchName())){
- batches.get(fish.getBatchName()).add(fish);
- }
- else {
- List<Sturgeon> batch = new ArrayList<Sturgeon>();
- batch.add(fish);
- batches.put(fish.getBatchName(), batch);
- }
-
- }
-
- @Override
- public void removeAquaNism(Sturgeon fish) {
- // TODO Auto-generated method stub
- super.removeAquaNism(fish);
-
- batches.get(fish.getBatchName()).remove(fish);
- }
-
-
- public void printNumberInBatches(){
- int total=0;
- for (Entry<String, List<Sturgeon>> entry : batches.entrySet()){
- System.out.println(" "+ entry.getKey()+ ":\t"+entry.getValue().size());
- total += entry.getValue().size();
- }
- System.out.println("-->"+total+"vs"+this.getAquaNismsList().size());
- }
-
- @Observable(description = "Fish number")
- public int getFishNumber() {
- if ( this.getAquaNismsList() != null)
- return this.getAquaNismsList().size();
- else
- return 0;
- }
-
- public Integer[] getFemaleHistory() {
- return (Integer[]) femaleSpawnerNbHistory.toArray();
- }
-
- @Observable(description = "nb of female ready to spawn")
- public int getNumberOfFemaleInMaturation() {
- int nb=0;
- for (Sturgeon fish : this.getAquaNismsList()){
- if (fish.getGender() == Gender.FEMALE & fish.isReadyToSpawn()){
- nb++;
- }
- }
- return nb;
- }
-
- @Observable(description = "nb of male ready to spawn")
- public int getNumberOfMaleInMaturation() {
- int nb=0;
- for (Sturgeon fish : this.getAquaNismsList()){
- if (fish.getGender() == Gender.MALE & fish.isReadyToSpawn()){
- nb++;
- }
- }
- return nb;
- }
-
- @Observable(description = "nb of normal fish")
- public int getNormalFishNumber() {
- int nb=0;
- for (Sturgeon fish : this.getAquaNismsList()){
- if (fish.getStatus() == Status.NORMAL){
- nb++;
- }
- }
- return nb;
- }
-
- @Observable(description = "nb of deformed fish")
- public int getDeformedFishNumber() {
- int nb=0;
- for (Sturgeon fish : this.getAquaNismsList()){
- if (fish.getStatus() == Status.DEFORMED){
- nb++;
- }
- }
- return nb;
- }
-
- @Observable(description = "annual larvae production")
- public double getAnnualLarvaeProduction() {
- return Math.round(annualLarvaeProduction * 1000.)/1000.;
- }
-
- public void setAnnualLarvaeProduction(double annualLarvaeProduction) {
- this.annualLarvaeProduction = annualLarvaeProduction;
- }
-
- public void setLarvaeProductionHistory(List<Double> larvaeProductionHistory) {
- this.larvaeProductionHistory = larvaeProductionHistory;
- }
-
- public Map<String, List<Sturgeon>> getBatches() {
- return batches;
- }
-
- public List<Integer> getFemaleSpawnerNbHistory() {
- return femaleSpawnerNbHistory;
- }
-
- public List<Double> getLarvaeProductionHistory() {
- return larvaeProductionHistory;
- }
-
- @Observable(description = "female spawner history")
- public Integer[] getFemaleSpawnersArray() {
- Integer[] output= new Integer[femaleSpawnerNbHistory.size()];
- for(int i=0; i < femaleSpawnerNbHistory.size(); i++){
- output[i] =femaleSpawnerNbHistory.get(i);
- }
- return output;
- }
-
- @Observable(description = "female spawner history")
- public String getFemaleSpawnersString() {
- String output="";
- String sep="";
- for (int i=0; i< femaleSpawnerNbHistory.size(); i++){
- output=output.concat(sep).concat(femaleSpawnerNbHistory.get(i).toString());
- sep=", ";
- }
- return output;
- }
-
- @Observable(description = "larvae hsitory history")
- public String getLarvaeProductionString() {
- String output="";
- String sep="";
- for (int i=0; i< larvaeProductionHistory.size(); i++){
- output=output.concat(sep).concat(larvaeProductionHistory.get(i).toString());
- sep=", ";
- }
- return output;
- }
-}
diff --git a/.svn/pristine/0f/0fb6877ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base b/.svn/pristine/0f/0fb6877ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base
deleted file mode 100644
index b8a62ef..0000000
--- a/.svn/pristine/0f/0fb6877ccd1a8bd8ba27aafa0bc880517de4bdac.svn-base
+++ /dev/null
@@ -1,140 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <!-- ************************************************************* -->
- <!-- *** POM Relationships *************************************** -->
- <!-- ************************************************************* -->
- <groupId>SturioSaintSeurin</groupId>
- <artifactId>SturioSaintSeurin</artifactId>
- <version>0.0.1-SNAPSHOT</version>
-
- <dependencies>
- <dependency>
- <groupId>fr.cemagref</groupId>
- <artifactId>simaqualife</artifactId>
- <version>2.0</version>
- </dependency>
-
- <dependency>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- <version>2.6</version>
- <type>jar</type>
- </dependency>
- </dependencies>
-
- <!-- ************************************************************* -->
- <!-- *** Project Information ************************************* -->
- <!-- ************************************************************* -->
-
- <name>${project.artifactId} ${project.version}</name>
- <description></description>
- <url></url>
-
- <licenses>
- <license>
- <name>GPL</name>
- <url>http://www.gnu.org/copyleft/gpl.html</url>
- <distribution>repo</distribution>
- </license>
- </licenses>
-
- <!-- ************************************************************* -->
- <!-- *** Build Settings ****************************************** -->
- <!-- ************************************************************* -->
- <packaging>jar</packaging>
-
- <build>
- <sourceDirectory>src</sourceDirectory>
-
- <plugins>
-
- <plugin>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>2.3.2</version>
- <configuration>
- <source>1.6</source>
- <target>1.6</target>
- </configuration>
- </plugin>
-
- <plugin>
- <artifactId>maven-assembly-plugin</artifactId>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>assembly</goal>
- </goals>
- <configuration>
- <appendAssemblyId>false</appendAssemblyId>
- <descriptorRefs>
- <descriptorRef>jar-with-dependencies</descriptorRef>
- </descriptorRefs>
- </configuration>
- </execution>
- </executions>
- </plugin>
-
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-resources-plugin</artifactId>
- <configuration>
- <encoding>${project.build.sourceEncoding}</encoding>
- </configuration>
- <executions>
- <execution>
- <phase>package</phase>
- <goals>
- <goal>resources</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
-
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- <configuration>
- <manifestLocation>target/META-INF</manifestLocation>
- <finalName>${symbolic.name}_${project.version}</finalName>
- <instructions>
- <Bundle-Name>${project.groupId}.${project.artifactId}</Bundle-Name>
- <Bundle-SymbolicName>${project.groupId}.${project.artifactId}</Bundle-SymbolicName>
- <Import-Package>*;resolution:=optional</Import-Package>
- <Export-Package>fr.cemagref.simaqualife.extensions.pilot.BatchRunner;fr.cemagref.simaqualife.*;miscellaneous.*</Export-Package>
- <Embed-Dependency>*;scope=!provided;inline=true</Embed-Dependency>
- <Embed-Transitive>true</Embed-Transitive>
- <eclipse.buddypolicy>global</eclipse.buddypolicy>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
-
- </build>
-
-
- <repositories>
- <repository>
- <id>trac.clermont.cemagref.fr.nexus.public</id>
- <url>http://trac.clermont.cemagref.fr/nexus/content/groups/public</url>
- </repository>
- <repository>
- <id>trac.clermont.cemagref.fr.nexus.snapshots</id>
- <url>http://trac.clermont.cemagref.fr/nexus/content/repositories/snapshots</url>
- </repository>
- <repository>
- <id>maven2-repository.dev.java.net</id>
- <name>Java.net repository</name>
- <url>http://download.java.net/maven/2</url>
- </repository>
- </repositories>
-
- <properties>
- <project.build.sourceEncoding>ISO-8859-15</project.build.sourceEncoding>
- <build.timestamp>${maven.build.timestamp}</build.timestamp>
- <netbeans.hint.license>gpl30</netbeans.hint.license>
- </properties>
-</project>
\ No newline at end of file
diff --git a/.svn/pristine/16/165a0396af4cd4e5d2a986c7688a6eeefa80191b.svn-base b/.svn/pristine/16/165a0396af4cd4e5d2a986c7688a6eeefa80191b.svn-base
deleted file mode 100644
index 89135df..0000000
--- a/.svn/pristine/16/165a0396af4cd4e5d2a986c7688a6eeefa80191b.svn-base
+++ /dev/null
@@ -1,23 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-/**
- *
- */
-package environment;
\ No newline at end of file
diff --git a/.svn/pristine/1b/1b6713d3bad9b10658390d20fdac65c5e656b1c2.svn-base b/.svn/pristine/1b/1b6713d3bad9b10658390d20fdac65c5e656b1c2.svn-base
deleted file mode 100644
index 6e8fab9..0000000
--- a/.svn/pristine/1b/1b6713d3bad9b10658390d20fdac65c5e656b1c2.svn-base
+++ /dev/null
@@ -1,126 +0,0 @@
-package observer;
-
-import java.lang.reflect.InvocationTargetException;
-
-import fr.cemagref.observation.kernel.ObservablesHandler;
-import fr.cemagref.observation.observers.ConsoleObserver;
-import fr.cemagref.ohoui.annotations.Description;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-
-public class MyCSVObserver extends ConsoleObserver {
-
- @Description(name = "Field separator", tooltip = "")
- protected char separator = ';';
- private List<String> observables;
- protected transient List<ObservablesHandler.ObservableFetcher> fetchers;
- /**
- * <code>classObservable</code> is used to display name of attributes as
- * header
- */
- private transient ObservablesHandler classObservable;
-
- public MyCSVObserver() {
- }
-
- public MyCSVObserver(boolean sysout, String outputFile) {
- super(sysout, outputFile);
- }
-
- public MyCSVObserver(boolean sysout, String outputFile, String... obsvervables) {
- super(sysout, outputFile);
- this.observables = Arrays.asList(obsvervables);
- }
-
- public List<String> getObservables() {
- return observables;
- }
-
- @Override
- public void addObservable(ObservablesHandler classObservable) {
- ObservablesHandler bak = this.classObservable;
- this.classObservable = classObservable;
- if (bak != null) // The observable has been changed
- {
- this.init();
- }
- }
-
- @Override
- public void valueChanged(ObservablesHandler clObservable, Object instance, long t) {
- if (isInDates(t)) {
- StringBuffer buf = new StringBuffer();
- StringBuffer sbSeparator = new StringBuffer(" " + this.separator + " ");
- // print current Time
- buf.append(t);
-
- // print value of each field
- for (ObservablesHandler.ObservableFetcher fetcher : fetchers) {
- buf.append(sbSeparator);
- Object value = getValue(fetcher, instance);
- buf.append(value == null ? "N/A" : value);
- }
- outputStream.println(buf);
- }
- }
-
- /**
- *
- * @param fetcher
- * @param instance
- * @return the value returned by the fetcher or null if a problem has
- * occured due to the introspection.
- */
- protected Object getValue(ObservablesHandler.ObservableFetcher fetcher, Object instance) {
- try {
- return fetcher.fetchValue(instance);
- } catch (IllegalArgumentException ex) {
- Logger.getLogger(MyCSVObserver.class.getName()).log(Level.SEVERE, null, ex);
- return null;
- } catch (IllegalAccessException ex) {
- Logger.getLogger(MyCSVObserver.class.getName()).log(Level.SEVERE, null, ex);
- return null;
- } catch (InvocationTargetException ex) {
- Logger.getLogger(MyCSVObserver.class.getName()).log(Level.SEVERE, null, ex);
- return null;
- }
- }
-
- @Override
- public void init() {
- super.init();
- if (classObservable != null) {
- fetchers = new ArrayList<ObservablesHandler.ObservableFetcher>();
- if (observables != null) {
- for (String name : observables) {
- fetchers.add(classObservable.getObservableFetcherByName(name));
- }
- } else {
- fetchers.addAll(Arrays.asList(classObservable.getObservableFetchers()));
- }
- // Headers printing
- StringBuffer buf = new StringBuffer();
- StringBuffer sbSeparator = new StringBuffer(" " + this.separator + " ");
- buf.append("Year");
- buf.append(sbSeparator);
- buf.append("Season");
- for (ObservablesHandler.ObservableFetcher fetcher : fetchers) {
- buf.append(sbSeparator);
- buf.append(fetcher.getDescription());
- }
- outputStream.println(buf);
- }
- }
-
- @Override
- public String toString() {
- if (observables != null) {
- return observables.toString() + " " + super.toString();
- } else {
- return super.toString();
- }
- }
-}
diff --git a/.svn/pristine/27/2708e0bf6b4154efd48681b889b1f6c996506960.svn-base b/.svn/pristine/27/2708e0bf6b4154efd48681b889b1f6c996506960.svn-base
deleted file mode 100644
index 081fc9c..0000000
--- a/.svn/pristine/27/2708e0bf6b4154efd48681b889b1f6c996506960.svn-base
+++ /dev/null
@@ -1,118 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.io.FileReader;
-import java.util.Locale;
-import java.util.Scanner;
-import java.util.regex.Pattern;
-
-import species.Sturgeon.Diet;
-import species.Sturgeon.Gender;
-import species.Sturgeon.Stage;
-import species.Sturgeon.Status;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-
-/**
- *
- */
-public class PopulateWithActualCaptiveStock extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private String sturgeonStockName ="data/input/maturation geniteurs juin2014.csv";
- private Boolean fishWithPb = true;
- private int presentYear = 2014;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new PopulateWithActualCaptiveStock())); }
-
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup group) {
-
- int cohort, birthYear, YearlastMaturation,pb;
- String alim, stage, sex, name, status;
-
- try {
- // open the file
- FileReader reader = new FileReader(sturgeonStockName);
-
- // Parsing the file
- Scanner scanner = new Scanner(reader);
- scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
- scanner.useDelimiter(Pattern.compile("(;|\r\n|\n)"));
-
- // skip the first line
- scanner.nextLine();
- //System.out.println(scanner.nextLine());
- while (scanner.hasNext()) {
- cohort = scanner.nextInt();
- birthYear = scanner.nextInt();
- name= scanner.next();
- //System.out.print(name+ " ");
- scanner.next(); // skip colum
- scanner.next(); // skip colum
- sex = scanner.next();
- alim= scanner.next();
- status = scanner.next();
- stage = scanner.next();
- YearlastMaturation = scanner.nextInt();
- pb = scanner.nextInt();
- scanner.next(); // skip colum
- scanner.next(); // skip colum
- scanner.next(); // skip colum
-
- //public Sturgeon(Tanks position, int cohort, int age, Stage stage, Gender gender, Diet diet,
- // Status status, String name, double ageAtLastReproduction);
-
- if (fishWithPb | (!fishWithPb & pb == 0 )){
- Sturgeon sturgeon = new Sturgeon(group.getPilot(), group.getEnvironment().getTanks(), cohort, (presentYear-birthYear),
- (stage.equalsIgnoreCase("mature") ? Stage.MATURE : Stage.IMMATURE),
- (sex.equalsIgnoreCase("femelle") ? Gender.FEMALE : Gender.MALE),
- (alim.equalsIgnoreCase("alim naturelle") ? Diet.NATURAL : Diet.MIXED),
- (status.equalsIgnoreCase("tordu") ? Status.DEFORMED : Status.NORMAL),
- name,
- (YearlastMaturation==-1 ? Double.NaN :(presentYear-birthYear-YearlastMaturation)));
- group.addAquaNism(sturgeon);
- }
- }
- //System.out.println();
- //System.out.println(group.getFishNumber()+" fish in the captive stock");
- scanner.close();
- reader.close();
- }
- catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- //System.out.println(group.getFishNumber());
- //group.printNumberInBatches();
-
- }
-
-
-}
diff --git a/.svn/pristine/29/29012f70b994318fc090429771a6dc7470cba503.svn-base b/.svn/pristine/29/29012f70b994318fc090429771a6dc7470cba503.svn-base
deleted file mode 100644
index 7fad85a..0000000
--- a/.svn/pristine/29/29012f70b994318fc090429771a6dc7470cba503.svn-base
+++ /dev/null
@@ -1,87 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.Locale;
-import java.util.Scanner;
-import java.util.regex.Pattern;
-
-import species.Sturgeon.Diet;
-import species.Sturgeon.Gender;
-import species.Sturgeon.Stage;
-import species.Sturgeon.Status;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class Enter extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private int nbWithNaturalDiet=25;
- private int nbWithMixedDiet=25;
-
- private transient UniformGen genUniform;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Enter())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen(pilot.getRandomStream(),0.,1.);
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup group) {
-
- int cohort = (int) group.getPilot().getCurrentTime();
- int age = 0;
-
- // fish with natural diet ( not deformed)
- for (int i=0; i < nbWithNaturalDiet; i++){
- Sturgeon sturgeon = new Sturgeon(group.getPilot(), group.getEnvironment().getTanks(), cohort, age, Stage.IMMATURE,
- (genUniform.nextDouble() <0.5) ? Gender.FEMALE : Gender.MALE,
- Diet.NATURAL, Status.NORMAL);
- group.addAquaNism(sturgeon);
- }
- // fish with mixed diet (not Deformed)
- for (int i=0; i < nbWithMixedDiet; i++){
- Sturgeon sturgeon = new Sturgeon(group.getPilot(), group.getEnvironment().getTanks(), cohort, age, Stage.IMMATURE,
- (genUniform.nextDouble() <0.5) ? Gender.FEMALE : Gender.MALE,
- Diet.MIXED, Status.NORMAL);
- group.addAquaNism(sturgeon);
- }
-
- //System.out.println(group.getFishNumber());
- //group.printNumberInBatches();
- }
-}
diff --git a/.svn/pristine/2c/2c1d6d58ef110c51c396b85a6352a4fbcd7fe475.svn-base b/.svn/pristine/2c/2c1d6d58ef110c51c396b85a6352a4fbcd7fe475.svn-base
deleted file mode 100644
index 0322ae0..0000000
--- a/.svn/pristine/2c/2c1d6d58ef110c51c396b85a6352a4fbcd7fe475.svn-base
+++ /dev/null
@@ -1,85 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import umontreal.iro.lecuyer.randvar.ExponentialGen;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class DieByAccident extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private double probaAccident= 0.65;
- private double dieScaleAccident = 11.85746 ;
-
- private transient UniformGen genUniform;
- private transient ExponentialGen exponentialGen;
-
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new DieByAccident())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen( pilot.getRandomStream(),0.,1.);
- exponentialGen = new ExponentialGen(pilot.getRandomStream(), dieScaleAccident);
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup stock) {
- List<Sturgeon> deadFish = new ArrayList<Sturgeon>();
- double probaToDie =0;
-
- for (List<Sturgeon> batch : stock.getBatches().values()){
- if (! batch.isEmpty()){
- if (genUniform.nextDouble() < probaAccident){
- probaToDie =exponentialGen.nextDouble();
- //System.out.println(" proba to die:" + probaToDie );
- for (Sturgeon fish : batch){
- if (genUniform.nextDouble() < probaToDie){
- deadFish.add(fish);
- }
- }
- }
- }
- }
-
- // remove fish from the list
- for (Sturgeon fish : deadFish){
- stock.removeAquaNism(fish);
- }
-
- //stock.printNumberInBatches();
- }
-}
diff --git a/.svn/pristine/34/347ffdcb69b47a6e335d0724cc20ee1263fb9c07.svn-base b/.svn/pristine/34/347ffdcb69b47a6e335d0724cc20ee1263fb9c07.svn-base
deleted file mode 100644
index 6428c68..0000000
--- a/.svn/pristine/34/347ffdcb69b47a6e335d0724cc20ee1263fb9c07.svn-base
+++ /dev/null
@@ -1,12 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
-org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
-org.eclipse.jdt.core.compiler.compliance=1.6
-org.eclipse.jdt.core.compiler.debug.lineNumber=generate
-org.eclipse.jdt.core.compiler.debug.localVariable=generate
-org.eclipse.jdt.core.compiler.debug.sourceFile=generate
-org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
-org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.6
diff --git a/.svn/pristine/36/361c5a629a2404bf1299b4ffdaaa53bbeaaf1591.svn-base b/.svn/pristine/36/361c5a629a2404bf1299b4ffdaaa53bbeaaf1591.svn-base
deleted file mode 100644
index f298254..0000000
--- a/.svn/pristine/36/361c5a629a2404bf1299b4ffdaaa53bbeaaf1591.svn-base
+++ /dev/null
@@ -1,29 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package environment;
-
-import fr.cemagref.simaqualife.kernel.spatial.Position;
-
-/**
- *
- */
-public class Tanks implements Position {
-
-}
diff --git a/.svn/pristine/43/432db9fec18773650423aab6f3c0ede28f5c6a02.svn-base b/.svn/pristine/43/432db9fec18773650423aab6f3c0ede28f5c6a02.svn-base
deleted file mode 100644
index 3978042..0000000
--- a/.svn/pristine/43/432db9fec18773650423aab6f3c0ede28f5c6a02.svn-base
+++ /dev/null
@@ -1,72 +0,0 @@
-<list>
- <species.SturgeonGroup>
- <processes>
- <processesAtBegin>
- <species.PopulateWithActualCaptiveStock>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <sturgeonStockName>data/input/MaturationGeniteursJuin14.csv</sturgeonStockName>
- <fishWithPb>true</fishWithPb>
- <presentYear>2014</presentYear>
- </species.PopulateWithActualCaptiveStock>
- </processesAtBegin>
-
- <processesEachStep>
-
- <species.Deform>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <scaleDeform>0.3203588</scaleDeform>
- <shapeDeform>6.55763282</shapeDeform>
- <piDeformForNaturalDiet>0.05565945</piDeformForNaturalDiet>
- <piDeformForMixedDiet>0.5463054</piDeformForMixedDiet>
- </species.Deform>
-
- <species.DieByAccident>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probaAccident>0.65</probaAccident>
- <dieScaleAccident>11.85746</dieScaleAccident>
- </species.DieByAccident>
-
- <species.Die>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <dieScaleForNormal>0.01877447</dieScaleForNormal>
- <dieScaleForDeformed>0.40354444</dieScaleForDeformed>
- <dieShape>1.0</dieShape>
- </species.Die>
-
- <species.MatureWithTruncatedDistribution>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probTruncature>0.01</probTruncature>
- <femaleMeanAgeAtMaturation>16.4</femaleMeanAgeAtMaturation>
- <femaleSdAgeAtMaturation>2.7</femaleSdAgeAtMaturation>
- <femaleMeanInterSpawningInterval>4.0
- </femaleMeanInterSpawningInterval>
- <maleMeanAgeAtMaturation>8.0</maleMeanAgeAtMaturation>
- <maleSdAgeAtMaturation>1.4</maleSdAgeAtMaturation>
- <maleMeanInterSpawningInterval>1.5</maleMeanInterSpawningInterval>
- </species.MatureWithTruncatedDistribution>
-
- <species.ProduceLarvae>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <pi>0.75</pi>
- <mu>4.347</mu>
- <sigma>0.7806</sigma>
- <maxProd>250.0</maxProd>
- </species.ProduceLarvae>
-
-
- <species.Age>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Age>
-
- </processesEachStep>
-
- <processesAtEnd>
- <species.Analyse>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Analyse>
- </processesAtEnd>
- </processes>
-
- <useCemetery>false</useCemetery>
- </species.SturgeonGroup>
-</list>
\ No newline at end of file
diff --git a/.svn/pristine/46/46e8ddb19a22963124aef81d1ab465f8512aca66.svn-base b/.svn/pristine/46/46e8ddb19a22963124aef81d1ab465f8512aca66.svn-base
deleted file mode 100644
index fd4a4e0..0000000
--- a/.svn/pristine/46/46e8ddb19a22963124aef81d1ab465f8512aca66.svn-base
+++ /dev/null
@@ -1,279 +0,0 @@
-/*
- * Copyright (C) 2012 dumoulin
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-package miscellaneous;
-
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import org.apache.commons.lang.ArrayUtils;
-
-/**
- *
- * @author dumoulin
- */
-public class ReflectUtils {
-
- private static final Logger LOGGER = Logger.getLogger(ReflectUtils.class.getName());
-
- /**
- *
- * @param type
- * @param name
- * @return null if the field wasn't found
- */
- public static Field getField(Class type, String name) throws NoSuchFieldException {
- Class current = type;
- while (current != null) {
- for (Field f : current.getDeclaredFields()) {
- if (f.getName().equals(name)) {
- return f;
- }
- }
- current = current.getSuperclass();
- }
- throw new NoSuchFieldException("The field " + name + " hasn't been found in the class " + type.getName());
- }
-
- public static Fetcher getFetcher(Class type, String name) throws NoSuchFieldException {
- Class current = type;
- while (current != null) {
- for (Field f : current.getDeclaredFields()) {
- if (f.getName().equals(name)) {
- return new FieldFetcher(f);
- }
- }
- for (Method m : current.getDeclaredMethods()) {
- if (m.getName().equals(name)) {
- return new MethodFetcher(m);
- }
- }
- current = current.getSuperclass();
- }
- throw new NoSuchFieldException("The field or method " + name + " hasn't been found in the class " + type.getName());
- }
-
- /**
- *
- * @param field
- * @param instance
- * @return null if a problem has occured during the introspection.
- */
- public static Object getFieldValue(Field field, Object instance) {
- boolean old = field.isAccessible();
- field.setAccessible(true);
- Object value = null;
- try {
- value = field.get(instance);
- } catch (Exception ex) {
- LOGGER.log(Level.SEVERE, "Error during field value retrieving", ex);
- }
- field.setAccessible(old);
- return value;
- }
-
- /**
- *
- * @param fieldname
- * @param instance
- * @return null if a problem has occured during the introspection.
- */
- public static Object getFieldValue(String fieldname, Object instance) throws NoSuchFieldException {
- Object value = null;
- Field field = getField(instance.getClass(), fieldname);
- if (field != null) {
- value = getFieldValue(field, instance);
- }
- return value;
- }
-
- /**
- *
- * @param methodName
- * @param instance
- * @param parameters
- * @return null if a problem has occured during the introspection.
- */
- public static Object invokeMethod(String methodName, Object instance, Object... parameters) {
- Object result = null;
- Class[] parametersType = new Class[parameters.length];
- for (int i = 0; i < parameters.length; i++) {
- parametersType[i] = parameters[i].getClass();
- }
- try {
- Method method = instance.getClass().getDeclaredMethod(methodName, parametersType);
- boolean accessible = method.isAccessible();
- method.setAccessible(true);
- result = method.invoke(instance, parameters);
- method.setAccessible(accessible);
- } catch (Exception ex) {
- LOGGER.log(Level.SEVERE, "Error during method invocation " + instance.getClass() + "." + methodName + "(" + ArrayUtils.toString(parameters) + ")", ex);
- }
- return result;
- }
-
- public static void setField(Field field, Object instance, Object value) throws IllegalAccessException, IllegalArgumentException {
- boolean old = field.isAccessible();
- field.setAccessible(true);
- field.set(instance, value);
- field.setAccessible(old);
-
- }
-
- public static void setField(String fieldname, Object instance, Object value) throws IllegalAccessException, IllegalArgumentException, NoSuchFieldException {
- Field field = getField(instance.getClass(), fieldname);
- if (field != null) {
- setField(field, instance, value);
- }
- }
-
- /**
- *
- * @param instance
- * @param path The path of the field to retrieve from the class of the
- * instance given. The path must contain a dot "." for accessing nested
- * fields. The element of a list can be accessed by its index. For example :
- * <tt>elements.2.aField</tt>
- * @return
- * @throws NoSuchFieldException
- */
- public static FieldOnInstance getFieldOnInstance(Object instance, String path) throws NoSuchFieldException {
- if (path.contains(".")) {
- String[] nodes = path.split("\\.");
- for (int i = 0; i < nodes.length - 1; i++) {
- if (nodes[i].matches("[0-9]*")) {
- instance = ((List) instance).get(Integer.parseInt(nodes[i]));
- } else {
- instance = ReflectUtils.getFieldValue(nodes[i], instance);
- }
- }
- path = nodes[nodes.length - 1];
- }
- return new FieldOnInstance(instance, getField(instance.getClass(), path));
- }
-
- public static FetcherOnInstance getFetcherOnInstance(Object instance, String path) throws NoSuchFieldException {
- if (path.contains(".")) {
- String[] nodes = path.split("\\.");
- for (int i = 0; i < nodes.length - 1; i++) {
- if (nodes[i].matches("[0-9]*")) {
- instance = ((List) instance).get(Integer.parseInt(nodes[i]));
- } else {
- instance = ReflectUtils.getFieldValue(nodes[i], instance);
- }
- }
- path = nodes[nodes.length - 1];
- }
- return new FetcherOnInstance(instance, getFetcher(instance.getClass(), path));
- }
-
- public static void setFieldValueFromPath(Object instance, String path, Object value) throws NoSuchFieldException, IllegalArgumentException, IllegalAccessException {
- getFieldOnInstance(instance, path).setValue(value);
- }
-
- public static Object getValueFromPath(Object instance, String path) throws NoSuchFieldException, IllegalArgumentException, IllegalAccessException, InvocationTargetException {
- return getFetcherOnInstance(instance, path).getValue();
- }
-
- public static abstract class Fetcher {
-
- public abstract Object getValue(Object instance) throws IllegalArgumentException, IllegalAccessException,
- InvocationTargetException;
- }
-
- public static class MethodFetcher extends Fetcher {
-
- private Method method;
-
- public MethodFetcher(Method method) {
- this.method = method;
- }
-
- @Override
- public Object getValue(Object instance) throws IllegalArgumentException, IllegalAccessException,
- InvocationTargetException {
- return method.invoke(instance, new Object[]{});
- }
- }
-
- public static class FieldFetcher extends Fetcher {
-
- private Field field;
-
- public FieldFetcher(Field field) {
- this.field = field;
- }
-
- @Override
- public Object getValue(Object instance) throws IllegalArgumentException, IllegalAccessException,
- InvocationTargetException {
- return field.get(instance);
- }
- }
-
- public static class FetcherOnInstance {
-
- private final Object instance;
- private final Fetcher fetcher;
-
- public FetcherOnInstance(Object instance, Fetcher fetcher) {
- this.instance = instance;
- this.fetcher = fetcher;
- }
-
- public Object getInstance() {
- return instance;
- }
-
- public Object getValue() throws IllegalAccessException, IllegalArgumentException, InvocationTargetException {
- return fetcher.getValue(instance);
- }
- }
-
- /**
- * Class that wraps a field with an instance on which will be
- * retrieved/update a field.
- */
- public static class FieldOnInstance {
-
- private final Object instance;
- private final Field field;
-
- public FieldOnInstance(Object instance, Field field) {
- this.instance = instance;
- this.field = field;
- }
-
- public Field getField() {
- return field;
- }
-
- public Object getInstance() {
- return instance;
- }
-
- public void setValue(Object value) throws IllegalAccessException {
- setField(field, instance, value);
- }
-
- public Object getValue() throws IllegalAccessException {
- return getFieldValue(field, instance);
- }
- }
-}
diff --git a/.svn/pristine/5c/5c0fa9fa45e00f89e1d164f1b101181624fed021.svn-base b/.svn/pristine/5c/5c0fa9fa45e00f89e1d164f1b101181624fed021.svn-base
deleted file mode 100644
index 8270ff6..0000000
--- a/.svn/pristine/5c/5c0fa9fa45e00f89e1d164f1b101181624fed021.svn-base
+++ /dev/null
@@ -1,43 +0,0 @@
-package miscellaneous;
-
-import fr.cemagref.simaqualife.pilot.Pilot;
-import umontreal.iro.lecuyer.randvar.NormalGen;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-
-public class Miscellaneous {
-
- static public long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba, long threshold) {
- long amountWithSuccess;
- if (amount > threshold) { // use a normal approximation for huge amount
- amountWithSuccess= -1;
- while (amountWithSuccess <0 | amountWithSuccess>amount){
- amountWithSuccess = Math.round(NormalGen.nextDouble(pilot.getRandomStream(),0.,1.) * Math.sqrt(succesProba * (1 - succesProba) * amount)
- + succesProba * amount);
- }
- }
- else {
- amountWithSuccess= 0;
- for (long i=0; i < amount; i++){
- if (UniformGen.nextDouble(pilot.getRandomStream(), 0.,1.) < succesProba)
- amountWithSuccess++;
- }
- }
- return amountWithSuccess;
- }
-
- static public long binomialForSuperIndividual(Pilot pilot, long amount, double succesProba) {
- return binomialForSuperIndividual(pilot, amount, succesProba, 50);
- }
-
- static public double logNormalAlea(Pilot pilot, double mean, double cv){
- if (cv > 0.){
- double mu=Math.log(mean)- (cv *cv)/2.;
- double sigma = Math.sqrt(Math.log(cv*cv +1));
- return Math.exp((UniformGen.nextDouble(pilot.getRandomStream(),0.,1. ) * sigma + mu));
- }
- else
- return mean;
- }
-
-
-}
diff --git a/.svn/pristine/5d/5d8750dc847f6c3cf61cb64ffad3d915ee1a67e2.svn-base b/.svn/pristine/5d/5d8750dc847f6c3cf61cb64ffad3d915ee1a67e2.svn-base
deleted file mode 100644
index 985de6a..0000000
--- a/.svn/pristine/5d/5d8750dc847f6c3cf61cb64ffad3d915ee1a67e2.svn-base
+++ /dev/null
@@ -1,22 +0,0 @@
-
-obsFile = newFile();
-obsFile << "<hashtable></hashtable>";
-
-arguments = ['-simDuration','44','-simBegin','2007','-timeStepDuration','1',
- '-groups', groupFile.getAbsolutePath(),'-env',envFile.getAbsolutePath(),'-observers',obsFile.getAbsolutePath(),
- '-RNGStatusIndex', replicat
- ] as String[]
-
-path = "aquaticWorld.aquaNismsGroupsList.0.processes.processesEachStep."
-
-Pilot.init()
-
-BatchRunner.parseArgs(arguments,false,true,false);
-
-BatchRunner.load();
-ReflectUtils.setFieldValueFromPath(Pilot.getInstance(), path+"0.nbWithNaturalDiet", nbIn);
-
-Pilot.run()
-femaleInLastReproduction = ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getNumberOfFemaleInMaturation");
-femaleInReproductions = ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getFemaleSpawnersString");
-larvaeProductions = ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getLarvaeProductionString");
\ No newline at end of file
diff --git a/.svn/pristine/69/69ae76376936d0f6f255b7510fbe974add550c00.svn-base b/.svn/pristine/69/69ae76376936d0f6f255b7510fbe974add550c00.svn-base
deleted file mode 100644
index 0762ff0..0000000
--- a/.svn/pristine/69/69ae76376936d0f6f255b7510fbe974add550c00.svn-base
+++ /dev/null
@@ -1,142 +0,0 @@
-/**
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import environment.Tanks;
-import environment.Station;
-import fr.cemagref.simaqualife.kernel.AquaNism;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class Sturgeon extends AquaNism<Tanks, Station>{
-
- public static enum Stage {IMMATURE, MATURE};
- public static enum Gender {FEMALE, MALE};
- public static enum Diet {NATURAL, MIXED};
- public static enum Status {NORMAL, DEFORMED};
-
- private final int cohort;
- private final Gender gender;
- private final Diet diet;
- private Stage stage;
- private Status status;
- private int age;
- private String name;
-
- private int numberOfReproduction;
- private double ageAtLastReproduction;
- private boolean readyToSpawn;
-
- /**
- *
- * @param position
- * @param stage
- * @param gender
- * @param diet
- * @param isDeformed
- */
-
- public Sturgeon(Pilot pilot, Tanks position, int cohort, int age, Stage stage, Gender gender, Diet diet,
- Status status, String name, double ageAtLastReproduction) {
- super(pilot, position);
- this.cohort = cohort;
- this.age = age;
- this.stage = stage;
- this.gender = gender;
- this.diet = diet;
- this.status = status;
- this.ageAtLastReproduction = ageAtLastReproduction;
- this.name = name;
-
- this.numberOfReproduction = 0;
- this.readyToSpawn = false;
- }
-
- public Sturgeon(Pilot pilot, Tanks position, int cohort, int age, Stage stage, Gender gender, Diet diet,
- Status status) {
- this(pilot, position, cohort, age, stage, gender, diet, status, "", Double.NaN );
- }
-
- public Status getStatus() {
- return status;
- }
-
- public void setStatus(Status status) {
- this.status = status;
- }
-
- public Gender getGender() {
- return gender;
- }
-
- public Diet getDiet() {
- return diet;
- }
-
- public Stage getStage() {
- return stage;
- }
-
- public void setStage(Stage stage) {
- this.stage = stage;
- }
-
- public int getAge() {
- return age;
- }
-
- public void incrementAge(){
- this.age++;
- }
-
- public int getCohort() {
- return cohort;
- }
-
- public String getBatchName(){
- return String.valueOf(this.getCohort()).concat("-").concat(this.getDiet().toString());
- }
-
- public int getNumberOfReproduction() {
- return numberOfReproduction;
- }
-
- public void incrementNumberOfReproduction() {
- this.numberOfReproduction += 1;
- }
-
- public double getAgeAtLastReproduction() {
- return ageAtLastReproduction;
- }
-
- public void setAgeAtLastReproduction() {
- this.ageAtLastReproduction = this.age;
- }
-
- public boolean isReadyToSpawn() {
- return readyToSpawn;
- }
-
- public void setReadyToSpawn(boolean readyToSpawn) {
- this.readyToSpawn = readyToSpawn;
- }
-
-}
diff --git a/.svn/pristine/6a/6ab0a26199c4d28b30319d02f8fcffbc62beb770.svn-base b/.svn/pristine/6a/6ab0a26199c4d28b30319d02f8fcffbc62beb770.svn-base
deleted file mode 100644
index 044f966..0000000
--- a/.svn/pristine/6a/6ab0a26199c4d28b30319d02f8fcffbc62beb770.svn-base
+++ /dev/null
@@ -1,12 +0,0 @@
-Cohorte;Aliment Nat Exclusif;Age;survivant;normal;deform
-2007;oui;6;73;72;1
-2007;non;6;76;57;19
-2008;oui;5;87;85;2
-2008;non;5;179;127;52
-2009;oui;4;36;35;1
-2009;non;4;88;62;26
-2011;oui;2;50;50;0
-2011;non;2;83;79;4
-2012;oui;1;27;27;0
-2012;non;1;25;25;0
-2013;oui;0;80;80;0
diff --git a/.svn/pristine/83/839d12205b3ef9fe5bbc8f128e4ce7e50d26e601.svn-base b/.svn/pristine/83/839d12205b3ef9fe5bbc8f128e4ce7e50d26e601.svn-base
deleted file mode 100644
index 33abdc5..0000000
--- a/.svn/pristine/83/839d12205b3ef9fe5bbc8f128e4ce7e50d26e601.svn-base
+++ /dev/null
@@ -1,66 +0,0 @@
-<list>
- <species.SturgeonGroup>
- <processes>
- <processesAtBegin>
- <species.PopulateWithActualCaptiveStock>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <sturgeonStockName>D:/workspace/SturioSaintSeurin/data/input/MaturationGeniteursJuin14.csv</sturgeonStockName>
- <fishWithPb>true</fishWithPb>
- <presentYear>2014</presentYear>
- </species.PopulateWithActualCaptiveStock>
- </processesAtBegin>
-
- <processesEachStep>
-
- <species.Deform>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <scaleDeform>0.3203588</scaleDeform>
- <shapeDeform>6.55763282</shapeDeform>
- <piDeformForNaturalDiet>0.05565945</piDeformForNaturalDiet>
- <piDeformForMixedDiet>0.5463054</piDeformForMixedDiet>
- </species.Deform>
-
- <species.Die>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <dieScaleForNormal>0.01877447</dieScaleForNormal>
- <dieScaleForDeformed>0.40354444</dieScaleForDeformed>
- <dieShape>1.0</dieShape>
- </species.Die>
-
- <species.MatureWithTruncatedDistribution>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probTruncature>0.01</probTruncature>
- <femaleMeanAgeAtMaturation>16.4</femaleMeanAgeAtMaturation>
- <femaleSdAgeAtMaturation>2.7</femaleSdAgeAtMaturation>
- <femaleMeanInterSpawningInterval>4.0
- </femaleMeanInterSpawningInterval>
- <maleMeanAgeAtMaturation>8.0</maleMeanAgeAtMaturation>
- <maleSdAgeAtMaturation>1.4</maleSdAgeAtMaturation>
- <maleMeanInterSpawningInterval>1.5</maleMeanInterSpawningInterval>
- </species.MatureWithTruncatedDistribution>
-
- <species.ProduceLarvae>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <pi>0.75</pi>
- <mu>4.347</mu>
- <sigma>0.7806</sigma>
- <maxProd>250.0</maxProd>
- </species.ProduceLarvae>
-
-
- <species.Age>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Age>
-
- </processesEachStep>
-
- <processesAtEnd>
- <species.Analyse>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Analyse>
- </processesAtEnd>
- </processes>
-
- <useCemetery>false</useCemetery>
- </species.SturgeonGroup>
-</list>
\ No newline at end of file
diff --git a/.svn/pristine/88/88234ca9a82458ac8c31e81ade3dec2acef32c2f.svn-base b/.svn/pristine/88/88234ca9a82458ac8c31e81ade3dec2acef32c2f.svn-base
deleted file mode 100644
index 29ab8ae..0000000
--- a/.svn/pristine/88/88234ca9a82458ac8c31e81ade3dec2acef32c2f.svn-base
+++ /dev/null
@@ -1,23 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-/**
- *
- */
-package species;
\ No newline at end of file
diff --git a/.svn/pristine/89/890cd70d2816e4a86c9e30d6bae6c34bec25bcaf.svn-base b/.svn/pristine/89/890cd70d2816e4a86c9e30d6bae6c34bec25bcaf.svn-base
deleted file mode 100644
index 8c2ea43..0000000
--- a/.svn/pristine/89/890cd70d2816e4a86c9e30d6bae6c34bec25bcaf.svn-base
+++ /dev/null
@@ -1,118 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.io.FileReader;
-import java.util.Locale;
-import java.util.Scanner;
-import java.util.regex.Pattern;
-
-import species.Sturgeon.Diet;
-import species.Sturgeon.Gender;
-import species.Sturgeon.Stage;
-import species.Sturgeon.Status;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class Populate extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private String sturgeonStockName ="data/input/stockSaintSeurin.csv";
-
- private transient UniformGen genUniform;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Populate())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen(pilot.getRandomStream(),0.,1.);
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup group) {
-
- int cohort, age, nbNormal, nbDeformed;
- String alim;
-
- try {
- // open the file
- FileReader reader = new FileReader(sturgeonStockName);
-
- // Parsing the file
- Scanner scanner = new Scanner(reader);
- scanner.useLocale(Locale.ENGLISH); // to have a comma as decimal separator !!!
- scanner.useDelimiter(Pattern.compile("(;|\r\n|\n)"));
-
- // skip the first line
- scanner.nextLine();
- //System.out.println(scanner.nextLine());
- while (scanner.hasNext()) {
- cohort = scanner.nextInt();
- alim= scanner.next();
- age = scanner.nextInt();
- scanner.next(); // skip nb survival
- nbNormal = scanner.nextInt();
- nbDeformed = scanner.nextInt();
-
- // normal fish
- for (int i=0; i < nbNormal; i++){
- Sturgeon sturgeon = new Sturgeon(group.getPilot(), group.getEnvironment().getTanks(), cohort, age, Stage.IMMATURE,
- (genUniform.nextDouble() <0.5) ? Gender.FEMALE : Gender.MALE,
- (alim.equalsIgnoreCase("oui")) ? Diet.NATURAL : Diet.MIXED,
- Status.NORMAL);
- group.addAquaNism(sturgeon);
- }
- // deformed fish
- for (int i=0; i < nbDeformed; i++){
- Sturgeon sturgeon = new Sturgeon(group.getPilot(), group.getEnvironment().getTanks(), cohort, age, Stage.IMMATURE,
- (genUniform.nextDouble() <0.5) ? Gender.FEMALE : Gender.MALE,
- (alim.equalsIgnoreCase("oui")) ? Diet.NATURAL : Diet.MIXED,
- Status.DEFORMED);
- group.addAquaNism(sturgeon);
- }
- }
- scanner.close();
- reader.close();
- }
- catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- //System.out.println(group.getFishNumber());
- //group.printNumberInBatches();
-
- }
-
-
-}
diff --git a/.svn/pristine/96/960e25840b92b7ffb0b4e12474e6e08d0a9871a3.svn-base b/.svn/pristine/96/960e25840b92b7ffb0b4e12474e6e08d0a9871a3.svn-base
deleted file mode 100644
index 2a990e6..0000000
--- a/.svn/pristine/96/960e25840b92b7ffb0b4e12474e6e08d0a9871a3.svn-base
+++ /dev/null
@@ -1,80 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import species.Sturgeon.Diet;
-import species.Sturgeon.Status;
-import umontreal.iro.lecuyer.probdist.GammaDist;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class Deform extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private double scaleDeform = 0.3203588; // as in R: (inverse in in Lecuyer)
- private double shapeDeform = 6.55763282;
- private double piDeformForNaturalDiet = 0.05565945;
- private double piDeformForMixedDiet = 0.5463054;
-
- private transient UniformGen genUniform;
- private transient GammaDist gammaDist;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Deform())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen( pilot.getRandomStream(),0.,1.);
- gammaDist = new GammaDist(shapeDeform, 1/scaleDeform);
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup stock) {
- for (Sturgeon fish : stock.getAquaNismsList()){
- if (fish.getStatus() == Status.NORMAL){
- //System.out.println(" "+fish.getAge()+" : " + getProbaToDeform(fish));
- if (genUniform.nextDouble() < getProbaToDeform(stock.getPilot(), fish)){
- fish.setStatus(Status.DEFORMED);
- }
- }
- }
- }
-
- public double getProbaToDeform(Pilot pilot, Sturgeon fish){
- double proba=0.;
- double pi = (fish.getDiet() == Diet.NATURAL) ? piDeformForNaturalDiet : piDeformForMixedDiet;
- double probaT = gammaDist.cdf(fish.getAge());
- double probaTplus = gammaDist.cdf(fish.getAge() + pilot.getTimeStepDuration());
- proba = pi * (probaTplus - probaT) / (1 - pi * probaT);
- return proba;
- }
-
-}
diff --git a/.svn/pristine/97/9712c4489898442d011ad0dad23fc8a4dec8d7b7.svn-base b/.svn/pristine/97/9712c4489898442d011ad0dad23fc8a4dec8d7b7.svn-base
deleted file mode 100644
index 6f74d81..0000000
--- a/.svn/pristine/97/9712c4489898442d011ad0dad23fc8a4dec8d7b7.svn-base
+++ /dev/null
@@ -1,58 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>SturioSaintSeurin</groupId>
- <artifactId>SturioSaintSeurin</artifactId>
- <version>0.0.1-SNAPSHOT</version>
- <build>
- <sourceDirectory>src</sourceDirectory>
- <plugins>
- <plugin>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>3.1</version>
- <configuration>
- <source>1.7</source>
- <target>1.7</target>
- </configuration>
- </plugin>
-
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- <configuration>
- <manifestLocation>target/META-INF</manifestLocation>
- <finalName>${symbolic.name}_${project.version}</finalName>
- <instructions>
- <Bundle-Name>${project.groupId}.${project.artifactId}</Bundle-Name>
- <Bundle-SymbolicName>${project.groupId}.${project.artifactId}</Bundle-SymbolicName>
- <Import-Package>*;resolution:=optional</Import-Package>
- <Export-Package>fr.cemagref.simaqualife.extensions.pilot.BatchRunner;fr.cemagref.simaqualife.*;miscellaneous.*</Export-Package>
- <Embed-Dependency>*;scope=!provided;inline=true</Embed-Dependency>
- <Embed-Transitive>true</Embed-Transitive>
- <eclipse.buddypolicy>global</eclipse.buddypolicy>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>fr.cemagref</groupId>
- <artifactId>simaqualife</artifactId>
- <version>1.4</version>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <id>trac.clermont.cemagref.fr.nexus.public</id>
- <url>http://trac.clermont.cemagref.fr/nexus/content/groups/public</url>
- </repository>
- <repository>
- <id>trac.clermont.cemagref.fr.nexus.snapshots</id>
- <url>http://trac.clermont.cemagref.fr/nexus/content/repositories/snapshots</url>
- </repository>
- </repositories>
-
-</project>
\ No newline at end of file
diff --git a/.svn/pristine/9c/9c52379c20f0afbc186e26cb897f085366a789e9.svn-base b/.svn/pristine/9c/9c52379c20f0afbc186e26cb897f085366a789e9.svn-base
deleted file mode 100644
index 0f0d0c5..0000000
--- a/.svn/pristine/9c/9c52379c20f0afbc186e26cb897f085366a789e9.svn-base
+++ /dev/null
@@ -1,69 +0,0 @@
-<list>
- <species.SturgeonGroup>
- <processes>
- <processesAtBegin>
-
- </processesAtBegin>
-
- <processesEachStep>
- <species.Enter>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <nbWithNaturalDiet>40</nbWithNaturalDiet>
- <nbWithMixedDiet>0</nbWithMixedDiet>
- </species.Enter>
-
- <species.Deform>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <scaleDeform>0.3203588</scaleDeform>
- <shapeDeform>6.55763282</shapeDeform>
- <piDeformForNaturalDiet>0.05565945</piDeformForNaturalDiet>
- <piDeformForMixedDiet>0.5463054</piDeformForMixedDiet>
- </species.Deform>
-
- <species.DieByAccident>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probaAccident>0.65</probaAccident>
- <dieScaleAccident>11.85746</dieScaleAccident>
- </species.DieByAccident>
-
- <species.Die>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <dieScaleForNormal>0.01877447</dieScaleForNormal>
- <dieScaleForDeformed>0.40354444</dieScaleForDeformed>
- <dieShape>1.0</dieShape>
- </species.Die>
-
- <species.MatureWithTruncatedDistribution>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probTruncature>0.01</probTruncature>
- <femaleMeanAgeAtMaturation>16.4</femaleMeanAgeAtMaturation>
- <femaleSdAgeAtMaturation>2.7</femaleSdAgeAtMaturation>
- <femaleMeanInterSpawningInterval>4.0
- </femaleMeanInterSpawningInterval>
- <maleMeanAgeAtMaturation>8.0</maleMeanAgeAtMaturation>
- <maleSdAgeAtMaturation>1.4</maleSdAgeAtMaturation>
- <maleMeanInterSpawningInterval>1.5</maleMeanInterSpawningInterval>
- </species.MatureWithTruncatedDistribution>
-
- <species.ProduceLarvae>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <pi>0.75</pi>
- <mu>4.347</mu>
- <sigma>0.7806</sigma>
- <maxProd>250.0</maxProd>
- </species.ProduceLarvae>
-
-
- <species.Age>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Age>
-
- </processesEachStep>
-
- <processesAtEnd>
- </processesAtEnd>
- </processes>
-
- <useCemetery>false</useCemetery>
- </species.SturgeonGroup>
-</list>
\ No newline at end of file
diff --git a/.svn/pristine/a1/a112be21c325d37ebc17baafd40c0386b5d09df1.svn-base b/.svn/pristine/a1/a112be21c325d37ebc17baafd40c0386b5d09df1.svn-base
deleted file mode 100644
index 14b697b..0000000
--- a/.svn/pristine/a1/a112be21c325d37ebc17baafd40c0386b5d09df1.svn-base
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/.svn/pristine/a1/a1445bee6c80c4ba1df383b332984d83c507d474.svn-base b/.svn/pristine/a1/a1445bee6c80c4ba1df383b332984d83c507d474.svn-base
deleted file mode 100644
index 171c83a..0000000
--- a/.svn/pristine/a1/a1445bee6c80c4ba1df383b332984d83c507d474.svn-base
+++ /dev/null
@@ -1,80 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import species.Sturgeon.Gender;
-import umontreal.iro.lecuyer.probdist.LognormalDist;
-import umontreal.iro.lecuyer.probdist.NormalDist;
-import umontreal.iro.lecuyer.randvar.LognormalGen;
-import umontreal.iro.lecuyer.randvar.NormalGen;
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class ProduceLarvae extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private double pi=.75;
- private double mu=4.3470;
- private double sigma=0.7806;
- private double maxProd=250.;
- transient NormalGen genAleaNormal;
- transient LognormalGen genAleaLognormal;
-
- @Override
- public void initTransientParameters(Pilot pilot) {
- super.initTransientParameters(pilot);
-
- genAleaNormal = new NormalGen(pilot.getRandomStream(), new NormalDist(0.,1.));
- genAleaLognormal = new LognormalGen(pilot.getRandomStream(), new LognormalDist(mu, sigma));
- }
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new ProduceLarvae())); }
-
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup group) {
- int nbFemale=0;
- double nbLarvae=0.; // in thousound of fish
- for (Sturgeon fish : group.getAquaNismsList()){
- if (fish.getGender() == Gender.FEMALE & fish.isReadyToSpawn()){
- nbFemale++;
-
- if (genAleaNormal.nextDouble()<pi){
- double nlarvae=Math.min(maxProd,genAleaLognormal.nextDouble());
- nbLarvae +=nlarvae;
- //System.out.println(nlarvae);
- }
- }
- }
- group.getFemaleSpawnerNbHistory().add(nbFemale);
- group.getLarvaeProductionHistory().add(nbLarvae);
- group.setAnnualLarvaeProduction(nbLarvae);
- }
-
-}
diff --git a/.svn/pristine/a1/a1c6e6d38346e9008f73c721f76668cee1c0f01e.svn-base b/.svn/pristine/a1/a1c6e6d38346e9008f73c721f76668cee1c0f01e.svn-base
deleted file mode 100644
index d99be84..0000000
--- a/.svn/pristine/a1/a1c6e6d38346e9008f73c721f76668cee1c0f01e.svn-base
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-
-import species.Sturgeon.Status;
-import umontreal.iro.lecuyer.probdist.WeibullDist;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- *
- */
-public class Die extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- private double dieScaleForNormal = 0.01877447;
- private double dieScaleForDeformed = 0.40354444;
- private double dieShape = 1.;
-
- private transient UniformGen genUniform;
- private transient WeibullDist weibullDistForNormal;
- private transient WeibullDist weibullDistForDeformed;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Die())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen( pilot.getRandomStream(),0.,1.);
- weibullDistForNormal = new WeibullDist(dieShape, dieScaleForNormal, 0.);
- weibullDistForDeformed = new WeibullDist(dieShape, dieScaleForDeformed, 0.);
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup stock) {
- List<Sturgeon> deadFish = new ArrayList<Sturgeon>();
- for (Sturgeon fish : stock.getAquaNismsList()){
- //System.out.println(fish.getAge()+":"+getProbaToDie(fish));
- if (genUniform.nextDouble() < getProbaToDie(stock.getPilot(), fish)){
- deadFish.add(fish);
- }
- }
- // remove fish from the list
- for (Sturgeon fish : deadFish){
- stock.removeAquaNism(fish);
- }
-
- //stock.printNumberInBatches();
- }
-
- public double getProbaToDie(Pilot pilot, Sturgeon fish){
- double probaT, probaTplus;
- if (fish.getStatus() == Status.DEFORMED){
- probaT = weibullDistForDeformed.cdf(fish.getAge());
- probaTplus = weibullDistForDeformed.cdf(fish.getAge() + pilot.getTimeStepDuration());
- }
- else {
- probaT = weibullDistForNormal.cdf(fish.getAge());
- probaTplus = weibullDistForNormal.cdf(fish.getAge() + pilot.getTimeStepDuration());
- }
-
- return ((probaTplus - probaT) / (1 - probaT));
-
- }
-
-}
diff --git a/.svn/pristine/a4/a480ba770bb5c18ee3c407f189a2451ff6e0e186.svn-base b/.svn/pristine/a4/a480ba770bb5c18ee3c407f189a2451ff6e0e186.svn-base
deleted file mode 100644
index 99465e1..0000000
--- a/.svn/pristine/a4/a480ba770bb5c18ee3c407f189a2451ff6e0e186.svn-base
+++ /dev/null
@@ -1,3 +0,0 @@
-<environment.Station>
-
-</environment.Station>
\ No newline at end of file
diff --git a/.svn/pristine/ad/adfb7cb2023625e3c8ba6ccdbd4a5982933751d8.svn-base b/.svn/pristine/ad/adfb7cb2023625e3c8ba6ccdbd4a5982933751d8.svn-base
deleted file mode 100644
index 4014af0..0000000
--- a/.svn/pristine/ad/adfb7cb2023625e3c8ba6ccdbd4a5982933751d8.svn-base
+++ /dev/null
@@ -1,23 +0,0 @@
-package miscellaneous;
-
-import umontreal.iro.lecuyer.probdist.GammaDist;
-
-public class TruncatedGammaDist {
-
- private final double probTroncature;
- private GammaDist gammaDist;
-
- public TruncatedGammaDist(double alpha, double lambda, double probTroncature) {
- gammaDist = new GammaDist(alpha, lambda);
- this.probTroncature = probTroncature;
- }
-
- public double cdf(double x) {
- return Math.max(0, (gammaDist.cdf(x)- probTroncature) / (1-probTroncature));
- }
-
- public double getXTrucature(){
- return gammaDist.inverseF(probTroncature);
- }
-
-}
diff --git a/.svn/pristine/c0/c0cd8a1ebd097b94487ff2b13441cbe94a9509f6.svn-base b/.svn/pristine/c0/c0cd8a1ebd097b94487ff2b13441cbe94a9509f6.svn-base
deleted file mode 100644
index d5a8271..0000000
--- a/.svn/pristine/c0/c0cd8a1ebd097b94487ff2b13441cbe94a9509f6.svn-base
+++ /dev/null
@@ -1,76 +0,0 @@
-package miscellaneous;
-
-import java.util.concurrent.ArrayBlockingQueue;
-
-public class QueueMemory<E> extends ArrayBlockingQueue<E> {
-
- private int memorySize;
-
- public QueueMemory(int memorySize) {
- super(memorySize);
- this.memorySize = memorySize;
- }
-
- public void push(E item){
- try {
- if (this.size() == this.memorySize){
- this.poll();
- }
- this.put(item);
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
-
- public E getLastItem(){
- E[] items= (E[]) this.toArray();
- if (items.length > 0)
- return items[items.length-1];
- else
- return null;
- }
-
- public double getMean(){
- double sum= 0;
- for (E item : this){
- sum += this.doubleValue(item);
- }
- sum = sum / memorySize ;
- return (sum);
- }
-
- public double getGeometricMean(){
- double sum= 0;
- for (E item : this){
- sum += Math.log(this.doubleValue(item));
- }
- return (Math.exp(sum / memorySize));
- }
-
- public double getStandartDeviation(){
- double mean= this.getMean();
- double sse= 0;
- for (E item : this){
- sse += Math.pow(this.doubleValue(item) - mean, 2.);
- }
- return (Math.sqrt(sse /(memorySize -1.)));
- }
-
- public double getCoefficientVariation(){
- return (this.getStandartDeviation() / this.getMean());
- }
-
- private double doubleValue(E item){
- if (item instanceof Double)
- return ((Double) item);
- else if (item instanceof Float)
- return ((Float) item).doubleValue();
- else if (item instanceof Long)
- return ((Long) item).doubleValue();
- else if (item instanceof Integer)
- return ((Integer) item).doubleValue();
- else
- return Double.NaN;
- }
-}
diff --git a/.svn/pristine/ce/ce816ea457800c0961dac1151087ae25753ac0ab.svn-base b/.svn/pristine/ce/ce816ea457800c0961dac1151087ae25753ac0ab.svn-base
deleted file mode 100644
index dbf82ad..0000000
--- a/.svn/pristine/ce/ce816ea457800c0961dac1151087ae25753ac0ab.svn-base
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/.svn/pristine/d1/d10271adacf2a350183ab3df355b7f4bb5163568.svn-base b/.svn/pristine/d1/d10271adacf2a350183ab3df355b7f4bb5163568.svn-base
deleted file mode 100644
index 0242966..0000000
--- a/.svn/pristine/d1/d10271adacf2a350183ab3df355b7f4bb5163568.svn-base
+++ /dev/null
@@ -1,45 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-
-/**
- *
- */
-public class Age extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Age())); }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup stock) {
- for (Sturgeon fish : stock.getAquaNismsList()){
- fish.incrementAge();
- }
- }
-
-}
diff --git a/.svn/pristine/d4/d4a815491319c64e6bb16de9ec68d1f39bd923a3.svn-base b/.svn/pristine/d4/d4a815491319c64e6bb16de9ec68d1f39bd923a3.svn-base
deleted file mode 100644
index 06afb52..0000000
--- a/.svn/pristine/d4/d4a815491319c64e6bb16de9ec68d1f39bd923a3.svn-base
+++ /dev/null
@@ -1,45 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package species;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-
-/**
- *
- */
-public class Analyse extends AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.processes.Process#doProcess(java.lang.Object)
- */
- @Override
- public void doProcess(SturgeonGroup group) {
- // TODO Auto-generated method stub
- System.out.println(group.getLarvaeProductionString());
- System.out.println(group.getFemaleSpawnersString());
- }
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new Analyse())); }
-
-}
diff --git a/.svn/pristine/d6/d6dad07ac6f2338d6acaf267057c979e724ebe64.svn-base b/.svn/pristine/d6/d6dad07ac6f2338d6acaf267057c979e724ebe64.svn-base
deleted file mode 100644
index 96dfd26..0000000
--- a/.svn/pristine/d6/d6dad07ac6f2338d6acaf267057c979e724ebe64.svn-base
+++ /dev/null
@@ -1,138 +0,0 @@
-/**
- *
- */
-package species;
-
-import miscellaneous.TruncatedGammaDist;
-
-import org.openide.util.lookup.ServiceProvider;
-
-import species.Sturgeon.Gender;
-import species.Sturgeon.Stage;
-import umontreal.iro.lecuyer.probdist.PoissonDist;
-import umontreal.iro.lecuyer.randvar.UniformGen;
-
-import com.thoughtworks.xstream.XStream;
-import com.thoughtworks.xstream.io.xml.DomDriver;
-
-import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
-import fr.cemagref.simaqualife.kernel.util.TransientParameters.InitTransientParameters;
-import fr.cemagref.simaqualife.pilot.Pilot;
-
-/**
- * @author Patrick.Lambert
- *
- */
-
-@ServiceProvider(service = AquaNismsGroupProcess.class)
-public class MatureWithTruncatedDistribution extends
-AquaNismsGroupProcess<Sturgeon, SturgeonGroup> {
-
-
- private double probTruncature = 0.01;
-
- private double femaleMeanAgeAtMaturation = 16.4; // in year
- private double femaleSdAgeAtMaturation = 2.7;
- private double femaleMeanInterSpawningInterval = 4.;
-
- private double maleMeanAgeAtMaturation = 8; // in year
- private double maleSdAgeAtMaturation = 1.4;
- private double maleMeanInterSpawningInterval = 1.5;
-
- private transient double lag;
- private transient TruncatedGammaDist femaleMaturationDist;
- private transient TruncatedGammaDist maleMaturationDist;
- private transient PoissonDist femaleInterSpawningIntervalDist;
- private transient PoissonDist maleInterSpawningIntervalDist;
- private transient UniformGen genUniform;
-
- public static void main(String[] args) { System.out.println((new
- XStream(new DomDriver())) .toXML(new MatureWithTruncatedDistribution())); }
-
- @Override
- @InitTransientParameters
- public void initTransientParameters(Pilot pilot) {
- genUniform = new UniformGen(pilot.getRandomStream(),0.,1.);
-
- // for female first maturation
- double alpha, lambda;
- alpha = Math.pow( femaleMeanAgeAtMaturation / femaleSdAgeAtMaturation, 2);
- lambda = femaleMeanAgeAtMaturation /Math.pow(femaleSdAgeAtMaturation, 2);
- femaleMaturationDist = new TruncatedGammaDist(alpha, lambda, probTruncature);
-
- // for male first maturation
- alpha = Math.pow(maleMeanAgeAtMaturation / maleSdAgeAtMaturation, 2);
- lambda = maleMeanAgeAtMaturation / Math.pow(maleSdAgeAtMaturation, 2);
- maleMaturationDist = new TruncatedGammaDist(alpha, lambda, probTruncature);
-
- // interval between maturation
- lag =1.; // to avoid forgetting the proba for interval =0
- femaleInterSpawningIntervalDist = new PoissonDist(femaleMeanInterSpawningInterval-lag);
- maleInterSpawningIntervalDist = new PoissonDist(maleMeanInterSpawningInterval-lag);
-
- }
-
- @Override
- public void doProcess(SturgeonGroup group) {
-
- double age, laggedTimeFromLastReproduction, probaToMature;
-
- for (Sturgeon fish : group.getAquaNismsList()) {
- age = fish.getAge();
-
- // new maturation
- if (fish.getStage() == Stage.MATURE){
- laggedTimeFromLastReproduction = age - fish.getAgeAtLastReproduction() - lag;
- if (fish.getGender() == Gender.FEMALE){
- probaToMature = (femaleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction) -
- femaleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction -1.))
- / (1 - femaleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction - 1.));
- }
- else {
- probaToMature = (maleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction) -
- maleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction -1.))
- / (1 - maleInterSpawningIntervalDist.cdf(laggedTimeFromLastReproduction - 1.));
- }
-
- //
- if (genUniform.nextDouble() < probaToMature){
- fish.setReadyToSpawn(true);
- fish.setAgeAtLastReproduction();
- }
- else {
- fish.setReadyToSpawn(false);
- }
- }
- // first maturation
- else {
- if (fish.getGender() == Gender.FEMALE){
- // compute the prob to mature between age and age-1
- // knowing that it was not mature before
- probaToMature = (femaleMaturationDist.cdf(age) - femaleMaturationDist.cdf(age -1.))
- / (1 - femaleMaturationDist.cdf(age - 1.));
- }
- else {
- probaToMature = (maleMaturationDist.cdf(age) - maleMaturationDist.cdf(age -1.))
- / (1 - maleMaturationDist.cdf(age - 1.));
- }
- //System.out.println(fish.getGender() +": "+fish.getAge() + "-->"+ probaToMature);
-
- if (genUniform.nextDouble() < probaToMature){
- fish.setStage(Stage.MATURE);
- fish.setReadyToSpawn(true);
- fish.setAgeAtLastReproduction();
- }
- }
- }
-
-/* int nb=0;
- for (Sturgeon fish : group.getAquaNismsList()){
- if (fish.getGender() == Gender.FEMALE & fish.isReadyToSpawn()){
- nb++;
- }
- }
- group.getFemaleSpawnerNbHistory().add(nb);*/
- }
- //System.out.println(this.getClass()+ " is finished");
-}
-
diff --git a/.svn/pristine/e1/e1d718cd7e12cadaf53b18520d4255b15150f25e.svn-base b/.svn/pristine/e1/e1d718cd7e12cadaf53b18520d4255b15150f25e.svn-base
deleted file mode 100644
index ebc65b1..0000000
--- a/.svn/pristine/e1/e1d718cd7e12cadaf53b18520d4255b15150f25e.svn-base
+++ /dev/null
@@ -1,72 +0,0 @@
-<list>
- <species.SturgeonGroup>
- <processes>
- <processesAtBegin>
- <species.PopulateWithActualCaptiveStock>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <sturgeonStockName>D:/workspace/SturioSaintSeurin/data/input/MaturationGeniteursJuin14.csv</sturgeonStockName>
- <fishWithPb>true</fishWithPb>
- <presentYear>2014</presentYear>
- </species.PopulateWithActualCaptiveStock>
- </processesAtBegin>
-
- <processesEachStep>
-
- <species.Deform>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <scaleDeform>0.3203588</scaleDeform>
- <shapeDeform>6.55763282</shapeDeform>
- <piDeformForNaturalDiet>0.05565945</piDeformForNaturalDiet>
- <piDeformForMixedDiet>0.5463054</piDeformForMixedDiet>
- </species.Deform>
-
- <species.DieByAccident>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probaAccident>0.65</probaAccident>
- <dieScaleAccident>11.85746</dieScaleAccident>
- </species.DieByAccident>
-
- <species.Die>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <dieScaleForNormal>0.01877447</dieScaleForNormal>
- <dieScaleForDeformed>0.40354444</dieScaleForDeformed>
- <dieShape>1.0</dieShape>
- </species.Die>
-
- <species.MatureWithTruncatedDistribution>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <probTruncature>0.01</probTruncature>
- <femaleMeanAgeAtMaturation>16.4</femaleMeanAgeAtMaturation>
- <femaleSdAgeAtMaturation>2.7</femaleSdAgeAtMaturation>
- <femaleMeanInterSpawningInterval>4.0
- </femaleMeanInterSpawningInterval>
- <maleMeanAgeAtMaturation>8.0</maleMeanAgeAtMaturation>
- <maleSdAgeAtMaturation>1.4</maleSdAgeAtMaturation>
- <maleMeanInterSpawningInterval>1.5</maleMeanInterSpawningInterval>
- </species.MatureWithTruncatedDistribution>
-
- <species.ProduceLarvae>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- <pi>0.75</pi>
- <mu>4.347</mu>
- <sigma>0.7806</sigma>
- <maxProd>250.0</maxProd>
- </species.ProduceLarvae>
-
-
- <species.Age>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Age>
-
- </processesEachStep>
-
- <processesAtEnd>
- <species.Analyse>
- <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
- </species.Analyse>
- </processesAtEnd>
- </processes>
-
- <useCemetery>false</useCemetery>
- </species.SturgeonGroup>
-</list>
\ No newline at end of file
diff --git a/.svn/pristine/e3/e3327ad96e179b6763c9a7ef5402ccfe04a5f1f0.svn-base b/.svn/pristine/e3/e3327ad96e179b6763c9a7ef5402ccfe04a5f1f0.svn-base
deleted file mode 100644
index 8a3975a..0000000
--- a/.svn/pristine/e3/e3327ad96e179b6763c9a7ef5402ccfe04a5f1f0.svn-base
+++ /dev/null
@@ -1,38 +0,0 @@
-<hashtable>
- <entry>
- <java-class>species.SturgeonGroup</java-class>
- <fr.cemagref.observation.kernel.ObservablesHandler>
- <observers>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Total Abundance</title>
- <xAxisLabel>Time (year)</xAxisLabel>
- <yAxisLabel>number of fish</yAxisLabel>
- <variableName>getFishNumber</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Total Larvae production</title>
- <xAxisLabel>Time (year)</xAxisLabel>
- <yAxisLabel>annual number of larvae</yAxisLabel>
- <variableName>getAnnualLarvaeProduction</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
-
- <observer.MyCSVObserver>
- <separator>;</separator>
- <sysout>true</sysout>
- <outputFile>data/output/totalAbundance.csv</outputFile>
- <observables>
- <string>getNormalFishNumber</string>
- <string>getDeformedFishNumber</string>
- <string>getNumberOfMaleInMaturation</string>
- <string>getNumberOfFemaleInMaturation</string>
- <string>getAnnualLarvaeProduction</string>
- </observables>
- </observer.MyCSVObserver>
-
- </observers>
- </fr.cemagref.observation.kernel.ObservablesHandler>
- </entry>
-</hashtable>
\ No newline at end of file
diff --git a/.svn/pristine/e5/e506a5bff87cde0595b5024f67733ea8122261cc.svn-base b/.svn/pristine/e5/e506a5bff87cde0595b5024f67733ea8122261cc.svn-base
deleted file mode 100644
index 323365d..0000000
--- a/.svn/pristine/e5/e506a5bff87cde0595b5024f67733ea8122261cc.svn-base
+++ /dev/null
@@ -1,25 +0,0 @@
-
-obsFile = newFile();
-obsFile << "<hashtable></hashtable>";
-
-arguments = ['-simDuration','36','-simBegin','2015','-timeStepDuration','1',
- '-groups', groupFile.getAbsolutePath(),'-env',envFile.getAbsolutePath(),'-observers',obsFile.getAbsolutePath(),
- '-RNGStatusIndex', replicat
- ] as String[]
-
-path = "aquaticWorld.aquaNismsGroupsList.0.processes.processesEachStep."
-
-Pilot.init()
-
-BatchRunner.parseArgs(arguments,false,true,false);
-
-BatchRunner.load();
-//ReflectUtils.setFieldValueFromPath(Pilot.getInstance(), path+"0.nbWithNaturalDiet", nbIn);
-
-Pilot.run()
-femaleInLastReproduction =
-ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getNumberOfFemaleInMaturation");
-femaleInReproductions =
-ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getFemaleSpawnersString");
-larvaeProductions =
-ReflectUtils.getValueFromPath(Pilot.getInstance(),"aquaticWorld.aquaNismsGroupsList.0.getLarvaeProductionString");
\ No newline at end of file
diff --git a/.svn/pristine/ea/eaba64b90ac859b9e02cbe2e020a68f4d40e9a3a.svn-base b/.svn/pristine/ea/eaba64b90ac859b9e02cbe2e020a68f4d40e9a3a.svn-base
deleted file mode 100644
index 1d44b6b..0000000
--- a/.svn/pristine/ea/eaba64b90ac859b9e02cbe2e020a68f4d40e9a3a.svn-base
+++ /dev/null
@@ -1,81 +0,0 @@
-/**
- * Patrick.Lambert
- * @author Patrick Lambert
- * @copyright Copyright (c) 2014, Irstea
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
-
- */
-package environment;
-
-import java.util.List;
-
-import species.Sturgeon;
-import fr.cemagref.simaqualife.kernel.AquaNismsGroup;
-import fr.cemagref.simaqualife.kernel.spatial.Environment;
-
-/**
- *
- */
-public class Station extends Environment<Tanks, Sturgeon> {
-
- Tanks tanks;
-
- public Station() {
- super();
- tanks = new Tanks();
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.spatial.Environment#addAquaNism(fr.cemagref.simaqualife.kernel.AquaNism, fr.cemagref.simaqualife.kernel.AquaNismsGroup)
- */
- @Override
- public void addAquaNism(Sturgeon aquaNism, AquaNismsGroup group) {
- // TODO Auto-generated method stub
-
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.spatial.Environment#removeAquaNism(fr.cemagref.simaqualife.kernel.AquaNism, fr.cemagref.simaqualife.kernel.AquaNismsGroup)
- */
- @Override
- public void removeAquaNism(Sturgeon aquaNism, AquaNismsGroup group) {
- // TODO Auto-generated method stub
-
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.spatial.Environment#moveAquaNism(fr.cemagref.simaqualife.kernel.AquaNism, fr.cemagref.simaqualife.kernel.AquaNismsGroup, fr.cemagref.simaqualife.kernel.spatial.Position)
- */
- @Override
- public void moveAquaNism(Sturgeon aquaNism, AquaNismsGroup group,
- Tanks destination) {
- // nothing to do
-
- }
-
- /* (non-Javadoc)
- * @see fr.cemagref.simaqualife.kernel.spatial.Environment#getNeighbours(fr.cemagref.simaqualife.kernel.spatial.Position)
- */
- @Override
- public List<Tanks> getNeighbours(Tanks position) {
- // TODO Auto-generated method stub
- return null;
- }
-
- public Tanks getTanks(){
- return tanks;
- }
-
-}
diff --git a/.svn/pristine/f0/f0ab6cdf18ff816ab9386ae70b586063bbee403f.svn-base b/.svn/pristine/f0/f0ab6cdf18ff816ab9386ae70b586063bbee403f.svn-base
deleted file mode 100644
index f3813f5..0000000
--- a/.svn/pristine/f0/f0ab6cdf18ff816ab9386ae70b586063bbee403f.svn-base
+++ /dev/null
@@ -1,76 +0,0 @@
-// pour une execution sur ma machine
-// cd C:\Program Files\OpenMOLE
-// openmole.bat -c -p D:\workspace\SturioSaintSeurin\target\${symbolic.name}_0.0.1-SNAPSHOT.jar -s D:\workspace\SturioSaintSeurin\openMole\ddpSaintSeurin.scala 2>D:\workspace\SturioSaintSeurin\openMole\erreur.txt
-
-//1>&2
-
-// pour un lancement sur le serveur de calcul
-// /usr/local/openmole/openmole -c -configuration /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/ -p /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/target/SturioSaintSeurin-0.0.1-SNAPSHOT.jar -s /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/openMole/SD4ref.scala 2>/home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/openMole/erreur.txt
-
-import org.openmole.plugin.task.groovy._
-import org.openmole.plugin.domain.range._
-import org.openmole.plugin.hook.display._
-import org.openmole.core.model.execution.Environment
-import org.openmole.plugin.domain.collection._
-import org.openmole.plugin.sampling.combine._
-import org.openmole.plugin.domain.distribution._
-import org.openmole.plugin.hook.display._
-import org.openmole.plugin.hook.file._
-import org.openmole.plugin.environment.pbs._
-
-// pour une execution sur ma machine
-val wd = "D:/workspace/SturioSaintSeurin/"
-
-// pour une execution sur le serveur
-//val wd ="/home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/"
-
-// lancement sur la ferme de calcul de Clermont
-//logger.level("FINE")
-//val env = PBSEnvironment("rougier", "calcul64.clermont.cemagref.fr")
-
-// ================================= prototype
-// ----------- input
-val replicat = Prototype[Int]("replicat")
-
-val nbIn = Prototype[Int]("nbIn")
-
-val groupFile = Prototype[File]("groupFile")
-val envFile = Prototype[File]("envFile")
-
-// ---------------- output
-val femaleInLastReproduction = Prototype[Int]("femaleInLastReproduction")
-val femaleInReproductions = Prototype[String]("femaleInReproductions")
-val larvaeProductions = Prototype[String]("larvaeProductions")
-
-// ======================================== exploration
-val explo = ExplorationTask("explo",
- Factor(nbIn, 25 to 50 by 5 toDomain) x
- Factor(replicat, 1 to 10000 by 1 toDomain)
- )
-
-// tache Groovy
-val model = GroovyTask("model", scala.io.Source.fromFile(wd + "openMole/ddpSaintSeurin.groovy").mkString)
-model addImport "fr.cemagref.simaqualife.extensions.pilot.BatchRunner"
-model addImport "fr.cemagref.simaqualife.pilot.Pilot"
-model addImport "miscellaneous.ReflectUtils"
-model addInput replicat
-model addInput nbIn
-model addParameter (groupFile -> new File(wd+"data/input/juvenileStock.xml"))
-model addParameter (envFile -> new File(wd+"data/input/SaintSeurin.xml"))
-
-model addOutput replicat
-model addOutput nbIn
-model addOutput femaleInLastReproduction
-model addOutput femaleInReproductions
-model addOutput larvaeProductions
-
- // sur l'ordi
- val h = AppendToCSVFileHook(wd + "data/output/ddpSaintSeurin.txt")
-
- //sur le serveur de calcul (pas la même version d'openMole que sur ma machine)
- //val h = new AppendToCSVFileHook(wd + "data/output/ddpSaintSeurin.txt")
-
-
-val ex = explo -< (model hook h) toExecution
-ex.start
-ex.waitUntilEnded
\ No newline at end of file
diff --git a/.svn/pristine/f3/f3b8f77a424c79ff067bd6ecf4e09a73442bb497.svn-base b/.svn/pristine/f3/f3b8f77a424c79ff067bd6ecf4e09a73442bb497.svn-base
deleted file mode 100644
index 3aba822..0000000
--- a/.svn/pristine/f3/f3b8f77a424c79ff067bd6ecf4e09a73442bb497.svn-base
+++ /dev/null
@@ -1,76 +0,0 @@
-// pour une execution sur ma machine
-// cd C:\Program Files\OpenMOLE
-// openmole.bat -c -p D:\workspace\SturioSaintSeurin\target\${symbolic.name}_0.0.1-SNAPSHOT.jar -s D:\workspace\SturioSaintSeurin\openMole\GENddpSaintSeurin.scala 2>D:\workspace\SturioSaintSeurin\openMole\erreur.txt
-
-//1>&2
-
-// pour un lancement sur le serveur de calcul
-// /usr/local/openmole/openmole -c -configuration /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/ -p /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/target/SturioSaintSeurin-0.0.1-SNAPSHOT.jar -s /home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/openMole/SD4ref.scala 2>/home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/openMole/erreur.txt
-
-import org.openmole.plugin.task.groovy._
-import org.openmole.plugin.domain.range._
-import org.openmole.plugin.hook.display._
-import org.openmole.core.model.execution.Environment
-import org.openmole.plugin.domain.collection._
-import org.openmole.plugin.sampling.combine._
-import org.openmole.plugin.domain.distribution._
-import org.openmole.plugin.hook.display._
-import org.openmole.plugin.hook.file._
-import org.openmole.plugin.environment.pbs._
-
-// pour une execution sur ma machine
-val wd = "D:/workspace/SturioSaintSeurin/"
-
-// pour une execution sur le serveur
-//val wd ="/home/win/BORDEAUX/patrick.lambert/SturioSaintSeurin/"
-
-// lancement sur la ferme de calcul de Clermont
-//logger.level("FINE")
-//val env = PBSEnvironment("rougier", "calcul64.clermont.cemagref.fr")
-
-// ================================= prototype
-// ----------- input
-val replicat = Prototype[Int]("replicat")
-
-//val nbIn = Prototype[Int]("nbIn")
-
-val groupFile = Prototype[File]("groupFile")
-val envFile = Prototype[File]("envFile")
-
-// ---------------- output
-val femaleInLastReproduction = Prototype[Int]("femaleInLastReproduction")
-val femaleInReproductions = Prototype[String]("femaleInReproductions")
-val larvaeProductions = Prototype[String]("larvaeProductions")
-
-// ======================================== exploration
-val explo = ExplorationTask("explo",
- //Factor(nbIn, 25 to 50 by 5 toDomain) x
- Factor(replicat, 1 to 10000 by 1 toDomain)
- )
-
-// tache Groovy
-val model = GroovyTask("model", scala.io.Source.fromFile(wd + "openMole/GENddpSaintSeurin.groovy").mkString)
-model addImport "fr.cemagref.simaqualife.extensions.pilot.BatchRunner"
-model addImport "fr.cemagref.simaqualife.pilot.Pilot"
-model addImport "miscellaneous.ReflectUtils"
-model addInput replicat
-//model addInput nbIn
-model addParameter (groupFile -> new File(wd+"data/input/geniteurStockSansAccidentOM.xml"))
-model addParameter (envFile -> new File(wd+"data/input/SaintSeurin.xml"))
-
-model addOutput replicat
-//model addOutput nbIn
-model addOutput femaleInLastReproduction
-model addOutput femaleInReproductions
-model addOutput larvaeProductions
-
- // sur l'ordi
- val h = AppendToCSVFileHook(wd + "data/output/GENddpSaintSeurinSansAccident.txt")
-
- //sur le serveur de calcul (pas la même version d'openMole que sur ma machine)
- //val h = new AppendToCSVFileHook(wd + "data/output/GENddpSaintSeurin.txt")
-
-
-val ex = explo -< (model hook h) toExecution
-ex.start
-ex.waitUntilEnded
\ No newline at end of file
diff --git a/.svn/pristine/f5/f55c8c416469a5b5605c3038ce6a7f0d1175b55c.svn-base b/.svn/pristine/f5/f55c8c416469a5b5605c3038ce6a7f0d1175b55c.svn-base
deleted file mode 100644
index 188c02e..0000000
--- a/.svn/pristine/f5/f55c8c416469a5b5605c3038ce6a7f0d1175b55c.svn-base
+++ /dev/null
@@ -1,54 +0,0 @@
-Cohorte;année Naissance;Appellation;Matricule;Pit-tag;Sexe;alim;tordus;stade;dernière maturation;bête à pb;expulsion gamètes;pré-sélection échec repro;Particip_repro
-9495;1994;LEONCE;30401;3D49;femelle;alim naturelle;;mature;2014;0;2014;;2012 /2014
-9495;1994;ALEXIS;70101;21D5 ou 41BC;femelle;alim naturelle;;mature;2011;0;2011;;2011
-1988;1988;D.N.;930102;OD01;femelle;alim naturelle;;mature;2013;0;2013;;2013
-1994;1994;JEANNETTE / Jeanne;951401;041121EAOC;femelle;alim naturelle;;mature;2012;0;2012;;2008 / 2012
-1994;1994;ODILE;951504;4.11E+165;femelle;alim naturelle;;mature;2012;0;2012;;2008 / 2012
-1994;1994;KARINE;951402;041121EFF7;femelle;alim naturelle;;mature;2012;0;;2008 / 2012;
-1994;1994;950212;950212;041121E4A5;femelle;alim naturelle;;mature;2011;0;2011;;2011
-1994;1994;HENRIETTE;951202;041121CACF;femelle;alim naturelle;;mature;2011;0;2011;2013;2 011
-1994;1994;SEVERINE;10202;3B2B;femelle;alim naturelle;;mature;2012;0;2012;;2012
-1994;1994;MARTINE;951502;041121FO7D;femelle;alim naturelle;;mature;2012;0;2012;;2012
-1994;1994;951201;951201;041121F065;femelle;alim naturelle;;mature;2012;0;;2012;2012
-1994;1994;JULES;30102;279C;femelle;alim naturelle;;mature;2013;0;2013;2011;2013
-1994;1994;FIACRE;10102;3480;femelle;alim naturelle;;mature;2013;0;2013;;2011 / 2013
-1994;1994;LUCETTE;951501;041121E82D;femelle;alim naturelle;;mature;2013;0;2013;;2011 / 2013
-1994;1994;FRANCINE;951001;041121E7E8;femelle;alim naturelle;;mature;2013;0;2013;;2007 / 2009 / 2011 / 2013
-1995;1995;THIERRY;20201;41BO;femelle;alim naturelle;;mature;2013;0;2013;;2012 / 2013
-1995;1995;JULIE;30101;3CBE;femelle;alim naturelle;;mature;2014;0;2014;;2008 / 2012 / 2014
-1995;1995;ARISTIDE;10103;31AB;femelle;alim naturelle;;mature;2013;0;2013;2009;2011 / 2013
-1995;1995;EDITH;20301;2F5D;femelle;alim naturelle;;mature;2013;0;2013;;2011 / 2013
-1995;1995;FULBERT;30202;4278;femelle;alim naturelle;;mature;2013;0;2013;;2013
-1995;1995;309;95309;04108E12A8;femelle;alim naturelle;;immature;-1;1;;;
-1995;1995;349;95349;O4108E2670;femelle;alim naturelle;;immature;-1;1;;;
-1995;1995;316;95316;041121D0D6;femelle;alim naturelle;;mature;2012;0;;2012;
-1995;1995;355;95355;04108E136D;femelle;alim naturelle;;immature;-1;0;;;
-1995;1995;360;95360;04108E0E9C;femelle;alim naturelle;;mature;2014;0;2012 / 2014 ?;2010;2008 / 2012 / 2014 ?
-1995;1995;313;95313;04108E1A85;femelle;alim naturelle;;mature;2012;0;;2012;
-1995;1995;337;95337;04108E1E16;femelle;alim naturelle;;mature;2012;0;;2010 / 2012 ?;
-1995;1995;361;95361;04108E15A2;femelle;alim naturelle;;immature;-1;1;;;
-8485;8485;JUSTIN;950901;OD61;mâle;alim naturelle;;mature;2014;0;2012 / 2014 ?;;1995 / 2007 / 2011 / 2012 / 2014 ?
-8788;8788;MARIETTE;951103;OD48;mâle;alim naturelle;;mature;2014;0;2013 / 2014 ? ;;2011 / 2012 / 2013 / 2014 ?
-8889;8889;EMELINE;940301;1439;mâle;alim naturelle;;mature;2013;0;2013;;2008 / 2010 / 2011 / 2013
-0;1994;GAUTIER;30201;1F1A;mâle;alim naturelle;;mature;2013;0;2013;;2013
-0;1994;PACO;70201;0411285OE5;mâle;alim naturelle;;mature;2013;0;2013;;2012 / 2013
-1984;1984;PHILIPPE;970101;OD20;mâle;alim naturelle;;mature;2011;0;2008;2011;2008
-1988;1988;ASCENSION;950801;111A;mâle;alim naturelle;;mature;2012;0;;2010 / 2011 / 2012;
-1988;1988;BLEU;930201;1A29;mâle;alim naturelle;;mature;2013;0;2013;;2008 / 2010 / 2011 / 2012 / 2013
-1992;1992;DELPHINE;10201;3EF1;mâle;alim naturelle;;mature;2014;0;2014 ? ;2010 / 2012;2014 ?
-1994;1994;PASCAL;951601;041121FO8A;mâle;alim naturelle;;mature;2014;0;2014;2010 / 2011 / 2012;2013 / 2014
-1994;1994;NORMAN;951503;041121CADA;mâle;alim naturelle;;mature;2013;0;2013;2010 / 2012;2011 / 2013
-1994;1994;CAROL;950210;O41121E3C4;mâle;alim naturelle;;mature;2014;0;2014;2010 / 2011 / 2012;2012 / 2014
-1994;1994;ISABEAU;951301;041121E82C;mâle;alim naturelle;;mature;2014;0;2008 / 2014 ? ;2010 / 2011 / 2012;2008 / 2014 ?
-1994;1994;NATHALIE;101;4.11E+98;mâle;alim naturelle;;mature;2013;0;2013;2014;2010 / 2012 / 2013
-1995;1995;GILLES;10104;479C;mâle;alim naturelle;;immature;-1;1;;;
-1995;1995;HERVE;20101;5AA5;mâle;alim naturelle;;mature;2014;0;2014;;2009 / 2014
-1995;1995;MARTINIEN;20202;3FC6;mâle;alim naturelle;;mature;2013;0;2013;2008 / 2011;2009 / 2013
-1995;1995;137;95137;041121CDEC;mâle;alim artificielle;;mature;2012;0;2012;2010 / 2011 ;2012 / 2013
-1995;1995;365;95365;1159;mâle;alim naturelle;;mature;2012;0;;2010 / 2011 / 2012;
-1995;1995;4;95004;04108E1EEF;mâle;alim artificielle;tordu;immature;-1;1;;;
-1995;1995;353;95353;04108E10AC;mâle;alim naturelle;tordu;mature;2010;1;;2010;
-1995;1995;328;95328;041121DFB4;mâle;alim naturelle;;mature;2013;0;2013;2010 / 2011 / 2012;2013
-1995;1995;364;95364;04108E233D;mâle;alim naturelle;;mature;2013;0;2013;;2013
-1995;1995;338;95338;04108E16B9;mâle;alim naturelle;;mature;2013;0;2013;2010 / 2011 / 2012;2009 / 2013
-1995;1995;163;95163;04108E1CDC;mâle;alim artificielle;;mature;2012;0;;2012;
diff --git a/.svn/wc.db b/.svn/wc.db
deleted file mode 100644
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