creation of analysis package

data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml

@@ -283,18 +283,18 @@
 				<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason> 
 					<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> -->
 
-				<species.AnalyseSpawnerFeatures>
+				<analysis.AnalyseSpawnerFeatures>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<analysisSeason>SPRING</analysisSeason>
 					<memorySize>30</memorySize>
-				</species.AnalyseSpawnerFeatures>
+				</analysis.AnalyseSpawnerFeatures>
 
-				<species.AnalyseFishDistribution>
+				<analysis.AnalyseFishDistribution>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<analysisSeason>SPRING</analysisSeason>
 					<memorySize>30</memorySize>
 					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
-				</species.AnalyseFishDistribution>
+				</analysis.AnalyseFishDistribution>
 
 				<species.ReproduceAndSurviveAfterReproductionWithDiagnose>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
@@ -342,15 +342,15 @@
 			</processesEachStep>
 
 			<processesAtEnd>
-				<species.AnalyseLikelihoodOfPresence>
+				<analysis.AnalyseLikelihoodOfPresence>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
 					<period>obs_1900_1950</period>
 					<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
 					<epsilon>0.001</epsilon>
-				</species.AnalyseLikelihoodOfPresence>
+				</analysis.AnalyseLikelihoodOfPresence>
 
-				<species.IdentifyPopulation>
+				<analysis.IdentifyPopulation>
 					<synchronisationMode>ASYNCHRONOUS</synchronisationMode>
 					<consoleDisplay>false</consoleDisplay>
 					<years>
@@ -358,7 +358,7 @@
 					</years>
 					<fluxesSeason>SPRING</fluxesSeason>
 					<fileNameOutput>effectiveFluxes</fileNameOutput>
-				</species.IdentifyPopulation>
+				</analysis.IdentifyPopulation>
 			</processesAtEnd>
 		</processes>
 		<useCemetery>false</useCemetery>

src/main/java/species/AnalyseFishDistribution.java → src/main/java/analysis/AnalyseFishDistribution.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -34,6 +34,8 @@ import fr.cemagref.simaqualife.pilot.Pilot;
 import miscellaneous.QueueMemory;
 import miscellaneous.TreeMapForCentile;
 import observer.ObservableRecord;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 /**
  *

src/main/java/species/AnalyseLikelihoodOfPresence.java → src/main/java/analysis/AnalyseLikelihoodOfPresence.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.FileReader;
 import java.util.Locale;
@@ -31,6 +31,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
 import environment.RiverBasin;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 /**
  *

src/main/java/species/AnalyseSpawnerFeatures.java → src/main/java/analysis/AnalyseSpawnerFeatures.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -31,6 +31,8 @@ import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import miscellaneous.QueueMemory;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 import species.DiadromousFish.Gender;
 
 /**

src/main/java/species/AnalyseSpawnerRun.java → src/main/java/analysis/AnalyseSpawnerRun.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -33,6 +33,8 @@ import fr.cemagref.observation.kernel.ObservablesHandler;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
 import observer.ObservableRecord;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 /**
  *

src/main/java/species/Calibrate.java → src/main/java/analysis/Calibrate.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 
 import java.io.IOException;

src/main/java/species/ExportLenghtAgeDistribution.java → src/main/java/analysis/ExportLenghtAgeDistribution.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -32,6 +32,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
 
 /**

src/main/java/species/ExportMeanRecruitment.java → src/main/java/analysis/ExportMeanRecruitment.java

-package species;
+package analysis;
 
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.io.xml.DomDriver;
@@ -9,6 +9,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 import java.io.BufferedWriter;
 import java.io.File;

src/main/java/species/ExportPopulationStatus.java → src/main/java/analysis/ExportPopulationStatus.java

-package species;
+package analysis;
 
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.io.xml.DomDriver;
@@ -9,6 +9,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 import java.io.BufferedWriter;
 import java.io.File;

src/main/java/species/ExportRecruitment.java → src/main/java/analysis/ExportRecruitment.java

-package species;
+package analysis;
 
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.io.xml.DomDriver;
@@ -9,6 +9,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 import java.io.BufferedWriter;
 import java.io.File;

src/main/java/species/ExportSpeciesRange.java → src/main/java/analysis/ExportSpeciesRange.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -30,6 +30,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
 import environment.Time;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 /**
  *

src/main/java/species/IdentifyPopulation.java → src/main/java/analysis/IdentifyPopulation.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -34,6 +34,8 @@ import environment.RiverBasin;
 import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 /**
  *

src/main/java/species/TypeTrajectoryCV.java → src/main/java/analysis/TypeTrajectoryCV.java

-package species;
+package analysis;
 
 import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.io.xml.DomDriver;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
+
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileReader;

src/main/java/species/WriteBiomassFluxes.java → src/main/java/analysis/WriteBiomassFluxes.java

-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -15,6 +15,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
 
 /**

src/main/java/species/WriteCurrentNutrientExportFluxes.java → src/main/java/analysis/WriteCurrentNutrientExportFluxes.java

-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
 import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 

src/main/java/species/WriteCurrentNutrientImportFluxes.java → src/main/java/analysis/WriteCurrentNutrientImportFluxes.java

-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
 import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 

src/main/java/species/WriteEffectiveAndBiomassExportFluxes.java → src/main/java/analysis/WriteEffectiveAndBiomassExportFluxes.java

-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -17,6 +17,8 @@ import environment.RiverBasin;
 import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
 
 public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {

src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java → src/main/java/analysis/WriteEffectiveAndBiomassImportFluxes.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -34,6 +34,8 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 import species.DiadromousFish.Stage;
 
 /**

src/main/java/species/WriteEffectivesFluxes.java → src/main/java/analysis/WriteEffectivesFluxes.java

@@ -17,7 +17,7 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
  */
-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -34,7 +34,9 @@ import environment.Time;
 import environment.Time.Season;
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
 import fr.cemagref.simaqualife.pilot.Pilot;
+import species.DiadromousFish;
 import species.DiadromousFish.Stage;
+import species.DiadromousFishGroup;
 
 @Deprecated
 /**

src/main/java/species/WriteNutrientExportFluxes.java → src/main/java/analysis/WriteNutrientExportFluxes.java

-package species;
+package analysis;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -13,13 +13,14 @@ import com.thoughtworks.xstream.XStream;
 import com.thoughtworks.xstream.io.xml.DomDriver;
 
 import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
+import species.DiadromousFish;
+import species.DiadromousFishGroup;
 
 @Deprecated
 public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
 
 	private String fileName = "nutrientExportFluxes";
 
-
 	public static void main(String[] args) {
 		System.out.println((new XStream(new DomDriver())).toXML(new WriteNutrientExportFluxes()));