Commit 7e0f088b authored by patrick.lambert's avatar patrick.lambert
Browse files

creation of analysis package

parent 6bf85149
......@@ -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>
......
......@@ -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;
/**
*
......
......@@ -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;
/**
*
......
......@@ -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;
/**
......
......@@ -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;
/**
*
......
......@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package species;
package analysis;
import java.io.IOException;
......
......@@ -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;
/**
......
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;
......
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;
......
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;
......
......@@ -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;
/**
*
......
......@@ -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;
/**
*
......
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;
......
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;
/**
......
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> {
......
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> {
......
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> {
......
......@@ -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;
/**
......
......@@ -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
/**
......
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()));
......
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