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

creation of analysis package

parent 6bf85149
...@@ -283,18 +283,18 @@ ...@@ -283,18 +283,18 @@
<!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason> <!--<species.WriteEffectiveAndBiomassImportFluxes> <synchronisationMode>ASYNCHRONOUS</synchronisationMode> <exportSeason>SPRING</exportSeason>
<fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> --> <fileNameOutput>effectiveBiomassFluxesBeforeReproduction</fileNameOutput> </species.WriteEffectiveAndBiomassImportFluxes> -->
<species.AnalyseSpawnerFeatures> <analysis.AnalyseSpawnerFeatures>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<analysisSeason>SPRING</analysisSeason> <analysisSeason>SPRING</analysisSeason>
<memorySize>30</memorySize> <memorySize>30</memorySize>
</species.AnalyseSpawnerFeatures> </analysis.AnalyseSpawnerFeatures>
<species.AnalyseFishDistribution> <analysis.AnalyseFishDistribution>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<analysisSeason>SPRING</analysisSeason> <analysisSeason>SPRING</analysisSeason>
<memorySize>30</memorySize> <memorySize>30</memorySize>
<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin> <minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
</species.AnalyseFishDistribution> </analysis.AnalyseFishDistribution>
<species.ReproduceAndSurviveAfterReproductionWithDiagnose> <species.ReproduceAndSurviveAfterReproductionWithDiagnose>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
...@@ -342,15 +342,15 @@ ...@@ -342,15 +342,15 @@
</processesEachStep> </processesEachStep>
<processesAtEnd> <processesAtEnd>
<species.AnalyseLikelihoodOfPresence> <analysis.AnalyseLikelihoodOfPresence>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName> <presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
<period>obs_1900_1950</period> <period>obs_1900_1950</period>
<minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin> <minimumRecruitsForPopulatedBasin>50</minimumRecruitsForPopulatedBasin>
<epsilon>0.001</epsilon> <epsilon>0.001</epsilon>
</species.AnalyseLikelihoodOfPresence> </analysis.AnalyseLikelihoodOfPresence>
<species.IdentifyPopulation> <analysis.IdentifyPopulation>
<synchronisationMode>ASYNCHRONOUS</synchronisationMode> <synchronisationMode>ASYNCHRONOUS</synchronisationMode>
<consoleDisplay>false</consoleDisplay> <consoleDisplay>false</consoleDisplay>
<years> <years>
...@@ -358,7 +358,7 @@ ...@@ -358,7 +358,7 @@
</years> </years>
<fluxesSeason>SPRING</fluxesSeason> <fluxesSeason>SPRING</fluxesSeason>
<fileNameOutput>effectiveFluxes</fileNameOutput> <fileNameOutput>effectiveFluxes</fileNameOutput>
</species.IdentifyPopulation> </analysis.IdentifyPopulation>
</processesAtEnd> </processesAtEnd>
</processes> </processes>
<useCemetery>false</useCemetery> <useCemetery>false</useCemetery>
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
...@@ -34,6 +34,8 @@ import fr.cemagref.simaqualife.pilot.Pilot; ...@@ -34,6 +34,8 @@ import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.QueueMemory; import miscellaneous.QueueMemory;
import miscellaneous.TreeMapForCentile; import miscellaneous.TreeMapForCentile;
import observer.ObservableRecord; import observer.ObservableRecord;
import species.DiadromousFish;
import species.DiadromousFishGroup;
/** /**
* *
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.FileReader; import java.io.FileReader;
import java.util.Locale; import java.util.Locale;
...@@ -31,6 +31,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver; ...@@ -31,6 +31,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.RiverBasin; import environment.RiverBasin;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
/** /**
* *
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
...@@ -31,6 +31,8 @@ import environment.Time.Season; ...@@ -31,6 +31,8 @@ import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import miscellaneous.QueueMemory; import miscellaneous.QueueMemory;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import species.DiadromousFish.Gender; import species.DiadromousFish.Gender;
/** /**
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
...@@ -33,6 +33,8 @@ import fr.cemagref.observation.kernel.ObservablesHandler; ...@@ -33,6 +33,8 @@ import fr.cemagref.observation.kernel.ObservablesHandler;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import observer.ObservableRecord; import observer.ObservableRecord;
import species.DiadromousFish;
import species.DiadromousFishGroup;
/** /**
* *
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.IOException; import java.io.IOException;
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -32,6 +32,8 @@ import environment.Time; ...@@ -32,6 +32,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import species.DiadromousFish.Stage; import species.DiadromousFish.Stage;
/** /**
......
package species; package analysis;
import com.thoughtworks.xstream.XStream; import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver; import com.thoughtworks.xstream.io.xml.DomDriver;
...@@ -9,6 +9,8 @@ import environment.Time; ...@@ -9,6 +9,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
......
package species; package analysis;
import com.thoughtworks.xstream.XStream; import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver; import com.thoughtworks.xstream.io.xml.DomDriver;
...@@ -9,6 +9,8 @@ import environment.Time; ...@@ -9,6 +9,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
......
package species; package analysis;
import com.thoughtworks.xstream.XStream; import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver; import com.thoughtworks.xstream.io.xml.DomDriver;
...@@ -9,6 +9,8 @@ import environment.Time; ...@@ -9,6 +9,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -30,6 +30,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver; ...@@ -30,6 +30,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Time; import environment.Time;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
/** /**
* *
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -34,6 +34,8 @@ import environment.RiverBasin; ...@@ -34,6 +34,8 @@ import environment.RiverBasin;
import environment.Time; import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; 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.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver; import com.thoughtworks.xstream.io.xml.DomDriver;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
import java.io.FileReader; import java.io.FileReader;
......
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -15,6 +15,8 @@ import environment.Time; ...@@ -15,6 +15,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import species.DiadromousFish.Stage; import species.DiadromousFish.Stage;
/** /**
......
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver; ...@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Time; import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import species.DiadromousFish;
import species.DiadromousFishGroup;
public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { public class WriteCurrentNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
......
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver; ...@@ -12,6 +12,8 @@ import com.thoughtworks.xstream.io.xml.DomDriver;
import environment.Time; import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import species.DiadromousFish;
import species.DiadromousFishGroup;
public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { public class WriteCurrentNutrientImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
......
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -17,6 +17,8 @@ import environment.RiverBasin; ...@@ -17,6 +17,8 @@ import environment.RiverBasin;
import environment.Time; import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import species.DiadromousFish.Stage; import species.DiadromousFish.Stage;
public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { public class WriteEffectiveAndBiomassExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -34,6 +34,8 @@ import environment.Time; ...@@ -34,6 +34,8 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFishGroup;
import species.DiadromousFish.Stage; import species.DiadromousFish.Stage;
/** /**
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>. * along with this program. If not, see <http://www.gnu.org/licenses/>.
*/ */
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -34,7 +34,9 @@ import environment.Time; ...@@ -34,7 +34,9 @@ import environment.Time;
import environment.Time.Season; import environment.Time.Season;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import fr.cemagref.simaqualife.pilot.Pilot; import fr.cemagref.simaqualife.pilot.Pilot;
import species.DiadromousFish;
import species.DiadromousFish.Stage; import species.DiadromousFish.Stage;
import species.DiadromousFishGroup;
@Deprecated @Deprecated
/** /**
......
package species; package analysis;
import java.io.BufferedWriter; import java.io.BufferedWriter;
import java.io.File; import java.io.File;
...@@ -13,13 +13,14 @@ import com.thoughtworks.xstream.XStream; ...@@ -13,13 +13,14 @@ import com.thoughtworks.xstream.XStream;
import com.thoughtworks.xstream.io.xml.DomDriver; import com.thoughtworks.xstream.io.xml.DomDriver;
import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess; import fr.cemagref.simaqualife.kernel.processes.AquaNismsGroupProcess;
import species.DiadromousFish;
import species.DiadromousFishGroup;
@Deprecated @Deprecated
public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { public class WriteNutrientExportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> {
private String fileName = "nutrientExportFluxes"; private String fileName = "nutrientExportFluxes";
public static void main(String[] args) { public static void main(String[] args) {
System.out.println((new XStream(new DomDriver())).toXML(new WriteNutrientExportFluxes())); System.out.println((new XStream(new DomDriver())).toXML(new WriteNutrientExportFluxes()));
......
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