diff --git a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml b/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml index 2678c280162c0308b89d371e7ea114427ca5eacf..1775d48381aaac99c2d9fc3e7fbbe515e77971d3 100644 --- a/data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml +++ b/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> diff --git a/src/main/java/species/AnalyseFishDistribution.java b/src/main/java/analysis/AnalyseFishDistribution.java similarity index 98% rename from src/main/java/species/AnalyseFishDistribution.java rename to src/main/java/analysis/AnalyseFishDistribution.java index 70681aba2ecffae4529ab246df98cd419388db7b..fee2d2e442cdd407c68c96611ede7faf96016619 100644 --- a/src/main/java/species/AnalyseFishDistribution.java +++ b/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; /** * diff --git a/src/main/java/species/AnalyseLikelihoodOfPresence.java b/src/main/java/analysis/AnalyseLikelihoodOfPresence.java similarity index 98% rename from src/main/java/species/AnalyseLikelihoodOfPresence.java rename to src/main/java/analysis/AnalyseLikelihoodOfPresence.java index ca4a12344da3d34812486036a6b46d445f774415..fe406f7dd70deb683b66c25a3565971799527b63 100644 --- a/src/main/java/species/AnalyseLikelihoodOfPresence.java +++ b/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; /** * diff --git a/src/main/java/species/AnalyseSpawnerFeatures.java b/src/main/java/analysis/AnalyseSpawnerFeatures.java similarity index 98% rename from src/main/java/species/AnalyseSpawnerFeatures.java rename to src/main/java/analysis/AnalyseSpawnerFeatures.java index d3ddb75f99f6ba9184caead4df3dec284ace3277..4eae1a88cc3c0670fd40dd3c669b1ea43c928b3f 100644 --- a/src/main/java/species/AnalyseSpawnerFeatures.java +++ b/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; /** diff --git a/src/main/java/species/AnalyseSpawnerRun.java b/src/main/java/analysis/AnalyseSpawnerRun.java similarity index 98% rename from src/main/java/species/AnalyseSpawnerRun.java rename to src/main/java/analysis/AnalyseSpawnerRun.java index e2210335ece40af5fe0d1967d1ac8445ef7e1438..05caa25bf8eb657ddeac6ec8371e8e59e07e61b9 100644 --- a/src/main/java/species/AnalyseSpawnerRun.java +++ b/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; /** * diff --git a/src/main/java/species/Calibrate.java b/src/main/java/analysis/Calibrate.java similarity index 99% rename from src/main/java/species/Calibrate.java rename to src/main/java/analysis/Calibrate.java index 840a641c62a7f980058b874adf2d27687e3e8c16..d19950ae33f660b43e8366eedf2d0f0863daa12f 100644 --- a/src/main/java/species/Calibrate.java +++ b/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; diff --git a/src/main/java/species/ExportLenghtAgeDistribution.java b/src/main/java/analysis/ExportLenghtAgeDistribution.java similarity index 97% rename from src/main/java/species/ExportLenghtAgeDistribution.java rename to src/main/java/analysis/ExportLenghtAgeDistribution.java index 709ff4b1e5ceaf00ed07b0ca89a24024c99f3244..6e73a4c5c496d4ae6f50d8bdbef2a62529ebf4d3 100644 --- a/src/main/java/species/ExportLenghtAgeDistribution.java +++ b/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; /** diff --git a/src/main/java/species/ExportMeanRecruitment.java b/src/main/java/analysis/ExportMeanRecruitment.java similarity index 93% rename from src/main/java/species/ExportMeanRecruitment.java rename to src/main/java/analysis/ExportMeanRecruitment.java index 59e1d33f1dde0d607ddc172906fcc70420aa21e8..3fab68d71a7f5e0165736f21939d90ac5aab1950 100644 --- a/src/main/java/species/ExportMeanRecruitment.java +++ b/src/main/java/analysis/ExportMeanRecruitment.java @@ -1,4 +1,4 @@ -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; diff --git a/src/main/java/species/ExportPopulationStatus.java b/src/main/java/analysis/ExportPopulationStatus.java similarity index 95% rename from src/main/java/species/ExportPopulationStatus.java rename to src/main/java/analysis/ExportPopulationStatus.java index ab9edaf3547db6c5874db9a731819fb964f9e172..9f55605b45b3822325bd804ce35a9c17abfb141a 100644 --- a/src/main/java/species/ExportPopulationStatus.java +++ b/src/main/java/analysis/ExportPopulationStatus.java @@ -1,4 +1,4 @@ -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; diff --git a/src/main/java/species/ExportRecruitment.java b/src/main/java/analysis/ExportRecruitment.java similarity index 93% rename from src/main/java/species/ExportRecruitment.java rename to src/main/java/analysis/ExportRecruitment.java index b29699e09ed252025266ccddbd855a1bc31b37ae..6d7f23d6d7d19b01ea8b2cfc4c6d7047617abb8f 100644 --- a/src/main/java/species/ExportRecruitment.java +++ b/src/main/java/analysis/ExportRecruitment.java @@ -1,4 +1,4 @@ -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; diff --git a/src/main/java/species/ExportSpeciesRange.java b/src/main/java/analysis/ExportSpeciesRange.java similarity index 93% rename from src/main/java/species/ExportSpeciesRange.java rename to src/main/java/analysis/ExportSpeciesRange.java index f580e1aa64cb7e030041bdda16e42ac9dec46f0d..f9ca25e32ea39e137681c74efa449fa160c21122 100644 --- a/src/main/java/species/ExportSpeciesRange.java +++ b/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; /** * diff --git a/src/main/java/species/IdentifyPopulation.java b/src/main/java/analysis/IdentifyPopulation.java similarity index 94% rename from src/main/java/species/IdentifyPopulation.java rename to src/main/java/analysis/IdentifyPopulation.java index d6d5961157ba0dc8f7e01e5120a39b1aa6818e33..670d818b5c534c7a9d8b353fe9b89525107cdbc9 100644 --- a/src/main/java/species/IdentifyPopulation.java +++ b/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; /** * diff --git a/src/main/java/species/TypeTrajectoryCV.java b/src/main/java/analysis/TypeTrajectoryCV.java similarity index 97% rename from src/main/java/species/TypeTrajectoryCV.java rename to src/main/java/analysis/TypeTrajectoryCV.java index 5dfcbef96d8765d1436a52553d7e412b068166b5..c76340cf5746a44fea5df49a358e5aad980f0ee3 100644 --- a/src/main/java/species/TypeTrajectoryCV.java +++ b/src/main/java/analysis/TypeTrajectoryCV.java @@ -1,8 +1,11 @@ -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; diff --git a/src/main/java/species/WriteBiomassFluxes.java b/src/main/java/analysis/WriteBiomassFluxes.java similarity index 97% rename from src/main/java/species/WriteBiomassFluxes.java rename to src/main/java/analysis/WriteBiomassFluxes.java index 0c18ddce51d960b3901a11d9f7b1317de40f0194..54efdad39e466033f1100dcbace54a5f80455613 100644 --- a/src/main/java/species/WriteBiomassFluxes.java +++ b/src/main/java/analysis/WriteBiomassFluxes.java @@ -1,4 +1,4 @@ -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; /** diff --git a/src/main/java/species/WriteCurrentNutrientExportFluxes.java b/src/main/java/analysis/WriteCurrentNutrientExportFluxes.java similarity index 93% rename from src/main/java/species/WriteCurrentNutrientExportFluxes.java rename to src/main/java/analysis/WriteCurrentNutrientExportFluxes.java index 7840608caec64651d317b4c3f2bf7253beab1703..1815f4181626bea5f40a533fd3798128a5ff807d 100644 --- a/src/main/java/species/WriteCurrentNutrientExportFluxes.java +++ b/src/main/java/analysis/WriteCurrentNutrientExportFluxes.java @@ -1,4 +1,4 @@ -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> { diff --git a/src/main/java/species/WriteCurrentNutrientImportFluxes.java b/src/main/java/analysis/WriteCurrentNutrientImportFluxes.java similarity index 93% rename from src/main/java/species/WriteCurrentNutrientImportFluxes.java rename to src/main/java/analysis/WriteCurrentNutrientImportFluxes.java index 06ca76fa4617cf7ac3e9d4ebc114f47530f87d5b..5b95342b40223559cc045c881204db9c01c730be 100644 --- a/src/main/java/species/WriteCurrentNutrientImportFluxes.java +++ b/src/main/java/analysis/WriteCurrentNutrientImportFluxes.java @@ -1,4 +1,4 @@ -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> { diff --git a/src/main/java/species/WriteEffectiveAndBiomassExportFluxes.java b/src/main/java/analysis/WriteEffectiveAndBiomassExportFluxes.java similarity index 97% rename from src/main/java/species/WriteEffectiveAndBiomassExportFluxes.java rename to src/main/java/analysis/WriteEffectiveAndBiomassExportFluxes.java index c106bda8d56f59ecf600ff4a0b29d102081d5169..5464b93b75f79e71179ca354adaab1a6e1c229c1 100644 --- a/src/main/java/species/WriteEffectiveAndBiomassExportFluxes.java +++ b/src/main/java/analysis/WriteEffectiveAndBiomassExportFluxes.java @@ -1,4 +1,4 @@ -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> { diff --git a/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java b/src/main/java/analysis/WriteEffectiveAndBiomassImportFluxes.java similarity index 98% rename from src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java rename to src/main/java/analysis/WriteEffectiveAndBiomassImportFluxes.java index 4d19b1702af27f1ec932eb2b4ef0627e6f999bc0..4be8260f7daded2c20bf031b446fa256f54e4a0e 100644 --- a/src/main/java/species/WriteEffectiveAndBiomassImportFluxes.java +++ b/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; /** diff --git a/src/main/java/species/WriteEffectivesFluxes.java b/src/main/java/analysis/WriteEffectivesFluxes.java similarity index 98% rename from src/main/java/species/WriteEffectivesFluxes.java rename to src/main/java/analysis/WriteEffectivesFluxes.java index 1a927259e8495229d76c4b642bc9b70603d2443b..34829a76373893bf455374e8fa77b67c426b8c4b 100644 --- a/src/main/java/species/WriteEffectivesFluxes.java +++ b/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 /** diff --git a/src/main/java/species/WriteNutrientExportFluxes.java b/src/main/java/analysis/WriteNutrientExportFluxes.java similarity index 92% rename from src/main/java/species/WriteNutrientExportFluxes.java rename to src/main/java/analysis/WriteNutrientExportFluxes.java index 3ab9320febddb43a3855d50a240ec36d0cb730fe..018a46f6a4687d9ba359455620037d748cb26451 100644 --- a/src/main/java/species/WriteNutrientExportFluxes.java +++ b/src/main/java/analysis/WriteNutrientExportFluxes.java @@ -1,4 +1,4 @@ -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())); diff --git a/src/main/java/species/WriteNutrientImportFluxes.java b/src/main/java/analysis/WriteNutrientImportFluxes.java similarity index 93% rename from src/main/java/species/WriteNutrientImportFluxes.java rename to src/main/java/analysis/WriteNutrientImportFluxes.java index 127f05a169d81268421e2d69e4f38e3c0039b772..10a34e7af7d817dbff5cc3ecfe410c2a7d7f734b 100644 --- a/src/main/java/species/WriteNutrientImportFluxes.java +++ b/src/main/java/analysis/WriteNutrientImportFluxes.java @@ -1,4 +1,4 @@ -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 WriteNutrientImportFluxes extends AquaNismsGroupProcess<DiadromousFish, DiadromousFishGroup> { private String fileName = "fluxes"; - public static void main(String[] args) { System.out.println((new XStream(new DomDriver())).toXML(new WriteNutrientImportFluxes()));