continue moving classes out of AlgorithmFactories

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/SpeciesCodesFromFileFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class SpeciesCodesFromFileFactorySupplier
+    extends BasicFactorySupplier<SpeciesCodesFromFileFactory> {
+    public SpeciesCodesFromFileFactorySupplier() {
+        super(SpeciesCodesFromFileFactory.class);
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/boxcars/SPRAgentBuilderFixedSampleSupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.boxcars;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class SPRAgentBuilderFixedSampleSupplier
+    extends BasicFactorySupplier<SPRAgentBuilderFixedSample> {
+    public SPRAgentBuilderFixedSampleSupplier() {
+        super(SPRAgentBuilderFixedSample.class, "SPR Fixed Sample Agent");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/boxcars/SPRAgentBuilderSelectiveSamplingSupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.boxcars;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class SPRAgentBuilderSelectiveSamplingSupplier
+    extends BasicFactorySupplier<SPRAgentBuilderSelectiveSampling> {
+    public SPRAgentBuilderSelectiveSamplingSupplier() {
+        super(SPRAgentBuilderSelectiveSampling.class, "SPR Selective Agent");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/boxcars/SPRAgentBuilderSupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.boxcars;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class SPRAgentBuilderSupplier
+    extends BasicFactorySupplier<SPRAgentBuilder> {
+    public SPRAgentBuilderSupplier() {
+        super(SPRAgentBuilder.class, "SPR Agent");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/AbundanceReallocatorFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.tuna;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class AbundanceReallocatorFactorySupplier
+    extends BasicFactorySupplier<AbundanceReallocatorFactory> {
+    public AbundanceReallocatorFactorySupplier() {
+        super(AbundanceReallocatorFactory.class);
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/AbundanceRestorerFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.tuna;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class AbundanceRestorerFactorySupplier
+    extends BasicFactorySupplier<AbundanceRestorerFactory> {
+    public AbundanceRestorerFactorySupplier() {
+        super(AbundanceRestorerFactory.class);
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/BiomassReallocatorFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.tuna;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class BiomassReallocatorFactorySupplier
+    extends BasicFactorySupplier<BiomassReallocatorFactory> {
+    public BiomassReallocatorFactorySupplier() {
+        super(BiomassReallocatorFactory.class);
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/biology/tuna/BiomassRestorerFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.biology.tuna;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class BiomassRestorerFactorySupplier
+    extends BasicFactorySupplier<BiomassRestorerFactory> {
+    public BiomassRestorerFactorySupplier() {
+        super(BiomassRestorerFactory.class);
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/fisher/log/timeScalarFunctions/factory/ExponentialTimeScalarFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.fisher.log.timeScalarFunctions.factory;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class ExponentialTimeScalarFactorySupplier
+    extends BasicFactorySupplier<ExponentialTimeScalarFactory> {
+    public ExponentialTimeScalarFactorySupplier() {
+        super(ExponentialTimeScalarFactory.class, "Exponential");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/fisher/log/timeScalarFunctions/factory/InverseTimeScalarFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.fisher.log.timeScalarFunctions.factory;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class InverseTimeScalarFactorySupplier
+    extends BasicFactorySupplier<InverseTimeScalarFactory> {
+    public InverseTimeScalarFactorySupplier() {
+        super(InverseTimeScalarFactory.class, "Inverse");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/fisher/log/timeScalarFunctions/factory/SigmoidalTimeScalarFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.fisher.log.timeScalarFunctions.factory;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class SigmoidalTimeScalarFactorySupplier
+    extends BasicFactorySupplier<SigmoidalTimeScalarFactory> {
+    public SigmoidalTimeScalarFactorySupplier() {
+        super(SigmoidalTimeScalarFactory.class, "Sigmoidal");
+    }
+}

POSEIDON/src/main/java/uk/ac/ox/oxfish/fisher/purseseiner/planner/factories/DiscretizedOwnFadPlanningFactorySupplier.java

@@ -0,0 +1,30 @@
+/*
+ * POSEIDON: an agent-based model of fisheries
+ * Copyright (c) 2024 CoHESyS Lab cohesys.lab@gmail.com
+ *
+ * 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 uk.ac.ox.oxfish.fisher.purseseiner.planner.factories;
+
+import com.google.auto.service.AutoService;
+import uk.ac.ox.poseidon.common.api.FactorySupplier;
+import uk.ac.ox.poseidon.common.core.BasicFactorySupplier;
+
+@AutoService(FactorySupplier.class)
+public class DiscretizedOwnFadPlanningFactorySupplier
+    extends BasicFactorySupplier<DiscretizedOwnFadPlanningFactory> {
+    public DiscretizedOwnFadPlanningFactorySupplier() {
+        super(DiscretizedOwnFadPlanningFactory.class, "Centroid FAD Planning");
+    }
+}