diff --git a/src/arcade/patch/agent/action/PatchActionConvert.java b/src/arcade/patch/agent/action/PatchActionConvert.java index acab7dd4..de82d525 100644 --- a/src/arcade/patch/agent/action/PatchActionConvert.java +++ b/src/arcade/patch/agent/action/PatchActionConvert.java @@ -4,14 +4,14 @@ import sim.engine.SimState; import sim.util.Bag; import arcade.core.agent.action.Action; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.agent.cell.PatchCell; import arcade.patch.agent.cell.PatchCellContainer; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.Coordinate; +import arcade.patch.env.location.Coordinate; import arcade.patch.sim.PatchSimulation; import static arcade.patch.util.PatchEnums.Ordering; diff --git a/src/arcade/patch/agent/action/PatchActionInsert.java b/src/arcade/patch/agent/action/PatchActionInsert.java index 0635d16d..49992be6 100644 --- a/src/arcade/patch/agent/action/PatchActionInsert.java +++ b/src/arcade/patch/agent/action/PatchActionInsert.java @@ -4,7 +4,7 @@ import sim.engine.Schedule; import sim.engine.SimState; import arcade.core.agent.action.Action; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; @@ -12,8 +12,8 @@ import arcade.patch.agent.cell.PatchCell; import arcade.patch.agent.cell.PatchCellContainer; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.Coordinate; -import arcade.patch.env.loc.PatchLocationContainer; +import arcade.patch.env.location.Coordinate; +import arcade.patch.env.location.PatchLocationContainer; import arcade.patch.sim.PatchSeries; import arcade.patch.sim.PatchSimulation; import static arcade.patch.util.PatchEnums.Ordering; diff --git a/src/arcade/patch/agent/action/PatchActionRemove.java b/src/arcade/patch/agent/action/PatchActionRemove.java index f676cc30..938afcbe 100644 --- a/src/arcade/patch/agent/action/PatchActionRemove.java +++ b/src/arcade/patch/agent/action/PatchActionRemove.java @@ -6,12 +6,12 @@ import sim.util.Bag; import arcade.core.agent.action.Action; import arcade.core.agent.cell.Cell; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.Coordinate; +import arcade.patch.env.location.Coordinate; import arcade.patch.sim.PatchSeries; import arcade.patch.sim.PatchSimulation; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/cell/PatchCell.java b/src/arcade/patch/agent/cell/PatchCell.java index fd7713ce..43b01e4c 100644 --- a/src/arcade/patch/agent/cell/PatchCell.java +++ b/src/arcade/patch/agent/cell/PatchCell.java @@ -11,7 +11,7 @@ import arcade.core.agent.cell.CellContainer; import arcade.core.agent.module.Module; import arcade.core.agent.process.Process; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.agent.module.PatchModuleApoptosis; @@ -20,7 +20,7 @@ import arcade.patch.agent.process.PatchProcessMetabolism; import arcade.patch.agent.process.PatchProcessSignaling; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.PatchLocation; import static arcade.core.util.Enums.Domain; import static arcade.core.util.Enums.Region; import static arcade.core.util.Enums.State; @@ -65,7 +65,7 @@ public abstract class PatchCell implements Cell { /** Stopper used to stop this agent from being stepped in the schedule. */ Stoppable stopper; - /** Cell {@link arcade.core.env.loc.Location} object. */ + /** Cell {@link Location} object. */ final PatchLocation location; /** Unique cell ID. */ diff --git a/src/arcade/patch/agent/cell/PatchCellCancer.java b/src/arcade/patch/agent/cell/PatchCellCancer.java index c7f6c6e8..9b8de1a7 100644 --- a/src/arcade/patch/agent/cell/PatchCellCancer.java +++ b/src/arcade/patch/agent/cell/PatchCellCancer.java @@ -2,7 +2,7 @@ import sim.engine.SimState; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/cell/PatchCellCancerStem.java b/src/arcade/patch/agent/cell/PatchCellCancerStem.java index 8955ee62..74ff0197 100644 --- a/src/arcade/patch/agent/cell/PatchCellCancerStem.java +++ b/src/arcade/patch/agent/cell/PatchCellCancerStem.java @@ -1,7 +1,7 @@ package arcade.patch.agent.cell; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.util.MiniBox; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/cell/PatchCellContainer.java b/src/arcade/patch/agent/cell/PatchCellContainer.java index 443a315f..1e538a43 100644 --- a/src/arcade/patch/agent/cell/PatchCellContainer.java +++ b/src/arcade/patch/agent/cell/PatchCellContainer.java @@ -3,7 +3,7 @@ import arcade.core.agent.cell.Cell; import arcade.core.agent.cell.CellContainer; import arcade.core.agent.cell.CellFactory; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.util.MiniBox; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/cell/PatchCellTissue.java b/src/arcade/patch/agent/cell/PatchCellTissue.java index a6a4a4ed..5c389439 100644 --- a/src/arcade/patch/agent/cell/PatchCellTissue.java +++ b/src/arcade/patch/agent/cell/PatchCellTissue.java @@ -1,7 +1,7 @@ package arcade.patch.agent.cell; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.util.MiniBox; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/module/PatchModule.java b/src/arcade/patch/agent/module/PatchModule.java index c050b083..854969fc 100644 --- a/src/arcade/patch/agent/module/PatchModule.java +++ b/src/arcade/patch/agent/module/PatchModule.java @@ -2,7 +2,7 @@ import arcade.core.agent.module.Module; import arcade.patch.agent.cell.PatchCell; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.PatchLocation; /** * Abstract implementation of {@link Module} for {@link PatchCell} agents. diff --git a/src/arcade/patch/agent/module/PatchModuleMigration.java b/src/arcade/patch/agent/module/PatchModuleMigration.java index ac01c48f..2ed40c02 100644 --- a/src/arcade/patch/agent/module/PatchModuleMigration.java +++ b/src/arcade/patch/agent/module/PatchModuleMigration.java @@ -4,7 +4,7 @@ import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.agent.cell.PatchCell; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.PatchLocation; import static arcade.core.util.Enums.State; /** diff --git a/src/arcade/patch/agent/module/PatchModuleProliferation.java b/src/arcade/patch/agent/module/PatchModuleProliferation.java index 14f1798b..46750113 100644 --- a/src/arcade/patch/agent/module/PatchModuleProliferation.java +++ b/src/arcade/patch/agent/module/PatchModuleProliferation.java @@ -7,7 +7,7 @@ import arcade.patch.agent.cell.PatchCell; import arcade.patch.agent.process.PatchProcess; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.PatchLocation; import static arcade.core.util.Enums.Domain; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/agent/process/PatchProcess.java b/src/arcade/patch/agent/process/PatchProcess.java index 0792cff3..c3913176 100644 --- a/src/arcade/patch/agent/process/PatchProcess.java +++ b/src/arcade/patch/agent/process/PatchProcess.java @@ -2,7 +2,7 @@ import arcade.core.agent.process.Process; import arcade.patch.agent.cell.PatchCell; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.PatchLocation; /** * Abstract implementation of {@link Process} for {@link PatchCell} agents. diff --git a/src/arcade/patch/env/comp/PatchComponentCycle.java b/src/arcade/patch/env/component/PatchComponentCycle.java similarity index 95% rename from src/arcade/patch/env/comp/PatchComponentCycle.java rename to src/arcade/patch/env/component/PatchComponentCycle.java index 4dd399cb..24c46eaa 100644 --- a/src/arcade/patch/env/comp/PatchComponentCycle.java +++ b/src/arcade/patch/env/component/PatchComponentCycle.java @@ -1,17 +1,17 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import sim.engine.Schedule; import sim.engine.SimState; -import arcade.core.env.comp.Component; -import arcade.core.env.lat.Lattice; +import arcade.core.env.component.Component; +import arcade.core.env.lattice.Lattice; import arcade.core.env.operation.Operation; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.env.operation.PatchOperationGenerator; import static arcade.core.util.Enums.Category; -import static arcade.patch.env.comp.PatchComponentSites.SiteLayer; +import static arcade.patch.env.component.PatchComponentSites.SiteLayer; import static arcade.patch.util.PatchEnums.Ordering; /** diff --git a/src/arcade/patch/env/comp/PatchComponentDegrade.java b/src/arcade/patch/env/component/PatchComponentDegrade.java similarity index 93% rename from src/arcade/patch/env/comp/PatchComponentDegrade.java rename to src/arcade/patch/env/component/PatchComponentDegrade.java index d134c918..bc695fd8 100644 --- a/src/arcade/patch/env/comp/PatchComponentDegrade.java +++ b/src/arcade/patch/env/component/PatchComponentDegrade.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import java.util.HashSet; @@ -6,17 +6,17 @@ import sim.engine.SimState; import sim.util.Bag; import arcade.core.agent.cell.Cell; -import arcade.core.env.comp.Component; -import arcade.core.env.loc.Location; +import arcade.core.env.component.Component; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.Graph; import arcade.core.util.MiniBox; import arcade.patch.agent.cell.PatchCellCancer; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.loc.CoordinateXYZ; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.MINIMUM_WALL_THICKNESS; +import arcade.patch.env.location.CoordinateXYZ; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.MINIMUM_WALL_THICKNESS; import static arcade.patch.util.PatchEnums.Ordering; /** diff --git a/src/arcade/patch/env/comp/PatchComponentPulse.java b/src/arcade/patch/env/component/PatchComponentPulse.java similarity index 97% rename from src/arcade/patch/env/comp/PatchComponentPulse.java rename to src/arcade/patch/env/component/PatchComponentPulse.java index 7a7307e5..24030357 100644 --- a/src/arcade/patch/env/comp/PatchComponentPulse.java +++ b/src/arcade/patch/env/component/PatchComponentPulse.java @@ -1,10 +1,10 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import sim.engine.Schedule; import sim.engine.SimState; -import arcade.core.env.comp.Component; -import arcade.core.env.lat.Lattice; +import arcade.core.env.component.Component; +import arcade.core.env.lattice.Lattice; import arcade.core.env.operation.Operation; import arcade.core.sim.Series; import arcade.core.sim.Simulation; @@ -12,7 +12,7 @@ import arcade.patch.env.operation.PatchOperationGenerator; import arcade.patch.sim.PatchSeries; import static arcade.core.util.Enums.Category; -import static arcade.patch.env.comp.PatchComponentSites.SiteLayer; +import static arcade.patch.env.component.PatchComponentSites.SiteLayer; import static arcade.patch.util.PatchEnums.Ordering; /** diff --git a/src/arcade/patch/env/comp/PatchComponentRemodel.java b/src/arcade/patch/env/component/PatchComponentRemodel.java similarity index 93% rename from src/arcade/patch/env/comp/PatchComponentRemodel.java rename to src/arcade/patch/env/component/PatchComponentRemodel.java index faa583a7..957e14e7 100644 --- a/src/arcade/patch/env/comp/PatchComponentRemodel.java +++ b/src/arcade/patch/env/component/PatchComponentRemodel.java @@ -1,18 +1,18 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import sim.engine.Schedule; import sim.engine.SimState; import sim.util.Bag; -import arcade.core.env.comp.Component; +import arcade.core.env.component.Component; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.Graph; import arcade.core.util.MiniBox; -import arcade.patch.env.loc.CoordinateXYZ; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.MAXIMUM_WALL_RADIUS_FRACTION; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.MINIMUM_CAPILLARY_RADIUS; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.MINIMUM_WALL_THICKNESS; +import arcade.patch.env.location.CoordinateXYZ; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.MAXIMUM_WALL_RADIUS_FRACTION; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.MINIMUM_CAPILLARY_RADIUS; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.MINIMUM_WALL_THICKNESS; import static arcade.patch.util.PatchEnums.Ordering; /** @@ -68,7 +68,7 @@ public class PatchComponentRemodel implements Component { private Graph graph; /** - * Creates a {@link arcade.core.env.comp.Component} object for remodeling. + * Creates a {@link arcade.core.env.component.Component} object for remodeling. *
* Loaded parameters include: *
* Method is equivalent to the step used with - * {@link arcade.patch.env.comp.PatchComponentSitesSource} and - * {@link arcade.patch.env.comp.PatchComponentSitesPattern} where the amount + * {@link arcade.patch.env.component.PatchComponentSitesSource} and + * {@link arcade.patch.env.component.PatchComponentSitesPattern} where the amount * of concentration added is the difference between the source concentration * and the current concentration for a given molecule. */ diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactory.java b/src/arcade/patch/env/component/PatchComponentSitesGraphFactory.java similarity index 99% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphFactory.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphFactory.java index b7614ac1..e56630f9 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactory.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphFactory.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import java.util.HashMap; @@ -11,9 +11,9 @@ import arcade.core.util.Graph; import arcade.core.util.Graph.Node; import arcade.core.util.Utilities; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteNode; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.*; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteNode; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.*; /** * Factory for building a {@link Graph} for {@link PatchComponentSitesGraph}. diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryRect.java b/src/arcade/patch/env/component/PatchComponentSitesGraphFactoryRect.java similarity index 98% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryRect.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphFactoryRect.java index 07999b12..eecb1b68 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryRect.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphFactoryRect.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import java.util.EnumMap; @@ -9,9 +9,9 @@ import arcade.core.util.Graph; import arcade.core.util.Utilities; import static arcade.core.util.Graph.Node; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteNode; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.*; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteNode; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.*; /** * Concrete implementation of {@link PatchComponentSitesGraphFactory} for diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryTri.java b/src/arcade/patch/env/component/PatchComponentSitesGraphFactoryTri.java similarity index 98% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryTri.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphFactoryTri.java index 78c664f8..bd5bef33 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphFactoryTri.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphFactoryTri.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import java.util.EnumMap; @@ -9,9 +9,9 @@ import arcade.core.util.Graph; import arcade.core.util.Utilities; import static arcade.core.util.Graph.Node; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteNode; -import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.*; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteNode; +import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.*; /** * Concrete implementation of {@link PatchComponentSitesGraphFactory} for diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphRect.java b/src/arcade/patch/env/component/PatchComponentSitesGraphRect.java similarity index 96% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphRect.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphRect.java index e8641aaf..f674b68a 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphRect.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphRect.java @@ -1,13 +1,13 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import sim.engine.SimState; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.util.MiniBox; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocationRect; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocationRect; /** * Extension of {@link PatchComponentSitesGraph} for rectangular geometry. diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphTri.java b/src/arcade/patch/env/component/PatchComponentSitesGraphTri.java similarity index 97% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphTri.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphTri.java index 89fd68a5..4adc3823 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphTri.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphTri.java @@ -1,14 +1,14 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import sim.engine.SimState; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import arcade.core.sim.Series; import arcade.core.util.MiniBox; -import arcade.patch.env.loc.CoordinateUVWZ; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocationHex; +import arcade.patch.env.location.CoordinateUVWZ; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocationHex; /** * Extension of {@link PatchComponentSitesGraph} for triangular geometry. diff --git a/src/arcade/patch/env/comp/PatchComponentSitesGraphUtilities.java b/src/arcade/patch/env/component/PatchComponentSitesGraphUtilities.java similarity index 98% rename from src/arcade/patch/env/comp/PatchComponentSitesGraphUtilities.java rename to src/arcade/patch/env/component/PatchComponentSitesGraphUtilities.java index 8b56ef04..a7088bf5 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesGraphUtilities.java +++ b/src/arcade/patch/env/component/PatchComponentSitesGraphUtilities.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.ArrayList; import java.util.HashSet; @@ -9,12 +9,12 @@ import arcade.core.util.Matrix; import arcade.core.util.Solver; import static arcade.core.util.Graph.Edge; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import static arcade.patch.env.comp.PatchComponentSitesGraph.SiteNode; -import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeCategory; -import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeLevel; -import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeType; -import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.Root; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import static arcade.patch.env.component.PatchComponentSitesGraph.SiteNode; +import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeCategory; +import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeLevel; +import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeType; +import static arcade.patch.env.component.PatchComponentSitesGraphFactory.Root; /** * Container for utility functions used by {@link PatchComponentSitesGraph}. diff --git a/src/arcade/patch/env/comp/PatchComponentSitesPattern.java b/src/arcade/patch/env/component/PatchComponentSitesPattern.java similarity index 99% rename from src/arcade/patch/env/comp/PatchComponentSitesPattern.java rename to src/arcade/patch/env/component/PatchComponentSitesPattern.java index 0264c5fe..803b7015 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesPattern.java +++ b/src/arcade/patch/env/component/PatchComponentSitesPattern.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.EnumMap; import sim.engine.SimState; diff --git a/src/arcade/patch/env/comp/PatchComponentSitesPatternRect.java b/src/arcade/patch/env/component/PatchComponentSitesPatternRect.java similarity index 99% rename from src/arcade/patch/env/comp/PatchComponentSitesPatternRect.java rename to src/arcade/patch/env/component/PatchComponentSitesPatternRect.java index a49d5a3d..288c4831 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesPatternRect.java +++ b/src/arcade/patch/env/component/PatchComponentSitesPatternRect.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.EnumMap; import arcade.core.sim.Series; diff --git a/src/arcade/patch/env/comp/PatchComponentSitesPatternTri.java b/src/arcade/patch/env/component/PatchComponentSitesPatternTri.java similarity index 99% rename from src/arcade/patch/env/comp/PatchComponentSitesPatternTri.java rename to src/arcade/patch/env/component/PatchComponentSitesPatternTri.java index 100c0237..fd6d63ae 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesPatternTri.java +++ b/src/arcade/patch/env/component/PatchComponentSitesPatternTri.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import java.util.EnumMap; import arcade.core.sim.Series; diff --git a/src/arcade/patch/env/comp/PatchComponentSitesSource.java b/src/arcade/patch/env/component/PatchComponentSitesSource.java similarity index 99% rename from src/arcade/patch/env/comp/PatchComponentSitesSource.java rename to src/arcade/patch/env/component/PatchComponentSitesSource.java index 6c03b1f0..9a1df1af 100644 --- a/src/arcade/patch/env/comp/PatchComponentSitesSource.java +++ b/src/arcade/patch/env/component/PatchComponentSitesSource.java @@ -1,4 +1,4 @@ -package arcade.patch.env.comp; +package arcade.patch.env.component; import sim.engine.SimState; import arcade.core.sim.Series; diff --git a/src/arcade/patch/env/grid/PatchGrid.java b/src/arcade/patch/env/grid/PatchGrid.java index 1be564fc..81a763ed 100644 --- a/src/arcade/patch/env/grid/PatchGrid.java +++ b/src/arcade/patch/env/grid/PatchGrid.java @@ -5,8 +5,8 @@ import sim.util.Bag; import arcade.core.agent.cell.Cell; import arcade.core.env.grid.Grid; -import arcade.core.env.loc.Location; -import arcade.patch.env.loc.PatchLocation; +import arcade.core.env.location.Location; +import arcade.patch.env.location.PatchLocation; /** * Implementation of {@link Grid} for patch models. diff --git a/src/arcade/patch/env/lat/PatchLattice.java b/src/arcade/patch/env/lattice/PatchLattice.java similarity index 96% rename from src/arcade/patch/env/lat/PatchLattice.java rename to src/arcade/patch/env/lattice/PatchLattice.java index 23e208b6..89c8be92 100644 --- a/src/arcade/patch/env/lat/PatchLattice.java +++ b/src/arcade/patch/env/lattice/PatchLattice.java @@ -1,16 +1,16 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import java.util.HashMap; import java.util.Map; import sim.engine.Schedule; import sim.engine.SimState; -import arcade.core.env.lat.Lattice; -import arcade.core.env.loc.Location; +import arcade.core.env.lattice.Lattice; +import arcade.core.env.location.Location; import arcade.core.env.operation.Operation; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocation; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocation; import static arcade.core.util.Enums.Category; import static arcade.patch.util.PatchEnums.Ordering; diff --git a/src/arcade/patch/env/lat/PatchLatticeFactory.java b/src/arcade/patch/env/lattice/PatchLatticeFactory.java similarity index 96% rename from src/arcade/patch/env/lat/PatchLatticeFactory.java rename to src/arcade/patch/env/lattice/PatchLatticeFactory.java index fce34bc2..3bdffeee 100644 --- a/src/arcade/patch/env/lat/PatchLatticeFactory.java +++ b/src/arcade/patch/env/lattice/PatchLatticeFactory.java @@ -1,8 +1,8 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import java.util.HashMap; import ec.util.MersenneTwisterFast; -import arcade.core.env.lat.LatticeFactory; +import arcade.core.env.lattice.LatticeFactory; import arcade.core.sim.Series; import arcade.core.util.MiniBox; diff --git a/src/arcade/patch/env/lat/PatchLatticeFactoryRect.java b/src/arcade/patch/env/lattice/PatchLatticeFactoryRect.java similarity index 94% rename from src/arcade/patch/env/lat/PatchLatticeFactoryRect.java rename to src/arcade/patch/env/lattice/PatchLatticeFactoryRect.java index c373da10..65f64020 100644 --- a/src/arcade/patch/env/lat/PatchLatticeFactoryRect.java +++ b/src/arcade/patch/env/lattice/PatchLatticeFactoryRect.java @@ -1,4 +1,4 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import arcade.core.util.MiniBox; diff --git a/src/arcade/patch/env/lat/PatchLatticeFactoryTri.java b/src/arcade/patch/env/lattice/PatchLatticeFactoryTri.java similarity index 94% rename from src/arcade/patch/env/lat/PatchLatticeFactoryTri.java rename to src/arcade/patch/env/lattice/PatchLatticeFactoryTri.java index 5da7feac..52f458de 100644 --- a/src/arcade/patch/env/lat/PatchLatticeFactoryTri.java +++ b/src/arcade/patch/env/lattice/PatchLatticeFactoryTri.java @@ -1,4 +1,4 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import arcade.core.util.MiniBox; diff --git a/src/arcade/patch/env/lat/PatchLatticeRect.java b/src/arcade/patch/env/lattice/PatchLatticeRect.java similarity index 97% rename from src/arcade/patch/env/lat/PatchLatticeRect.java rename to src/arcade/patch/env/lattice/PatchLatticeRect.java index 1b8c67ce..11a1628b 100644 --- a/src/arcade/patch/env/lat/PatchLatticeRect.java +++ b/src/arcade/patch/env/lattice/PatchLatticeRect.java @@ -1,4 +1,4 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import arcade.core.env.operation.Operation; import arcade.core.util.MiniBox; diff --git a/src/arcade/patch/env/lat/PatchLatticeTri.java b/src/arcade/patch/env/lattice/PatchLatticeTri.java similarity index 97% rename from src/arcade/patch/env/lat/PatchLatticeTri.java rename to src/arcade/patch/env/lattice/PatchLatticeTri.java index d43b5aaa..aec892ec 100644 --- a/src/arcade/patch/env/lat/PatchLatticeTri.java +++ b/src/arcade/patch/env/lattice/PatchLatticeTri.java @@ -1,4 +1,4 @@ -package arcade.patch.env.lat; +package arcade.patch.env.lattice; import arcade.core.env.operation.Operation; import arcade.core.util.MiniBox; diff --git a/src/arcade/patch/env/loc/Coordinate.java b/src/arcade/patch/env/location/Coordinate.java similarity index 96% rename from src/arcade/patch/env/loc/Coordinate.java rename to src/arcade/patch/env/location/Coordinate.java index 0b56d66f..12b46c52 100644 --- a/src/arcade/patch/env/loc/Coordinate.java +++ b/src/arcade/patch/env/location/Coordinate.java @@ -1,4 +1,4 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; /** * Representation of a coordinate. diff --git a/src/arcade/patch/env/loc/CoordinateUVWZ.java b/src/arcade/patch/env/location/CoordinateUVWZ.java similarity index 97% rename from src/arcade/patch/env/loc/CoordinateUVWZ.java rename to src/arcade/patch/env/location/CoordinateUVWZ.java index ce165949..41da1da5 100644 --- a/src/arcade/patch/env/loc/CoordinateUVWZ.java +++ b/src/arcade/patch/env/location/CoordinateUVWZ.java @@ -1,4 +1,4 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; /** * Representation of (u, v, w, z) coordinate. diff --git a/src/arcade/patch/env/loc/CoordinateXYZ.java b/src/arcade/patch/env/location/CoordinateXYZ.java similarity index 97% rename from src/arcade/patch/env/loc/CoordinateXYZ.java rename to src/arcade/patch/env/location/CoordinateXYZ.java index f84d649f..584ffe59 100644 --- a/src/arcade/patch/env/loc/CoordinateXYZ.java +++ b/src/arcade/patch/env/location/CoordinateXYZ.java @@ -1,4 +1,4 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; /** * Representation of (x, y, z) coordinates. diff --git a/src/arcade/patch/env/loc/PatchLocation.java b/src/arcade/patch/env/location/PatchLocation.java similarity index 90% rename from src/arcade/patch/env/loc/PatchLocation.java rename to src/arcade/patch/env/location/PatchLocation.java index c5ddfc11..86744940 100644 --- a/src/arcade/patch/env/loc/PatchLocation.java +++ b/src/arcade/patch/env/location/PatchLocation.java @@ -1,8 +1,8 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; import java.util.EnumSet; -import arcade.core.env.loc.Location; +import arcade.core.env.location.Location; import static arcade.core.util.Enums.Region; /** @@ -10,10 +10,10 @@ *
* {@code PatchLocation} objects define where agents are within the * {@link arcade.core.env.grid.Grid} (relative to other agents) and relative to - * the {@link arcade.core.env.lat.Lattice} (local molecule concentrations). The - * coordinate defines the location in the + * the {@link arcade.core.env.lattice.Lattice} (local molecule concentrations). + * Thecoordinate defines the location in the * {@link arcade.core.env.grid.Grid} while the term subcoordinate(s) - * defines the location(s) in the {@link arcade.core.env.lat.Lattice}. + * defines the location(s) in the {@link arcade.core.env.lattice.Lattice}. *
* There may be multiple subcoordinates associated with the same * coordinate (therefore there may be more than one agent per @@ -28,8 +28,8 @@ *
* Regardless of geometry, the center of the model should have * {@link arcade.core.env.grid.Grid} location coordinate (0,0,0) or (0,0,0,0). - * {@link arcade.core.env.lat.Lattice} arrays cannot have negative indices, so - * (0,0,0) is located at the top left of the 2D array and the bottom layer of + * {@link arcade.core.env.lattice.Lattice} arrays cannot have negative indices, + * so (0,0,0) is located at the top left of the 2D array and the bottom layer of * the 3D stack. */ @@ -98,14 +98,14 @@ public PatchLocation(Coordinate coordinate, int n) { * Gets the patch coordinate in the {@link arcade.core.env.grid.Grid}. *
* These are not necessarily the same as the - * {@link arcade.core.env.lat.Lattice} coordinates. + * {@link arcade.core.env.lattice.Lattice} coordinates. * * @return the coordinate */ public Coordinate getCoordinate() { return coordinate; } /** - * Gets the patch subcoordinate in the {@link arcade.core.env.lat.Lattice}. + * Gets the patch subcoordinate in the {@link arcade.core.env.lattice.Lattice}. *
* These are not necessarily the same as the * {@link arcade.core.env.grid.Grid} coordinates. @@ -115,7 +115,7 @@ public PatchLocation(Coordinate coordinate, int n) { public Coordinate getSubcoordinate() { return subcoordinates.get(0); } /** - * Gets all subcoordinates in the {@link arcade.core.env.lat.Lattice} that + * Gets all subcoordinates in the {@link arcade.core.env.lattice.Lattice} that * correspond to the {@link arcade.core.env.grid.Grid} location. * * @return the array of subcoordinates @@ -131,7 +131,7 @@ public PatchLocation(Coordinate coordinate, int n) { public abstract double getCoordinateSize(); /** - * Gets the {@link arcade.core.env.lat.Lattice} coordinate size in the xy + * Gets the {@link arcade.core.env.lattice.Lattice} coordinate size in the xy * plane. * * @return the subcoordinate size @@ -154,7 +154,7 @@ public PatchLocation(Coordinate coordinate, int n) { /** * Gets the {@link arcade.core.env.grid.Grid} offset relative to the - * {@link arcade.core.env.lat.Lattice}. + * {@link arcade.core.env.lattice.Lattice}. */ abstract void calculateOffset(); diff --git a/src/arcade/patch/env/loc/PatchLocationContainer.java b/src/arcade/patch/env/location/PatchLocationContainer.java similarity index 87% rename from src/arcade/patch/env/loc/PatchLocationContainer.java rename to src/arcade/patch/env/location/PatchLocationContainer.java index 1f614f00..dcc77a1f 100644 --- a/src/arcade/patch/env/loc/PatchLocationContainer.java +++ b/src/arcade/patch/env/location/PatchLocationContainer.java @@ -1,9 +1,9 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import arcade.core.agent.cell.CellContainer; -import arcade.core.env.loc.Location; -import arcade.core.env.loc.LocationContainer; -import arcade.core.env.loc.LocationFactory; +import arcade.core.env.location.Location; +import arcade.core.env.location.LocationContainer; +import arcade.core.env.location.LocationFactory; /** * Implementation of {@link LocationContainer} for {@link PatchLocation} diff --git a/src/arcade/patch/env/loc/PatchLocationFactory.java b/src/arcade/patch/env/location/PatchLocationFactory.java similarity index 95% rename from src/arcade/patch/env/loc/PatchLocationFactory.java rename to src/arcade/patch/env/location/PatchLocationFactory.java index 0c0dc332..2e796844 100644 --- a/src/arcade/patch/env/loc/PatchLocationFactory.java +++ b/src/arcade/patch/env/location/PatchLocationFactory.java @@ -1,11 +1,11 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; import java.util.Comparator; import java.util.HashMap; import ec.util.MersenneTwisterFast; -import arcade.core.env.loc.LocationContainer; -import arcade.core.env.loc.LocationFactory; +import arcade.core.env.location.LocationContainer; +import arcade.core.env.location.LocationFactory; import arcade.core.sim.Series; import arcade.core.util.Utilities; import arcade.patch.sim.PatchSeries; diff --git a/src/arcade/patch/env/loc/PatchLocationFactoryHex.java b/src/arcade/patch/env/location/PatchLocationFactoryHex.java similarity index 97% rename from src/arcade/patch/env/loc/PatchLocationFactoryHex.java rename to src/arcade/patch/env/location/PatchLocationFactoryHex.java index 33cd19b4..1c1fefcc 100644 --- a/src/arcade/patch/env/loc/PatchLocationFactoryHex.java +++ b/src/arcade/patch/env/location/PatchLocationFactoryHex.java @@ -1,4 +1,4 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; diff --git a/src/arcade/patch/env/loc/PatchLocationFactoryRect.java b/src/arcade/patch/env/location/PatchLocationFactoryRect.java similarity index 97% rename from src/arcade/patch/env/loc/PatchLocationFactoryRect.java rename to src/arcade/patch/env/location/PatchLocationFactoryRect.java index 9342dc57..3a9e2130 100644 --- a/src/arcade/patch/env/loc/PatchLocationFactoryRect.java +++ b/src/arcade/patch/env/location/PatchLocationFactoryRect.java @@ -1,4 +1,4 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; diff --git a/src/arcade/patch/env/loc/PatchLocationHex.java b/src/arcade/patch/env/location/PatchLocationHex.java similarity index 95% rename from src/arcade/patch/env/loc/PatchLocationHex.java rename to src/arcade/patch/env/location/PatchLocationHex.java index 51d09995..d9472094 100644 --- a/src/arcade/patch/env/loc/PatchLocationHex.java +++ b/src/arcade/patch/env/location/PatchLocationHex.java @@ -1,18 +1,18 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; -import arcade.core.env.loc.Location; -import arcade.core.env.loc.LocationContainer; +import arcade.core.env.location.Location; +import arcade.core.env.location.LocationContainer; import arcade.patch.sim.PatchSeries; /** * Concrete implementation of {@link PatchLocation} for hexagonal * {@link arcade.core.env.grid.Grid} to a triangular - * {@link arcade.core.env.lat.Lattice}. + * {@link arcade.core.env.lattice.Lattice}. *
* {@link arcade.core.env.grid.Grid} coordinates are in terms of (u, v, w) and - * the {@link arcade.core.env.lat.Lattice} coordinates are in (x, y). Hexagons - * are flat side up. Triangular {@link arcade.core.env.lat.Lattice} + * the {@link arcade.core.env.lattice.Lattice} coordinates are in (x, y). + * Hexagons are flat side up. Triangular {@link arcade.core.env.lattice.Lattice} * subcoordinates are ordered 0 - 5, with 0 at the top center and going * clockwise around. *
@@ -247,8 +247,8 @@ public LocationContainer convert(int id) { } /** - * Converts triangular {@link arcade.core.env.lat.Lattice} coordinates into - * a hexagonal {@link arcade.core.env.grid.Grid} coordinate. + * Converts triangular {@link arcade.core.env.lattice.Lattice} coordinates + * into a hexagonal {@link arcade.core.env.grid.Grid} coordinate. * * @param coordinate the triangular coordinate * @return the corresponding hexagonal coordinate diff --git a/src/arcade/patch/env/loc/PatchLocationRect.java b/src/arcade/patch/env/location/PatchLocationRect.java similarity index 94% rename from src/arcade/patch/env/loc/PatchLocationRect.java rename to src/arcade/patch/env/location/PatchLocationRect.java index 261904a4..2863ba39 100644 --- a/src/arcade/patch/env/loc/PatchLocationRect.java +++ b/src/arcade/patch/env/location/PatchLocationRect.java @@ -1,19 +1,19 @@ -package arcade.patch.env.loc; +package arcade.patch.env.location; import java.util.ArrayList; -import arcade.core.env.loc.Location; -import arcade.core.env.loc.LocationContainer; +import arcade.core.env.location.Location; +import arcade.core.env.location.LocationContainer; import arcade.patch.sim.PatchSeries; /** * Concrete implementation of {@link PatchLocation} for rectangular * {@link arcade.core.env.grid.Grid} to a rectangular - * {@link arcade.core.env.lat.Lattice}. + * {@link arcade.core.env.lattice.Lattice}. ** {@link arcade.core.env.grid.Grid} coordinates are in terms of (x, y) and the - * {@link arcade.core.env.lat.Lattice} coordinates are in (a, b). Rectangular - * {@link arcade.core.env.lat.Lattice} subcoordinates are ordered 0 - 3, with 0 - * at the top left and going clockwise around. + * {@link arcade.core.env.lattice.Lattice} coordinates are in (a, b). + * Rectangular {@link arcade.core.env.lattice.Lattice} subcoordinates are + * ordered 0 - 3, with 0 at the top left and going clockwise around. *
* --------- * | 0 | 1 | @@ -236,8 +236,8 @@ public LocationContainer convert(int id) { } /** - * Converts rectangular {@link arcade.core.env.lat.Lattice} coordinates into - * a rectangular {@link arcade.core.env.grid.Grid} coordinate. + * Converts rectangular {@link arcade.core.env.lattice.Lattice} coordinates + * into a rectangular {@link arcade.core.env.grid.Grid} coordinate. * * @param coordinate the rectangular coordinate * @return the corresponding rectangular coordinate diff --git a/src/arcade/patch/env/operation/PatchOperation.java b/src/arcade/patch/env/operation/PatchOperation.java index 8f50fb5b..8f8b25ee 100644 --- a/src/arcade/patch/env/operation/PatchOperation.java +++ b/src/arcade/patch/env/operation/PatchOperation.java @@ -1,7 +1,7 @@ package arcade.patch.env.operation; import arcade.core.env.operation.Operation; -import arcade.patch.env.lat.PatchLattice; +import arcade.patch.env.lattice.PatchLattice; /** * Abstract implementation of {@link Operation} for {@link PatchLattice} diff --git a/src/arcade/patch/env/operation/PatchOperationDiffuser.java b/src/arcade/patch/env/operation/PatchOperationDiffuser.java index 0707139a..3bdb787c 100644 --- a/src/arcade/patch/env/operation/PatchOperationDiffuser.java +++ b/src/arcade/patch/env/operation/PatchOperationDiffuser.java @@ -4,7 +4,7 @@ import arcade.core.env.operation.Operation; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; -import arcade.patch.env.lat.PatchLattice; +import arcade.patch.env.lattice.PatchLattice; import static arcade.core.util.Enums.Category; /** diff --git a/src/arcade/patch/env/operation/PatchOperationDiffuserRect.java b/src/arcade/patch/env/operation/PatchOperationDiffuserRect.java index 08613072..db36b158 100644 --- a/src/arcade/patch/env/operation/PatchOperationDiffuserRect.java +++ b/src/arcade/patch/env/operation/PatchOperationDiffuserRect.java @@ -1,6 +1,6 @@ package arcade.patch.env.operation; -import arcade.patch.env.lat.PatchLattice; +import arcade.patch.env.lattice.PatchLattice; /** * Extension of {@link PatchOperationDiffuser} for rectangular lattices. diff --git a/src/arcade/patch/env/operation/PatchOperationDiffuserTri.java b/src/arcade/patch/env/operation/PatchOperationDiffuserTri.java index ca67c01d..0eda8668 100644 --- a/src/arcade/patch/env/operation/PatchOperationDiffuserTri.java +++ b/src/arcade/patch/env/operation/PatchOperationDiffuserTri.java @@ -1,6 +1,6 @@ package arcade.patch.env.operation; -import arcade.patch.env.lat.PatchLattice; +import arcade.patch.env.lattice.PatchLattice; /** * Extension of {@link PatchOperationDiffuser} for triangular lattices. diff --git a/src/arcade/patch/env/operation/PatchOperationGenerator.java b/src/arcade/patch/env/operation/PatchOperationGenerator.java index 01add776..f2ac8e90 100644 --- a/src/arcade/patch/env/operation/PatchOperationGenerator.java +++ b/src/arcade/patch/env/operation/PatchOperationGenerator.java @@ -4,7 +4,7 @@ import arcade.core.env.operation.Operation; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; -import arcade.patch.env.lat.PatchLattice; +import arcade.patch.env.lattice.PatchLattice; import static arcade.core.util.Enums.Category; /** diff --git a/src/arcade/patch/sim/PatchSimulation.java b/src/arcade/patch/sim/PatchSimulation.java index 02a79c68..9b6505ad 100644 --- a/src/arcade/patch/sim/PatchSimulation.java +++ b/src/arcade/patch/sim/PatchSimulation.java @@ -8,20 +8,20 @@ import arcade.core.agent.action.Action; import arcade.core.agent.cell.Cell; import arcade.core.agent.cell.CellContainer; -import arcade.core.env.comp.Component; +import arcade.core.env.component.Component; import arcade.core.env.grid.Grid; -import arcade.core.env.lat.Lattice; -import arcade.core.env.loc.Location; -import arcade.core.env.loc.LocationContainer; +import arcade.core.env.lattice.Lattice; +import arcade.core.env.location.Location; +import arcade.core.env.location.LocationContainer; import arcade.core.sim.Series; import arcade.core.sim.Simulation; import arcade.core.util.MiniBox; import arcade.patch.agent.cell.PatchCell; import arcade.patch.agent.cell.PatchCellFactory; import arcade.patch.env.grid.PatchGrid; -import arcade.patch.env.lat.PatchLattice; -import arcade.patch.env.lat.PatchLatticeFactory; -import arcade.patch.env.loc.PatchLocationFactory; +import arcade.patch.env.lattice.PatchLattice; +import arcade.patch.env.lattice.PatchLatticeFactory; +import arcade.patch.env.location.PatchLocationFactory; /** * Abstract implementation for patch {@link Simulation} instances. @@ -167,21 +167,21 @@ public void finish() { /** * Creates a factory for locations. * - * @return a {@link arcade.core.env.loc.Location} factory + * @return a {@link Location} factory */ public abstract PatchLocationFactory makeLocationFactory(); /** * Creates a factory for cells. * - * @return a {@link arcade.core.agent.cell.Cell} factory + * @return a {@link Cell} factory */ public abstract PatchCellFactory makeCellFactory(); /** * Creates a factory for lattices. * - * @return a {@link arcade.core.env.lat.Lattice} factory + * @return a {@link Lattice} factory */ public abstract PatchLatticeFactory makeLatticeFactory(); diff --git a/src/arcade/patch/sim/PatchSimulationHex.java b/src/arcade/patch/sim/PatchSimulationHex.java index 53d6ea71..8aed4da5 100644 --- a/src/arcade/patch/sim/PatchSimulationHex.java +++ b/src/arcade/patch/sim/PatchSimulationHex.java @@ -1,25 +1,25 @@ package arcade.patch.sim; import arcade.core.agent.action.Action; -import arcade.core.env.comp.Component; +import arcade.core.env.component.Component; import arcade.core.sim.Series; import arcade.core.util.MiniBox; import arcade.patch.agent.action.PatchActionConvert; import arcade.patch.agent.action.PatchActionInsert; import arcade.patch.agent.action.PatchActionRemove; import arcade.patch.agent.cell.PatchCellFactory; -import arcade.patch.env.comp.PatchComponentCycle; -import arcade.patch.env.comp.PatchComponentDegrade; -import arcade.patch.env.comp.PatchComponentPulse; -import arcade.patch.env.comp.PatchComponentRemodel; -import arcade.patch.env.comp.PatchComponentSitesGraphTri; -import arcade.patch.env.comp.PatchComponentSitesPatternTri; -import arcade.patch.env.comp.PatchComponentSitesSource; -import arcade.patch.env.lat.PatchLatticeFactory; -import arcade.patch.env.lat.PatchLatticeFactoryTri; -import arcade.patch.env.loc.PatchLocationFactory; -import arcade.patch.env.loc.PatchLocationFactoryHex; -import arcade.patch.env.loc.PatchLocationHex; +import arcade.patch.env.component.PatchComponentCycle; +import arcade.patch.env.component.PatchComponentDegrade; +import arcade.patch.env.component.PatchComponentPulse; +import arcade.patch.env.component.PatchComponentRemodel; +import arcade.patch.env.component.PatchComponentSitesGraphTri; +import arcade.patch.env.component.PatchComponentSitesPatternTri; +import arcade.patch.env.component.PatchComponentSitesSource; +import arcade.patch.env.lattice.PatchLatticeFactory; +import arcade.patch.env.lattice.PatchLatticeFactoryTri; +import arcade.patch.env.location.PatchLocationFactory; +import arcade.patch.env.location.PatchLocationFactoryHex; +import arcade.patch.env.location.PatchLocationHex; /** * Extension of {@link PatchSimulation} for hexagonal geometry. diff --git a/src/arcade/patch/sim/PatchSimulationRect.java b/src/arcade/patch/sim/PatchSimulationRect.java index 25cd329b..ea614f01 100644 --- a/src/arcade/patch/sim/PatchSimulationRect.java +++ b/src/arcade/patch/sim/PatchSimulationRect.java @@ -1,25 +1,25 @@ package arcade.patch.sim; import arcade.core.agent.action.Action; -import arcade.core.env.comp.Component; +import arcade.core.env.component.Component; import arcade.core.sim.Series; import arcade.core.util.MiniBox; import arcade.patch.agent.action.PatchActionConvert; import arcade.patch.agent.action.PatchActionInsert; import arcade.patch.agent.action.PatchActionRemove; import arcade.patch.agent.cell.PatchCellFactory; -import arcade.patch.env.comp.PatchComponentCycle; -import arcade.patch.env.comp.PatchComponentDegrade; -import arcade.patch.env.comp.PatchComponentPulse; -import arcade.patch.env.comp.PatchComponentRemodel; -import arcade.patch.env.comp.PatchComponentSitesGraphRect; -import arcade.patch.env.comp.PatchComponentSitesPatternRect; -import arcade.patch.env.comp.PatchComponentSitesSource; -import arcade.patch.env.lat.PatchLatticeFactory; -import arcade.patch.env.lat.PatchLatticeFactoryRect; -import arcade.patch.env.loc.PatchLocationFactory; -import arcade.patch.env.loc.PatchLocationFactoryRect; -import arcade.patch.env.loc.PatchLocationRect; +import arcade.patch.env.component.PatchComponentCycle; +import arcade.patch.env.component.PatchComponentDegrade; +import arcade.patch.env.component.PatchComponentPulse; +import arcade.patch.env.component.PatchComponentRemodel; +import arcade.patch.env.component.PatchComponentSitesGraphRect; +import arcade.patch.env.component.PatchComponentSitesPatternRect; +import arcade.patch.env.component.PatchComponentSitesSource; +import arcade.patch.env.lattice.PatchLatticeFactory; +import arcade.patch.env.lattice.PatchLatticeFactoryRect; +import arcade.patch.env.location.PatchLocationFactory; +import arcade.patch.env.location.PatchLocationFactoryRect; +import arcade.patch.env.location.PatchLocationRect; /** * Extension of {@link PatchSimulation} for rectangular geometry. diff --git a/src/arcade/patch/sim/input/PatchInputBuilder.java b/src/arcade/patch/sim/input/PatchInputBuilder.java index 68f3c1ee..ac28eb90 100644 --- a/src/arcade/patch/sim/input/PatchInputBuilder.java +++ b/src/arcade/patch/sim/input/PatchInputBuilder.java @@ -6,11 +6,11 @@ import arcade.core.sim.input.InputBuilder; import arcade.core.util.Box; import arcade.core.util.MiniBox; -import arcade.patch.env.loc.CoordinateUVWZ; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocation; -import arcade.patch.env.loc.PatchLocationHex; -import arcade.patch.env.loc.PatchLocationRect; +import arcade.patch.env.location.CoordinateUVWZ; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocation; +import arcade.patch.env.location.PatchLocationHex; +import arcade.patch.env.location.PatchLocationRect; import arcade.patch.sim.PatchSeries; import static arcade.core.util.Box.KEY_SEPARATOR; import static arcade.core.util.MiniBox.TAG_SEPARATOR; diff --git a/src/arcade/patch/sim/output/PatchOutputDeserializer.java b/src/arcade/patch/sim/output/PatchOutputDeserializer.java index 8a895648..7966226d 100644 --- a/src/arcade/patch/sim/output/PatchOutputDeserializer.java +++ b/src/arcade/patch/sim/output/PatchOutputDeserializer.java @@ -11,13 +11,13 @@ import com.google.gson.JsonObject; import com.google.gson.JsonParseException; import arcade.core.agent.cell.CellContainer; -import arcade.core.env.loc.LocationContainer; +import arcade.core.env.location.LocationContainer; import arcade.core.sim.output.OutputDeserializer; import arcade.patch.agent.cell.PatchCellContainer; -import arcade.patch.env.loc.Coordinate; -import arcade.patch.env.loc.CoordinateUVWZ; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocationContainer; +import arcade.patch.env.location.Coordinate; +import arcade.patch.env.location.CoordinateUVWZ; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocationContainer; import static arcade.core.sim.Simulation.DEFAULT_LOCATION_TYPE; import static arcade.core.util.Enums.State; diff --git a/src/arcade/patch/sim/output/PatchOutputSerializer.java b/src/arcade/patch/sim/output/PatchOutputSerializer.java index e25fdbb1..1e20b4a1 100644 --- a/src/arcade/patch/sim/output/PatchOutputSerializer.java +++ b/src/arcade/patch/sim/output/PatchOutputSerializer.java @@ -11,14 +11,14 @@ import com.google.gson.JsonSerializationContext; import com.google.gson.JsonSerializer; import arcade.core.agent.cell.CellContainer; -import arcade.core.env.loc.LocationContainer; +import arcade.core.env.location.LocationContainer; import arcade.core.sim.Series; import arcade.core.sim.output.OutputSerializer; import arcade.patch.agent.cell.PatchCellContainer; -import arcade.patch.env.loc.Coordinate; -import arcade.patch.env.loc.CoordinateUVWZ; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocationContainer; +import arcade.patch.env.location.Coordinate; +import arcade.patch.env.location.CoordinateUVWZ; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocationContainer; import arcade.patch.sim.PatchSeries; import static arcade.core.sim.Simulation.DEFAULT_LOCATION_TYPE; diff --git a/src/arcade/patch/vis/PatchDrawer.java b/src/arcade/patch/vis/PatchDrawer.java index 7eef9c4c..d7e63085 100644 --- a/src/arcade/patch/vis/PatchDrawer.java +++ b/src/arcade/patch/vis/PatchDrawer.java @@ -26,9 +26,9 @@ import arcade.core.util.Graph.Node; import arcade.core.vis.Drawer; import arcade.core.vis.Panel; -import arcade.patch.env.comp.PatchComponentSitesGraph; -import arcade.patch.env.comp.PatchComponentSitesGraph.SiteEdge; -import arcade.patch.env.comp.PatchComponentSitesGraph.SiteNode; +import arcade.patch.env.component.PatchComponentSitesGraph; +import arcade.patch.env.component.PatchComponentSitesGraph.SiteEdge; +import arcade.patch.env.component.PatchComponentSitesGraph.SiteNode; import arcade.patch.sim.PatchSimulation; import static arcade.patch.vis.PatchColorMaps.*; diff --git a/src/arcade/patch/vis/PatchDrawerHex.java b/src/arcade/patch/vis/PatchDrawerHex.java index 27017fbb..ef91d0cf 100644 --- a/src/arcade/patch/vis/PatchDrawerHex.java +++ b/src/arcade/patch/vis/PatchDrawerHex.java @@ -7,16 +7,16 @@ import sim.util.gui.ColorMap; import arcade.core.vis.Panel; import arcade.patch.agent.cell.PatchCell; -import arcade.patch.env.comp.PatchComponentSites; -import arcade.patch.env.comp.PatchComponentSitesPattern; -import arcade.patch.env.comp.PatchComponentSitesSource; -import arcade.patch.env.loc.Coordinate; -import arcade.patch.env.loc.CoordinateUVWZ; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocation; -import arcade.patch.env.loc.PatchLocationContainer; -import arcade.patch.env.loc.PatchLocationFactory; -import arcade.patch.env.loc.PatchLocationFactoryHex; +import arcade.patch.env.component.PatchComponentSites; +import arcade.patch.env.component.PatchComponentSitesPattern; +import arcade.patch.env.component.PatchComponentSitesSource; +import arcade.patch.env.location.Coordinate; +import arcade.patch.env.location.CoordinateUVWZ; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocation; +import arcade.patch.env.location.PatchLocationContainer; +import arcade.patch.env.location.PatchLocationFactory; +import arcade.patch.env.location.PatchLocationFactoryHex; import arcade.patch.sim.PatchSeries; import arcade.patch.sim.PatchSimulation; diff --git a/src/arcade/patch/vis/PatchDrawerRect.java b/src/arcade/patch/vis/PatchDrawerRect.java index 5fa498c2..a6e73bae 100644 --- a/src/arcade/patch/vis/PatchDrawerRect.java +++ b/src/arcade/patch/vis/PatchDrawerRect.java @@ -7,15 +7,15 @@ import sim.util.gui.ColorMap; import arcade.core.vis.Panel; import arcade.patch.agent.cell.PatchCell; -import arcade.patch.env.comp.PatchComponentSites; -import arcade.patch.env.comp.PatchComponentSitesPattern; -import arcade.patch.env.comp.PatchComponentSitesSource; -import arcade.patch.env.loc.Coordinate; -import arcade.patch.env.loc.CoordinateXYZ; -import arcade.patch.env.loc.PatchLocation; -import arcade.patch.env.loc.PatchLocationContainer; -import arcade.patch.env.loc.PatchLocationFactory; -import arcade.patch.env.loc.PatchLocationFactoryRect; +import arcade.patch.env.component.PatchComponentSites; +import arcade.patch.env.component.PatchComponentSitesPattern; +import arcade.patch.env.component.PatchComponentSitesSource; +import arcade.patch.env.location.Coordinate; +import arcade.patch.env.location.CoordinateXYZ; +import arcade.patch.env.location.PatchLocation; +import arcade.patch.env.location.PatchLocationContainer; +import arcade.patch.env.location.PatchLocationFactory; +import arcade.patch.env.location.PatchLocationFactoryRect; import arcade.patch.sim.PatchSeries; import arcade.patch.sim.PatchSimulation;