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: *