Rename comp/lat/loc packages in patch

bagherilab · Jan 31, 2023 · 21a5581 · 21a5581
1 parent 0fd72b1
commit 21a5581
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Showing 59 changed files with 216 additions and 216 deletions.
diff --git 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
@@ -4,16 +4,16 @@
 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;
 import arcade.core.util.Utilities;
 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/...e/patch/env/comp/PatchComponentCycle.java → ...ch/env/component/PatchComponentCycle.java b/...e/patch/env/comp/PatchComponentCycle.java → ...ch/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/...patch/env/comp/PatchComponentDegrade.java → .../env/component/PatchComponentDegrade.java b/...patch/env/comp/PatchComponentDegrade.java → .../env/component/PatchComponentDegrade.java
@@ -1,22 +1,22 @@
-package arcade.patch.env.comp;
+package arcade.patch.env.component;
 
 import java.util.ArrayList;
 import java.util.HashSet;
 import sim.engine.Schedule;
 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/...e/patch/env/comp/PatchComponentPulse.java → ...ch/env/component/PatchComponentPulse.java b/...e/patch/env/comp/PatchComponentPulse.java → ...ch/env/component/PatchComponentPulse.java
@@ -1,18 +1,18 @@
-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 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/...patch/env/comp/PatchComponentRemodel.java → .../env/component/PatchComponentRemodel.java b/...patch/env/comp/PatchComponentRemodel.java → .../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.
      * <p>
      * Loaded parameters include:
      * <ul>

diff --git a/...e/patch/env/comp/PatchComponentSites.java → ...ch/env/component/PatchComponentSites.java b/...e/patch/env/comp/PatchComponentSites.java → ...ch/env/component/PatchComponentSites.java
@@ -1,9 +1,9 @@
-package arcade.patch.env.comp;
+package arcade.patch.env.component;
 
 import java.util.ArrayList;
 import sim.engine.Schedule;
-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;

diff --git a/...ch/env/comp/PatchComponentSitesGraph.java → ...v/component/PatchComponentSitesGraph.java b/...ch/env/comp/PatchComponentSitesGraph.java → ...v/component/PatchComponentSitesGraph.java
@@ -1,24 +1,24 @@
-package arcade.patch.env.comp;
+package arcade.patch.env.component;
 
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashSet;
 import sim.util.Bag;
 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.Graph;
 import arcade.core.util.Graph.Edge;
 import arcade.core.util.Graph.Node;
 import arcade.core.util.MiniBox;
 import arcade.core.util.Solver;
 import arcade.core.util.Solver.Function;
-import arcade.patch.env.loc.CoordinateXYZ;
+import arcade.patch.env.location.CoordinateXYZ;
 import arcade.patch.sim.PatchSeries;
-import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeLevel;
-import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeTag;
-import static arcade.patch.env.comp.PatchComponentSitesGraphFactory.EdgeType;
-import static arcade.patch.env.comp.PatchComponentSitesGraphUtilities.*;
+import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeLevel;
+import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeTag;
+import static arcade.patch.env.component.PatchComponentSitesGraphFactory.EdgeType;
+import static arcade.patch.env.component.PatchComponentSitesGraphUtilities.*;
 
 /**
  * Extension of {@link PatchComponentSites} for graph sites.
@@ -191,8 +191,8 @@ Graph initializeGraph(MersenneTwisterFast random) {
      * Graph step that only considers differences in concentration.
      * <p>
      * 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/...comp/PatchComponentSitesGraphFactory.java → ...nent/PatchComponentSitesGraphFactory.java b/...comp/PatchComponentSitesGraphFactory.java → ...nent/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/.../PatchComponentSitesGraphFactoryRect.java → .../PatchComponentSitesGraphFactoryRect.java b/.../PatchComponentSitesGraphFactoryRect.java → .../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/...p/PatchComponentSitesGraphFactoryTri.java → ...t/PatchComponentSitesGraphFactoryTri.java b/...p/PatchComponentSitesGraphFactoryTri.java → ...t/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/...nv/comp/PatchComponentSitesGraphRect.java → ...mponent/PatchComponentSitesGraphRect.java b/...nv/comp/PatchComponentSitesGraphRect.java → ...mponent/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.