Refactor to read/write files of graph and map data

src/main/java/GraphWithMapData.java

@@ -3,52 +3,91 @@ import org.jgrapht.graph.SimpleWeightedGraph;
 import java.time.Duration;
 import java.util.Map;
 
-public class GraphWithMapData {
+//Can't just write the graph, because I need the occupancy data too.
+//Makes most sense to serialize object and write that to a file.
+//Which means there's no reason to split map data and graph data up.
+public class GraphWithMapData implements java.io.Serializable {
+
+    private String sourceFilename;
     private final SimpleWeightedGraph graph;
-    private final MapData maps;
+    private Integer numWells;
+    private Integer lowThreshold;
+    private Integer highThreshold;
+    private final Map<Integer, Integer> distCellsMapAlphaKey;
+    private final Map<Integer, Integer> allAlphas;
+    private final Map<Integer, Integer> allBetas;
+    private final Map<Integer, Integer> plateVtoAMap;
+    private final Map<Integer, Integer> plateVtoBMap;
+    private final Map<Integer, Integer> plateAtoVMap;
+    private final Map<Integer, Integer> plateBtoVMap;
     private final Map<Integer, Integer> alphaWellCounts;
     private final Map<Integer, Integer> betaWellCounts;
     private final Duration time;
 
-    public GraphWithMapData(SimpleWeightedGraph graph, MapData maps, Map<Integer, Integer> alphaWellCounts,
+    public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer lowThreshold, Integer highThreshold,
+                            Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> allAlphas,
+                            Map<Integer, Integer> allBetas, Map<Integer, Integer> plateVtoAMap,
+                            Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
+                            Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
                             Map<Integer, Integer> betaWellCounts, Duration time) {
         this.graph = graph;
-        this.maps = maps;
+        this.numWells = numWells;
+        this.lowThreshold = lowThreshold;
+        this.highThreshold = highThreshold;
+        this.distCellsMapAlphaKey = distCellsMapAlphaKey;
+        this.allAlphas = allAlphas;
+        this.allBetas = allBetas;
+        this.plateVtoAMap = plateVtoAMap;
+        this.plateVtoBMap = plateVtoBMap;
+        this.plateAtoVMap = plateAtoVMap;
+        this.plateBtoVMap = plateBtoVMap;
         this.alphaWellCounts = alphaWellCounts;
         this.betaWellCounts = betaWellCounts;
-        this.time = time.plus(maps.getTime());
+        this.time = time;
     }
 
     public SimpleWeightedGraph getGraph() {
         return graph;
     }
 
+    public Integer getNumWells() {
+        return numWells;
+    }
+
+    public Integer getLowThreshold() {
+        return lowThreshold;
+    }
+
+    public Integer getHighThreshold() {
+        return highThreshold;
+    }
+
     public Map<Integer, Integer> getDistCellsMapAlphaKey() {
-        return maps.getDistCellsMapAlphaKey();
+        return distCellsMapAlphaKey;
     }
 
     public Map<Integer, Integer> getAllAlphas() {
-        return maps.getAllAlphas();
+        return allAlphas;
     }
 
     public Map<Integer, Integer> getAllBetas() {
-        return maps.getAllBetas();
+        return allBetas;
     }
 
     public Map<Integer, Integer> getPlateVtoAMap() {
-        return maps.getPlateVtoAMap();
+        return plateVtoAMap;
     }
 
     public Map<Integer, Integer> getPlateVtoBMap() {
-        return maps.getPlateVtoBMap();
+        return plateVtoBMap;
     }
 
     public Map<Integer, Integer> getPlateAtoVMap() {
-        return maps.getPlateAtoVMap();
+        return plateAtoVMap;
     }
 
     public Map<Integer, Integer> getPlateBtoVMap() {
-        return maps.getPlateBtoVMap();
+        return plateBtoVMap;
     }
 
     public Map<Integer, Integer> getAlphaWellCounts() {
@@ -62,4 +101,12 @@ public class GraphWithMapData {
     public Duration getTime() {
         return time;
     }
+
+    public void setSourceFilename(String filename) {
+        this.sourceFilename = filename;
+    }
+
+    public String getSourceFilename() {
+        return sourceFilename;
+    }
 }