Merge pull request #396 from mstevens-uk/UpdateCellsRefactor

Added Cell/Hosts helper functions to Update.cpp

src/Update.cpp

@@ -25,6 +25,10 @@ void LatentToInfectious(int cellIndex);
 void InfectiousToRecovered(int cellIndex);
 void InfectiousToDeath(int cellIndex);
 
+// if the dest cell state == src cell state, use this
+void UpdateCell(int* cellPeople, int index, int srcIndex);
+void UpdateCell(int* cellPeople, int* srcCellPeople, int index, int srcIndex);
+
 void DoImmune(int ai)
 {
 	// This transfers a person straight from susceptible to immune. Used to start a run with a partially immune population.
@@ -41,19 +45,19 @@ void DoImmune(int ai)
 
 		if (a->listpos < Cells[c].S)
 		{
-			Cells[c].susceptible[a->listpos] = Cells[c].susceptible[Cells[c].S];
-			Hosts[Cells[c].susceptible[a->listpos]].listpos = a->listpos;
+			UpdateCell(Cells[c].susceptible, a->listpos, Cells[c].S);
 		}
 		if (Cells[c].L > 0)
 		{
-			Cells[c].susceptible[Cells[c].S] = Cells[c].susceptible[Cells[c].S + Cells[c].L];
-			Hosts[Cells[c].susceptible[Cells[c].S]].listpos = Cells[c].S;
+			UpdateCell(Cells[c].susceptible, Cells[c].S, Cells[c].S + Cells[c].L);
 		}
+
 		if (Cells[c].I > 0)
 		{
-			Cells[c].susceptible[Cells[c].S + Cells[c].L] = Cells[c].susceptible[Cells[c].S + Cells[c].L + Cells[c].I];
-			Hosts[Cells[c].susceptible[Cells[c].S + Cells[c].L]].listpos = Cells[c].S + Cells[c].L;
+			UpdateCell(Cells[c].susceptible, Cells[c].S + Cells[c].L, Cells[c].S + Cells[c].L + Cells[c].I);
+
 		}
+
 		if (a->listpos < Cells[c].S + Cells[c].L + Cells[c].I)
 		{
 			Cells[c].susceptible[Cells[c].S + Cells[c].L + Cells[c].I] = ai;
@@ -107,8 +111,8 @@ void DoInfect(int ai, double t, int tn, int run) // Change person from susceptib
 
 			if (a->listpos < Cells[a->pcell].S)
 			{
-				Cells[a->pcell].susceptible[a->listpos] = Cells[a->pcell].susceptible[Cells[a->pcell].S];
-				Hosts[Cells[a->pcell].susceptible[a->listpos]].listpos = a->listpos;
+				UpdateCell(Cells[a->pcell].susceptible, a->listpos, Cells[a->pcell].S);
+
 				a->listpos = Cells[a->pcell].S;	//// person a's position with cell.members now equal to number of susceptibles in cell.
 				Cells[a->pcell].latent[0] = ai; //// person ai joins front of latent queue.
 			}
@@ -540,8 +544,8 @@ void DoIncub(int ai, unsigned short int ts, int tn, int run)
 
 		if (Cells[a->pcell].L > 0)
 		{
-			Cells[a->pcell].susceptible[a->listpos] = Cells[a->pcell].latent[Cells[a->pcell].L]; //// reset pointers.
-			Hosts[Cells[a->pcell].susceptible[a->listpos]].listpos = a->listpos;
+			UpdateCell(Cells[a->pcell].susceptible, Cells[a->pcell].latent, a->listpos, Cells[a->pcell].L);
+
 			a->listpos = Cells[a->pcell].S + Cells[a->pcell].L; //// change person a's listpos, which will now refer to their position among infectious people, not latent.
 			Cells[a->pcell].infected[0] = ai; //// this person is now first infectious person in the array. Pointer was moved back one so now that memory address refers to person ai. Alternative would be to move everyone back one which would take longer.
 		}
@@ -935,8 +939,7 @@ void DoRecover(int ai, int tn, int run)
 		j = Cells[a->pcell].S + Cells[a->pcell].L + Cells[a->pcell].I;
 		if (i < Cells[a->pcell].S + Cells[a->pcell].L + Cells[a->pcell].I)
 		{
-			Cells[a->pcell].susceptible[i] = Cells[a->pcell].susceptible[j];
-			Hosts[Cells[a->pcell].susceptible[i]].listpos = i;
+			UpdateCell(Cells[a->pcell].susceptible, i, j);
 			a->listpos = j;
 			Cells[a->pcell].susceptible[j] = ai;
 		}
@@ -979,8 +982,7 @@ void DoDeath(int ai, int tn, int run)
 		i = a->listpos;
 		if (i < Cells[a->pcell].S + Cells[a->pcell].L + Cells[a->pcell].I)
 		{
-			Cells[a->pcell].susceptible[a->listpos] = Cells[a->pcell].infected[Cells[a->pcell].I];
-			Hosts[Cells[a->pcell].susceptible[a->listpos]].listpos = i;
+			UpdateCell(Cells[a->pcell].susceptible, Cells[a->pcell].infected, a->listpos, Cells[a->pcell].I);
 			a->listpos = Cells[a->pcell].S + Cells[a->pcell].L + Cells[a->pcell].I;
 			Cells[a->pcell].susceptible[a->listpos] = ai;
 		}
@@ -1431,3 +1433,40 @@ void InfectiousToDeath(int cellIndex)
 	Cells[cellIndex].D++; //// one more dead person
 }
 
+/**
+ * Function: UpdateCell
+ *
+ * Purpose: update Cells and Hosts
+ * @param cellPeople - pointer to people in cell. e.g. *susceptible identifies where the final susceptible member of cell is.
+ * @param index - index into cellPeople to update
+ * @param srcIndex - index into cellPeople to update from
+ * @return void
+ */
+void UpdateCell(int* cellPeople,
+	int index,
+	int srcIndex)
+{
+	UpdateCell(cellPeople, cellPeople, index, srcIndex);
+}
+
+/**
+ * Function: UpdateCell
+ *
+ * Purpose: update Cells and Hosts 
+ * @param cellPeople - pointer to people in cell to update. e.g. *susceptible identifies where the final susceptible member of cell is.
+ * @param srcCellPeople - pointer to people in cell to update from. e.g. *infected identifies where the final infected member of cell is.
+ * @param index - index into cellPeople to update
+ * @param srcIndex - index into srcCellPeople to update from
+ * @return void
+ */
+void UpdateCell(int* cellPeople,
+	int* srcCellPeople,
+	int index,
+	int srcIndex)
+{
+	cellPeople[index] = srcCellPeople[srcIndex];
+
+	// update the listpos
+	Hosts[cellPeople[index]].listpos = index;
+}
+