From a5f7c0641d30a368f6527e13fa7b4ccec91561b9 Mon Sep 17 00:00:00 2001
From: efischer <ej@eugenefischer.com>
Date: Sun, 27 Feb 2022 14:51:53 -0600
Subject: [PATCH] Refactor for better encapsulation with CellSamples

---
 src/main/java/InteractiveInterface.java | 3 +--
 src/main/java/Simulator.java            | 3 ++-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java
index 0de7a8e..d826b1f 100644
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -304,8 +304,7 @@ public class InteractiveInterface {
             System.out.println("Returning to main menu.");
         }
         else{
-            List<Integer[]> cells = cellSample.getCells();
-            GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
+            GraphWithMapData data = Simulator.makeGraph(cellSample, plate, true);
             assert filename != null;
             if(BiGpairSEQ.outputBinary()) {
                 GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 0cc6df1..da13878 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -24,8 +24,9 @@ public class Simulator implements GraphModificationFunctions {
     private static final int cdr1BetaIndex = 3;
 
     //Make the graph needed for matching CDR3s
-    public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
+    public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
         Instant start = Instant.now();
+        List<Integer[]> distinctCells = cellSample.getCells();
         int[] alphaIndex = {cdr3AlphaIndex};
         int[] betaIndex = {cdr3BetaIndex};