From 19a2a35f07d46f76bdffd59906d6f9af011fe44e Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Mon, 26 Sep 2022 17:00:25 -0500
Subject: [PATCH] Refactor plate assay methods to use maps passed as parameters
 rather than returning maps

---
 src/main/java/Plate.java     | 14 ++++++--------
 src/main/java/Simulator.java | 16 ++++++++++------
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java
index 5d4ea60..75ca2c8 100644
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -149,24 +149,22 @@ public class Plate {
     }
 
     //returns a map of the counts of the sequence at cell index sIndex, in all wells
-    public Map<String, Integer> assayWellsSequenceS(int... sIndices){
-        return this.assayWellsSequenceS(0, size, sIndices);
+    public void assayWellsSequenceS(Map<String, Integer> sequences, int... sIndices){
+        this.assayWellsSequenceS(sequences, 0, size, sIndices);
     }
 
     //returns a map of the counts of the sequence at cell index sIndex, in a specific well
-    public Map<String, Integer> assayWellsSequenceS(int n, int... sIndices) {
-        return this.assayWellsSequenceS(n, n+1, sIndices);
+    public void assayWellsSequenceS(Map<String, Integer> sequences, int n, int... sIndices) {
+        this.assayWellsSequenceS(sequences, n, n+1, sIndices);
     }
 
     //returns a map of the counts of the sequence at cell index sIndex, in a range of wells
-    public Map<String, Integer> assayWellsSequenceS(int start, int end, int... sIndices) {
-        Map<String, Integer> assay = new HashMap<>();
+    public void assayWellsSequenceS(Map<String, Integer> sequences, int start, int end, int... sIndices) {
         for(int sIndex: sIndices){
             for(int i = start; i < end; i++){
-                countSequences(assay, wells.get(i), sIndex);
+                countSequences(sequences, wells.get(i), sIndex);
             }
         }
-        return assay;
     }
     //For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
     private void countSequences(Map<String, Integer> wellMap, List<String[]> well, int... sIndices) {
diff --git a/src/main/java/Simulator.java b/src/main/java/Simulator.java
index 698993c..1db1853 100644
--- a/src/main/java/Simulator.java
+++ b/src/main/java/Simulator.java
@@ -36,8 +36,10 @@ public class Simulator implements GraphModificationFunctions {
 
         if(verbose){System.out.println("Making well maps");}
 
-        Map<String, Integer> allAlphas = samplePlate.assayWellsSequenceS(alphaIndices);
-        Map<String, Integer> allBetas = samplePlate.assayWellsSequenceS(betaIndices);
+        Map<String, Integer> allAlphas = new HashMap<>();
+        samplePlate.assayWellsSequenceS(allAlphas, alphaIndices);
+        Map<String, Integer> allBetas = new HashMap<>();
+        samplePlate.assayWellsSequenceS(allBetas, betaIndices);
         int alphaCount = allAlphas.size();
         if(verbose){System.out.println("All alphas count: " + alphaCount);}
         int betaCount = allBetas.size();
@@ -658,18 +660,20 @@ public class Simulator implements GraphModificationFunctions {
                                                     Map<String, Integer> rowSequenceCounts,
                                                     Map<String, Integer> columnSequenceCounts,
                                                     double[][] weights){
-        Map<String, Integer> wellNRowSequences = null;
-        Map<String, Integer> wellNColumnSequences = null;
+        Map<String, Integer> wellNRowSequences;
+        Map<String, Integer> wellNColumnSequences;
         int vertexStartValue = rowSequenceToVertexMap.size();
         int numWells = samplePlate.getSize();
         for (int n = 0; n < numWells; n++) {
-            wellNRowSequences = samplePlate.assayWellsSequenceS(n, rowSequenceIndices);
+            wellNRowSequences = new HashMap<>();
+            samplePlate.assayWellsSequenceS(wellNRowSequences, n, rowSequenceIndices);
             for (String a : wellNRowSequences.keySet()) {
                 if(allRowSequences.containsKey(a)){
                     rowSequenceCounts.merge(a, 1, (oldValue, newValue) -> oldValue + newValue);
                 }
             }
-            wellNColumnSequences = samplePlate.assayWellsSequenceS(n, colSequenceIndices);
+            wellNColumnSequences = new HashMap<>();
+            samplePlate.assayWellsSequenceS(wellNColumnSequences, n, colSequenceIndices);
             for (String b : wellNColumnSequences.keySet()) {
                 if(allColumnSequences.containsKey(b)){
                     columnSequenceCounts.merge(b, 1, (oldValue, newValue) -> oldValue + newValue);