From c30167d5ec2b7c46ef49bf7d40c3d09ae11d1090 Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 28 Sep 2022 23:15:55 -0500
Subject: [PATCH] Change real sequence collision so it isn't biased toward
 sequences in the earlier wells.

---
 src/main/java/Plate.java | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/main/java/Plate.java b/src/main/java/Plate.java
index b81a140..c790be8 100644
--- a/src/main/java/Plate.java
+++ b/src/main/java/Plate.java
@@ -166,6 +166,8 @@ public class Plate {
         Map<String, List<String>> sequencesAndMisreads = new HashMap<>();
         //Map of all sequences read. Keys are sequences, values are associated SequenceRecords
         Map<String, SequenceRecord> sequenceMap = new LinkedHashMap<>();
+        //get list of all distinct, real sequences
+        String[] realSequences = assayWells(sIndices).toArray(new String[0]);
         for (int well = 0; well < size; well++) {
             for (String[] cell: wells.get(well)) {
                 for (int sIndex: sIndices) {
@@ -201,8 +203,8 @@ public class Plate {
                                         String wrongSequence;
                                         do{
                                             //get a random real sequence that's been read from the plate before
-                                            int index = rand.nextInt(sequencesAndMisreads.size());
-                                            wrongSequence = sequencesAndMisreads.keySet().toArray(new String[0])[index];
+                                            int index = rand.nextInt(realSequences.length);
+                                            wrongSequence = realSequences[index];
                                             //make sure it's not accidentally the *right* sequence
                                             //Also that it's not a wrong sequence already in the misread list
                                         } while(currentSequence.equals(wrongSequence) || sequencesAndMisreads.get(currentSequence).contains(wrongSequence));
@@ -240,6 +242,18 @@ public class Plate {
         return sequenceMap;
     }
 
+    private HashSet<String> assayWells(int[] indices) {
+        HashSet<String> allSequences = new HashSet<>();
+        for (List<String[]> well: wells) {
+            for (String[] cell: well) {
+                for(int index: indices) {
+                    allSequences.add(cell[index]);
+                }
+            }
+        }
+        return allSequences;
+    }
+
     public String getSourceFileName() {
         return sourceFile;
     }