From 9dacd8cd3488cced5142aecfa76d8035513bb75d Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Wed, 28 Sep 2022 17:43:21 -0500
Subject: [PATCH] Add real sequence collision rate

---
 src/main/java/InteractiveInterface.java | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java
index 5c1f14f..4c568c4 100644
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -255,6 +255,7 @@ public class InteractiveInterface {
         int readDepth = 1;
         double readErrorRate = 0.0;
         double errorCollisionRate = 0.0;
+        double realSequenceCollisionRate = 0.0;
         try {
             String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
             str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -271,22 +272,29 @@ public class InteractiveInterface {
                 simulateReadDepth = true;
             }
             if (simulateReadDepth) {
-                System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
+                System.out.print("\nPlease enter the read depth (the integer number of times a sequence is read): ");
                 readDepth = sc.nextInt();
                 if(readDepth < 1) {
                     throw new InputMismatchException("The read depth must be an integer >= 1");
                 }
-                System.out.print("\nPlease enter probability of a sequence read error (0.0 to 1.0): ");
+                System.out.println("\nPlease enter the read error probability (0.0 to 1.0)");
+                System.out.print("(The probability that a sequence will be misread): ");
                 readErrorRate = sc.nextDouble();
                 if(readErrorRate < 0.0 || readErrorRate > 1.0) {
                     throw new InputMismatchException("The read error probability must be in the range [0.0, 1.0]");
                 }
-                System.out.println("\nPlease enter the probability of read error collision (0.0 to 1.0)");
-                System.out.print("(The probability that two misreads produce the same spurious sequence): ");
+                System.out.println("\nPlease enter the error collision probability (0.0 to 1.0)");
+                System.out.print("(The probability of a sequence being misread in a way it has been misread before): ");
                 errorCollisionRate = sc.nextDouble();
                 if(errorCollisionRate < 0.0 || errorCollisionRate > 1.0) {
                     throw new InputMismatchException("The error collision probability must be an in the range [0.0, 1.0]");
                 }
+                System.out.println("\nPlease enter the real sequence collision probability (0.0 to 1.0)");
+                System.out.print("(The probability that a (non-collision) misread produces a different, real sequence): ");
+                realSequenceCollisionRate = sc.nextDouble();
+                if(realSequenceCollisionRate < 0.0 || realSequenceCollisionRate > 1.0) {
+                    throw new InputMismatchException("The real sequence collision probability must be an in the range [0.0, 1.0]");
+                }
             }
             System.out.println("\nThe graph and occupancy data will be written to a file.");
             System.out.print("Please enter a name for the output file: ");
@@ -334,7 +342,8 @@ public class InteractiveInterface {
             System.out.println("Returning to main menu.");
         }
         else{
-            GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate, errorCollisionRate, true);
+            GraphWithMapData data = Simulator.makeCDR3Graph(cellSample, plate, readDepth, readErrorRate,
+                    errorCollisionRate, realSequenceCollisionRate, true);
             assert filename != null;
             if(BiGpairSEQ.outputBinary()) {
                 GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);