From e795b4cdd072aa497d07be239e57fed2f5779f3f Mon Sep 17 00:00:00 2001
From: eugenefischer <66030419+eugenefischer@users.noreply.github.com>
Date: Mon, 26 Sep 2022 14:25:47 -0500
Subject: [PATCH] Add read depth option to interface

---
 src/main/java/InteractiveInterface.java | 28 +++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/main/java/InteractiveInterface.java b/src/main/java/InteractiveInterface.java
index f37d923..87d1fa1 100644
--- a/src/main/java/InteractiveInterface.java
+++ b/src/main/java/InteractiveInterface.java
@@ -250,6 +250,11 @@ public class InteractiveInterface {
         String filename = null;
         String cellFile = null;
         String plateFile = null;
+        Boolean simulateReadDepth = false;
+        //number of times to read each sequence in a well
+        Integer readDepth = 1;
+        Double readErrorRate = 0.0;
+        Double errorCollisionRate = 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.");
@@ -258,6 +263,23 @@ public class InteractiveInterface {
             cellFile = sc.next();
             System.out.print("\nPlease enter name of an existing sample plate file: ");
             plateFile = sc.next();
+            System.out.println("\nEnable simulation of sequence read depth and sequence read errors? (y/n)");
+            String ans = sc.next();
+            Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
+            Matcher matcher = pattern.matcher(ans);
+            if(matcher.matches()){
+                simulateReadDepth = true;
+            }
+            if (simulateReadDepth) {
+                System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
+                readDepth = sc.nextInt();
+                System.out.print("\nPlease enter probability of a sequence read error (0.0 to 1.0): ");
+                readErrorRate = sc.nextDouble();
+                System.out.println("\nPlease enter the probability of read error collision");
+                System.out.println("(the likelihood that two read errors produce the same spurious sequence)");
+                System.out.print("(0.0 to 1.0): ");
+                errorCollisionRate = sc.nextDouble();
+            }
             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: ");
             filename = sc.next();
@@ -505,8 +527,7 @@ public class InteractiveInterface {
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
             System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
             System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
-            System.out.println("6) Turn " + getOnOff(!BiGpairSEQ.simulateReadDepth()) + " simulation of read depth and sequence read errors");
-            System.out.println("7) Maximum weight matching algorithm options");
+            System.out.println("6) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {
                 input = sc.nextInt();
@@ -516,8 +537,7 @@ public class InteractiveInterface {
                     case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
                     case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
                     case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
-                    case 6 -> BiGpairSEQ.setSimulateReadDepth(!BiGpairSEQ.simulateReadDepth());
-                    case 7 -> algorithmOptions();
+                    case 6 -> algorithmOptions();
                     case 0 -> backToMain = true;
                     default -> System.out.println("Invalid input");
                 }