From 44b09bb4965aa3b8a7248874b075efcf6e035a62 Mon Sep 17 00:00:00 2001
From: Anthony Wang <ta180m@gmail.com>
Date: Wed, 2 Jun 2021 16:38:58 -0500
Subject: [PATCH] Add latest files

---
 .gitignore |  2 ++
 main.cpp   | 38 ++++++++++++++++++++++----------------
 2 files changed, 24 insertions(+), 16 deletions(-)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..59be43b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+*
+!*.*
diff --git a/main.cpp b/main.cpp
index c651f76..e80b645 100644
--- a/main.cpp
+++ b/main.cpp
@@ -5,7 +5,7 @@ using ll = long long;
 string P[3];
 double score[3][7];
 
-vector<string> variant[7];
+vector<string> vrt[7];
 
 ll levenshtein(string &s, string &t){
   int n = s.size(), m = t.size();
@@ -44,31 +44,37 @@ bitset<k> test(string & probe) {
 	bitset<k> bs;
 	double avg[7];
 	for (int i = 0; i < 7; ++i) {
-		avg[i] = 0;
-		for (int j = 0; j < 20; ++j)
-			avg[i] += sequenceCmp(probe, variant[i][j]);
-		avg[i] /= 20;
+		for (int j = 0; j < 10; ++j) {
+			int r = rand()%20;
+			avg[i] += sequenceCmp(probe, vrt[i][r]);
+		}
+		avg[i] /= 2;
 	}
 	int cnt = 0;
 	for (int i = 0; i < 7; ++i)
 		for (int j = i+1; j < 7; ++j)
-			if (abs(avg[i]-avg[j]) > 10) bs[cnt++] = 1;
-	return cnt;
+			{
+				if (abs(avg[i]-avg[j]) > 10) bs[cnt] = 1;
+				cnt++;
+			}
+	return bs;
 }
 
 vector<string> dp[4][1 << k];
 void analyze_spike_sequences(){
 	freopen("spike_sequences.txt", "r", stdin);
-	for (int i = 0; i < 7; ++i) { // 7 variants
+	for (int i = 0; i < 7; ++i) { // 7 vrts
 		for (int j = 0; j < 20; ++j) {
 			string s, t; cin >> s >> t;
-			variant[i].push_back(t);
+			vrt[i].push_back(t);
 		}
 	}
+	int cnt = 0;
   for (int i = 0; i < 7; ++i) {
-		for (int j = 0; j <= variant[i][0].size()-150; ++j) {
-			string probe(begin(variant[i][0]), begin(variant[i][0])+150);
+		for (int j = 0; j <= vrt[i][0].size()-150; j += rand()%100) {
+			string probe(begin(vrt[i][0])+j, begin(vrt[i][0])+j+150);
 			bitset<k> bs = test(probe);
+            cout << probe << ' ' << cnt++ << endl;
 
       int bsint = 0; //change to int
       for(int i = 0; i < k; i++) bsint |= bs[i] << i;
@@ -89,7 +95,7 @@ void analyze_spike_sequences(){
   
   int retx = 0, rety = 0;
   //find best dp coverage
-  for(int i = 1; i <= 3; i++)
+  for(int i = 3; i <= 3; i++)
   for(int j = 0; j < (1 << k); j++){
     if(!dp[i][j].empty() && __builtin_popcount(j) > __builtin_popcount(rety)){
       retx = i, rety = j;
@@ -111,7 +117,7 @@ void mkscores() {
 		for (int j = 0; j < 7; ++j) {
 			score[i][j] = 0;
 			for (int k = 0; k < 20; ++k)
-				score[i][j] += sequenceCmp(P[i], variant[j][k]);
+				score[i][j] += sequenceCmp(P[i], vrt[j][k]);
 			score[i][j] /= 20;
 			cout << score[i][j];
 			if (j < 6) cout << ",";
@@ -137,7 +143,7 @@ string types[7] = {"original",
 "B.1.427",
 "P.1",
 "B.1.351",
-"other_variant",
+"other_vrt",
 "not_sars_cov2"};
 
 void answer(){
@@ -156,10 +162,10 @@ int main(){
   ios::sync_with_stdio(0);
   cin.tie(0);
   if (fopen("spike_sequences.txt", "r")) {
-		analyze_spike_sequences();
 		if (P[0] != "") mkscores();
+        else analyze_spike_sequences();
 		return 0;
   }
   answer();
   return 0;
-}
\ No newline at end of file
+}