From 77983064295ac225b58da552c21cdc4d875beb27 Mon Sep 17 00:00:00 2001
From: Ben Coleman <brc7@rice.edu>
Date: Mon, 20 Jul 2020 21:42:56 -0400
Subject: [PATCH] Change uint to unsigned int

---
 include/MyBloom.h            |  6 +++---
 include/Rambo_construction.h |  4 ++--
 include/bitArray.h           |  6 +++---
 src/MyBloom.cpp              | 10 +++++-----
 src/Rambo_construction.cpp   | 32 ++++++++++++++++----------------
 src/bitArray.cpp             |  8 ++++----
 src/main.cpp                 |  4 ++--
 src/utils.cpp                |  8 ++++----
 8 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/include/MyBloom.h b/include/MyBloom.h
index ca32aef..e32edc7 100644
--- a/include/MyBloom.h
+++ b/include/MyBloom.h
@@ -5,14 +5,14 @@
 #include <bitset>
 #include "bitArray.h"
 
-std::vector<uint> myhash(std::string key, int len, int k, int r, int range);
+std::vector<unsigned int> myhash(std::string key, int len, int k, int r, int range);
 
 class BloomFiler{
     public:
         // BloomFiler(int capacity, float FPR, int k);
         BloomFiler(int sz, float FPR, int k);
-        void insert(std::vector<uint> a);
-        bool test(std::vector<uint> a);
+        void insert(std::vector<unsigned int> a);
+        bool test(std::vector<unsigned int> a);
         void serializeBF(std::string BF_file);
         void deserializeBF(std::vector<std::string> BF_file);
 
diff --git a/include/Rambo_construction.h b/include/Rambo_construction.h
index 2411169..3ac48ba 100644
--- a/include/Rambo_construction.h
+++ b/include/Rambo_construction.h
@@ -8,14 +8,14 @@
 #include "bitArray.h"
 
 
-// vector<uint> hashfunc( void* key, int len, int R, int B){
+// vector<unsigned int> hashfunc( void* key, int len, int R, int B){
 // }
 
 class RAMBO{
     public:
 
         RAMBO(int n, int r1, int b1, int K);
-        std::vector<uint> hashfunc( std::string key, int len);
+        std::vector<unsigned int> hashfunc( std::string key, int len);
         void insertion (std::string setID, std::vector<std::string> keys);
         std::set<int> takeunion(std::set<int> set1, std::set<int> set2);
         std::set<int> takeIntrsec(std::set<int>* setArray);
diff --git a/include/bitArray.h b/include/bitArray.h
index 73165f0..a02e08e 100644
--- a/include/bitArray.h
+++ b/include/bitArray.h
@@ -10,9 +10,9 @@ class bitArray{
         // friend class boost::serialization::access;
 
         bitArray(int size);
-        void SetBit(uint k);
-        void ClearBit( uint k);
-        bool TestBit( uint k);
+        void SetBit(unsigned int k);
+        void ClearBit( unsigned int k);
+        bool TestBit( unsigned int k);
         void ANDop(char* B);
         void serializeBitAr(std::string BF_file);
         void deserializeBitAr(std::vector<std::string> BF_file);
diff --git a/src/MyBloom.cpp b/src/MyBloom.cpp
index d03da14..0b52f52 100644
--- a/src/MyBloom.cpp
+++ b/src/MyBloom.cpp
@@ -11,10 +11,10 @@
 
 using namespace std;
 
-vector<uint> myhash( std::string key, int len, int k, int r, int range){
+vector<unsigned int> myhash( std::string key, int len, int k, int r, int range){
   // int hashvals[k];
-  vector <uint> hashvals;
-  uint op; // takes 4 byte
+  vector <unsigned int> hashvals;
+  unsigned int op; // takes 4 byte
 
   for (int i=0+ k*r; i<k+ k*r; i++){
     MurmurHash3_x86_32(key.c_str(), len, i, &op);
@@ -29,14 +29,14 @@ BloomFiler::BloomFiler(int sz, float FPR, int k){
       m_bits = new bitArray(sz);
       }
 
-void BloomFiler::insert(vector<uint> a){
+void BloomFiler::insert(vector<unsigned int> a){
   int N = a.size();
   for (int n =0 ; n<N; n++){
     m_bits->SetBit(a[n]);
   }
 }
 
-bool BloomFiler::test(vector<uint> a){
+bool BloomFiler::test(vector<unsigned int> a){
   int N = a.size();
   for (int n =0 ; n<N; n++){
       if (!m_bits->TestBit(a[n])){
diff --git a/src/Rambo_construction.cpp b/src/Rambo_construction.cpp
index 5185646..7205264 100644
--- a/src/Rambo_construction.cpp
+++ b/src/Rambo_construction.cpp
@@ -20,10 +20,10 @@
 
 using namespace std;
 
-vector<uint> RAMBO:: hashfunc( std::string key, int len){
+vector<unsigned int> RAMBO:: hashfunc( std::string key, int len){
   // int hashvals[k];
-  vector <uint> hashvals;
-  uint op;
+  vector <unsigned int> hashvals;
+  unsigned int op;
   for (int i=0; i<R; i++){
     MurmurHash3_x86_32(key.c_str(), len, 10, &op); //seed i
     hashvals.push_back(op%B);
@@ -43,7 +43,7 @@ std::vector <std::string>  RAMBO:: getdata(string filenameSet){
               stringstream is;
               is<<line1;
               if (line1[0]!= '>' && line1.size()>30 ){
-                for (uint idx =0; idx<line1.size()-31 +1; idx++){
+                for (unsigned int idx =0; idx<line1.size()-31 +1; idx++){
                   allKeys.push_back(line1.substr(idx, 31));
                   totKmerscnt++;
                 }
@@ -78,7 +78,7 @@ RAMBO::RAMBO(int n, int r1, int b1, int K){
 // one time process- a preprocess step
 void RAMBO::createMetaRambo(int K, bool verbose){
   for(int i=0;i<K;i++){
-    vector<uint> hashvals = RAMBO::hashfunc(std::to_string(i), std::to_string(i).size()); // R hashvals, each with max value B
+    vector<unsigned int> hashvals = RAMBO::hashfunc(std::to_string(i), std::to_string(i).size()); // R hashvals, each with max value B
     for(int r=0; r<R; r++){
       metaRambo[hashvals[r] + B*r].push_back(i);
     }
@@ -99,13 +99,13 @@ void RAMBO::createMetaRambo(int K, bool verbose){
 
 // give set and keys in the set
 void RAMBO::insertion (std::string setID, std::vector<std::string> keys){
-  vector<uint> hashvals = RAMBO::hashfunc(setID, setID.size()); // R hashvals
+  vector<unsigned int> hashvals = RAMBO::hashfunc(setID, setID.size()); // R hashvals
 
   //make this loop parallel
   #pragma omp parallel for
   for(std::size_t i=0; i<keys.size(); ++i){
     for(int r=0; r<R; r++){
-      vector<uint> temp = myhash(keys[i].c_str(), keys[i].size() , k,r, range);
+      vector<unsigned int> temp = myhash(keys[i].c_str(), keys[i].size() , k,r, range);
       Rambo_array[hashvals[r] + B*r]->insert(temp);
     }
   }
@@ -120,10 +120,10 @@ void RAMBO::insertion2 (std::vector<string> alllines){
     std::vector<string>KeySets =  line2array(alllines[i], d);//sets for a key
 
     std::vector<string>KeySet = line2array(KeySets[1], ',');
-    for (uint j = 0; j<KeySet.size(); j++){
-      vector<uint> hashvals = RAMBO::hashfunc(KeySet[j], KeySet[j].size()); // R hashvals
+    for (unsigned int j = 0; j<KeySet.size(); j++){
+      vector<unsigned int> hashvals = RAMBO::hashfunc(KeySet[j], KeySet[j].size()); // R hashvals
       for(int r=0; r<R; r++){
-	vector<uint> temp = myhash(KeySets[0].c_str(), KeySets[0].size() , k, r, range);// i is the key
+	vector<unsigned int> temp = myhash(KeySets[0].c_str(), KeySets[0].size() , k, r, range);// i is the key
         Rambo_array[hashvals[r] + B*r]->insert(temp);
       }
     }
@@ -132,7 +132,7 @@ void RAMBO::insertion2 (std::vector<string> alllines){
 
 // // give set and keys in the set
 // void RAMBO::insertionRare (std::string setID, std::vector<std::string> keys){
-//   vector<uint> hashvals = RAMBO::hashfunc(setID, setID.size()); // R hashvals
+//   vector<unsigned int> hashvals = RAMBO::hashfunc(setID, setID.size()); // R hashvals
 //
 //   //make this loop parallel
 //   int skip =0;
@@ -141,7 +141,7 @@ void RAMBO::insertion2 (std::vector<string> alllines){
 //     bitArray MemVec = RAMBO::query(keys[i].c_str(), keys[i].size());
 //     if ( MemVec.getcount() <10 ){
 //       for(int r=0; r<R; r++){
-//       vector<uint> temp = myhash(keys[i].c_str(), keys[i].size() , k, r, range);
+//       vector<unsigned int> temp = myhash(keys[i].c_str(), keys[i].size() , k, r, range);
 //         Rambo_array[hashvals[r] + B*r]->insert(temp);
 //     }
 //   }
@@ -157,7 +157,7 @@ bitArray RAMBO::query (string query_key, int len){
   // bitset<Ki> bitarray_K;
   // set<int> res;
   float count=0.0;
-  vector<uint> check;
+  vector<unsigned int> check;
   for(int r=0; r<R; r++){
     check = myhash(query_key, len , k, r,range); //hash values correspondign to the keys
     bitArray bitarray_K1(Ki);
@@ -165,7 +165,7 @@ bitArray RAMBO::query (string query_key, int len){
     for(int b=0; b<B; b++){
         if (Rambo_array[b + B*r]->test(check)){
           chrono::time_point<chrono::high_resolution_clock> t5 = chrono::high_resolution_clock::now();
-          for (uint j=0; j<metaRambo[b + B*r].size(); j++){
+          for (unsigned int j=0; j<metaRambo[b + B*r].size(); j++){
             bitarray_K1.SetBit(metaRambo[b + B*r][j]);
         }
         chrono::time_point<chrono::high_resolution_clock> t6 = chrono::high_resolution_clock::now();
@@ -179,7 +179,7 @@ bitArray RAMBO::query (string query_key, int len){
       bitarray_K.ANDop(bitarray_K1.A);
     }
   }
-  vector<uint>().swap(check);
+  vector<unsigned int>().swap(check);
   return bitarray_K;
 }
 
@@ -196,7 +196,7 @@ void RAMBO::deserializeRAMBO(vector<string> dir){
   for(int b=0; b<B; b++){
     for(int r=0; r<R; r++){
       vector<string> br;
-     	for (uint j=0; j<dir.size(); j++){
+     	for (unsigned int j=0; j<dir.size(); j++){
 	  br.push_back(dir[j] + to_string(b) + "_" + to_string(r) + ".txt");
 	}
       Rambo_array[b + B*r]->deserializeBF(br);
diff --git a/src/bitArray.cpp b/src/bitArray.cpp
index e466039..7af8041 100644
--- a/src/bitArray.cpp
+++ b/src/bitArray.cpp
@@ -13,15 +13,15 @@ bitArray::bitArray(int size){
    }
 }
 
-void bitArray::SetBit(uint k) {
+void bitArray::SetBit(unsigned int k) {
    A[(k/8)] |= (1 << (k%8));
 }
 
-void bitArray::ClearBit(uint k) {
+void bitArray::ClearBit(unsigned int k) {
    A[(k/8)] &= ~(1 << (k%8));
 }
 
-bool bitArray::TestBit(uint k) {
+bool bitArray::TestBit(unsigned int k) {
    return (A[(k/8)] & (1 << (k%8)));
 }
 
@@ -55,7 +55,7 @@ void bitArray::serializeBitAr(string BF_file){
 }
 
 void bitArray::deserializeBitAr(std::vector<string> BF_file){
-  for(uint j =0; j<BF_file.size(); j++){
+  for(unsigned int j =0; j<BF_file.size(); j++){
     char* C;
     C = new char[ar_size/8 +1];
     ifstream in(BF_file[j]);
diff --git a/src/main.cpp b/src/main.cpp
index 8aca529..6a2edd9 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -61,7 +61,7 @@ if (insert == true){
     int stpt;
 	stpt = 5;
     //}
-    for (uint ss=0; ss<setIDs.size(); ss++){
+    for (unsigned int ss=0; ss<setIDs.size(); ss++){
       stpCnt++;
       char d = ',';
       vector<std::string> setID = line2array(setIDs[ss], d);
@@ -111,7 +111,7 @@ if(test){
   //std::vector<string> alllines = readlines("data/query.txt", 0);
   std::vector<string> testKeys;
   std::vector<int> gt_size;
-  for(uint i=0; i<alllines.size(); i++){
+  for(unsigned int i=0; i<alllines.size(); i++){
         std::vector<string>KeySets =  line2array(alllines[i], ';');//sets for a key
         testKeys.push_back(KeySets[0]);
         gt_size.push_back( line2array(KeySets[1], ',').size() );
diff --git a/src/utils.cpp b/src/utils.cpp
index aac01dc..08753f8 100644
--- a/src/utils.cpp
+++ b/src/utils.cpp
@@ -146,14 +146,14 @@ return s;
 
 std::map<std::string, vector<int>> makeInvIndex(int n, vector<std::string> foldernames){
   std::map<std::string, vector<int>> m;
-  for (uint f=0; f<foldernames.size(); f++){
+  for (unsigned int f=0; f<foldernames.size(); f++){
     string foldername = foldernames[f];
     for (int batch=0; batch<47; batch++){
   	string dataPath = foldername + to_string(batch)+ "_indexed.txt";
   	std::vector<string> setIDs = readlines(dataPath, 0);
   	cout<<setIDs[0]<<endl;
 
-  	for (uint ss=0; ss<setIDs.size(); ss++){
+  	for (unsigned int ss=0; ss<setIDs.size(); ss++){
     	  char d = ',';
     	  vector<std::string> setID = line2array(setIDs[ss], d);
           string mainfile = foldername + setID[1]+ ".out";
@@ -172,7 +172,7 @@ std::map<std::string, vector<int>> makeInvIndex(int n, vector<std::string> folde
     	   }
     	  else{
 
-    		for (uint i =0; i<keys.size(); i++){
+    		for (unsigned int i =0; i<keys.size(); i++){
       		   if (m.find(keys[i]) != m.end()){
         	     std::cout << "map contains the key!\n";
         	     m[keys[i]].push_back(std::stoi(setID[0]));
@@ -188,7 +188,7 @@ std::map<std::string, vector<int>> makeInvIndex(int n, vector<std::string> folde
 
 std::vector<std::string> getkmers(std::string query_key, int kmersize){
   std::vector<std::string> query_kmers;
-  for (uint idx =0; idx<query_key.size()-kmersize +1; idx++){
+  for (unsigned int idx =0; idx<query_key.size()-kmersize +1; idx++){
     query_kmers.push_back(query_key.substr(idx, kmersize));
   }
  return query_kmers;