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Change uint to unsigned int #1

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6 changes: 3 additions & 3 deletions include/MyBloom.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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);

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4 changes: 2 additions & 2 deletions include/Rambo_construction.h
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Expand Up @@ -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);
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6 changes: 3 additions & 3 deletions include/bitArray.h
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Expand Up @@ -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);
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10 changes: 5 additions & 5 deletions src/MyBloom.cpp
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Expand Up @@ -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);
Expand All @@ -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])){
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32 changes: 16 additions & 16 deletions src/Rambo_construction.cpp
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Expand Up @@ -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);
Expand All @@ -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++;
}
Expand Down Expand Up @@ -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);
}
Expand All @@ -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);
}
}
Expand All @@ -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);
}
}
Expand All @@ -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;
Expand All @@ -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);
// }
// }
Expand All @@ -157,15 +157,15 @@ 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);
// bitset<Ki> bitarray_K1;
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();
Expand All @@ -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;
}

Expand All @@ -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);
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8 changes: 4 additions & 4 deletions src/bitArray.cpp
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Expand Up @@ -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)));
}

Expand Down Expand Up @@ -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]);
Expand Down
4 changes: 2 additions & 2 deletions src/main.cpp
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Expand Up @@ -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);
Expand Down Expand Up @@ -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() );
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8 changes: 4 additions & 4 deletions src/utils.cpp
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Expand Up @@ -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";
Expand All @@ -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]));
Expand All @@ -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;
Expand Down