Remove "using namespace std" from all cpp files

src/filepattern/cpp/external/external_filepattern.cpp

@@ -1,8 +1,6 @@
 #include "external_filepattern.hpp"
 
-using namespace std;
-
-ExternalFilePattern::ExternalFilePattern(const string& path, const string& filePattern, const string& block_size, bool recursive, bool suppressWarnings, bool sorted):
+ExternalFilePattern::ExternalFilePattern(const std::string& path, const std::string& filePattern, const std::string& block_size, bool recursive, bool suppressWarnings, bool sorted):
 ExternalPattern(path, block_size, recursive) {
 
     this->setSuppressWarnings(suppressWarnings);
@@ -53,7 +51,7 @@ ExternalFilePattern::~ExternalFilePattern(){
 
 void ExternalFilePattern::printFiles(){
 
-    vector<Tuple> files;
+    std::vector<Tuple> files;
 
     while(true){
         files = this->stream_.getValidFilesBlock();
@@ -62,12 +60,12 @@ void ExternalFilePattern::printFiles(){
             if(std::get<0>(file).size() < this->stream_.map_size_) continue;
 
             for(const auto& element: std::get<0>(file)){
-               cout << element.first << ":" << s::to_string(element.second) << endl;
+               std::cout << element.first << ":" << s::to_string(element.second) << std::endl;
             }
             for(const auto& element: std::get<1>(file)){
-                cout << "file: " << element << endl;
+                std::cout << "file: " << element << std::endl;
             }
-            cout << endl;
+            std::cout << std::endl;
         }
 
         if (this->stream_.endOfValidFiles()) break;
@@ -90,11 +88,11 @@ void ExternalFilePattern::matchFiles() {
 }
 
 void ExternalFilePattern::matchFilesOneDir(){
-    vector<string> block;
+    std::vector<std::string> block;
 
-    regex pattern_regex = regex(this->getRegexFilePattern());
-    string file;
-    smatch sm;
+    std::regex pattern_regex = std::regex(this->getRegexFilePattern());
+    std::string file;
+    std::smatch sm;
 
     // iterate over files
     while(!this->stream_.isEmpty()){

src/filepattern/cpp/external/external_stringpattern.cpp

@@ -1,8 +1,6 @@
 #include "external_stringpattern.hpp"
 
-using namespace std;
-
-ExternalStringPattern::ExternalStringPattern(const string& path, const string& file_pattern, const string& block_size, bool suppress_warnings, bool sorted):
+ExternalStringPattern::ExternalStringPattern(const std::string& path, const std::string& file_pattern, const std::string& block_size, bool suppress_warnings, bool sorted):
 ExternalPattern(path, block_size, false) {
     this->setSuppressWarnings(suppress_warnings);
     this->setPath(path); // store path to target directory
@@ -43,11 +41,11 @@ void ExternalStringPattern::matchFiles(){
 
     this->setMapSize(this->variables_.size());
 
-    vector<string> block;
+    std::vector<std::string> block;
 
-    regex pattern_regex = regex(this->getRegexFilePattern());
-    string file;
-    smatch sm;
+    std::regex pattern_regex = std::regex(this->getRegexFilePattern());
+    std::string file;
+    std::smatch sm;
 
     // iterate over files
     while(!this->stream_.isEmpty()){

src/filepattern/cpp/external/external_vectorpattern.cpp

@@ -1,12 +1,10 @@
 #include "external_vectorpattern.hpp"
 
-using namespace std;
-
 const std::regex ExternalVectorPattern::STITCH_REGEX_ = std::regex("(corr): (.*); (position): \\((.*), (.*)\\); (grid): \\((.*), (.*)\\);"); // regex of a stitching vector line
 const std::vector<std::regex> ExternalVectorPattern::STITCH_REGEX_VECTOR_ = {std::regex("(corr):\\s*(.*?);"), std::regex("(position):\\s*\\((.*?),\\s*(.*?)\\);"), std::regex("(grid):\\s*\\((.*),\\s*(.*)\\);")};
 const std::vector<std::string> ExternalVectorPattern::STITCH_VARIABLES_ = {"correlation","posX","posY","gridX","gridY"}; // stitching vector variables
 
-ExternalVectorPattern::ExternalVectorPattern(const string& path, const string& file_pattern, const string& block_size, bool suppress_warnings, bool sorted):
+ExternalVectorPattern::ExternalVectorPattern(const std::string& path, const std::string& file_pattern, const std::string& block_size, bool suppress_warnings, bool sorted):
 ExternalPattern(path, block_size, false){
     this->setSuppressWarnings(suppress_warnings);
     this->path_ = path; // store path to target directory
@@ -15,7 +13,7 @@ ExternalPattern(path, block_size, false){
     this->setBlockSize(Block::parseblockSize(block_size));
 
     this->vector_reader_.open(path);
-    if(!this->vector_reader_.is_open()) throw invalid_argument("Invalid path \"" + path + "\".");
+    if(!this->vector_reader_.is_open()) throw std::invalid_argument("Invalid path \"" + path + "\".");
 
     this->setFilePattern(file_pattern); // cast input string to regex
     this->setRegexFilePattern(""); // Regex version of pattern
@@ -45,13 +43,13 @@ void ExternalVectorPattern::matchFiles(){
 
     this->setMapSize(this->variables_.size() + this->STITCH_VARIABLES_.size()); // Change the size of the map to include stitching variables
 
-    this->setRegexExpression(regex(this->getRegexFilePattern()));
+    this->setRegexExpression(std::regex(this->getRegexFilePattern()));
 
-    string line, file;
+    std::string line, file;
     Tuple temp;
-    smatch sm;
+    std::smatch sm;
 
-    while(getline(this->vector_reader_, line)){
+    while(std::getline(this->vector_reader_, line)){
         file = VectorParser::getFileName(line);
         if(regex_match(file, sm, this->getRegexExpression())){
             temp = getVariableMap(file, sm);
@@ -62,17 +60,17 @@ void ExternalVectorPattern::matchFiles(){
     this->vector_reader_.close();
 }
 
-string ExternalVectorPattern::inferPattern(const string& path, string& variables, const string& block_size){
+std::string ExternalVectorPattern::inferPattern(const std::string& path, std::string& variables, const std::string& block_size){
 
     long block = Block::parseblockSize(block_size); // parse string
 
-    vector<string> files;
-    string file;
-    ifstream infile(path);
+    std::vector<std::string> files;
+    std::string file;
+    std::ifstream infile(path);
 
-    long size = sizeof(vector<string>) + sizeof(vector<vector<int>>); // memory footprint
+    long size = sizeof(std::vector<std::string>) + sizeof(std::vector<std::vector<int>>); // memory footprint
 
-    string pattern = "";
+    std::string pattern = "";
     // while the stitching vector contains another line:
     //      get block of file from stitching vector and call internal memory version of infer pattern on the block
     while(getline(infile, file)){
@@ -81,11 +79,11 @@ string ExternalVectorPattern::inferPattern(const string& path, string& variables
 
         files.push_back(s::escape_regex_characters(file));
 
-        size += sizeof(string) + file.length() + sizeof(int)*2*file.length(); // account for size of filenames
+        size += sizeof(std::string) + file.length() + sizeof(int)*2*file.length(); // account for size of filenames
 
          if(size >= block) {
             pattern = inferPatternInternal(files, variables, pattern);
-            size = sizeof(vector<string>) + sizeof(vector<vector<int>>);
+            size = sizeof(std::vector<std::string>) + sizeof(std::vector<std::vector<int>>);
             files.clear();
         }
     }

src/filepattern/cpp/internal/filepattern.cpp

@@ -2,9 +2,7 @@
 #include "../util/util.hpp"
 #include <chrono>
 
-using namespace std;
-
-FilePatternObject::FilePatternObject(const string& path, const string& file_pattern, bool recursive, bool suppress_warnings, bool sorted) {
+FilePatternObject::FilePatternObject(const std::string& path, const std::string& file_pattern, bool recursive, bool suppress_warnings, bool sorted) {
 
     this->setSuppressWarnings(suppress_warnings);
 
@@ -17,7 +15,7 @@ FilePatternObject::FilePatternObject(const string& path, const string& file_patt
             this->recursive_ = true;
             this->setJustPath(true);
         } catch (const std::runtime_error& e) {
-            string error = "No directory found. Invalid path \"" + path + "\".";
+            std::string error = "No directory found. Invalid path \"" + path + "\".";
             throw std::runtime_error(error);
         }
 
@@ -46,7 +44,7 @@ FilePatternObject::FilePatternObject(const string& path, const string& file_patt
                 this->iterator_ = fs::directory_iterator(fs::path(this->getPath())); // store iterator for target directory
             }
         } catch (const std::runtime_error& e) {
-            string error = "No directory found. Invalid path \"" + path + "\".";
+            std::string error = "No directory found. Invalid path \"" + path + "\".";
             throw std::runtime_error(error);
         }
     }
@@ -64,10 +62,10 @@ FilePatternObject::FilePatternObject(const string& path, const string& file_patt
 void FilePatternObject::matchFilesOneDir(){
 
     Map mapping;
-    vector<string> parsed_regex;
+    std::vector<std::string> parsed_regex;
 
-    string s;
-    string file, file_path;
+    std::string s;
+    std::string file, file_path;
     Tuple member;
     // Iterate over every file in directory
 
@@ -76,11 +74,11 @@ void FilePatternObject::matchFilesOneDir(){
         auto start = this->getRegexFilePattern().find('{');
         auto end = this->getRegexFilePattern().find('}');
         auto length = end - start;
-        throw invalid_argument("Invalid pattern found in bracket expressions in filepattern: \"" + this->getRegexFilePattern().substr(start, length+1) + "\"");
+        throw std::invalid_argument("Invalid pattern found in bracket expressions in filepattern: \"" + this->getRegexFilePattern().substr(start, length+1) + "\"");
     }
 
-    regex pattern_regex = regex(this->getRegexFilePattern());
-    smatch sm;
+    std::regex pattern_regex = std::regex(this->getRegexFilePattern());
+    std::smatch sm;
 
     for (const auto& entry : this->iterator_) {
         // Get the current file
@@ -96,11 +94,11 @@ void FilePatternObject::matchFilesOneDir(){
 
 void FilePatternObject::matchFilesMultDir(){
 
-    regex pattern_regex = regex(this->getRegexFilePattern());
+    std::regex pattern_regex = std::regex(this->getRegexFilePattern());
 
     Tuple tup;
-    smatch sm;
-    string file, file_path;
+    std::smatch sm;
+    std::string file, file_path;
 
     bool is_pushed = false;
 
@@ -125,7 +123,7 @@ void FilePatternObject::matchFilesMultDir(){
                 tup = getVariableMapMultDir(file_path, sm);
             }
 
-            if(get<0>(tup).size() > 0){
+            if(std::get<0>(tup).size() > 0){
                 this->valid_files_.push_back(tup); 
                 is_pushed = true;
             } else {
@@ -134,7 +132,7 @@ void FilePatternObject::matchFilesMultDir(){
         }
     }
 
-    if (!is_pushed && get<1>(tup).size() > 0) {
+    if (!is_pushed && std::get<1>(tup).size() > 0) {
          this->valid_files_.push_back(tup); 
     }
 }