/usr/include/pbseq/alignment/tuples/TupleListImpl.hpp is in libblasr-dev 0~20161219-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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TupleList<T>::TupleList() {
listLength = 0;
}
template<typename T>
void TupleList<T>::Reset() {
std::vector<T>().swap(tupleList);
}
template<typename T>
T& TupleList<T>::operator[](int index) {
return tupleList[index];
}
template<typename T>
void TupleList<T>::GetTupleMetrics(TupleMetrics &ptm) {
ptm = tm;
}
template<typename T>
void TupleList<T>::SetTupleMetrics(TupleMetrics &ptm) {
tm = ptm;
}
template<typename T>
int TupleList<T>::size() {
return tupleList.size();
}
template<typename T>
int TupleList<T>::GetLength() {
return tupleList.size();
}
template<typename T>
int TupleList<T>::InitFromFile(std::string &fileName) {
std::ifstream listIn;
listIn.open(fileName.c_str(), std::ios_base::binary);
if (!listIn)
return 0;
listIn.read((char*) &listLength, sizeof(int));
listIn.read((char*) &tm.tupleSize, sizeof(int));
tm.InitializeMask();
tupleList.resize(listLength);
listIn.read((char*) &tupleList[0], sizeof(T) * listLength);
return 1;
}
template<typename T>
void TupleList<T>::clear() {
tupleList.clear();
listLength = 0;
}
template<typename T>
int TupleList<T>::WriteToFile(std::string &fileName) {
std::ofstream listOut;
listOut.open(fileName.c_str(), std::ios_base::binary);
if (!listOut)
return 0;
listLength = tupleList.size();
std::cout << "writing tuple lis of length " << listLength << std::endl;
listOut.write((char*) &listLength, sizeof(int));
listOut.write((char*) &tm.tupleSize, sizeof(int));
listOut.write((char*) &tupleList[0], sizeof(T)*listLength);
return 1;
}
//
// Find one instance of a match.
//
template<typename T>
int TupleList<T>::Find( T& tuple) {
typename std::vector<T>::const_iterator begin, end, matchIt;
begin = tupleList.begin();
end = tupleList.end();
matchIt = lower_bound(begin, end, tuple);
if (*matchIt != tuple) {
return -1;
}
else {
return matchIt - tupleList.begin();
}
}
//
// Find the boundaries of all instances of a match.
//
template<typename T>
void TupleList<T>::FindAll(T &tuple,
typename std::vector<T>::const_iterator &firstPos,
typename std::vector<T>::const_iterator &endPos ) {
firstPos = lower_bound(tupleList.begin(), tupleList.end(), tuple);
typename std::vector<T>::const_iterator firstPos2;
endPos = tupleList.end();
endPos = upper_bound(firstPos, endPos, tuple);
while (endPos != tupleList.end()) {
if (*endPos != tuple) {
return;
}
else {
endPos++;
}
}
}
template<typename T>
void TupleList<T>::Append( T&tuple) {
tupleList.push_back(tuple);
}
template<typename T>
void TupleList<T>::Insert(T&tuple) {
// insert and maintain order.
typename std::vector<T>::iterator pos;
pos = std::lower_bound(tupleList.begin(), tupleList.end(), tuple);
tupleList.insert(pos, tuple);
}
template<typename T>
void TupleList<T>::Sort() {
sort(tupleList.begin(), tupleList.end());
}
template<typename T>
void TupleList<T>::Print() {
int i;
for (i = 0; i< tupleList.size(); i++) {
std::cout << tupleList[i].tuple << std::endl;
}
}
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