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#ifndef _BLASR_SHARED_SUFFIX_ARRAY_HPP_
#define _BLASR_SHARED_SUFFIX_ARRAY_HPP_
#include <cstdlib>
#include <fstream>
#include <sstream>
#include <alignment/algorithms/compare/CompareStrings.hpp>
#include <alignment/ipc/SharedMemoryAllocator.hpp>
#include <alignment/suffixarray/SuffixArray.hpp>
#include <alignment/tuples/CompressedDNATuple.hpp>
#include <alignment/tuples/DNATuple.hpp>
template <typename T, typename Sigma, typename Compare = DefaultCompareStrings<T>,
typename Tuple = DNATuple>
class SharedSuffixArray : public SuffixArray<T, Sigma, Compare, Tuple>
{
public:
std::string shmIdTag;
SAIndex *indexShared;
int indexID;
std::string indexHandle;
SAIndex *lookupTableShared;
int lookupTableID;
std::string lookupTableHandle;
int lookupPrefixLength;
void InitShmIdTag()
{
std::stringstream tagStrm;
tagStrm << "_" << getpid();
shmIdTag = tagStrm.str();
}
void ReadSharedArray(std::ifstream &saIn)
{
std::cout << "reading a shared suffix array index." << std::endl;
saIn.read((char *)&this->length, sizeof(int));
indexHandle = "suffixarray.index." + shmIdTag;
AllocateMappedShare(indexHandle, this->length + 1, indexShared, indexID);
std::cout << "the shared index is: " << indexShared << std::endl;
this->index = indexShared;
std::cout << "the index used is: " << this->index << std::endl;
this->ReadAllocatedArray(saIn);
}
void ReadSharedLookupTable(std::ifstream &saIn)
{
this->ReadLookupTableLengths(saIn);
lookupTableHandle = "suffixarray.lookuptable." + shmIdTag;
AllocateMappedShare(lookupTableHandle, this->lookupTableLength + 1, lookupTableShared,
lookupTableID);
this->lookupTable = lookupTableShared;
this->ReadAllocatedLookupTable(saIn);
}
void ReadShared(std::string &inFileName)
{
std::ifstream saIn;
InitShmIdTag();
saIn.open(inFileName.c_str(), std::ios::binary);
this->ReadComponentList(saIn);
if (this->componentList[SuffixArray<T, Sigma, Compare, Tuple>::CompArray]) {
this->ReadSharedArray(saIn);
}
if (this->componentList[SuffixArray<T, Sigma, Compare, Tuple>::CompLookupTable]) {
this->ReadSharedLookupTable(saIn);
}
saIn.close();
}
void FreeShared()
{
if (this->componentList[SuffixArray<T, Sigma, Compare, Tuple>::CompArray]) {
shm_unlink(indexHandle.c_str());
}
if (this->componentList[SuffixArray<T, Sigma, Compare, Tuple>::CompLookupTable]) {
shm_unlink(lookupTableHandle.c_str());
}
}
};
#endif // _BLASR_SHARED_SUFFIX_ARRAY_HPP_
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