/usr/include/blasr/suffixarray/SharedSuffixArray.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | #ifndef _BLASR_SHARED_SUFFIX_ARRAY_HPP_
#define _BLASR_SHARED_SUFFIX_ARRAY_HPP_
#include <stdlib.h>
#include <fstream>
#include <sstream>
#include "SuffixArray.hpp"
#include "ipc/SharedMemoryAllocator.hpp"
#include "tuples/DNATuple.hpp"
#include "tuples/CompressedDNATuple.hpp"
#include "algorithms/compare/CompareStrings.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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