/usr/include/pbseq/alignment/suffixarray/LCPTable.hpp is in libblasr-dev 0~20161219-1.
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 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 | #ifndef _BLASR_LCP_TABLE_HPP_
#define _BLASR_LCP_TABLE_HPP_
#include <map>
#include <fstream>
#include "../../pbdata/utils.hpp"
template <typename T>
class LCPTable {
//
// Change the following TWO type defs if
// the max LCP is changed.
//
typedef short SignedPrefixLength;
typedef unsigned short PrefixLength;
typedef std::map<int, int> LongPrefixMap;
PrefixLength maxPrefixLength;
LongPrefixMap llongPrefixMap, rlongPrefixMap;
int tableLength;
public:
PrefixLength *llcp, *rlcp;
LCPTable() {
tableLength =0;
llcp = rlcp = NULL;
}
LCPTable(T* data, unsigned int pTableLength) {
Init(data, pTableLength);
}
inline int LengthLongestCommonPrefix(T* a, int alen, T* b, int blen) {
int i;
for (i = 0 ; i < alen and i < blen; i++ )
if (a[i] != b[i])
break;
return i;
}
void Init(T* data, unsigned int pTableLength, unsigned int *index) {
tableLength = pTableLength;
maxPrefixLength = (PrefixLength) (SignedPrefixLength(-1));
llcp = ProtectedNew<PrefixLength>(tableLength);
rlcp = ProtectedNew<PrefixLength>(tableLength);
std::fill(llcp, llcp + tableLength, 0);
std::fill(rlcp, rlcp + tableLength, 0);
FillTable(data, index);
}
int SetL(int index, int length) {
assert(index >= 0);
assert(index < tableLength);
if (index >= maxPrefixLength) {
llcp[index] = maxPrefixLength;
llongPrefixMap[index] = length;
}
else {
llcp[index] = length;
}
return llcp[index];
}
int SetR(int index, int length) {
assert(index >= 0);
assert(index < tableLength);
if (index >= maxPrefixLength) {
rlcp[index] = maxPrefixLength;
rlongPrefixMap[index] = length;
}
else {
rlcp[index] = length;
}
return rlcp[index];
}
int GetL(int index) {
if (llcp[index] == maxPrefixLength) {
assert(llongPrefixMap.find(index) != llongPrefixMap.end());
return llongPrefixMap[index];
}
else {
return llcp[index];
}
}
int GetR(int index) {
if (rlcp[index] == maxPrefixLength) {
assert(rlongPrefixMap.find(index) != llongPrefixMap.end());
return rlongPrefixMap[index];
}
else {
return rlcp[index];
}
}
~LCPTable() {
if (llcp != NULL) {
delete[] llcp;
llcp = NULL;
}
if (rlcp != NULL) {
delete[] rlcp;
rlcp = NULL;
}
// the two maps automatically go away.
}
void WriteLCPTable(std::ofstream &out) {
out.write((char*) &tableLength, sizeof(tableLength));
out.write((char*) llcp, sizeof(PrefixLength)*tableLength);
out.write((char*) rlcp, sizeof(PrefixLength)*tableLength);
typename LongPrefixMap::iterator llcpTableIt, llcpTableEnd;
int llongPrefixMapSize = llongPrefixMap.size();
out.write((char*) &llongPrefixMapSize, sizeof(llongPrefixMapSize));
for((llcpTableIt = llongPrefixMap.begin(),
llcpTableEnd = llongPrefixMap.end());
llcpTableIt != llcpTableEnd;
++llcpTableIt) {
out.write((char*) &llcpTableIt->first, sizeof(typename LongPrefixMap::key_type));
out.write((char*) &llcpTableIt->second, sizeof(typename LongPrefixMap::mapped_type));
}
typename LongPrefixMap::iterator rlcpTableIt, rlcpTableEnd;
int rlongPrefixMapSize = rlongPrefixMap.size();
out.write((char*) &rlongPrefixMapSize, sizeof(rlongPrefixMapSize));
for((rlcpTableIt = rlongPrefixMap.begin(),
rlcpTableEnd = rlongPrefixMap.end());
rlcpTableIt != rlcpTableEnd;
++rlcpTableIt) {
out.write((char*) &rlcpTableIt->first, sizeof(typename LongPrefixMap::key_type));
out.write((char*) &rlcpTableIt->second, sizeof(typename LongPrefixMap::mapped_type));
}
}
void ReadLCPTables(std::ifstream &in) {
in.read((char*) &tableLength, sizeof(tableLength));
in.read((char*) &llcp, sizeof(PrefixLength)*tableLength);
in.read((char*) &rlcp, sizeof(PrefixLength)*tableLength);
int longPrefixMapSize;
in.read((char*) &longPrefixMapSize, sizeof(longPrefixMapSize));
int i;
int index, lcpLength;
// The rest is stored as a tree, but read and construct this on the fly.
for (i = 0; i < longPrefixMapSize; i++) {
in.read((char*) &index, sizeof(index));
in.read((char*) &lcpLength, sizeof(lcpLength));
llongPrefixMap[index] = lcpLength;
}
// Read the rlcp
in.read((char*) &longPrefixMapSize, sizeof(longPrefixMapSize));
for (i = 0; i < longPrefixMapSize; i++) {
in.read((char*) &index, sizeof(index));
in.read((char*) &lcpLength, sizeof(lcpLength));
rlongPrefixMap[index] = lcpLength;
}
}
void FillTable(T* data, unsigned int *index) {
//
// This assumes that the index table is now in sorted order.
//
FillTable(0, tableLength, data, index);
}
void FillTable(unsigned int low, unsigned int high, T* data, unsigned int *index) {
if (low == high)
return;
unsigned int mid = (low + high) / 2;
assert (mid != low);
SetL(mid, LengthLongestCommonPrefix(&data[index[low]], tableLength - index[low],
&data[index[mid]], tableLength - index[mid]));
FillTable(low, mid, data, index);
assert(mid != high);
SetR(mid, LengthLongestCommonPrefix(&data[index[mid]], tableLength - index[mid],
&data[index[high]], tableLength - index[high]));
FillTable(mid+1, high, data, index);
}
};
#endif // _BLASR_LCP_TABLE_HPP_
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