/usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.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.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 | #ifndef SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
#define SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
#include <stdlib.h>
#include <stdint.h>
#include <algorithm>
#include <cassert>
#include <set>
#include <limits.h>
#include <ostream>
#include "SDPSet.hpp"
#include "SDPFragment.hpp"
#include "SDPColumn.hpp"
#include "FragmentSort.hpp"
template<typename T_Fragment>
void StoreAbove(std::vector<T_Fragment> &fragmentSet, DNALength fragmentLength) {
(void)(fragmentLength);
std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSortByY<T_Fragment>());
for (size_t i = 1; i < fragmentSet.size(); i++) {
if (fragmentSet[i-1].x <= fragmentSet[i].x
and fragmentSet[i-1].x + fragmentSet[i-1].length > fragmentSet[i].x
and fragmentSet[i-1].y < fragmentSet[i].y) {
fragmentSet[i].SetAbove(fragmentSet[i-1].index);
}
}
// Place back in original order.
std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<T_Fragment>());
}
template<typename T_Fragment>
int SDPLongestCommonSubsequence(DNALength queryLength,
std::vector<T_Fragment> &fragmentSet,
DNALength fragmentLength,
int insertion, int deletion, int match,
std::vector<int> &maxFragmentChain, AlignmentType alignType) {
maxFragmentChain.clear();
if (fragmentSet.size() < 1)
return 0;
std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<T_Fragment>());
SDPSet<Fragment> sweepSet;
SDPSet<SDPColumn> colSet;
unsigned int sweepRow;
unsigned int trailRow;
VectorIndex fSweep, fTrail;
VectorIndex fi;
for (fi = 0; fi < fragmentSet.size(); fi++) {
fragmentSet[fi].index = fi;
}
StoreAbove(fragmentSet, fragmentLength);
sweepRow = fragmentSet[0].x;
Fragment pred, succ;
fSweep = 0;
fTrail = 0;
unsigned int maxChainLength = 0;
int maxChainFragment = -1;
int minFragmentCost, minFragmentIndex;
minFragmentCost = INF_INT;
minFragmentIndex = -1;
for (; sweepRow < queryLength + fragmentLength; sweepRow++) {
//
// Add all elements on the sweep row to the sweep set. Note that when
// fSweep is past query.length.
int startF = fSweep;
size_t fragmentSetSize = fragmentSet.size();
while (fSweep < fragmentSetSize and
fragmentSet[fSweep].x == sweepRow) {
//
// Compute the cost of every fragment in the sweep.
//
int cp = INF_INT, cl = INF_INT, ca = INF_INT;
SDPColumn curCol, predCol;
curCol.col = fragmentSet[fSweep].y;
//
// Search preceeding fragments.
//
//
// Compute the cost of fragment_f
int foundPrev = 0;
int driftPenalty;
if (colSet.Predecessor(curCol, predCol)) {
//
// predCol points to the fragment with greatest value less than curCol.
//
// Baker and Giancarlo LCS cost
driftPenalty = IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
fragmentSet[predCol.optFragment].x,
fragmentSet[predCol.optFragment].y,
insertion, deletion);
cp = fragmentSet[predCol.optFragment].cost + driftPenalty;
foundPrev = 1;
}
// Search overlapping fragments.
if (sweepSet.Predecessor(fragmentSet[fSweep], pred)) {
//
// Baker and Giancarlo LCS cost
// Cost with insertion and deletion penalty.
//
cl = pred.cost +
MIN((int)(fragmentLength - (fragmentSet[fSweep].y - pred.y)) * match, 0) +
IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
pred.x, pred.y, insertion, deletion);
foundPrev = 1;
}
int aboveIndex;
if (fragmentSet[fSweep].GetAbove(aboveIndex)) {
// Baker and Giancarlo LCS cost
ca = fragmentSet[aboveIndex].cost +
(fragmentLength - (int)(fragmentSet[fSweep].y - fragmentSet[aboveIndex].y)) * match +
IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
fragmentSet[aboveIndex].x,
fragmentSet[aboveIndex].y,
insertion, deletion);
foundPrev = 1;
}
//
// Now compute the minimum of all these.
//
int minCost;
minCost = MIN(cp, MIN(cl, ca));
//
// If doing a global alignment, chain is always extended. If local, the chain may not be.
//
if (foundPrev and
(alignType == Global or
(alignType == Local and minCost < 0))) {
fragmentSet[fSweep].cost = minCost - fragmentSet[fSweep].weight;
if (minCost == cp) {
fragmentSet[fSweep].chainPrev = predCol.optFragment;
}
else if (minCost == cl) {
fragmentSet[fSweep].chainPrev = pred.index;
}
else if (minCost == ca) {
fragmentSet[fSweep].chainPrev = aboveIndex;
}
assert(fragmentSet[fSweep].chainPrev >= 0 and
fragmentSet[fSweep].chainPrev < (int)fragmentSet.size());
fragmentSet[fSweep].chainLength = fragmentSet[fragmentSet[fSweep].chainPrev].chainLength + 1;
}
else {
if (alignType == Global) {
fragmentSet[fSweep].chainPrev = (int) -1;
fragmentSet[fSweep].cost = (fragmentSet[fSweep].x + fragmentSet[fSweep].y) * deletion +
fragmentLength * match - fragmentSet[fSweep].weight;
fragmentSet[fSweep].chainLength = 1;
}
else if (alignType == Local) {
fragmentSet[fSweep].chainPrev = (int) -1;
fragmentSet[fSweep].cost = fragmentLength * match - fragmentSet[fSweep].weight;
fragmentSet[fSweep].chainLength = 1;
}
}
if (minFragmentCost > fragmentSet[fSweep].cost) {
minFragmentCost = fragmentSet[fSweep].cost;
minFragmentIndex = fSweep;
// maxChainLength = fragmentSet[fSweep].chainLength;
}
if (fragmentSet[fSweep].chainLength > maxChainLength) {
maxChainLength = fragmentSet[fSweep].chainLength;
maxChainFragment = fSweep;
}
// Done computing the optimal score for this fragment.
fSweep++;
}
//
// Insert all fragments in the sweep set
//
fSweep = startF;
while (fSweep < fragmentSetSize and
fragmentSet[fSweep].x == sweepRow) {
// cout << "inserting sweep set with index" << fragmentSet[fSweep].index << endl;
sweepSet.Insert(fragmentSet[fSweep]);
++fSweep;
}
// Remove elements from the sweep set that are too far back.
if (sweepRow >= fragmentLength + 1) {
trailRow = sweepRow - fragmentLength - 1;
while (fTrail < fragmentSetSize and
fragmentSet[fTrail].x == trailRow) {
//
// These elements are removed from the sweep set since they are done being processed.
// If they are the lowest cost in the value, update colSet
//
SDPColumn col;
int storeCol = 0;
col.col = fragmentSet[fTrail].y;
if (colSet.Member(col)) {
if (fragmentSet[col.optFragment].cost < fragmentSet[fTrail].cost) {
storeCol = 1;
}
}
else {
storeCol = 1;
}
if (storeCol) {
col.col = fragmentSet[fTrail].y;
col.optFragment = fTrail;
//
// Insert new column or replace col with a more optimal one.
//
colSet.Insert(col);
//
// The invariant structure of the colSet is that
// after inserting a fragment of score S at column col,
// the score of all columns greater than 'col' in col set
// must be less than col.
//
// To preserve this invariant, when an element is inserted
// at 'col', look to columns greater. As long as any columns
// have scores that are greater than col, remove them.
// Once a column col_next has been found that has a score less than S
// by the structure of the loop invariant, all columns greater than col_next
// are guaranteed to have lower score than S, so we can continue searching
// through this loop.
//
// Since fragments are processed at most once, this remains O(M).
SDPColumn successorCol = col;
while (colSet.Successor(col, successorCol) and
fragmentSet[successorCol.optFragment].cost > fragmentSet[fTrail].cost) {
colSet.Delete(successorCol);
}
}
//
// Now remove this fragment, it is at the end of the sweep line.
//
int deleted;
deleted = sweepSet.Delete(fragmentSet[fTrail]);
assert(deleted);
++fTrail;
}
}
}
if (alignType == Local) {
maxChainFragment = minFragmentIndex;
}
while (maxChainFragment != -1) {
maxFragmentChain.push_back(maxChainFragment);
maxChainFragment = fragmentSet[maxChainFragment].chainPrev;
}
std::reverse(maxFragmentChain.begin(), maxFragmentChain.end());
return maxFragmentChain.size();
}
#endif // __SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
|