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
|
/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef BINARY_SA_SEARCH_H_
#define BINARY_SA_SEARCH_H_
#include <stdint.h>
#include <iostream>
#include <limits>
#include "alphabet.h"
#include "assert_helpers.h"
#include "ds.h"
#include "btypes.h"
/**
* Do a binary search using the suffix of 'host' beginning at offset
* 'qry' as the query and 'sa' as an already-lexicographically-sorted
* list of suffixes of host. 'sa' may be all suffixes of host or just
* a subset. Returns the index in sa of the smallest suffix of host
* that is larger than qry, or length(sa) if all suffixes of host are
* less than qry.
*
* We use the Manber and Myers optimization of maintaining a pair of
* counters for the longest lcp observed so far on the left- and right-
* hand sides and using the min of the two as a way of skipping over
* characters at the beginning of a new round.
*
* Returns maximum value if the query suffix matches an element of sa.
*/
template<typename TStr, typename TSufElt> inline
TIndexOffU binarySASearch(
const TStr& host,
TIndexOffU qry,
const EList<TSufElt>& sa)
{
TIndexOffU lLcp = 0, rLcp = 0; // greatest observed LCPs on left and right
TIndexOffU l = 0, r = (TIndexOffU)sa.size()+1; // binary-search window
TIndexOffU hostLen = (TIndexOffU)host.length();
while(true) {
assert_gt(r, l);
TIndexOffU m = (l+r) >> 1;
if(m == l) {
// Binary-search window has closed: we have an answer
if(m > 0 && sa[m-1] == qry) {
return std::numeric_limits<TIndexOffU>::max(); // qry matches
}
assert_leq(m, sa.size());
return m; // Return index of right-hand suffix
}
assert_gt(m, 0);
TIndexOffU suf = sa[m-1];
if(suf == qry) {
return std::numeric_limits<TIndexOffU>::max(); // query matches an elt of sa
}
TIndexOffU lcp = min(lLcp, rLcp);
#ifndef NDEBUG
if(sstr_suf_upto_neq(host, qry, host, suf, lcp)) {
assert(0);
}
#endif
// Keep advancing lcp, but stop when query mismatches host or
// when the counter falls off either the query or the suffix
while(suf+lcp < hostLen && qry+lcp < hostLen && host[suf+lcp] == host[qry+lcp]) {
lcp++;
}
// Fell off the end of either the query or the sa elt?
bool fell = (suf+lcp == hostLen || qry+lcp == hostLen);
if((fell && qry+lcp == hostLen) || (!fell && host[suf+lcp] < host[qry+lcp])) {
// Query is greater than sa elt
l = m; // update left bound
lLcp = max(lLcp, lcp); // update left lcp
}
else if((fell && suf+lcp == hostLen) || (!fell && host[suf+lcp] > host[qry+lcp])) {
// Query is less than sa elt
r = m; // update right bound
rLcp = max(rLcp, lcp); // update right lcp
} else {
assert(false); // Must be one or the other!
}
}
// Shouldn't get here
assert(false);
return std::numeric_limits<TIndexOffU>::max();
}
#endif /*BINARY_SA_SEARCH_H_*/
|
