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Description: Renamed seqan::fill function calls to use seqan::resize.
SeqAn 1.3 renamed seqan::fill() to seqan::resize().
SeqAn ticket: http://trac.seqan.de/ticket/77
Forwarded: no
Author: Ognyan Kulev <ogi@debian.org>
Last-Update: 2014-08-13
--- a/blockwise_sa.h
+++ b/blockwise_sa.h
@@ -456,8 +456,8 @@ void KarkkainenBlockwiseSA<TStr>::buildS
try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
- fill(bucketSzs, numBuckets, 0, Exact());
- fill(bucketReps, numBuckets, OFF_MASK, Exact());
+ resize(bucketSzs, numBuckets, 0, Exact());
+ resize(bucketReps, numBuckets, OFF_MASK, Exact());
} catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
@@ -816,7 +816,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
// Not the last bucket
assert_lt(_cur, length(_sampleSuffs));
hi = _sampleSuffs[_cur];
- fill(zHi, _dcV, 0, Exact());
+ resize(zHi, _dcV, 0, Exact());
assert_eq(zHi[0], 0);
calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
}
@@ -825,7 +825,7 @@ void KarkkainenBlockwiseSA<TStr>::nextBl
assert_gt(_cur, 0);
assert_leq(_cur, length(_sampleSuffs));
lo = _sampleSuffs[_cur-1];
- fill(zLo, _dcV, 0, Exact());
+ resize(zLo, _dcV, 0, Exact());
assert_gt(_dcV, 3);
assert_eq(zLo[0], 0);
calcZ(t, lo, zLo, this->verbose(), this->sanityCheck());
--- a/diff_sample.h
+++ b/diff_sample.h
@@ -452,7 +452,7 @@ static String<T> getDeltaMap(T v, const
// Declare anchor-map-related items
String<T> amap;
size_t amapEnts = 1;
- fill(amap, v, 0xffffffff, Exact());
+ resize(amap, v, 0xffffffff, Exact());
amap[0] = 0;
// Print out difference cover (and optionally calculate
// anchor map)
@@ -532,7 +532,7 @@ public:
assert_gt(_d, 0);
assert_eq(1, popCount(_v)); // must be power of 2
// Build map from d's to idx's
- fill(_dInv, _v, 0xffffffff, Exact());
+ resize(_dInv, _v, 0xffffffff, Exact());
uint32_t lim = (uint32_t)length(_ds);
for(uint32_t i = 0; i < lim; i++) {
_dInv[_ds[i]] = i;
@@ -656,7 +656,7 @@ void DifferenceCoverSample<TStr>::doBuil
VMSG_NL(" Doing sanity check");
TIndexOffU added = 0;
String<TIndexOffU> sorted;
- fill(sorted, length(_isaPrime), OFF_MASK, Exact());
+ resize(sorted, length(_isaPrime), OFF_MASK, Exact());
for(size_t di = 0; di < this->d(); di++) {
uint32_t d = _ds[di];
size_t i = 0;
@@ -717,7 +717,7 @@ void DifferenceCoverSample<TStr>::buildS
assert_eq(length(_doffs), d+1);
// Size sPrime appropriately
reserve(sPrime, sPrimeSz+1, Exact()); // reserve extra slot for LS
- fill(sPrime, sPrimeSz, OFF_MASK, Exact());
+ resize(sPrime, sPrimeSz, OFF_MASK, Exact());
// Slot suffixes from text into sPrime according to the mu
// mapping; where the mapping would leave a blank, insert a 0
TIndexOffU added = 0;
@@ -823,7 +823,7 @@ void DifferenceCoverSample<TStr>::build(
// arrays back into sPrime.
VMSG_NL(" Allocating rank array");
reserve(_isaPrime, length(sPrime)+1, Exact());
- fill(_isaPrime, length(sPrime), OFF_MASK, Exact());
+ resize(_isaPrime, length(sPrime), OFF_MASK, Exact());
assert_gt(length(_isaPrime), 0);
{
Timer timer(cout, " Ranking v-sort output time: ", this->verbose());
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