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General performance improvements #200

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General performance improvements #200

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12c0eb3
Added TODO to branches which may cause performance problems
Sep 5, 2014
72fa9dc
better language in comments
Sep 12, 2014
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2 changes: 1 addition & 1 deletion include/sdsl/bit_vector_il.hpp
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Expand Up @@ -130,7 +130,7 @@ class bit_vector_il
size_type cum_sum = 0;
size_type sample_rate = t_bs/64;
for (size_type i=0, sample_cnt=sample_rate; i < blocks; ++i, ++sample_cnt) {
if (sample_cnt == sample_rate) {
if (sample_cnt == sample_rate) { // TODO get rid of this branch
m_data[j] = cum_sum;
sample_cnt = 0;
j++;
Expand Down
8 changes: 4 additions & 4 deletions include/sdsl/bp_support_sada.hpp
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Expand Up @@ -369,7 +369,7 @@ class bp_support_sada
// calculate min/max excess values of the small blocks and medium blocks
difference_type min_ex = 1, max_ex = -1, curr_rel_ex = 0, curr_abs_ex = 0;
for (size_type i=0; i < m_size; ++i) {
if ((*bp)[i])
if ((*bp)[i]) // TODO This is not good
++curr_rel_ex;
else
--curr_rel_ex;
Expand Down Expand Up @@ -397,9 +397,9 @@ class bp_support_sada

for (size_type v = m_med_block_min_max.size()/2 - 1; !is_root(v); --v) {
size_type p = parent(v);
if (min_value(v) < min_value(p)) // update minimum
if (min_value(v) < min_value(p)) // update minimum TODO branch can be avoided
m_med_block_min_max[2*p] = m_med_block_min_max[2*v];
if (max_value(v) > max_value(p)) // update maximum
if (max_value(v) > max_value(p)) // update maximum TODO branch can be avoided
m_med_block_min_max[2*p+1] = m_med_block_min_max[2*v+1];
}
}
Expand Down Expand Up @@ -648,7 +648,7 @@ class bp_support_sada
l_sblock = 1;
}
for (size_type i=l_sblock; i <= r_sblock; ++i) {
if ((e = (excess(i*t_sml_blk-1) + sml_min_value(i))) <= min_ex) {
if ((e = (excess(i*t_sml_blk-1) + sml_min_value(i))) <= min_ex) { //TODO branch can be avoided
pos_min_block = i;
min_ex = e;
}
Expand Down
2 changes: 1 addition & 1 deletion include/sdsl/coder_comma.hpp
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Expand Up @@ -258,7 +258,7 @@ inline uint64_t comma<t_width>::decode(const uint64_t* data,
digit = (uint32_t)bits::read_int_and_move(data, offset, t_width)); //and read next digit
//now decide how to handle value
value = (t_sumup) ? value + v : v;
if (t_inc) *(it++) = value;
if (t_inc) *(it++) = value; // TODO can be done without the branch
}
return value;
}
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/coder_elias_delta.hpp
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Expand Up @@ -161,7 +161,7 @@ bool elias_delta::encode(const int_vector& v, int_vector& z)
uint64_t w;
const uint64_t zero_val = v.width() < 64 ? (1ULL)<<v.width() : 0;
for (typename int_vector::const_iterator it = v.begin(), end = v.end(); it != end; ++it) {
if ((w=*it) == 0) {
if ((w=*it) == 0) { // TODO get rid of this branch
w = zero_val;
}
z_bit_size += encoding_length(w);
Expand All @@ -176,7 +176,7 @@ bool elias_delta::encode(const int_vector& v, int_vector& z)
size_type len, len_1_len; // TODO: change to uint8_t and test it
for (typename int_vector::const_iterator it = v.begin(), end=v.end(); it != end; ++it) {
w = *it;
if (w == 0) {
if (w == 0) { // TODO get rid of this branch
w = zero_val;
}
// (number of bits to represent w)
Expand Down
10 changes: 5 additions & 5 deletions include/sdsl/coder_elias_gamma.hpp
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Expand Up @@ -157,7 +157,7 @@ bool elias_gamma::encode(const int_vector& v, int_vector& z)
uint64_t w;
const uint64_t zero_val = v.width() < 64 ? (1ULL)<<v.width() : 0;
for (typename int_vector::const_iterator it = v.begin(), end = v.end(); it != end; ++it) {
if ((w=*it) == 0) {
if ((w=*it) == 0) { // TODO not necessary
w = zero_val;
}
z_bit_size += encoding_length(w);
Expand All @@ -172,19 +172,19 @@ bool elias_gamma::encode(const int_vector& v, int_vector& z)
size_type len_1; // TODO: change to uint8_t and test it
for (typename int_vector::const_iterator it = v.begin(), end=v.end(); it != end; ++it) {
w = *it;
if (w == 0) {
if (w == 0) { // TODO not necessary
w = zero_val;
}
// (number of bits to represent w)-1
if (!w) {
if (!w) { // TODO get rid of this branch
len_1 = 64;
bits::write_int_and_move(z_data, 0ULL, offset, 64);
bits::write_int_and_move(z_data, 1ULL, offset, 1);
} else {
} else { // TODO get rid of this branch
len_1 = bits::hi(w);
bits::write_int_and_move(z_data, 1ULL << len_1, offset, len_1+1);
}
if (len_1) {
if (len_1) { // TODO get rid of this branch
bits::write_int_and_move(z_data, w, offset, len_1);
}
}
Expand Down
10 changes: 5 additions & 5 deletions include/sdsl/coder_fibonacci.hpp
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Expand Up @@ -55,9 +55,9 @@ class fibonacci

impl() {
for (uint32_t x=0; x <= 0x1FFF; ++x) {
if (bits::cnt11(x)) {
if (bits::cnt11(x)) { // TODO get rid of this branch
fib2bin_shift[x] = bits::sel11(x, 1)+1;
} else {
} else { // TODO get rid of this branch
fib2bin_shift[x] = 0;
}
}
Expand Down Expand Up @@ -169,8 +169,8 @@ inline bool fibonacci::encode(const int_vector1& v, int_vector2& z)
uint64_t w;
const uint64_t zero_val = v.width() < 64 ? (1ULL)<<v.width() : 0;
for (typename int_vector1::const_iterator it=v.begin(), end = v.end(); it != end; ++it) {
if ((w=*it) == 0) {
if (v.width() < 64) {
if ((w=*it) == 0) { // TODO unnecessary branch
if (v.width() < 64) { // TODO unnecessary branch
w = zero_val;
}
}
Expand All @@ -186,7 +186,7 @@ inline bool fibonacci::encode(const int_vector1& v, int_vector2& z)
uint64_t t;
for (typename int_vector1::const_iterator it=v.begin(), end = v.end(); it != end; ++it) {
w = *it;
if (w == 0) {
if (w == 0) { // TODO unnecessary branch
w = zero_val;
}
int8_t len_1 = encoding_length(w)-1,j;
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/construct_lcp.hpp
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Expand Up @@ -83,7 +83,7 @@ void construct_lcp_kasai(cache_config& config)
sa_1 = isa_buf[i]; // = isa[i]
if (sa_1) {
j = sa[sa_1-1];
if (l) --l;
if (l) --l; // TODO l changes in the else, could be unpredictable
assert(i!=j);
while (text[i+l]==text[j+l]) { // i+l < n and j+l < n are not necessary, since text[n]=0 and text[i]!=0 (i<n) and i!=j
++l;
Expand Down Expand Up @@ -158,7 +158,7 @@ void construct_lcp_PHI(cache_config& config)
++l;
}
plcp[i] = l;
if (l) {
if (l) { // TODO possible without the branch
max_l = std::max(max_l, l);
--l;
}
Expand Down
25 changes: 13 additions & 12 deletions include/sdsl/construct_sa_se.hpp
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Expand Up @@ -239,10 +239,10 @@ void _construct_sa_se(int_vector_type& text, std::string filename_sa, uint64_t s
bkt_s_last=0, bkt_s_sum=0;
for (size_t i=0; i<sigma; ++i) {
bkt_s_sum += bkt_s[i];
if (bkt_s[i]) {
if (bkt_s[i]) { // TODO possible without the branch
bkt_s[i] = bkt_s_sum;
bkt_s_last = bkt_s_sum;
} else {
} else { // TODO possible without the branch
bkt_s[i] = bkt_s_sum;
}
bkt_lms[i] = bkt_s[i];
Expand Down Expand Up @@ -348,7 +348,7 @@ void _construct_sa_se(int_vector_type& text, std::string filename_sa, uint64_t s
++a;
++b;
}
if (text[a] == text[b]) {
if (text[a] == text[b]) { // TODO possible without conditional
same_lms[i] = true;
--order;
}
Expand All @@ -373,17 +373,17 @@ void _construct_sa_se(int_vector_type& text, std::string filename_sa, uint64_t s
util::_set_zero_bits(text_rec);
order = 0;
for (size_t i=number_of_lms_strings-1; i<number_of_lms_strings; --i) {
if (!same_lms[i]) {
if (!same_lms[i]) { // TODO possible without conditional
++order;
}
if (left[i]/2 >= size_of_part) {
if (left[i]/2 >= size_of_part) { // TODO possible without conditional
text_rec[(left[i]/2)-size_of_part] = order;
}
}
std::string filename_text_rec_part2 = tmp_file(filename_sa, "_text_rec_part2"+util::to_string(recursion));
size_t pos = 0;
for (size_t i=0; i<size_of_part; ++i) {
if (text_rec[i]>0) {
if (text_rec[i]>0) { // TODO possible without conditional
text_rec[pos++] = text_rec[i];
}
}
Expand All @@ -392,23 +392,24 @@ void _construct_sa_se(int_vector_type& text, std::string filename_sa, uint64_t s
text_rec.resize(size_of_part);
util::_set_zero_bits(text_rec);
order = 0;
// TODO code duplication !!
for (size_t i=number_of_lms_strings-1; i<number_of_lms_strings; --i) {
if (!same_lms[i]) {
if (!same_lms[i]) { // TODO possible without conditional
++order;
}
if (left[i]/2 < size_of_part) {
if (left[i]/2 < size_of_part) { // TODO possible without conditional
text_rec[left[i]/2] = order;
}
}
pos = 0;
for (size_t i=0; i<size_of_part; ++i) {
if (text_rec[i]>0) {
if (text_rec[i]>0) { // TODO possible without conditional
text_rec[pos++] = text_rec[i];
}
}
text_rec.resize(number_of_lms_strings);
int_vector_buffer<> buf(filename_text_rec_part2, std::ios::in, 1024*1024);
for (size_t i=0; i<buf.size(); ++i) {
for (size_t i=0; i<buf.size(); ++i) { // TODO possible without conditional
text_rec[pos++] = buf[i];
}
buf.close(true);
Expand All @@ -418,13 +419,13 @@ void _construct_sa_se(int_vector_type& text, std::string filename_sa, uint64_t s
util::_set_zero_bits(text_rec);
order = 0;
for (size_t i=number_of_lms_strings-1; i<number_of_lms_strings; --i) {
if (!same_lms[i]) {
if (!same_lms[i]) { // TODO possible without conditional
++order;
}
text_rec[left[left_pointer--]/2] = order;
}
for (size_t i=0, pos=0; i<text_rec.size(); ++i) {
if (text_rec[i]>0) {
if (text_rec[i]>0) { // TODO possible without conditional
text_rec[pos++] = text_rec[i];
}
}
Expand Down
2 changes: 1 addition & 1 deletion include/sdsl/csa_alphabet_strategy.hpp
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Expand Up @@ -269,7 +269,7 @@ class succinct_byte_alphabet
assert(1 == D[0]); // null-byte should occur exactly once
m_sigma = 0;
for (int i=0; i<256; ++i)
if (D[i]) {
if (D[i]) { // TODO possible without conditional
tmp_char[i] = 1; // mark occurring character
D[m_sigma] = D[i]; // compactify m_C
++m_sigma;
Expand Down
14 changes: 7 additions & 7 deletions include/sdsl/csa_sampling_strategy.hpp
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Expand Up @@ -85,7 +85,7 @@ class _sa_order_sampling : public int_vector<t_width>

for (size_type i=0, cnt_mod=sample_dens, cnt_sum=0; i < n; ++i, ++cnt_mod) {
size_type sa = sa_buf[i];
if (sample_dens == cnt_mod) {
if (sample_dens == cnt_mod) { // TODO possible without conditional
cnt_mod = 0;
(*this)[cnt_sum++] = sa;
}
Expand Down Expand Up @@ -151,7 +151,7 @@ class _text_order_sampling : public int_vector<t_width>

for (size_type i=0, sa_cnt=0; i < n; ++i) {
size_type sa = sa_buf[i];
if (0 == (sa % sample_dens)) {
if (0 == (sa % sample_dens)) { // TODO possible without conditional
marked[i] = 1;
(*this)[sa_cnt++] = sa;
}
Expand Down Expand Up @@ -299,18 +299,18 @@ class _bwt_sampling : public int_vector<t_width>
size_type sa = sa_buf[i];
char_type bwt = bwt_buf[i];
if (0 == (sa % sample_dens)) {
marked[i] = 1;
++sa_cnt;
marked[i] = 1; // TODO same as below
++sa_cnt; // TODO same as below
} else if (char_map.find(bwt) != char_map.end()) {
marked[i] = 1;
++sa_cnt;
marked[i] = 1; // TODO same as above
++sa_cnt; // TODO same as above
}
}
this->resize(sa_cnt);
sa_cnt = 0;
for (size_type i=0; i < n; ++i) {
size_type sa = sa_buf[i];
if (marked[i]) {
if (marked[i]) { // TODO possible without conditional
(*this)[sa_cnt++] = sa;
}
}
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/cst_sada.hpp
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Expand Up @@ -157,9 +157,9 @@ class cst_sada
util::set_to_value(m_bp, 0);
size_type idx=0;
for (cst_sct3<>::const_iterator it=temp_cst.begin(), end=temp_cst.end(); it!=end; ++it) {
if (1 == it.visit())
if (1 == it.visit()) // TODO possible without conditional
m_bp[idx] = 1;
if (temp_cst.is_leaf(*it) and temp_cst.root()!= *it)
if (temp_cst.is_leaf(*it) and temp_cst.root()!= *it) // TODO possible without conditional
++idx;
++idx;
}
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/dac_vector.hpp
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Expand Up @@ -234,7 +234,7 @@ dac_vector<t_b, t_rank>::dac_vector(const Container& c)
t = sum_blocks;
sum_blocks += m_level_pointer_and_rank[i];
m_level_pointer_and_rank[i] = t;
if (sum_blocks > t) {
if (sum_blocks > t) { // TODO possible without conditional
++m_max_level;
last_block_size = sum_blocks - t;
}
Expand Down Expand Up @@ -311,7 +311,7 @@ dac_vector<t_b, t_rank>::dac_vector(int_vector_buffer<int_width>& v_buf)
t = sum_blocks;
sum_blocks += m_level_pointer_and_rank[i];
m_level_pointer_and_rank[i] = t;
if (sum_blocks > t) {
if (sum_blocks > t) { // TODO possible without conditional
++m_max_level;
last_block_size = sum_blocks - t;
}
Expand Down
8 changes: 4 additions & 4 deletions include/sdsl/enc_vector.hpp
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Expand Up @@ -222,7 +222,7 @@ enc_vector<t_coder, t_dens,t_width>::enc_vector(const Container& c)
v2 = *it;
if (!no_sample) { // add a sample
no_sample = get_sample_dens();
if (max_sample_value < v2) max_sample_value = v2;
if (max_sample_value < v2) max_sample_value = v2; // TODO possible without conditional
++samples;
} else {
z_size += t_coder::encoding_length(v2-v1);
Expand All @@ -242,11 +242,11 @@ enc_vector<t_coder, t_dens,t_width>::enc_vector(const Container& c)
size_type no_sample=0;
for (it = c.begin(); it != end; ++it, --no_sample) {
v2 = *it;
if (!no_sample) { // add a sample
if (!no_sample) { // add a sample // TODO possible without conditional
no_sample = get_sample_dens();
*sv_it = v2; ++sv_it;
*sv_it = z_size; ++sv_it;
} else {
} else { // TODO possible without conditional
x = v2-v1;
z_size += t_coder::encoding_length(x);
}
Expand Down Expand Up @@ -289,7 +289,7 @@ enc_vector<t_coder, t_dens,t_width>::enc_vector(int_vector_buffer<int_width>& v_
v2 = v_buf[i];
if (!no_sample) { // is sample
no_sample = sd;
if (max_sample_value < v2) max_sample_value = v2;
if (max_sample_value < v2) max_sample_value = v2; // TODO possible without conditional
++samples;
} else {
z_size += t_coder::encoding_length(v2-v1);
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/fast_cache.hpp
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Expand Up @@ -21,10 +21,10 @@ struct fast_cache {
// Returns true if the request i is cached and
// x is set to the answer of request i
bool exists(size_type i, size_type& x) {
if (m_table[(i&CACHE_SIZE)<<1 ] == i) {
if (m_table[(i&CACHE_SIZE)<<1 ] == i) { // TODO possible without conditional
x = m_table[((i&CACHE_SIZE)<<1) + 1 ];
return true;
} else
} else // TODO possible without conditional
return false;
}
// Writes the answer for request i to the cache
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/int_vector.hpp
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Expand Up @@ -304,7 +304,7 @@ class int_vector
int_vector(std::initializer_list<t_T> il) : int_vector() {
resize(il.size());
size_type idx = 0;
for (auto x : il) {
for (auto x : il) {
(*this)[idx++] = x;
}
}
Expand Down Expand Up @@ -1113,7 +1113,7 @@ template<class t_bv>
inline typename std::enable_if<std::is_same<typename t_bv::index_category ,bv_tag>::value, std::ostream&>::type
operator<<(std::ostream& os, const t_bv& bv)
{
for (auto b : bv) {
for (auto b : bv) {
os << b;
}
return os;
Expand Down
4 changes: 2 additions & 2 deletions include/sdsl/inv_perm_support.hpp
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Expand Up @@ -96,7 +96,7 @@ class inv_perm_support
back_pointer = j;
}
}
if (all_steps > t_s) {
if (all_steps > t_s) { // TODO possible without conditional
marked[i] = 1;
max_back_pointer = std::max(max_back_pointer, back_pointer);
}
Expand Down Expand Up @@ -125,7 +125,7 @@ class inv_perm_support
back_pointer = j;
}
}
if (all_steps > t_s) {
if (all_steps > t_s) { // TODO possible without conditional
m_back_pointer[m_rank_marked(i)] = back_pointer;
}
}
Expand Down
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