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Fix a bunch of compilation warnings from clang++. #43

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Fix a bunch of compilation warnings from clang++. #43

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3 changes: 2 additions & 1 deletion core/match_types.cpp
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@

#include <vector>
#include <string>
#include <utility>

#include "match_types.h"

namespace MOODS {

variant::variant(){}
variant::variant(size_t s, size_t e, std::string seq): start_pos(s), end_pos(e), modified_seq(seq) {}
variant::variant(size_t s, size_t e, std::string seq): start_pos(s), end_pos(e), modified_seq(std::move(seq)) {}

}
4 changes: 1 addition & 3 deletions core/moods_scan.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,6 @@ namespace MOODS { namespace scan{
}
}

bool done = 0;

int iteration = 0;


Expand Down Expand Up @@ -249,7 +247,7 @@ namespace MOODS { namespace scan{
}

for (size_t j = 0; j < cols; ++j){
CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
CODE = (MASK & (CODE << SHIFT)) | alphabet_map[seq[i+j+q-1]];
score += matrix[CODE][j];
}

Expand Down
60 changes: 30 additions & 30 deletions core/moods_tools.cpp
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Expand Up @@ -141,35 +141,35 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
{

// Approximate the scoring matrix with integer matrix for DP
long a = pssm.size();
long n = pssm[0].size();
size_t a = pssm.size();
size_t n = pssm[0].size();


vector<vector<long> > mat(a, vector<long>(n));
vector<vector<size_t> > mat(a, vector<size_t>(n));

long maxT = 0;
long minV = std::numeric_limits<long>::max();
size_t maxT = 0;
size_t minV = std::numeric_limits<size_t>::max();

for (size_t i = 0; i < n; ++i)
{
for (size_t j = 0; j < a; ++j)
{
if (pssm[j][i] > 0.0){
mat[j][i] = (long) ( precision * pssm[j][i] + 0.5 );
mat[j][i] = (size_t) ( precision * pssm[j][i] + 0.5 );
}
else {
mat[j][i] = (long) ( precision * pssm[j][i] - 0.5 );
mat[j][i] = (size_t) ( precision * pssm[j][i] - 0.5 );
}
}
}

for (size_t i = 0; i < n; ++i)
{
long max = mat[0][i];
long min = max;
size_t max = mat[0][i];
size_t min = max;
for (size_t j = 1; j < a; ++j)
{
long v = mat[j][i];
size_t v = mat[j][i];
if (max < v)
max = v;
else if (min > v)
Expand All @@ -180,7 +180,7 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
minV = min;
}

long R = maxT - n * minV;
size_t R = maxT - n * minV;

vector<double> table0(R + 1, 0.0);
vector<double> table1(R + 1, 0.0);
Expand All @@ -193,10 +193,10 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
for (size_t j = 0; j < a; ++j)
{
long s = mat[j][i] - minV;
for (long r = s; r <= R; ++r)
for (size_t r = s; r <= R; ++r)
table1[r] += bg[j] * table0[r - s];
}
for (long r = 0; r <= R; ++r)
for (size_t r = 0; r <= R; ++r)
{
table0[r] = table1[r];
table1[r] = 0.0;
Expand All @@ -211,7 +211,7 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
return max_score(pssm) - min_delta(pssm)/2;
}

for (long r = R-1; r >= 0; --r)
for (size_t r = R-1; r != ((size_t)-1); --r)
{
sum += table0[r];
if (sum > p)
Expand Down Expand Up @@ -439,8 +439,8 @@ double min_score(const score_matrix &mat, const size_t a){
double threshold_from_p_with_precision(const score_matrix &pssm, const vector<double> &bg, const double &p, const double precision, const size_t a)
{

long rows = pssm.size();
long cols = pssm[0].size();
size_t rows = pssm.size();
size_t cols = pssm[0].size();

unsigned int q = MOODS::misc::q_gram_size(rows, a);

Expand All @@ -449,32 +449,32 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
const bits_t Q_CODE_SIZE = (1 << (SHIFT * (q-1)));
const bits_t Q_MASK = Q_CODE_SIZE - 1;

vector<vector<long> > mat(rows, vector<long>(cols));
vector<vector<size_t> > mat(rows, vector<size_t>(cols));

long maxT = 0;
long minV = std::numeric_limits<long>::max();
size_t maxT = 0;
size_t minV = std::numeric_limits<size_t>::max();

for (size_t i = 0; i < cols; ++i)
{
for (size_t CODE = 0; CODE < rows; ++CODE)
{
if (pssm[CODE][i] > 0.0){
mat[CODE][i] = (long) ( precision * pssm[CODE][i] + 0.5 );
mat[CODE][i] = (size_t) ( precision * pssm[CODE][i] + 0.5 );
}
else {
mat[CODE][i] = (long) ( precision * pssm[CODE][i] - 0.5 );
mat[CODE][i] = (size_t) ( precision * pssm[CODE][i] - 0.5 );
}
}
}


for (size_t i = 0; i < cols; ++i)
{
long max = mat[0][i];
long min = max;
size_t max = mat[0][i];
size_t min = max;
for (size_t CODE = 1; CODE < rows; ++CODE)
{
long v = mat[CODE][i];
size_t v = mat[CODE][i];
if (max < v)
max = v;
else if (min > v)
Expand All @@ -485,7 +485,7 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
minV = min;
}

long R = maxT - cols * minV;
size_t R = maxT - cols * minV;

vector<vector<double>> table0(Q_CODE_SIZE, vector<double>(R + 1, 0));

Expand All @@ -508,16 +508,16 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
bits_t CODE_PREFIX = (CODE >> SHIFT) & Q_MASK;
bits_t CODE_SUFFIX = CODE & Q_MASK;
bits_t CHAR = CODE & A_MASK;
long s = mat[CODE][i] - minV;
for (long r = s; r <= R; ++r)
size_t s = mat[CODE][i] - minV;
for (size_t r = s; r <= R; ++r)
table1[CODE_SUFFIX][r] += bg[CHAR] * table0[CODE_PREFIX][r - s];
}
table0 = table1;
}


vector<double> table2(R+1, 0.0);
for (long r = 0; r < R+1; ++r){
for (size_t r = 0; r < R+1; ++r){
for (bits_t CODE = 0; CODE < Q_CODE_SIZE; ++CODE){
table2[r] += table0[CODE][r];
}
Expand All @@ -530,7 +530,7 @@ double threshold_from_p_with_precision(const score_matrix &pssm, const vector<do
return max_score(pssm, a) - min_delta(pssm)/2;;
}

for (long r = R-1; r >= 0; --r)
for (size_t r = R-1; r >= 0; --r)
{
sum += table2[r];
if (sum > p)
Expand Down Expand Up @@ -585,7 +585,7 @@ vector<MOODS::variant> snp_variants(const std::string &seq){

for (size_t i = 0; i < seq.size(); ++i){
for (size_t j = 0; j < snp_alt[seq[i]].size(); ++j){
ret.push_back(variant{i,i+1,snp_alt[seq[i]].substr(j,1)});
ret.emplace_back(i,i+1,snp_alt[seq[i]].substr(j,1));
}
}

Expand Down
2 changes: 2 additions & 0 deletions core/motif.h
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,8 @@ class Motif {
virtual unsigned int alphabet_size() = 0;
virtual unsigned int window_pos() = 0;
virtual double threshold() = 0;

virtual ~Motif() = default;
};


Expand Down
16 changes: 8 additions & 8 deletions core/motif_0.cpp
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Expand Up @@ -25,17 +25,17 @@ vector<double> expected_differences(const score_matrix &mat, const vector<double
size_t m = mat[0].size();
vector<double> ret(m);

for (int i = 0; i < m; ++i)
for (size_t i = 0; i < m; ++i)
{
double max = -std::numeric_limits<double>::infinity();
for (int j = 0; j < a; ++j)
for (size_t j = 0; j < a; ++j)
{
max = std::max(max, mat[j][i]);
}

ret[i] = max;

for (int j = 0; j < a; ++j)
for (size_t j = 0; j < a; ++j)
{
ret[i] -= bg[j] * mat[j][i];
}
Expand All @@ -59,9 +59,9 @@ unsigned int window_position(const vector<double> &ed, unsigned int l, unsigned
}

double max = current;
int window_pos = 0;
unsigned int window_pos = 0;

for (int i = 0; i < m - l; ++i)
for (unsigned int i = 0; i < m - l; ++i)
{
current -= ed[i];
current += ed[i+l];
Expand Down Expand Up @@ -93,11 +93,11 @@ vector<unsigned int> compute_lookahead_order(const vector<double> &ed, unsigned
else
{
vector<unsigned int> order(m-l, 0);
for (int i = 0; i < window_pos; ++i)
for (unsigned int i = 0; i < window_pos; ++i)
{
order[i] = i;
}
for (int i = window_pos+l; i < m; ++i)
for (unsigned int i = window_pos+l; i < m; ++i)
{
order[i-l] = i;
}
Expand All @@ -122,7 +122,7 @@ vector<double> compute_lookahead_scores(const score_matrix &mat, const vector<un
std::vector<double> scores(m-l,0);

double total = 0;
for (int i = m-l-1; i >= 0; --i)
for (unsigned int i = m-l-1; i != ((unsigned int)-1); --i)
{
double max = -std::numeric_limits<double>::infinity();
for (unsigned int j = 0; j < a; ++j)
Expand Down
20 changes: 13 additions & 7 deletions core/motif_h.cpp
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Expand Up @@ -23,8 +23,8 @@ vector<double> MotifH::expected_scores(const vector<double> &bg){
const bits_t A_MASK = (1 << (SHIFT)) - 1;

vector<double> ret(cols, 0);
for (int i = 0; i < cols; ++i){
for (int j = 0; j < rows; ++j){
for (unsigned int i = 0; i < cols; ++i){
for (unsigned int j = 0; j < rows; ++j){
double bg_prop = 1;
for (unsigned int k = 0; k < q; ++k){
bg_prop *= bg[A_MASK & (j >> (SHIFT * (q - 1 - k)))];
Expand All @@ -39,15 +39,18 @@ vector<double> MotifH::expected_scores(const vector<double> &bg){

vector<vector<double>> MotifH::max_scores_f(size_t start, size_t end){

double wsize = end - start;
size_t wsize = end - start;
if (end <= start) {
wsize = 0;
}
vector<vector<double>> max_scores (wsize, vector<double> (Q_CODE_SIZE, 0));

if (end > start){
for (unsigned int j = 0; j < rows; ++j){
max_scores[0][j & Q_MASK] = std::max(mat[j][start], max_scores[0][j & Q_MASK]);
}

for (unsigned int i = 1 ; i < wsize; ++i){
for (size_t i = 1 ; i < wsize; ++i){
for (unsigned int j = 0; j < rows; ++j){
max_scores[i][j & Q_MASK] = std::max(mat[j][i+start] + max_scores[i-1][j >> SHIFT], max_scores[i][j & Q_MASK]);
}
Expand All @@ -59,7 +62,10 @@ vector<vector<double>> MotifH::max_scores_f(size_t start, size_t end){

vector<vector<double>> MotifH::max_scores_b(size_t start, size_t end){

double wsize = end - start;
size_t wsize = end - start;
if (end <= start) {
wsize = 0;
}
vector<vector<double>> max_scores (wsize, vector<double> (Q_CODE_SIZE, 0));


Expand All @@ -70,7 +76,7 @@ vector<vector<double>> MotifH::max_scores_b(size_t start, size_t end){
max_scores[wsize-1][j >> SHIFT] = std::max(mat[j][end-1], max_scores[wsize-1][j >> SHIFT]);
}

for (unsigned int i = 1; i < wsize; ++i){
for (size_t i = 1; i < wsize; ++i){

for (unsigned int j = 0; j < rows; ++j){
max_scores[wsize-i-1][j >> SHIFT] = std::max(mat[j][end-i-1] + max_scores[wsize-i][j & Q_MASK], max_scores[wsize-i-1][j >> SHIFT]);
Expand Down Expand Up @@ -253,7 +259,7 @@ std::pair<bool, double> MotifH::check_hit(const std::string& s, const vector<uns
return std::make_pair(false, score);
}

CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
CODE = (MASK & (CODE << SHIFT)) ^ alphabet_map[s[ii + i + q - 1]];
score += mat[CODE][i];
}
}
Expand Down