Commit 2c6e657f authored by Mikael Salson's avatar Mikael Salson

algo/core: reindent

parent 7675f014
Pipeline #16530 passed with stages
in 26 minutes and 41 seconds
...@@ -289,7 +289,7 @@ string KmerAffectAnalyser::toString() const{ ...@@ -289,7 +289,7 @@ string KmerAffectAnalyser::toString() const{
} }
string KmerAffectAnalyser::toStringValues() const{ string KmerAffectAnalyser::toStringValues() const{
string kmer; string kmer;
for (size_t i = 0; i < affectations.size(); i++) { for (size_t i = 0; i < affectations.size(); i++) {
kmer += affectations[i].toStringValues(); kmer += affectations[i].toStringValues();
} }
......
...@@ -88,8 +88,8 @@ void comp_matrix::load(string file){ ...@@ -88,8 +88,8 @@ void comp_matrix::load(string file){
for(unsigned int i=0; i<sort_clones.size();i++){ for(unsigned int i=0; i<sort_clones.size();i++){
in_comp.read(tampon, sort_clones.size()*sizeof(char)); in_comp.read(tampon, sort_clones.size()*sizeof(char));
for(unsigned int j=0;j<sort_clones.size(); j++){ for(unsigned int j=0;j<sort_clones.size(); j++){
m[i][j]=tampon[j]; m[i][j]=tampon[j];
} }
} }
free(tampon); free(tampon);
...@@ -157,25 +157,25 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream ...@@ -157,25 +157,25 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream
size_t j = 0; size_t j = 0;
for (list <pair<junction,size_t> >::const_iterator it1 = sort_clones.begin(); for (list <pair<junction,size_t> >::const_iterator it1 = sort_clones.begin();
(it1 != sort_clones.end()) & (j<matrix_size); ++it1) (it1 != sort_clones.end()) & (j<matrix_size); ++it1)
{ {
j++; j++;
j2=it1->first; j2=it1->first;
int distance = (int)m[c2][c1]; int distance = (int)m[c2][c1];
if (distance <= epsilon){ if (distance <= epsilon){
neighbor[j1].push_back(j2); neighbor[j1].push_back(j2);
} }
c1++; c1++;
c++; c++;
}//fin it1 }//fin it1
c2++; c2++;
c1=0; c1=0;
}//fin it0 }//fin it0
///////////////////////// /////////////////////////
//Forced - edges //Forced - edges
if (forced_edges.size()) if (forced_edges.size())
{ {
ifstream fe(forced_edges.c_str()); ifstream fe(forced_edges.c_str());
...@@ -243,7 +243,7 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream ...@@ -243,7 +243,7 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream
nVoisins=0; nVoisins=0;
for (list<string>::iterator it1 = voisins1.begin(); for (list<string>::iterator it1 = voisins1.begin();
it1 != voisins1.end(); ++it1 ) nVoisins+=count[*it1]; it1 != voisins1.end(); ++it1 ) nVoisins+=count[*it1];
if (nVoisins<minPts){ if (nVoisins<minPts){
//noise //noise
...@@ -268,7 +268,7 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream ...@@ -268,7 +268,7 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream
nVoisins=0; nVoisins=0;
for (list<string>::iterator it1 = voisins2.begin();it1 != voisins2.end(); for (list<string>::iterator it1 = voisins2.begin();it1 != voisins2.end();
++it1 )nVoisins+=count[*it1]; ++it1 )nVoisins+=count[*it1];
//si la junction possede assez de voisins //si la junction possede assez de voisins
if (nVoisins>=minPts){ if (nVoisins>=minPts){
//on ajoute ses voisins a la liste des voisins du cluster //on ajoute ses voisins a la liste des voisins du cluster
...@@ -308,9 +308,9 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream ...@@ -308,9 +308,9 @@ list<list<junction> > comp_matrix::cluster(string forced_edges, int w, ostream
list< string > c2; list< string > c2;
for (list< pair<int,string> >::iterator c_it = c.begin(); c_it != c.end(); for (list< pair<int,string> >::iterator c_it = c.begin(); c_it != c.end();
++c_it ){ ++c_it ){
pair<int,string> pair=*c_it; pair<int,string> pair=*c_it;
c2.push_back(pair.second); c2.push_back(pair.second);
} }
c2.reverse(); c2.reverse();
cluster.push_back(c2); cluster.push_back(c2);
......
...@@ -38,7 +38,7 @@ SimilarityMatrix compare_all(list <Sequence> sequences, ...@@ -38,7 +38,7 @@ SimilarityMatrix compare_all(list <Sequence> sequences,
for (list <Sequence>::const_iterator it1 = sequences.begin(); for (list <Sequence>::const_iterator it1 = sequences.begin();
it1 != sequences.end(); ++it1 ) it1 != sequences.end(); ++it1 )
num = 0 ; num = 0 ;
list<string>::const_iterator itLabel = sequence_names.begin(); list<string>::const_iterator itLabel = sequence_names.begin();
for (list <Sequence>::const_iterator it1 = sequences.begin(); for (list <Sequence>::const_iterator it1 = sequences.begin();
......
...@@ -294,26 +294,26 @@ bool KmerRepresentativeComputer::tryToExtendRepresentative(const vector<Kmer> co ...@@ -294,26 +294,26 @@ bool KmerRepresentativeComputer::tryToExtendRepresentative(const vector<Kmer> co
else else
pos_of_interest = i - 1; pos_of_interest = i - 1;
if (pos_of_interest < (int) counts[current_seed].size() && pos_of_interest >= 0) { if (pos_of_interest < (int) counts[current_seed].size() && pos_of_interest >= 0) {
if (isSufficienlyExpressed(counts[current_seed][pos_of_interest].count, sequences.size())) { if (isSufficienlyExpressed(counts[current_seed][pos_of_interest].count, sequences.size())) {
i += direction; i += direction;
if (nb_seeds > 1) { if (nb_seeds > 1) {
size_t seed_length = seeds[current_seed].size(); size_t seed_length = seeds[current_seed].size();
for (size_t pos = 0; pos < seed_length; pos++) { for (size_t pos = 0; pos < seed_length; pos++) {
bool previous_cover = cover[pos_of_interest+pos]; bool previous_cover = cover[pos_of_interest+pos];
cover[pos_of_interest+pos] |= (seeds[current_seed][pos] == '#'); cover[pos_of_interest+pos] |= (seeds[current_seed][pos] == '#');
if (! previous_cover && cover[pos_of_interest+pos]) if (! previous_cover && cover[pos_of_interest+pos])
length_cover++; length_cover++;
} }
} else { } else {
int pos_modif = (direction == -1) ? pos_of_interest : i; int pos_modif = (direction == -1) ? pos_of_interest : i;
if (!cover[pos_modif]) if (!cover[pos_modif])
length_cover++; length_cover++;
cover[pos_modif] = true; cover[pos_modif] = true;
}
was_extended = true;
} }
was_extended = true;
}
} }
} }
return was_extended; return was_extended;
......
...@@ -1085,8 +1085,8 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c, ...@@ -1085,8 +1085,8 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,
box_J->end = sequence.length()-1; box_J->end = sequence.length()-1;
// Why could this happen ? // Why could this happen ?
if (box_J->start>=(int) sequence.length()) if (box_J->start>=(int) sequence.length())
box_J->start=sequence.length()-1; box_J->start=sequence.length()-1;
// seg_N will be recomputed in finishSegmentation() // seg_N will be recomputed in finishSegmentation()
......
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