Commit 10453486 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove old 'very_detailed_analysis' phase

Yes, we get rid of a very old duplicate in the code...
parent df50db08
......@@ -279,7 +279,6 @@ int main (int argc, char **argv)
bool output_sequences_by_cluster = false;
bool detailed_cluster_analysis = true ;
bool very_detailed_cluster_analysis = false ;
bool output_segmented = false;
bool output_unsegmented = false;
......@@ -305,7 +304,6 @@ int main (int argc, char **argv)
usage(argv[0]);
case 'a':
output_sequences_by_cluster = true;
very_detailed_cluster_analysis = true;
break;
case 'd':
segment_D = 1 ;
......@@ -1276,60 +1274,8 @@ int main (int argc, char **argv)
cout << endl ;
out_windows.close();
if (!very_detailed_cluster_analysis)
{
continue ;
}
//$$ Very detailed cluster analysis (with sequences, -a)
//$$ Second pass: output clone, all representatives
num_seq = 0 ;
list <Sequence> representatives_this_clone ;
string code_representative = "";
for (list <pair<junction, int> >::const_iterator it = sort_windows.begin();
it != sort_windows.end(); ++it) {
num_seq++ ;
string junc = it->first ;
// Output all sequences
Sequence representative
= windowsStorage->getRepresentative(it->first, seed,
min_cover_representative,
ratio_representative,
max_auditionned);
if (representative != NULL_SEQUENCE) {
representative.label = string_of_int(it->second) + "--"
+ representative.label;
representatives_this_clone.push_back(representative);
}
}
out_clone.close();
cout << endl;
//$$ Compare representatives of this clone
cout << "Comparing representatives of this clone 2 by 2" << endl ;
// compare_all(representatives_this_clone);
SimilarityMatrix matrix = compare_all(representatives_this_clone, true);
cout << RawOutputSimilarityMatrix(matrix, 90);
//Sort all windows
windowsStorage->sort();
//Compute all the edges
SimilarityMatrix matrixLevenshtein = compare_windows(*windowsStorage, Levenshtein, max_clones);
//Added distances matrix in the JsonTab
jsonLevenshtein << JsonOutputWindowsMatrix(matrixLevenshtein);
}
//$$ End of very_detailed_cluster_analysis
}
out_edges.close() ;
out_clones.close();
......
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