Commit 30abf568 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: remove msa

This code was wrote a long time ago and is not used anymore.
Now we have the browser to visualize alignments.
parent 350c55a6
......@@ -41,7 +41,6 @@
#include "core/dynprog.h"
#include "core/read_score.h"
#include "core/read_chooser.h"
#include "core/msa.h"
#include "core/compare-all.h"
#include "core/teestream.h"
#include "core/mkdir.h"
......@@ -1267,35 +1266,7 @@ int main (int argc, char **argv)
}
//$$ Very detailed cluster analysis (with sequences) // NOT USED NOW
list<string> msa;
bool good_msa = false ;
// TODO: do something if no sequences have been segmented !
if (!more_windows)
{
cout << "!! No segmented sequence, deleting clone" << endl ;
// continue ;
} else
{
msa = multiple_seq_align(windows_file_name);
// Alignment of windows
if (!msa.empty())
{
if (msa.size() == sort_windows.size() + more_windows)
{
// cout << "clustalw parse: success" << endl ;
good_msa = true ;
}
else
{
cout << "! clustalw parse: failed" << endl ;
}
}
}
//$$ Very detailed cluster analysis (with sequences, -a)
//$$ Second pass: output clone, all representatives
......@@ -1308,18 +1279,7 @@ int main (int argc, char **argv)
num_seq++ ;
string junc ;
if (!good_msa)
{
junc = it->first ;
}
else
{
junc = msa.back();
msa.pop_back();
}
string junc = it->first ;
// Output all sequences
......@@ -1381,22 +1341,6 @@ int main (int argc, char **argv)
}
}
//$$ Display msa
if (good_msa)
{
cout << setw(20) << best_V << " " << msa.back() << endl ;
msa.pop_back();
if (segment_D)
{
cout << setw(20) << best_D << " " << msa.back() << endl ;
msa.pop_back();
}
cout << setw(20) << best_J << " " << msa.back() << endl ;
msa.pop_back();
}
out_clone.close();
cout << endl;
......
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