Commit 85b8053f authored by Raquel Bromberg's avatar Raquel Bromberg

Code cleanup, mostly commented code deleted

parent 1cadca46
......@@ -234,7 +234,7 @@ int main(int argc, char* argv[])
exit(1);
}
ofstream outstream3;
/* ofstream outstream3;
string outfile3 = path+"/"+bfn+"/bin_corrections_unlikelies.txt";
outstream3.open(outfile3.c_str(), ios::out | ios::app);
if(outstream3.fail())
......@@ -242,6 +242,7 @@ int main(int argc, char* argv[])
cout<<"Failed to open outstream3 to "<<outfile3<<endl;
exit(1);
}
*/
outstream<<num_bins<<endl<<endl;
......@@ -330,8 +331,8 @@ int main(int argc, char* argv[])
}
outstream<<endl;
outstream3<<i<<" to "<<j<<endl;
outstream3<<uscore<<endl<<most_unlikely<<endl<<endl;
// outstream3<<i<<" to "<<j<<endl;
// outstream3<<uscore<<endl<<most_unlikely<<endl<<endl;
}
}
}
......
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......@@ -26,7 +26,7 @@ class org
int total_num_aa; //total number of amino acids in the proteome
int total_num_proteins; //total number of proteins in the proteome
int tag_length;
bool conserved; //what the hell is this?
bool conserved;
int filtering_steps;
vector<string> files; //e.g. NC_021726.faa
......@@ -93,14 +93,12 @@ class org
void fill_fields(string dir_par);
void generate_tags(bool do_scrambled, bool partial_run);
// void generate_scrambled_tags();
void clear_tags();
void clear_scr_tags();
void write_out_aa_array(ofstream& outstream);
int mark_keepers(vector<string> keepers);
void write_out_gene(int index);
void clear_proteins();
// void increment_ggs(int gene_id,int gnums_size,int vector_size);
void increment_ggs(int gene_id,int gnums_size,int vector_size,double d);
void write_out_new_proteome(int index);
void add_file(string s);
......@@ -115,14 +113,6 @@ class org
void write_filtered_set(ofstream& outstream, int filt_option);
//GETTERS AND SETTERS
//void add_file(string f);
//void set_uid(string u);
//vector<string> get_files();
//string get_uid();
//string get_path();
//string get_bfn();
int get_ordinal();
};
......@@ -161,11 +151,6 @@ void org::generate_tags(bool do_scrambled, bool partial_run)
p.generate_tags(ordinal,do_scrambled,partial_run);
}
/*void org::generate_scrambled_tags()
{
p.generate_scrambled_tags(ordinal);
}
*/
void org::set_ordinal(int i)
{
ordinal=i;
......@@ -173,7 +158,6 @@ void org::set_ordinal(int i)
void org::setp_set_keeper(int index,int i)
{
// cout<<"In setp_set_keeper(int,int): "<<index<<" "<<i<<endl;
p.set_keeper(index,i);
}
......@@ -202,12 +186,6 @@ void org::setp_size_real_tags(int i)
p.set_size_real_tags(i);
}
/*void org::setp_set_pv_val(int index,int i1, int i2, int i3, int i4, int i5)
{
p.set_pv_val(index,i1,i2,i3,i4,i5);
}
*/
void org::setp_set_pvv_gnums_val(int index, vector<int> vals)
{
p.set_pvv_gnums_val(index,vals);
......@@ -232,11 +210,6 @@ void org::setp_chosen_column(int i)
p.set_chosen_column(i);
}
/*void org::setp_set_pv_size(int i)
{
p.set_pv_size(i);
}*/
void org::setp_set_pvv_size(int i)
{
p.set_pvv_size(i);
......@@ -339,11 +312,7 @@ int org::read_faa_file(int i,int& total_aa)
instream>>eater;
}
//we now have both the info_line and the protein sequence.
//cout<<"Adding a protein"<<endl;
//cout<<info_line<<endl;
p.add_protein(info_line,aaseq);
//cout<<"info_line = "<<info_line<<endl;
//cout<<"aaseq = "<<aaseq<<endl;
add_aa_counts(aaseq);
result+=aaseq.length();
aaseq="";
......@@ -376,19 +345,6 @@ int org::get_tags_size()
return p.get_tags_size();
}
/*
//GETTERS AND SETTERS
void org::add_file(string f)
{
files.push_back(f);
}
vector<string> org::get_files()
{
return files;
}
*/
string org::get_file(int i)
{
if(i>=0 && i<files.size())
......@@ -421,18 +377,7 @@ string org::get_directory()
{
return directory;
}
/*
void org::set_uid(string u)
{
uid = u;
}
string org::get_uid()
{
return uid;
}
*/
void org::set_path(string p)
{
path = p;
......@@ -448,15 +393,6 @@ void org::set_dir(string s)
dir=s;
}
/*
string org::get_path()
{
return path;
}
*/
void org::add_aa_counts(string s)
{
for(int i=0; i<s.length(); i++)
......@@ -489,13 +425,6 @@ void org::write_out_aa_array(ofstream& outstream)
}
}
/*
string org::get_bfn()
{
return bfn;
}
*/
string org::get_dir()
{
return dir;
......@@ -520,7 +449,7 @@ void org::mark_gene_internal_repeats(int index)
void org::write_out_gene(int index)
{
p.print_protein_info(index);
// p.print_protein_info(index);
}
void org::clear_proteins()
......@@ -528,11 +457,6 @@ void org::clear_proteins()
p.clear_proteins();
}
/*void org::increment_ggs(int gene_id,int gnums_size,int vector_size)
{
p.increment_ggs(gene_id,gnums_size,vector_size);
}*/
void org::increment_ggs(int gene_id,int gnums_size,int vector_size,double d)
{
p.increment_ggs(gene_id,gnums_size,vector_size,d);
......@@ -546,24 +470,14 @@ void org::write_out_new_proteome(int index)
cout<<"dir = "<<dir<<endl;
cout<<"directory = "<<directory<<endl;
/*
string outcommand = "rm -r "+path+"/FAA_new/"+directory;
int system_return = system(outcommand.c_str());
outcommand = "mkdir "+path+"/FAA_new/"+directory;
system_return = system(outcommand.c_str());
*/
stringstream ss;
ss<<index;
string col;
ss>>col;
//string s = path+bfn+"/FAA_new_col"+col+"/"+directory;
//cout<<"s = "<<s<<endl;
vector<pair<int,int> > mscv;
populate_mscv(mscv);
p.write_out_new_proteome_v2(path,directory,files,ordinal,mscv,index);
//instream.open( (path+"/"+dir+"/"+directory+"/"+files.at(i)).c_str() );
}
void org::add_file(string s)
......@@ -636,7 +550,6 @@ void org::populate_mscv(vector<pair<int,int> >& mscv)
instream.open(infile.c_str());
if(instream.fail())
{
//Just leave it alone. File doesn't exist. Leave mscv empty.
}
else
{
......@@ -654,7 +567,6 @@ void org::populate_mscv(vector<pair<int,int> >& mscv)
foo.first=gene_id;
foo.second=count;
mscv.push_back(foo);
//mscv[gene_id]=count;
instream>>gnum>>gene_id>>count;
}
}
......
This diff is collapsed.
......@@ -17,13 +17,10 @@ class protein
int gene_ids;
bool deleter;
bool manually_include; //beats deleter.
//set<int> genome_hits;
public:
protein();
void mark_keeper();
//void add_hit(int i);
//void write_genome_hits(ofstream& outstream);
void add_gnums(int i);
void add_gis(int i);
void mark_for_deletion();
......@@ -40,7 +37,6 @@ class protein
//getters
string get_sequence();
string get_info_line();
//int get_genome_hits_size();
int get_gnums();
int get_geneids();
bool get_deleter();
......@@ -77,41 +73,16 @@ void protein::set_id(int i)
id = i;
}
/*void protein::add_hit(int i)
{
genome_hits.insert(i);
}
*/
string protein::get_sequence()
{
return sequence;
}
/*void protein::write_genome_hits(ofstream& outstream)
{
set<int>::iterator it;
for(it=genome_hits.begin(); it!=genome_hits.end(); ++it)
{
outstream<<*it<<" ";
}
outstream<<endl;
}
*/
string protein::get_info_line()
{
return info_line;
}
/*
int protein::get_genome_hits_size()
{
return genome_hits.size();
}
*/
void protein::add_gnums(int i)
{
gnums+=i;
......@@ -151,12 +122,8 @@ void protein::reset_deleters()
{
if(deleter)
{
cout<<"reset_deleters for: "<<endl;
print_protein_info();
gnums=0;
//int staller;
//cout<<"Stalling: ";
//cin>>staller;
}
}
......
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