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BioHPC
slopetree
Commits
1cadca46
Commit
1cadca46
authored
Jun 27, 2016
by
Raquel Bromberg
Browse files
Code cleaned up (commented code deleted)
parent
99830c1f
Changes
10
Hide whitespace changes
Inline
Side-by-side
Coptim1_layer.h
View file @
1cadca46
...
...
@@ -22,7 +22,6 @@ class Coptim1_layer
Coptim1_layer
::
Coptim1_layer
(
int
number_of_genomes
)
{
//array_size = (((number_of_genomes*number_of_genomes)-number_of_genomes)/2.0);
array_size
=
get_index
(
number_of_genomes
-
2
,
number_of_genomes
-
1
)
+
1
;
diagonal_size
=
number_of_genomes
;
array
=
new
int
[
array_size
];
...
...
amino_acids.h
View file @
1cadca46
...
...
@@ -22,7 +22,6 @@ amino_acids::amino_acids()
{
}
char
amino_acids
::
get_aa
(
int
i
)
{
if
(
i
==
0
)
...
...
cm.cpp
View file @
1cadca46
#include <iostream>
#include <fstream>
#include <cstdlib>
//#include <omp.h>
#include <getopt.h>
#include "mctr.h"
...
...
@@ -22,11 +21,6 @@ int main(int argc, char* argv[])
int
fs
=-
1
;
int
fo
=-
1
;
/* if(argc<2)
{
cout<<"Wrong input to cm.cpp: ./cm -p <full path> -f <filtering steps, =0 for unfiltered (e.g. all) data> -o <filtering option, =0 for unfiltered (e.g. all) data>"<<endl;
}*/
cout
<<
"Values stored in argv:"
<<
endl
;
for
(
int
i
=
0
;
i
<
argc
;
i
++
)
{
...
...
@@ -40,9 +34,6 @@ int main(int argc, char* argv[])
case
'o'
:
fo
=
atoi
(
optarg
);
break
;
/* case 'p':
full_path = optarg;
break;*/
case
'f'
:
fs
=
atoi
(
optarg
);
break
;
...
...
@@ -54,16 +45,12 @@ int main(int argc, char* argv[])
}
}
// cout<<"fo="<<fo<<endl;
// cout<<"p="<<full_path<<endl;
// cout<<"fs="<<fs<<endl;
cout
<<
"Calling run on real data"
<<
endl
;
mctr
m
(
full_path
,
""
,
fs
,
fo
,
partial_run
);
m
.
run_it0
();
cout
<<
"Calling run on scrambled data"
<<
endl
;
mctr
mscr
(
full_path
,
"scr"
,
fs
,
fo
,
partial_run
);
//scrambled
mctr
mscr
(
full_path
,
"scr"
,
fs
,
fo
,
partial_run
);
mscr
.
run_it0
();
return
0
;
...
...
dbc.cpp
View file @
1cadca46
...
...
@@ -21,7 +21,6 @@ struct avg
struct
Mproteome
{
vector
<
string
>
proteins
;
//vector<double> bit_scores;
double
bit_scores
[
20
];
vector
<
string
>
files
;
int
ordinal
;
...
...
@@ -47,7 +46,6 @@ struct v
};
void
do_counts
(
Mproteome
p1
,
Mproteome
p2
,
int
tag_length
,
vector
<
int
>&
array
,
int
&
max
,
int
&
min
,
string
&
most_unlikely
,
int
&
uscore
,
int
SOS_CUTOFF
,
bool
partial_run
,
char
partial_run_char
);
avg
calc_running_avgs
(
int
array
[],
int
max
,
int
min
);
bool
check_composition
(
string
s
,
int
tag_length
,
amino_acids
&
aas
,
int
SOSCUTOFF
);
int
get_num_bins
(
string
path
,
string
bfn
);
int
calc_sos_cutoff
(
string
path
,
string
bfn
);
...
...
@@ -92,11 +90,6 @@ int main(int argc, char* argv[])
abort
();
}
}
//string FM = argv[3]; //always set to true
// int num_bins=atoi(argv[4]); //set it from within
// string PS = argv[5]; //always set to P
//int SOS_CUTOFF=atoi(argv[6]); //set it from within
amino_acids
aas
;
if
(
partial_run
)
...
...
@@ -136,16 +129,11 @@ int main(int argc, char* argv[])
if
(
ordinal
==
proteomes
.
at
(
i
).
ordinal
&&
org_name
==
proteomes
.
at
(
i
).
org_name
)
{
proteomes
.
at
(
i
).
files
.
push_back
(
faa_path
);
//cout<<"Already there. ordinal="<<ordinal<<" org_name="<<org_name<<endl;
//cout<<"pushing back "<<faa_path<<endl;
already_there
=
true
;
}
}
if
(
!
already_there
)
{
//cout<<"Not already there."<<endl;
//cout<<"ordinal = "<<ordinal<<" org_name = "<<org_name<<endl;
//cout<<"adding file "<<faa_path<<endl;
Mproteome
mp_temp
;
mp_temp
.
ordinal
=
ordinal
;
mp_temp
.
org_name
=
org_name
;
...
...
@@ -191,11 +179,9 @@ int main(int argc, char* argv[])
instream
>>
eater
;
}
proteomes
.
at
(
i
).
proteins
.
push_back
(
protein
);
//cout<<"info_line = "<<info_line<<endl<<protein<<endl;
}
}
instream
.
close
();
// cout<<"Size of "<<i<<" proteins = "<<proteomes.at(i).proteins.size()<<endl;
}
for
(
int
j
=
0
;
j
<
20
;
j
++
)
...
...
@@ -229,26 +215,19 @@ int main(int argc, char* argv[])
for
(
int
i
=
0
;
i
<
proteomes
.
size
();
i
++
)
{
outstream2
<<
i
<<
" "
<<
proteomes
.
at
(
i
).
total
<<
endl
;
//cout<<"Doing bitting for proteome i="<<i<<endl;
for
(
int
j
=
0
;
j
<
20
;
j
++
)
{
//cout<<j<<" "<<proteomes.at(i).bit_scores[j]<<" ";
//outstream2<<aas.get_aa(j)<<" "<<proteomes.at(i).bit_scores[j]<<" ";
proteomes
.
at
(
i
).
bit_scores
[
j
]
/=
proteomes
.
at
(
i
).
total
;
//now frequencies.
//cout<<proteomes.at(i).bit_scores[j]<<" ";
//outstream2<<proteomes.at(i).bit_scores[j]<<" ";
proteomes
.
at
(
i
).
bit_scores
[
j
]
=
abs
(
log
(
proteomes
.
at
(
i
).
bit_scores
[
j
]));
//outstream2<<proteomes.at(i).bit_scores[j]<<" ";
proteomes
.
at
(
i
).
bit_scores
[
j
]
/=
2.0
;
outstream2
<<
proteomes
.
at
(
i
).
bit_scores
[
j
]
<<
endl
;
//cout<<proteomes.at(i).bit_scores[j]<<endl;
}
outstream2
<<
endl
;
}
ofstream
outstream
;
string
outfile
=
path
+
"/"
+
bfn
+
"/bin_corrections.txt"
;
outstream
.
open
(
outfile
.
c_str
());
//, ios::out | ios::app);
outstream
.
open
(
outfile
.
c_str
());
if
(
outstream
.
fail
())
{
cout
<<
"Failed to open outstream to "
<<
outfile
<<
endl
;
...
...
@@ -266,13 +245,9 @@ int main(int argc, char* argv[])
outstream
<<
num_bins
<<
endl
<<
endl
;
// int i_starter=32;
//int j_starter=1687;
//bool start_writing=false;
if
(
PS
==
"P"
)
{
cout
<<
"Using omp...
presumably...
"
<<
endl
;
cout
<<
"Using omp..."
<<
endl
;
vector
<
v
>
stored_counts
;
...
...
@@ -294,8 +269,6 @@ int main(int argc, char* argv[])
int
uscore
=
0
;
do_counts
(
proteomes
.
at
(
i
),
proteomes
.
at
(
j
),
tag_length
,
array
,
max
,
min
,
most_unlikely
,
uscore
,
SOS_CUTOFF
,
partial_run
,
partial_run_lead
);
do_counts
(
proteomes
.
at
(
j
),
proteomes
.
at
(
i
),
tag_length
,
array
,
max
,
min
,
most_unlikely
,
uscore
,
SOS_CUTOFF
,
partial_run
,
partial_run_lead
);
//avg result;
//result = calc_running_avgs(array,max,min);
v
vtemp
;
for
(
int
f
=
0
;
f
<
array
.
size
();
f
++
)
...
...
@@ -349,13 +322,8 @@ int main(int argc, char* argv[])
int
max
(
0
),
min
(
0
);
string
most_unlikely
=
""
;
int
uscore
=
0
;
//do_counts(proteomes.at(i),proteomes.at(j), tag_length, array,max,min,most_unlikely,uscore);
//do_counts(proteomes.at(j),proteomes.at(i), tag_length, array,max,min,most_unlikely,uscore);
//avg result;
//result = calc_running_avgs(array,max,min);
outstream
<<
i
<<
" to "
<<
j
<<
endl
;
//outstream<<result.index<<endl<<result.avg<<endl;
for
(
int
f
=
0
;
f
<
100
;
f
++
)
{
outstream
<<
array
[
f
]
<<
endl
;
...
...
@@ -368,22 +336,14 @@ int main(int argc, char* argv[])
}
}
}
//b. read them in from file
else
if
(
FM
==
"F"
)
{
vector
<
Fproteome
>
proteomes
;
}
else
{
cout
<<
"Invalid option for File/Memory (FM)."
<<
endl
;
exit
(
1
);
}
//3. do all comparisons and write out.
}
//void do_counts(Mproteome p1, Mproteome p2, int tag_length, int array[],int& max, int& min,string& most_unlikely,int& uscore)
void
do_counts
(
Mproteome
p1
,
Mproteome
p2
,
int
tag_length
,
vector
<
int
>&
array
,
int
&
max
,
int
&
min
,
string
&
most_unlikely
,
int
&
uscore
,
int
SOS_CUTOFF
,
bool
partial_run
,
char
partial_run_lead
)
{
int
sum
=
0
;
...
...
@@ -408,9 +368,6 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
double
score
=
0.0
;
for
(
int
k
=
0
;
k
<
tag_length
&&
(
j
+
k
)
<
p1
.
proteins
.
at
(
i
).
length
();
k
++
)
{
// bool composition_ok=check_composition(p1.proteins.at(i).substr(k,tag_length),tag_length,aas,SOS_CUTOFF);
// if(composition_ok)
// {
s
+=
p1
.
proteins
.
at
(
i
)[
j
+
k
];
int
index
=
aas
.
get_aa
(
p1
.
proteins
.
at
(
i
)[
j
+
k
]);
...
...
@@ -421,12 +378,10 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
if
(
(
score
+
.5
)
<
min
||
min
==
0
)
{
min
=
score
+
.5
;
//cout<<"min score = "<<min<<" sequence = "<<s<<endl;
}
if
(
(
score
+
.5
)
>
max
)
{
max
=
score
+
.5
;
//cout<<"max score = "<<max<<" sequence = "<<s<<endl;
uscore
=
max
;
most_unlikely
=
s
;
}
...
...
@@ -436,12 +391,6 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
k
=
tag_length
;
j
+=
k
-
1
;
}
// }
// else
// {
// k=tag_length;
// j+=k-1;
// }
}
}
}
...
...
@@ -458,9 +407,6 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
double
score
=
0.0
;
for
(
int
k
=
0
;
k
<
tag_length
&&
(
j
+
k
)
<
p1
.
proteins
.
at
(
i
).
length
();
k
++
)
{
// bool composition_ok=check_composition(p1.proteins.at(i).substr(k,tag_length),tag_length,aas,SOS_CUTOFF);
// if(composition_ok)
// {
s
+=
p1
.
proteins
.
at
(
i
)[
j
+
k
];
int
index
=
aas
.
get_aa
(
p1
.
proteins
.
at
(
i
)[
j
+
k
]);
...
...
@@ -471,12 +417,10 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
if
(
(
score
+
.5
)
<
min
||
min
==
0
)
{
min
=
score
+
.5
;
//cout<<"min score = "<<min<<" sequence = "<<s<<endl;
}
if
(
(
score
+
.5
)
>
max
)
{
max
=
score
+
.5
;
//cout<<"max score = "<<max<<" sequence = "<<s<<endl;
uscore
=
max
;
most_unlikely
=
s
;
}
...
...
@@ -486,12 +430,6 @@ void do_counts(Mproteome p1, Mproteome p2, int tag_length, vector<int>& array,in
k
=
tag_length
;
j
+=
k
-
1
;
}
// }
// else
// {
// k=tag_length;
// j+=k-1;
// }
}
}
}
...
...
@@ -539,56 +477,6 @@ bool check_composition(string s,int tag_length,amino_acids& aas,int SOSCUTOFF)
return
true
;
}
avg
calc_running_avgs
(
int
array
[],
int
max
,
int
min
)
{
/*
avg chosen_avg;
chosen_avg.avg=0;
chosen_avg.index=0;
cout<<"In calc_running_avgs"<<endl;
for(int i=0; i<1000; i++)
{
cout<<i<<" "<<array[i]<<endl;
}
vector<avg> rolling_avg;
//go forwards
double denom=0;
double sum=0;
double cur_avg=0;
for(int i=min; i<max; i++)
{
if(array[i]>0)
{
sum+=array[i];
denom+=1;
cur_avg=sum/denom;
avg atemp;
atemp.avg=log(cur_avg);
atemp.index=i;
rolling_avg.push_back(atemp);
}
}
for(int i=rolling_avg.size()-1; i>=0; i--)
{
double diff=log(array[rolling_avg.at(i).index])-rolling_avg.at(i).avg;
//double diff=log(counts.at(rolling_avg.at(i).index))-rolling_avg.at(i).avg;
//cout<<i<<" "<<rolling_avg.at(i).index<<" "<<rolling_avg.at(i).avg<<" "<<diff<<endl;
if(abs(diff)<0.08)
{
chosen_avg=rolling_avg.at(i);
//cout<<"Choosing the avg. This better only appear once."<<endl;
break;
}
}
//cout<<"chosen avg = "<<chosen_avg.index<<" "<<chosen_avg.avg<<endl;
return chosen_avg;
*/
}
int
get_num_bins
(
string
path
,
string
bfn
)
{
ifstream
instream
;
...
...
dentrop.cpp
View file @
1cadca46
...
...
@@ -50,8 +50,8 @@ int main(int argc, char* argv[])
for
(
int
j
=
i
+
1
;
j
<
ref_set_size
+
main_set_size
;
j
++
)
{
int
total_size_j
;
// = organisms.at(j).get_total_num_aa();
vector
<
int
>
aa_array_j
;
// = organisms.at(j).get_aa_array();
int
total_size_j
;
vector
<
int
>
aa_array_j
;
get_hist_data
(
u
.
int_to_string
(
j
),
total_size_j
,
aa_array_j
,
path_frag
);
double
entropy
=
0
;
...
...
directory_reader.h
View file @
1cadca46
...
...
@@ -43,7 +43,6 @@ vector<string> directory_reader::load_names(string dir)
}
else
{
//cout<<"Rejecting directory named "<<temp<<endl;
}
}
closedir
(
dp
);
...
...
exp_grid.h
View file @
1cadca46
...
...
@@ -63,14 +63,6 @@ void exp_grid::get_exps(double min_slope_par, double max_slope_par, vector<float
yvals
=
y_fit
;
wvals
=
w_fit
;
/* //for debugging
for(int i=0; i<x_fit.size(); i++)
{
cout<<i<<" "<<xvals.at(i)<<" "<<yvals.at(i)<<" "<<wvals.at(i)<<endl;
}
exit(1);
*/
min_slope_par
=
0
;
max_slope_par
=
0.3
;
...
...
@@ -88,15 +80,6 @@ void exp_grid::get_exps(double min_slope_par, double max_slope_par, vector<float
cout
<<
"wvals.size(0 = "
<<
wvals
.
size
()
<<
endl
;
exit
(
1
);
}
/* else
{
cout<<"Writing out values for xvals, yvals, and wvals"<<endl;
cout<<"Size of xvals = "<<xvals.size()<<endl;
for(int i=0; i<xvals.size(); i++)
{
cout<<i<<" "<<xvals.at(i)<<" "<<yvals.at(i)<<" "<<wvals.at(i)<<endl;
}
}*/
bool
done
=
false
;
int
previous_val
=-
1
;
...
...
@@ -166,27 +149,17 @@ void exp_grid::get_exps(double min_slope_par, double max_slope_par, vector<float
}
}
//cout<<"Calculating match_score_cutoff: ";
//cout<<"xvals.at(0) = "<<xvals.at(0)<<endl;
double
n1
=
0.1
*
F
/
G
;
//cout<<"n1="<<n1<<endl;
double
n2
=
b1
-
b2
;
//cout<<"n2="<<n2<<endl;
if
(
n1
<=
0
||
n2
==
0
)
{
//cout<<"setting match_score_cutoff to -1"<<endl;
match_score_cutoff
=-
1
;
}
else
{
// cout<<"n1 and n2 acceptable."<<endl;
match_score_cutoff
=
log
(
n1
)
/
(
n2
)
+
xvals
.
at
(
0
);
//cout<<"match_score_cutoff="<<match_score_cutoff<<endl;
}
msc_par
=
match_score_cutoff
;
/* int staller;
cout<<"Stalling: ";
cin>>staller;*/
}
void
exp_grid
::
assign_array
(
double
min_b1
,
double
max_b1
,
double
min_b2
,
double
max_b2
,
double
stepper
)
...
...
@@ -226,14 +199,6 @@ void exp_grid::calc_constants(double& alpha,double& alpha1,double& beta,double&
gamma
+=
wvals
.
at
(
i
)
*
yvals
.
at
(
i
)
*
exp
(
-
1.0
*
b1
*
xvals
.
at
(
i
));
gamma1
+=
wvals
.
at
(
i
)
*
yvals
.
at
(
i
)
*
exp
(
-
1.0
*
b2
*
xvals
.
at
(
i
));
}
/*
alpha*=2.0;
alpha1*=2.0;
beta*=2.0;
gamma*=2.0;
gamma1*=2.0;
*/
}
double
exp_grid
::
get_genomic_distance
()
...
...
@@ -296,7 +261,7 @@ double exp_grid::get_wt_rmsd(vector<float> rmsd_wts)
}
else
{
val
=
-
2
;
//according to Zbyszek.
val
=
-
2
;
}
if
(
yvals
.
at
(
i
)
>
0
)
...
...
file_info.h
View file @
1cadca46
...
...
@@ -17,14 +17,10 @@ class file_info
~
file_info
();
void
read_line
();
void
set_file_name
(
string
file_name_par
);
// char get_caa();
// void delete_pFile();
string
get_current_line
();
// void open(string path_par);
void
set_path
(
string
path_par
);
void
open
();
void
set_position
();
// string file_name;
string
path
;
int
total_tags
;
int
strings_read_in
;
...
...
@@ -49,9 +45,7 @@ file_info::file_info()
file_info
::~
file_info
()
{
cout
<<
"Top of file_info destructor."
<<
endl
;
// fclose(pFile);
cout
<<
"Closed the file."
<<
endl
;
//delete pFile;
cout
<<
"Bottom of file_info destructor."
<<
endl
;
}
...
...
@@ -98,8 +92,6 @@ void file_info::set_path(string path_par)
fgetpos
(
pFile
,
&
position
);
//point to the first sequence in the file.
// read_line();
if
(
DEBUG_FI
||
verbose
)
{
cout
<<
"total_tags in current TAGS file = "
<<
total_tags
<<
endl
;
...
...
@@ -127,8 +119,6 @@ void file_info::open()
fsetpos
(
pFile
,
&
position
);
//set the position to the last place we read from.
}
// strings_read_in=0;
// fgetpos(pFile,&position); //point to the first sequence in the file.
read_line
();
if
(
s
==
last_read
)
...
...
@@ -184,13 +174,3 @@ string file_info::get_current_line()
{
return
s
;
}
/*char file_info::get_caa()
{
cout<<"in get_caa(). last_read_sequence = "<<s<<endl;
return s[0];
}
*/
//void file_info::delete_pFile()
//{
//}
fmerg.cpp
View file @
1cadca46
...
...
@@ -171,7 +171,5 @@ int main(int argc, char* argv[])
otagstream
.
close
();
}
return
0
;
}
sttagger.h
View file @
1cadca46
...
...
@@ -27,9 +27,6 @@ const int SIZE_CUTOFF=140000; //SIZE_CUTOFF: A constant that ~identifies orga
//Any proteome with < SIZE_CUTOFF amino acids considered a reduced organism
//and flagged as potentially problematic in problematic_orgs.txt file.
const
int
TAGS_MAX
=
5000000
;
//TAGS_MAX: Maximum size of the vector holding/sorting the groups of tags.
//Can be increased when code is run on machines with more memory.
const
bool
DO_SCRAMBLING
=
true
;
//DO_SCRAMBLING: Can be set to false when user wants to maintain a previously generated background.
//Scrambling introduces a random element into the code, with each scramble
//generating very slightly different results; keeping this random background
...
...
@@ -88,8 +85,6 @@ class sttagger
void
do_tags
();
void
do_tags_v2
();
// void do_scr_tags();
void
write_out_aux_files
();
void
write_out_aux_files_v2
();
void
write_out_aahistogram
();
...
...
@@ -149,6 +144,7 @@ sttagger::sttagger(string path_par, string species_par, bool filtering_par, bool
keepers
.
push_back
(
"IDTPGHVDFTIEVERSMRVLDGAIVV"
);
keepers
.
push_back
(
"IDTPGHVDFTIEVERSMRVLDGAVMV"
);
}
//If we are filtering Archaea, "" "" "" (same as above)
else
if
(
filtering
&&
species
==
"A"
)
{
...
...
@@ -189,15 +185,13 @@ sttagger::sttagger(string path_par, string species_par, bool filtering_par, bool
keepers
.
push_back
(
"IDTPGHVDFTIEVERSMRVLDGAIVV"
);
keepers
.
push_back
(
"IDTPGHVDFTIEVERSMRVLDGAVMV"
);
}
//If we are filtering Archaea, "" "" "" (same as above)
else
if
(
filtering
&&
species
==
"A"
)
{
keepers
.
push_back
(
"YFTIIDAPGHRDFVKNMITGASQADAALLVV"
);
}
//string kfile = path+"/"+bfn+"/"+bfn+"_keepers_for_filtering.txt";
//u.open_ofile(keeperstream,kfile,"kfile");
complete_setup_v2
();
}
...
...
@@ -241,15 +235,6 @@ void sttagger::complete_setup_v2()
logstream
.
close
();
}
/*
problem_stream.open( (path+"/"+bfn+"/problematic_inputs.txt").c_str(), ios::out | ios::app);
if(problem_stream.fail())
{
cout<<"Failed to open problem_stream."<<endl;
exit(1);
}
*/
parse_if_v2
();
}
...
...
@@ -481,7 +466,6 @@ void sttagger::do_tags()
#pragma omp parallel for
for
(
int
i
=
0
;
i
<
organisms
.
size
();
i
++
)
{
cout
<<
"sttagger::do_tags(): i="
<<
i
<<
" "
<<
organisms
.
at
(
i
).
get_directory
()
<<
endl
;
// organisms.at(i).generate_tags(!filtering); //Only generate the scrambled tags if this is not a filtering run.
organisms
.
at
(
i
).
generate_tags
(
true
,
partial_run
);
//Only generate the scrambled tags if this is not a filtering run.
//Check the total number of amino acids.
...
...
@@ -528,7 +512,6 @@ void sttagger::do_tags_v2()
int
num_tags
=
0
;
cout
<<
"sttagger::do_tags_v2(): ordinal="
<<
ordinal
<<
" "
<<
organisms
.
at
(
0
).
get_directory
()
<<
endl
;
// organisms.at(i).generate_tags(!filtering); //Only generate the scrambled tags if this is not a filtering run.
organisms
.
at
(
0
).
generate_tags
(
true
,
partial_run
);
//Only generate the scrambled tags if this is not a filtering run.
//Check the total number of amino acids.
...
...
@@ -633,20 +616,6 @@ void sttagger::write_out_tags_v2()
organism_tags
.
clear
();
organisms
.
at
(
0
).
clear_tags
();
outstream
.
close
();
/*
ofstream histstream;
histstream.open( (path+"/"+bfn+"/"+bfn+"_hist.txt").c_str());
if(histstream.fail())
{
cout<<"Failed to open histstream "<<endl;
exit(1);
}
histstream<<ordinal<<endl<<organisms.at(0).get_total_num_aa()<<endl;
organisms.at(0).write_out_aa_array(outstream);
histstream<<endl;
histstream.close();*/
}
void
sttagger
::
write_out_scr_tags
(
int
organism
)
...
...
@@ -728,7 +697,6 @@ void sttagger::write_out_aux_files()
void
sttagger
::
write_out_aux_files_v2
()
{
write_out_aahistogram_v2
();
// write_out_aaentropies_v2();
if
(
filtering
)
{
write_out_keepers_log_v2
();
...
...
@@ -827,12 +795,6 @@ void sttagger::write_out_aaentropies()
outstream
.
close
();
}
/*vector<org> sttagger::return_organisms()
{
return organisms;
}
*/
void
sttagger
::
close_pstream
()
{
problem_stream
.
close
();
...
...
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