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fixed an issue with libraries order. It had to do with the freeze fun…
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…ction that was out of sync with the ordered inserzion of the CL->entries
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@cnotred
cnotred committed Mar 28, 2023
1 parent cd06c91 commit 70d88dd
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Showing 4 changed files with 91 additions and 51 deletions.
17 changes: 3 additions & 14 deletions lib/dp_lib/util_dp_drivers.c
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Original file line number Diff line number Diff line change
Expand Up @@ -556,26 +556,15 @@ Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL)
PW_CL->get_dp_cost=slow_get_dp_cost;
PW_CL->evaluate_residue_pair=evaluate_matrix_score;
PW_CL->extend_jit=0;


if (get_string_variable ("fs_matrix"))sprintf (PW_CL->method_matrix,"%s",get_string_variable ("fs_matrix"));
else sprintf (PW_CL->method_matrix,"idmat");



if (int_variable_isset ("fs_gop") && get_int_variable("fs_gop")<0)
PW_CL->gop=get_int_variable("fs_gop");
else
PW_CL->gop= get_avg_matrix_mm (PW_CL->M, AA_ALPHABET)*10;

if (int_variable_isset ("fs_gep") && get_int_variable("fs_gep")<0)
PW_CL->gep=get_int_variable("fs_gep");
else
PW_CL->gep= -1;


}
else if ( strm (mode, "proba_pair"))
{

PW_CL->maximise=1;
PW_CL->TG_MODE=1;
PW_CL->use_fragments=0;
Expand Down
27 changes: 19 additions & 8 deletions lib/dp_lib/util_dp_suboptimal_nw.c
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ int suboptimal_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL,
entry[R1]=i;entry[R2]=j;
entry[WE]=id;
entry[CONS]=1;

add_entry2list (entry,A->CL);
}
}
Expand Down Expand Up @@ -628,14 +628,15 @@ int proba_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
static int TinsProb_ml, TmatchProb_ml;
int i, j,I, J;
float *F, *B;

int l;
float thr=0.01;//ProbCons Default
char *alphabet;


int do_reset=0;
//HERE ("DO reset must be replaced by a higher order reset");

//Free all the memory
if (A==NULL)
if (A==NULL || do_reset)
{
free_float (transMat, -1);transMat=NULL;
free_float (insProb, -1);insProb=NULL;
Expand All @@ -653,7 +654,7 @@ int proba_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
forward_proba_pair_wise (NULL, NULL, 0,0,NULL,NULL,NULL,NULL,NULL);
backward_proba_pair_wise (NULL, NULL, 0,0,NULL,NULL,NULL,NULL,NULL);
ProbaMatrix2CL(NULL, NULL, NULL, 0, 0, NULL, NULL, 0, NULL);
return 0;
if (!do_reset || !A)return 0;
}

if (!transMat && (strm (retrieve_seq_type(), "DNA")))
Expand Down Expand Up @@ -1447,6 +1448,8 @@ Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixT
return NULL;
}



I=strlen (A->seq_al[ls[0][0]]);
J=strlen (A->seq_al[ls[1][0]]);

Expand Down Expand Up @@ -1485,21 +1488,29 @@ Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixT
if (v>0.01)old_n++;
}
}

sort_int_inv (list, 3, 2, 0, list_n-1);
if (!entry)entry=(int*)vcalloc ( CL->entry_len+1, CL->el_size);

list_n=MIN(list_n,(F*MIN(I,J)));
//list_n=MIN(list_n,(F*MIN(I,J)));



for (i=0; i<list_n; i++)
{
int x, y;

entry[SEQ1]=s1;
entry[SEQ2]=s2;
entry[R1] =list[i][0];
entry[R2] =list[i][1];
entry[WE] =list[i][2];
entry[CONS]=1;

add_entry2list (entry,A->CL);

}

tot_new+=list_n;
tot_old+=old_n;
// HERE ("LIB_SIZE NEW: %d (new) %d (old) [%.2f]", list_n, old_n, (float)tot_new/(float)tot_old);
Expand Down
17 changes: 9 additions & 8 deletions lib/t_coffee_lib/t_coffee.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5137,8 +5137,6 @@ get_cl_param(\
if ((CL->S)->nseq>1 && !do_convert)
{
CL=read_n_constraint_list (list_file,n_list,NULL, mem_mode,weight,type, le, CL, seq_source);

//CL=post_process_constraint_list (CL); //needed when constraints are added, for instance the RNA modes
}
else if ( do_convert && out_lib[0])
{
Expand All @@ -5151,12 +5149,12 @@ get_cl_param(\
CL=read_n_constraint_list (list_file,n_list,NULL, mem_mode,weight,type, le, CL, seq_source);
}
}

//This very important step insures the CL is symetrical
//This is essential for the remaining computation
//It should not be done before because some methods may not be symetrical for specific reasons
//And the CL may be used in different contexts
CL=CL2simCL (CL);


if ( CL->M)clean_aln=0;

Expand Down Expand Up @@ -5276,13 +5274,14 @@ get_cl_param(\

if (CL->ne>0 && out_lib[0]!='\0' && !strm (out_lib, "no"))
{

if (strstr (out_lib_mode, "extended"))
{
char emode[1000];
//Do the processing before saving the extended lib*/
processed_lib=1;

if ( filter_lib) CL=filter_constraint_list (CL,CL->weight_field, filter_lib);

for (a=0; a<relax_lib; a++)CL=relax_constraint_list (CL);
for (a=0; a<shrink_lib; a++)CL=shrink_constraint_list (CL);
sprintf ( emode, "lib_%s", out_lib_mode);
Expand Down Expand Up @@ -5316,11 +5315,13 @@ get_cl_param(\

if (!processed_lib)
{
if ( filter_lib) CL=filter_constraint_list (CL,CL->weight_field, filter_lib);
if (atoigetenv ("EXTEND4TC")==1)CL=extend_constraint_list(CL);

for (a=0; a<relax_lib; a++)CL=relax_constraint_list (CL);
for (a=0; a<shrink_lib; a++)CL=shrink_constraint_list (CL);
if ( filter_lib) CL=filter_constraint_list (CL,CL->weight_field, filter_lib);

if (atoigetenv ("EXTEND4TC")==1)CL=extend_constraint_list(CL);

for (a=0; a<relax_lib; a++)CL=relax_constraint_list (CL);
for (a=0; a<shrink_lib; a++)CL=shrink_constraint_list (CL);
}

CL=evaluate_constraint_list_reference (CL);
Expand Down
81 changes: 60 additions & 21 deletions lib/util_lib/util_constraints_list.c
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
#include "dp_lib_header.h"

static int entry_len;

int dump2ne (char*file, int entry_len);
/**
* \file util_constraints_list.c
* All utilities for the Constraint_list.
Expand Down Expand Up @@ -60,7 +60,7 @@ Constraint_list *produce_list ( Constraint_list *CL, Sequence *S, char * metho
njob=queue2n(job)+1;

nproc=get_nproc();

HERE ("CL->multi_thread=%s", CL->multi_thread);
if (strstr ( CL->multi_thread, "jobcells"))return fork_cell_produce_list (CL, S, method, weight, mem_mode,job,nproc,local_stderr);
else if (strstr ( CL->multi_thread, "joblines"))return fork_line_produce_list (CL, S, method, weight, mem_mode,job, nproc,local_stderr);
else if (strstr ( CL->multi_thread, "jobs"))return fork_subset_produce_list (CL, S, method, weight, mem_mode,job, nproc,local_stderr); //Recommended default
Expand Down Expand Up @@ -143,6 +143,7 @@ Constraint_list *fork_subset_produce_list ( Constraint_list *CL, Sequence *S,
done=0;
while (job!=end)
{
//empty_constraint_list (CL);
if (a==0)output_completion ( local_stderr,done,todo,1, "Submit Job");
job=print_lib_job (job, "io->CL=%p control->submitF=%p control->retrieveF=%p control->mode=%s",CL,submit_lib_job, retrieve_lib_job, CL->multi_thread );

Expand Down Expand Up @@ -1278,12 +1279,32 @@ char *make_aln_command(TC_method *m, char *seq, char *aln)
/* */
/* */
/*********************************************************************/
Constraint_list * unfreeze_constraint_list (Constraint_list *CL)
Constraint_list * unfreeze_constraint_list_old (Constraint_list *CL)
{
free_int (CL->freeze, -1);
CL->freeze=NULL;
}
Constraint_list * unfreeze_constraint_list (Constraint_list *CL)
{
int s1, r1, b;
Sequence *S=CL->S;
for (s1=0; s1<S->nseq; s1++)
for (r1=1; r1<=S->len[s1]; r1++)
for (b=1; b<CL->residue_index[s1][r1][0]; b+=ICHUNK)
CL->residue_index[s1][r1][b+MISC]=0;
return CL;
}
Constraint_list * freeze_constraint_list (Constraint_list *CL)
{
int s1, r1, b;
Sequence *S=CL->S;
for (s1=0; s1<S->nseq; s1++)
for (r1=1; r1<=S->len[s1]; r1++)
for (b=1; b<CL->residue_index[s1][r1][0]; b+=ICHUNK)
CL->residue_index[s1][r1][b+MISC]=CL->residue_index[s1][r1][b+WE];
return CL;
}
Constraint_list * freeze_constraint_list_old (Constraint_list *CL)
{
int a, b, d=0;
Sequence *S=CL->S;
Expand Down Expand Up @@ -1320,13 +1341,26 @@ Constraint_list * empty_constraint_list (Constraint_list *CL)
CL->ne=0;
return CL;
}

int dump2ne (char*file, int entry_len)
{
int *entry, b, c, e, tot;
FILE *fp;
int count=0;
if (!file) return 0;
entry=(int*)vcalloc ( entry_len+1, sizeof (int));
fp=vfopen (file, "rb");
if (!fp) return 0;
while ((b=fread (entry, sizeof(int), entry_len, fp))==entry_len)count++;
vfree(entry);
vfclose (fp);
return count;
}
Constraint_list * undump_constraint_list (Constraint_list *CL, char *file)
{

int *entry, b, c, e, tot;
FILE *fp;

if (!CL || !CL->residue_index)return CL;
entry=(int*)vcalloc ( CL->entry_len+1, sizeof (int));

Expand Down Expand Up @@ -1372,7 +1406,7 @@ int safe_dump_constraint_list (Constraint_list *CL,char *file, char *mode, Seque
if (entry[R1]<=0)continue;

b=(CL->freeze)?CL->freeze[s1][r1]:1;
for (;b<CL->residue_index[s1][r1][0]; b+=ICHUNK)
for (b=1;b<CL->residue_index[s1][r1][0]; b+=ICHUNK)
{
s2=CL->residue_index[s1][r1][b+SEQ2];
r2=CL->residue_index[s1][r1][b+R2];
Expand All @@ -1389,7 +1423,8 @@ int safe_dump_constraint_list (Constraint_list *CL,char *file, char *mode, Seque
entry[WE]=CL->residue_index[s1][r1][b+WE];
entry[CONS]=CL->residue_index[s1][r1][b+CONS];
entry[MISC]=CL->residue_index[s1][r1][b+MISC];
fwrite(entry, sizeof (int),CL->entry_len,fp);
if (entry[MISC]!=entry[WE])
fwrite(entry, sizeof (int),CL->entry_len,fp);
}
}
}
Expand Down Expand Up @@ -1745,8 +1780,11 @@ Constraint_list *add_entry2list( CLIST_TYPE *entry, Constraint_list *CL)
int r1=entry[R1];
int r2=entry[R2];

if (entry[INDEX])return add_entry2list2(entry, CL);

if (entry[INDEX])
{
return add_entry2list2(entry, CL);
}

entry[SEQ1]=s2;
entry[SEQ2]=s1;
entry[R1]=r2;
Expand Down Expand Up @@ -2169,12 +2207,7 @@ Constraint_list*reload_constraint_list (Constraint_list *CL)

Constraint_list* read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode, char *type,FILE *local_stderr, Constraint_list *CL, char *seq_source)
{


if (1==1 && !strstr (CL->multi_thread, "methods"))//deprecated
return fork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source, 1);
else
return fork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source, get_nproc());
return fork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode,type,local_stderr, CL, seq_source, get_nproc());
}


Expand Down Expand Up @@ -2226,19 +2259,20 @@ Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_m
n_list=1;

return read_constraint_list (CL, fname[0], in_mode, mem_mode,weight_mode);
// return fork_read_n_constraint_list(fname,n_list, in_mode,mem_mode,weight_mode, type,local_stderr, CL, seq_source,1);

}

if (!CL)CL=declare_constraint_list ( S,NULL, NULL, 0,(strm(mem_mode, "disk"))?tmpfile():NULL, NULL);

if (CL->ne)
{

dump_constraint_list(CL,tmp_list[n_list], "w");
CL->ne=0;
}

CL->local_stderr=local_stderr;

fprintf ( local_stderr, "\n\tMulti Core Mode (read): %d processor(s):\n", nproc);
for (ns=0,a=0; a< n_list; a++)
{
Expand All @@ -2251,7 +2285,9 @@ Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_m
initiate_vtmpnam (NULL);
CL->local_stderr=vfopen("/dev/null", "w");
in=CL->ne;

CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode);

if (CL->ne>in)dump_constraint_list(CL,tmp_list[a], "w");
myexit (EXIT_SUCCESS);
}
Expand All @@ -2264,6 +2300,7 @@ Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_m
{
b=proclist[vwait(NULL)];
fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);

if (tmp_list[b] && check_file_exists (tmp_list[b]))
{
CL=undump_constraint_list(CL,tmp_list[b]);
Expand All @@ -2280,8 +2317,9 @@ Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_m
a=proclist[pid2];
fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]);
if (tmp_list[a] && check_file_exists (tmp_list[a]))
{
CL=undump_constraint_list (CL,tmp_list[a]);
{

CL=undump_constraint_list (CL,tmp_list[a]);
}
ns--;
}
Expand All @@ -2291,7 +2329,7 @@ Constraint_list* fork_read_n_constraint_list(char **fname,int n_list, char *in_m
{
CL=undump_constraint_list(CL,tmp_list[n_list]);
}

CL->local_stderr=local_stderr;

vfree (proclist);
Expand Down Expand Up @@ -2367,6 +2405,7 @@ Constraint_list* read_constraint_list(Constraint_list *CL,char *in_fname,char *i
{

CL=produce_list ( CL, CL->S, fname,weight_mode,mem_mode);

}
else if (strm(read_mode, "matrix"))
{
Expand Down Expand Up @@ -4365,8 +4404,8 @@ Constraint_list *merge_constraint_list ( Constraint_list *SL, Constraint_list
entry[SEQ1]=(cache)?cache[s1][0]:s1;
entry[R1]=(cache)?cache[s1][r1]:r1;
if (entry[R1]<=0)continue;
b=(SL->freeze)?SL->freeze[s1][r1]:1;
for (;b<SL->residue_index[s1][r1][0]; b+=ICHUNK)

for (b=1;b<SL->residue_index[s1][r1][0]; b+=ICHUNK)
{
s2=SL->residue_index[s1][r1][b+SEQ2];
r2=SL->residue_index[s1][r1][b+R2];
Expand Down

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