Hscore * Hscore_from_ProteinABC(ProteinDB* querydb,ProteinDB* targetdb,CompMat* comp,int a,int b,int c,double bits_cutoff,int report_level,boolean die_on_error,DBSearchImpl* dbsi)
{
Hscore * out = NULL;
Search_Return_Type ret;
ret = SEARCH_ERROR;
out = std_score_Hscore(bits_cutoff,report_level);
if( dbsi == NULL ) {
warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
goto exit;
}
if( querydb == NULL ) {
warn("Passed a NULL querydb. Exiting without searching");
goto exit;
}
if( targetdb == NULL ) {
warn("Passed a NULL targetdb. Exiting without searching");
goto exit;
}
if( comp == NULL ) {
warn("Passed a NULL comparison matrix. Exiting without searching");
goto exit;
}
ret = search_abc(dbsi,out,querydb,targetdb,comp,a,b,c);
exit:
return out;
}
Hscore * Hscore_from_ProteinBA(ProteinDB* querydb,ProteinDB* targetdb,CompMat* comp,Score bentry,Score bexit,Score bfor_trans,Score b_self_trans,Score b3exit,double bits_cutoff,int report_level,DBSearchImpl* dbsi)
{
Hscore * out = NULL;
Search_Return_Type ret;
ret = SEARCH_ERROR;
out = std_score_Hscore(bits_cutoff,report_level);
if( dbsi == NULL ) {
warn("Passed a NULL dbsi search implementaion object. Exiting without searching");
goto exit;
}
if( querydb == NULL ) {
warn("Passed a NULL querydb. Exiting without searching");
goto exit;
}
if( targetdb == NULL ) {
warn("Passed a NULL targetdb. Exiting without searching");
goto exit;
}
if( comp == NULL ) {
warn("Passed a NULL comparison matrix. Exiting without searching");
goto exit;
}
ret = search_ProteinBlockAligner(dbsi,out,querydb,targetdb,comp,bentry,bexit,bfor_trans,b_self_trans,b3exit);
exit:
return out;
}
int main(int argc,char **argv)
{
FiveStateFrameSet * frame;
FiveStateModel * fsm;
FiveStateScore * fss;
RandomModel * rm;
ProteinDB * proteindb;
DBSearchImpl * dbsi;
Hscore * hs;
double gathering_cutoff = 0.0;
double bits;
int i;
dbsi = new_DBSearchImpl_from_argv(&argc,argv);
strip_out_float_argument(&argc,argv,"ga",&gathering_cutoff);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
rm = default_RandomModel();
frame = read_FiveStateFrameSet_file(argv[1],"block.str");
if( frame == NULL )
fatal("Unable to make FiveStateModel from context %s, block.str file",argv[1]);
fsm = FiveStateModel_from_FiveStateFrameSet(frame);
/* dump_FiveStateModel(fsm,stdout); */
fsm->name = stringalloc(argv[1]);
fold_RandomModel_into_FiveStateModel(fsm,rm);
/* converts probabilities to integers for calculation */
fss = FiveStateScore_from_FiveStateModel(fsm);
proteindb = single_fasta_ProteinDB(argv[2]);
if( proteindb== NULL )
fatal("Unable to make proteindb from %s",argv[2]);
hs = std_score_Hscore(Probability2Score(gathering_cutoff)-10,-1);
search_FiveStateProtein(dbsi,hs,fss,proteindb);
fprintf(stdout,"\n\n#High Score list\n");
fprintf(stdout,"#Protein ID DNA Str ID Bits Evalue\n");
fprintf(stdout,"--------------------------------------------------------------------------\n");
for(i=0;i<hs->len;i++) {
bits = Score2Bits(hs->ds[i]->score);
if( bits < gathering_cutoff ) {
break;
}
fprintf(stdout,"Protein %-20sDNA [%c] %-24s %.2f\n",hs->ds[i]->query->name,hs->ds[i]->target->is_reversed == TRUE ? '-' : '+',hs->ds[i]->target->name,bits);
}
}
