DPRunImpl * new_DPRunImpl_from_argv(int * argc,char ** argv)
{
DPRunImpl * out;
char * temp;
out = DPRunImpl_alloc();
if( (temp = strip_out_assigned_argument(argc,argv,"dymem")) != NULL ) {
if( strcmp(temp,"explicit") == 0) {
out->memory = DPIM_Explicit;
} else if( strcmp(temp,"linear") == 0 ) {
out->memory = DPIM_Linear;
} else if( strcmp(temp,"default") == 0 ) {
out->memory = DPIM_Default;
} else {
warn("String [%s] for dynamic memory layout is not recognised",temp);
free_DPRunImpl(out);
return NULL;
}
}
if( (temp = strip_out_assigned_argument(argc,argv,"kbyte")) != NULL ) {
if( is_integer_string(temp,&out->kbyte_size) == FALSE ) {
warn("String [%s] for dynamic memory size is not recognised",temp);
free_DPRunImpl(out);
return NULL;
}
}
if(strip_out_boolean_argument(argc,argv,"dydebug") == TRUE ) {
out->debug = 1;
out->memory = DPIM_Explicit;
}
return out;
}
/* Function: free_DnaProfileEnginePara(obj)
*
* Descrip: Free Function: removes the memory held by obj
* Will chain up to owned members and clear all lists
*
*
* Arg: obj [UNKN ] Object that is free'd [DnaProfileEnginePara *]
*
* Return [UNKN ] Undocumented return value [DnaProfileEnginePara *]
*
*/
DnaProfileEnginePara * free_DnaProfileEnginePara(DnaProfileEnginePara * obj)
{
int return_early = 0;
if( obj == NULL) {
warn("Attempting to free a NULL pointer to a DnaProfileEnginePara obj. Should be trappable");
return NULL;
}
#ifdef PTHREAD
assert(pthread_mutex_lock(&(obj->dynamite_mutex)) == 0);
#endif
if( obj->dynamite_hard_link > 1) {
return_early = 1;
obj->dynamite_hard_link--;
}
#ifdef PTHREAD
assert(pthread_mutex_unlock(&(obj->dynamite_mutex)) == 0);
#endif
if( return_early == 1)
return NULL;
if( obj->dpri != NULL)
free_DPRunImpl(obj->dpri);
if( obj->rm != NULL)
free_RandomModelDNA(obj->rm);
if( obj->setpara != NULL)
free_LocalCisHitSetPara(obj->setpara);
if( obj->lchs != NULL)
free_LocalCisHitScore(obj->lchs);
ckfree(obj);
return NULL;
}
int main(int argc,char ** argv)
{
DPRunImpl * dpri = NULL;
ScanWiseHSPImpl * scani = NULL;
HSP2HitListImpl * hsp2hiti = NULL;
HitListOutputImpl * hloi = NULL;
ProteinIndexConstructor * pic = NULL;
HSPScanInterface * hsi;
HSPScanInterfacePara * para;
SearchStatInterface * ssi;
SearchStatInterface * ssl;
SeqLookupLoadPara * slp;
HSPset2HitPairPara * hsp2hit;
CompMat * mat;
SequenceDB * db;
Sequence * seq;
int ret;
int i;
int effective_db_size = 300000;
int kk;
int count = 0;
LinearHSPmanager * lm;
HitList * hl;
boolean use_mott = 1;
boolean trunc_best_hsp = 0;
boolean verbose = 0;
static struct rusage use;
struct timeval t0, t1;
gettimeofday(&t0, NULL);
dpri = new_DPRunImpl_from_argv(&argc,argv);
dpri->memory = DPIM_Explicit;
scani = new_ScanWiseHSPImpl_from_argv(&argc,argv);
hsp2hiti = new_HSP2HitListImpl_from_argv(&argc,argv);
hloi = new_HitListOutputImpl_from_argv(&argc,argv);
slp = new_SeqLookupLoadPara_from_argv(&argc,argv);
pic = new_ProteinIndexConstructor_from_argv(&argc,argv);
hsp2hit = new_HSPset2HitPairPara_from_argv(&argc,argv);
para = new_HSPScanInterfacePara_from_argv(&argc,argv);
verbose = strip_out_boolean_argument(&argc,argv,"verbose") ;
strip_out_boolean_def_argument(&argc,argv,"mott",&use_mott);
strip_out_boolean_def_argument(&argc,argv,"besthsp",&trunc_best_hsp);
strip_out_integer_argument(&argc,argv,"dbsize",&effective_db_size);
#ifdef SCAN_CORBA
sorb = get_Wise2Corba_Singleton(&argc,argv,"orbit-local-orb");
#endif
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 2 ) {
show_help(stdout);
exit(12);
}
/* ugly, but we don't want to bounce matrices around the network... */
mat = read_Blast_file_CompMat("BLOSUM62.bla");
erroroff(REPORT);
hsi = new_HSPScanInterface_from_ScanWiseHSPImpl(scani,pic,slp);
ssi = new_Mott_SearchStatInterface();
ssl = new_lookup_SearchStatInterface(40,2.3);
if( verbose ) {
info("contacted database");
}
db = single_fasta_SequenceDB(argv[1]);
if( db == NULL ) {
fatal("Could not open sequence db...\n");
}
for(seq = init_SequenceDB(db,&ret); seq != NULL;seq = get_next_SequenceDB(db) ) {
count++;
for(i=0;i<seq->len;i++) {
if( !isalpha(seq->seq[i]) ) {
fatal("Sequence position %d [%c] is not valid",i,seq->seq[i]);
}
seq->seq[i] = toupper(seq->seq[i]);
}
info("Processing %s",seq->name);
getrusage(RUSAGE_SELF,&use);
/* info("Before query %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
lm = (*hsi->scan_query)(hsi->data,seq,para);
fprintf(stderr,"Got linear manager is %d entries\n",lm->len);
if( lm->mat == NULL ) {
lm->mat = hard_link_CompMat(mat);
}
getrusage(RUSAGE_SELF,&use);
/*
info("After query %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
sort_LinearHSPmanager(lm,compare_HSPset_score);
if( trunc_best_hsp == 1 ) {
for(kk=1;kk<lm->len;kk++) {
free_HSPset(lm->set[kk]);
lm->set[kk] = NULL;
}
lm->len = 1;
}
getrusage(RUSAGE_SELF,&use);
/*
info("After sort %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
hl = HitList_from_HSP_HSP2HitListImpl(hsp2hiti,lm,dpri,hsp2hit);
getrusage(RUSAGE_SELF,&use);
/*
info("After conversion %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
free_LinearHSPmanager(lm);
if( use_mott == 1 ) {
apply_SearchStat_to_HitList(hl,ssi,effective_db_size);
} else {
for(kk=0;kk<hl->len;kk++) {
hl->pair[kk]->bit_score = hl->pair[kk]->raw_score / 2.0;
}
}
sort_HitList_by_score(hl);
show_HitList_HitListOutputImpl(hloi,hl,stdout);
getrusage(RUSAGE_SELF,&use);
/*
info("After output %s %.3fu %.3fs\n", seq->name,
use.ru_utime.tv_sec + use.ru_utime.tv_usec*MICROSECOND,
use.ru_stime.tv_sec + use.ru_stime.tv_usec*MICROSECOND
);
*/
free_HitList(hl);
free_Sequence(seq);
}
free_DPRunImpl(dpri);
free_HSPScanInterface(hsi);
gettimeofday(&t1, NULL);
fprintf(stderr, "[client stats] queries, time (s): %d %f\n",
count,
(t1.tv_sec - t0.tv_sec) +
(t1.tv_usec - t0.tv_usec) * 1e-6);
return 0;
}