DycWarning * new_DycWarning_from_argstr(int * argc,char ** argv)
{
DycWarning * out;
boolean cwarn = TRUE;
out = DycWarning_alloc();
strip_out_boolean_def_argument(argc,argv,"cwarn",&cwarn);
if( cwarn == TRUE ) {
out->warn_extern = TRUE;
out->warn_extern_method = TRUE;
out->warn_c_type = TRUE;
} else {
out->warn_extern = FALSE;
out->warn_c_type = FALSE;
out->warn_extern_method = FALSE;
}
strip_out_boolean_def_argument(argc,argv,"extern",&out->warn_extern);
strip_out_boolean_def_argument(argc,argv,"ctype",&out->warn_c_type);
strip_out_boolean_def_argument(argc,argv,"methods",&out->warn_extern_method);
return out;
}
int main(int argc,char ** argv)
{
DnaMatchPara * para;
HitListOutputImpl * hitoutput;
HitList * hitlist;
Sequence * reference;
Sequence * swap;
Sequence * trans;
SequenceSet * amplimers;
int show_hitlist = 0;
int show_swapped = 1;
hitoutput = new_HitListOutputImpl_from_argv(&argc,argv);
para = new_DnaMatchPara_from_argv(&argc,argv);
strip_out_boolean_def_argument(&argc,argv,"hitlist",&show_hitlist);
strip_out_boolean_def_argument(&argc,argv,"swapped",&show_hitlist);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
reference = read_fasta_file_Sequence(argv[1]);
amplimers = read_fasta_SequenceSet_file(argv[2]);
hitlist = HitList_from_Sequence_SequenceSet_DNA(reference,amplimers,para);
if( show_hitlist ) {
show_HitList_HitListOutputImpl(hitoutput,hitlist,stdout);
}
swap = swapped_Sequence(reference,hitlist);
trans = translate_swapped(swap);
if( show_swapped ) {
write_fasta_Sequence(swap,stdout);
write_fasta_Sequence(trans,stdout);
}
}
DPImplementation * new_DPImplementation_from_argstr(int * argc,char ** argv)
{
DPImplementation * out;
char * temp;
out = DPImplementation_alloc();
if( (strip_out_boolean_argument(argc,argv,"pthreads")) == TRUE ) {
out->do_threads = TRUE;
}
if( (temp=strip_out_assigned_argument(argc,argv,"dbtrace")) != NULL ) {
if( is_integer_string(temp,&out->db_trace_level) == FALSE ) {
warn("%s is not an integer argument for dbtrace",temp);
}
}
if( strip_out_boolean_argument(argc,argv,"O") == TRUE ) {
out->largemem= TRUE;
/* other optimisations */
}
strip_out_boolean_def_argument(argc,argv,"largemem",&out->largemem);
strip_out_boolean_def_argument(argc,argv,"onemodel",&out->doone);
if( strip_out_boolean_argument(argc,argv,"prob") == TRUE ) {
out->doprob = TRUE;
}
if( strip_out_boolean_argument(argc,argv,"g") == TRUE ) {
out->dydebug = TRUE;
}
if( (temp=strip_out_assigned_argument(argc,argv,"logsum")) != NULL ) {
out->calcfunc = stringalloc(temp);
} else {
out->calcfunc = stringalloc("Probability_logsum");
}
out->dycw = new_DycWarning_from_argstr(argc,argv);
/* fprintf(stderr,"And %d is extern warning",out->dycw->warn_extern);*/
return out;
}
GeneModelParam * new_GeneModelParam_from_argv(int * argc,char ** argv)
{
GeneModelParam * out;
char * temp;
out = std_GeneModelParam();
if( (temp=strip_out_assigned_argument(argc,argv,"splice_min_collar")) != NULL ) {
if( is_double_string(temp,&out->min_collar) == FALSE ) {
warn("%s is not a floating point number. Can't be a splice_min_collar",temp);
free_GeneModelParam(out);
return NULL;
}
}
strip_out_boolean_def_argument(argc,argv,"splice_gtag",&out->use_gtag_splice);
if( (temp=strip_out_assigned_argument(argc,argv,"splice_max_collar")) != NULL ) {
if( is_double_string(temp,&out->max_collar) == FALSE ) {
warn("%s is not a floating point number. Can't be a splice_max_collar",temp);
free_GeneModelParam(out);
return NULL;
}
}
if( (temp=strip_out_assigned_argument(argc,argv,"splice_score_offset")) != NULL ) {
if( is_double_string(temp,&out->score_offset) == FALSE ) {
warn("%s is not a floating point number. Can't be a splice_score_offset",temp);
free_GeneModelParam(out);
return NULL;
}
}
if( (temp=strip_out_assigned_argument(argc,argv,"genestats")) != NULL ) {
if( out->gene_stats_file != NULL ) {
ckfree(out->gene_stats_file);
}
out->gene_stats_file = stringalloc(temp);
}
if( (temp=strip_out_assigned_argument(argc,argv,"splice_gtag_prob")) != NULL ) {
if( is_double_string(temp,&out->prob_for_gtag) == FALSE ) {
warn("%s is not a floating pointer number. Can't be a probability for gtag",temp);
free_GeneModelParam(out);
return NULL;
}
}
return out;
}
int main (int argc,char ** argv)
{
EditString * q;
EditString * t;
PackAln * pal;
AlnBlock * alb;
int match = 1;
int mismatch = -1;
int gap = -1;
boolean show_pretty = FALSE;
DPRunImpl * dpri = NULL;
StandardOutputOptions * std_opt = NULL;
strip_out_boolean_def_argument(&argc,argv,"pretty",&show_pretty);
dpri = new_DPRunImpl_from_argv(&argc,argv);
std_opt = new_StandardOutputOptions_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
q = new_EditString(argv[1]);
t = new_EditString(argv[2]);
pal = PackAln_bestmemory_EditDistance(q,t,match,mismatch,gap,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_EditDistance(pal);
fprintf(stdout,"Score %d\n",pal->score);
if( show_pretty == TRUE ) {
write_pretty_str_align(alb,"string1",q->string,"string2",t->string,12,60,stdout);
}
show_StandardOutputOptions(std_opt,alb,pal,"//",stdout);
return 0;
}
HSP2HitListImpl * new_HSP2HitListImpl_from_argv(int * argc,char ** argv)
{
HSP2HitListImpl * out;
char * temp;
out = malloc(sizeof(HSP2HitListImpl));
out->type = HSP2HitList_Heuristic;
if( (temp = strip_out_assigned_argument(argc,argv,"hspconvert")) != NULL ) {
out->type = HSP2HitListType_string_convert(temp);
}
strip_out_boolean_def_argument(argc,argv,"hspthread",&out->threaded);
out->no_threads = 4;
strip_out_integer_argument(argc,argv,"hspthreadno",&out->no_threads);
return out;
}
int main(int argc,char ** argv)
{
Sequence * gen;
Genomic * genomic;
CodonTable * ct = NULL;
GenomeEvidenceSet * ges = NULL;
RandomCodonScore * rcs;
FILE * ifp = NULL;
ComplexSequence * cs = NULL;
ComplexSequenceEvalSet * cses = NULL;
AlnBlock * alb;
PackAln * pal;
GenomicRegion * gr;
int i;
Protein * trans;
cDNA * cdna;
int kbyte = 10000;
int stop_codon_pen = 200;
int start_codon_pen = 30;
int new_gene = 5000;
int switch_cost = 100;
int smell = 8;
DPRunImpl * dpri = NULL;
EstEvidence * est;
boolean show_trans = TRUE;
boolean show_cdna = FALSE;
boolean show_genes = TRUE;
boolean show_alb = FALSE;
boolean show_pal = FALSE;
boolean show_gff = TRUE;
boolean show_debug = FALSE;
boolean show_geneu = TRUE;
char * divide_string = "//";
strip_out_boolean_def_argument(&argc,argv,"geneutr",&show_geneu);
strip_out_boolean_def_argument(&argc,argv,"genes",&show_genes);
strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);
strip_out_boolean_def_argument(&argc,argv,"gff",&show_gff);
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal);
strip_out_boolean_def_argument(&argc,argv,"debug",&show_debug);
strip_out_boolean_def_argument(&argc,argv,"cdna",&show_cdna);
strip_out_integer_argument(&argc,argv,"stop",&stop_codon_pen);
strip_out_integer_argument(&argc,argv,"start",&start_codon_pen);
strip_out_integer_argument(&argc,argv,"gene",&new_gene);
strip_out_integer_argument(&argc,argv,"switch",&switch_cost);
strip_out_integer_argument(&argc,argv,"smell",&smell);
dpri = new_DPRunImpl_from_argv(&argc,argv);
if( dpri == NULL ) {
fatal("Unable to build DPRun implementation. Bad arguments");
}
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
ct = read_CodonTable_file("codon.table");
gen = read_fasta_file_Sequence(argv[1]);
ifp = openfile(argv[2],"r");
ges = read_est_evidence(ifp,ct);
for(i=0;i<ges->len;i++) {
est = (EstEvidence *) ges->geu[i]->data;
est->in_smell = smell;
}
rcs= RandomCodonScore_alloc();
for(i=0;i<125;i++) {
if( is_stop_codon(i,ct) ) {
rcs->codon[i] = -1000000;
} else {
rcs->codon[i] = 0;
}
/* fprintf(stderr,"Got %d for %d\n",rcs->codon[i],i); */
}
cses = default_genomic_ComplexSequenceEvalSet();
cs = new_ComplexSequence(gen,cses);
pal = PackAln_bestmemory_GenomeWise9(ges,cs,-switch_cost,-new_gene,-start_codon_pen,-stop_codon_pen,rcs,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_GenomeWise9(pal);
genomic = Genomic_from_Sequence(gen);
gr = new_GenomicRegion(genomic);
add_Genes_to_GenomicRegion_GeneWise(gr,1,gen->len,alb,gen->name,0,NULL);
if( show_genes ) {
show_pretty_GenomicRegion(gr,0,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_gff ) {
show_GFF_GenomicRegion(gr,gen->name,"genomwise",stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_trans ) {
for(i=0;i<gr->len;i++) {
if( gr->gene[i]->ispseudo == TRUE ) {
fprintf(stdout,"#Gene %d is a pseudo gene - no translation possible\n",i);
} else {
trans = get_Protein_from_Translation(gr->gene[i]->transcript[0]->translation[0],ct);
write_fasta_Sequence(trans->baseseq,stdout);
}
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_cdna ) {
for(i=0;i<gr->len;i++) {
cdna = get_cDNA_from_Transcript(gr->gene[i]->transcript[0]);
write_fasta_Sequence(cdna->baseseq,stdout);
}
fprintf(stdout,"%s\n",divide_string);
}
if( show_geneu ) {
show_utr_exon_genomewise(alb,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_alb ) {
mapped_ascii_AlnBlock(alb,id,1,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_debug ) {
debug_genomewise(alb,ges,ct,gen,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_pal ) {
show_simple_PackAln(pal,stdout);
fprintf(stdout,"%s\n",divide_string);
}
return 0;
}
int main (int argc,char ** argv)
{
MappedCloneSet * trusted;
MappedCloneSet * weak;
MappedCloneMatch * match;
FILE * in;
int kbyte = 10000;
PackAln * pal;
AlnBlock * alb;
int spread = 30;
boolean show_alb = 0;
boolean show_pal = 0;
boolean show_zip = 1;
boolean show_path = 0;
char * alg_string = "local";
char * temp;
char * divide_string = "//";
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"pal",&show_pal);
strip_out_boolean_def_argument(&argc,argv,"zip",&show_zip);
strip_out_boolean_def_argument(&argc,argv,"path",&show_path);
strip_out_integer_argument(&argc,argv,"wgap",&query_gap_start);
strip_out_integer_argument(&argc,argv,"wext",&query_gap_extend);
strip_out_integer_argument(&argc,argv,"wswitch",&query_switch_cost);
strip_out_integer_argument(&argc,argv,"tgap",&target_gap_start);
strip_out_integer_argument(&argc,argv,"text",&target_gap_extend);
strip_out_integer_argument(&argc,argv,"match",&match_score);
strip_out_integer_argument(&argc,argv,"mismatch",&mismatch_score);
temp =strip_out_assigned_argument(&argc,argv,"alg");
if( temp != NULL ) {
alg_string = temp;
}
strip_out_integer_argument(&argc,argv,"spread",&spread);
strip_out_integer_argument(&argc,argv,"kbyte",&kbyte);
strip_out_standard_options(&argc,argv,show_help,show_version);
if( argc != 3 ) {
show_help(stdout);
exit(12);
}
in = fopen(argv[1],"r");
if( in == NULL ) {
fatal("Unable to open %s",argv[1]);
}
trusted = read_MappedCloneSet(in);
/* fprintf(stderr,"first start %d\n",trusted->clone[0]->start);*/
in = fopen(argv[2],"r");
if( in == NULL ) {
fatal("Unable to open %s",argv[2]);
}
change_max_BaseMatrix_kbytes(kbyte);
weak = read_MappedCloneSet(in);
synchronise_MappedCloneSets(trusted,weak);
/* fprintf(stderr,"score for 2,2 is %d\n",MappedCloneSet_match(weak,trusted,2,2,0,10,-5)); */
match = new_MappedCloneMatch(weak,trusted,match_score,mismatch_score);
fprintf(stderr,"Match matrix calculated\n");
if( strcmp(alg_string,"global") == 0 ) {
pal = PackAln_bestmemory_CloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL);
alb = convert_PackAln_to_AlnBlock_CloneWise(pal);
} else if ( strcmp(alg_string,"local") == 0 ) {
pal = PackAln_bestmemory_LocalCloneWise(weak,trusted,match,-query_gap_start,-query_gap_extend,-target_gap_start,-target_gap_extend,spread,-query_switch_cost,NULL);
alb = convert_PackAln_to_AlnBlock_LocalCloneWise(pal);
} else {
/* keep gcc happy */
pal = NULL;
alb = NULL;
fatal("Not a proper algorithm string %s",alg_string);
}
if( show_path ) {
extended_path(alb,weak,trusted,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_zip ) {
debug_zip(alb,weak,trusted,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_alb ) {
mapped_ascii_AlnBlock(alb,id,1,stdout);
fprintf(stdout,"%s\n",divide_string);
}
if( show_pal ) {
show_simple_PackAln(pal,stdout);
fprintf(stdout,"%s\n",divide_string);
}
return 0;
}
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;
}
ScanWiseHSPImpl * new_ScanWiseHSPImpl_from_argv(int * argc,char ** argv)
{
ScanWiseHSPImpl * out;
char * temp;
out = malloc(sizeof(ScanWiseHSPImpl));
out->use_corba = FALSE;
out->use_mysql = FALSE;
out->use_compress = FALSE;
out->use_multiscan = FALSE;
out->ior_file = NULL;
out->direct_sequence = NULL;
out->matrix_file = "BLOSUM62.bla";
out->step = 32;
out->host = "localhost";
out->port = 4050;
strip_out_boolean_def_argument(argc,argv,"corba",&out->use_corba);
strip_out_boolean_def_argument(argc,argv,"mysql",&out->use_mysql);
strip_out_boolean_def_argument(argc,argv,"wiseserver",&out->use_wiseserver);
strip_out_boolean_def_argument(argc,argv,"compress",&out->use_compress);
strip_out_boolean_def_argument(argc,argv,"multi",&out->use_multiscan);
if( (temp = strip_out_assigned_argument(argc,argv,"iorfile")) != NULL ) {
out->ior_file = temp;
}
if( (temp = strip_out_assigned_argument(argc,argv,"multiserver")) != NULL ) {
out->multiscan_file = temp;
}
if( (temp = strip_out_assigned_argument(argc,argv,"scan_host")) != NULL ) {
out->host = temp;
}
strip_out_integer_argument(argc,argv,"scan_port",&out->port);
if( (temp = strip_out_assigned_argument(argc,argv,"scan_dbname")) != NULL ) {
out->dbname = temp;
}
if( (temp = strip_out_assigned_argument(argc,argv,"scan_username")) != NULL ) {
out->username = temp;
}
if( (temp = strip_out_assigned_argument(argc,argv,"scan_password")) != NULL ) {
out->password = temp;
}
strip_out_integer_argument(argc,argv,"scan_step",&out->step);
if( (temp = strip_out_assigned_argument(argc,argv,"seqdb")) != NULL ) {
out->direct_sequence = temp;
}
if( (temp = strip_out_assigned_argument(argc,argv,"seqdbmat")) != NULL ) {
out->matrix_file = temp;
}
return out;
}
int main(int argc,char ** argv)
{
int i;
SequenceSet * in;
Sequence * trans;
ThreeStateDB * tsd;
DPRunImpl * dpri;
CodonTable * ct;
int return_status;
ThreeStateModel * tsm;
ThreeStateScore * tss;
Protein * hmmp;
ComplexSequence * cs;
ComplexSequenceEvalSet * cses;
PackAln * pal;
AlnBlock * alb;
int show_align = 0;
int show_alb = 0;
int show_verbose = 1;
int show_trans = 0;
ct = read_CodonTable_file("codon.table");
cses = default_aminoacid_ComplexSequenceEvalSet();
dpri = new_DPRunImpl_from_argv(&argc,argv);
strip_out_boolean_def_argument(&argc,argv,"pretty",&show_align);
strip_out_boolean_def_argument(&argc,argv,"alb",&show_alb);
strip_out_boolean_def_argument(&argc,argv,"trans",&show_trans);
if( argc != 3 ) {
show_help(stdout);
exit(63);
}
in = read_fasta_SequenceSet_file(argv[1]);
tsd = HMMer2_ThreeStateDB(argv[2]);
assert(in);
assert(tsd);
assert(in->len == 2);
trans = translate_Sequence(in->set[0],ct);
if( show_trans ) {
write_fasta_Sequence(trans,stdout);
}
cs = new_ComplexSequence(trans,cses);
open_ThreeStateDB(tsd);
while( (tsm = read_TSM_ThreeStateDB(tsd,&return_status)) != NULL ) {
fold_RandomModel_into_ThreeStateModel(tsm,tsm->rm);
set_startend_policy_ThreeStateModel(tsm,TSM_local,10,1.0);
tss = ThreeStateScore_from_ThreeStateModel(tsm);
hmmp = pseudo_Protein_from_ThreeStateModel(tsm);
pal = PackAln_bestmemory_ThreeStateLoop(tss,cs,NULL,dpri);
alb = convert_PackAln_to_AlnBlock_ThreeStateLoop(pal);
if( show_alb ) {
show_flat_AlnBlock(alb,stdout);
}
if( show_align ) {
write_pretty_seq_align(alb,hmmp->baseseq,trans,15,50,stdout);
}
if( show_verbose ) {
show_verbose_evo(alb,tsm,in->set[0],in->set[1],ct,stdout);
}
}
}