boolean build_alignment(void)
{
GeneParameter21 * gpara;
GeneModel * gm;
if( pal_file != NULL ) {
pal = read_simple_PackAln_file(pal_file);
}
if( use_new_stats == 0 ) {
gpara = GeneParameter21_wrap(gf,subs_error,indel_error,rmd,model_codon,model_splice,use_tied_model,ct,rnd_loop,cds_loop,rnd_to_model,link_loop,link_to_model);
} else {
gm = GeneModel_from_GeneStats(gs,gmp);
gpara= GeneParameter21_from_GeneModel(gm,ct,rnd_loop,cds_loop,rnd_to_model,link_loop,link_to_model,subs_error,indel_error);
}
if( gpara == NULL ) {
warn("Sorry - could not build gene parameters. Must be a bug of some sort");
return FALSE;
}
/* phased based proteins use a different source */
if( alg == GWWRAP_623P ) {
alb = AlnBlock_from_phased_protein_wrap(pro,tsm,gen,gpara->cm,rm,mat,ppp,gpara,dpri,&pal);
} else {
if( use_tsm == FALSE) {
alb = AlnBlock_from_protein_genewise_wrap(pro,gen,mat,-gap,-ext,gpara,rmd,rmd,alg,use_syn,rm,allN,startend,dpri,&pal,gwrp);
} else {
alb = AlnBlock_from_TSM_genewise_wrap(tsm,gen,gpara,rmd,rmd,use_syn,alg,allN,flat_insert,dpri,&pal,NULL);
}
}
free_GeneParameter21(gpara);
if( alb == NULL )
return FALSE;
gr = new_GenomicRegion(gen);
add_Genes_to_GenomicRegion_GeneWise(gr,gen->baseseq->offset,gen->baseseq->end,alb,use_tsm == TRUE ? tsm->name : pro->baseseq->name,pseudo,NULL);
if( use_tsm == TRUE)
mss = MatchSummarySet_from_AlnBlock_genewise(alb,tsm->name,1,gen->baseseq);
else
mss = MatchSummarySet_from_AlnBlock_genewise(alb,pro->baseseq->name,pro->baseseq->offset,gen->baseseq);
return TRUE;
}
GeneModel * GeneModel_from_GeneModelParam(GeneModelParam * p)
{
GeneStats * st;
GeneModel * out;
assert(p);
st = GeneStats_from_GeneModelParam(p);
out = GeneModel_from_GeneStats(st,p);
free_GeneStats(st);
return out;
}
int main(int argc,char ** argv)
{
Sequence * seq;
ComplexSequence * cs;
ComplexSequenceEvalSet * cset;
GeneStats * st;
GeneModel * gm;
GeneModelParam * gp;
FILE * ifp;
gp = std_GeneModelParam();
seq = read_fasta_file_Sequence("../../test_data/human.genomic");
ifp = openfile("gene.stat","r");
st = read_GeneStats(ifp);
/* dump_GeneStats(st,stdout); */
fflush(stdout);
gm = GeneModel_from_GeneStats(st,gp);
show_GeneModel(gm,stdout);
fflush(stdout);
cset = new_ComplexSequenceEvalSet_from_GeneModel(gm);
cs = new_ComplexSequence(seq,cset);
show_ComplexSequence(cs,stdout);
}
