static void make_sequence_region(GtHashmap *sequence_regions,
GtStr *sequenceid,
GthRegionFactory *srf,
GthInput *input,
GtUword filenum,
GtUword seqnum)
{
GtUword offset_is_defined = false;
GtRange range, descrange;
GtGenomeNode *sr = NULL;
gt_assert(sequence_regions && sequenceid && srf && input);
if (gth_input_use_substring_spec(input)) {
range.start = gth_input_genomic_substring_from(input);
range.end = gth_input_genomic_substring_to(input);
}
else {
range = gth_input_get_relative_genomic_range(input, filenum, seqnum);
}
if (srf->use_desc_ranges) {
GtStr *description = gt_str_new();
gth_input_get_genomic_description(input, description, filenum, seqnum);
if (!gt_parse_description_range(gt_str_get(description), &descrange))
offset_is_defined = true;
gt_str_delete(description);
}
if (offset_is_defined)
range = gt_range_offset(&range, descrange.start);
else
range = gt_range_offset(&range, 1); /* 1-based */
if (!gt_str_length(sequenceid) ||
(gt_cstr_table_get(srf->used_seqids, gt_str_get(sequenceid)) &&
!offset_is_defined)) {
/* sequenceid is empty or exists already (and no offset has been parsed)
-> make one up */
GtStr *seqid;
char *base;
base = gt_basename(gth_input_get_genomic_filename(input, filenum));
seqid = gt_str_new_cstr(base);
gt_free(base);
gt_str_append_char(seqid, '|');
gt_str_append_uword(seqid, seqnum + 1); /* 1-based */
seqid_store_add(srf->seqid_store, filenum, seqnum, seqid, GT_UNDEF_UWORD);
gt_assert(!gt_cstr_table_get(srf->used_seqids, gt_str_get(seqid)));
gt_cstr_table_add(srf->used_seqids, gt_str_get(seqid));
sr = gt_region_node_new(seqid_store_get(srf->seqid_store, filenum, seqnum),
range.start, range.end);
gt_hashmap_add(sequence_regions,
(void*) gt_cstr_table_get(srf->used_seqids,
gt_str_get(seqid)),
sr);
gt_str_delete(seqid);
}
else {
/* sequenceid does not exists already (or an offset has been parsed)
-> use this one */
if (!gt_cstr_table_get(srf->used_seqids, gt_str_get(sequenceid))) {
/* no sequence region with this id exists -> create one */
gt_cstr_table_add(srf->used_seqids, gt_str_get(sequenceid));
seqid_store_add(srf->seqid_store, filenum, seqnum, sequenceid,
offset_is_defined ? descrange.start : GT_UNDEF_UWORD);
sr = gt_region_node_new(seqid_store_get(srf->seqid_store, filenum,
seqnum), range.start, range.end);
gt_hashmap_add(sequence_regions,
(void*) gt_cstr_table_get(srf->used_seqids,
gt_str_get(sequenceid)),
sr);
}
else {
GtRange prev_range, new_range;
/* sequence region with this id exists already -> modify range */
sr = gt_hashmap_get(sequence_regions, gt_str_get(sequenceid));
gt_assert(sr);
prev_range = gt_genome_node_get_range(sr);
new_range = gt_range_join(&prev_range, &range);
gt_genome_node_set_range(sr, &new_range);
seqid_store_add(srf->seqid_store, filenum, seqnum, sequenceid,
offset_is_defined ? descrange.start : GT_UNDEF_UWORD);
}
}
gt_assert(sr);
}
static int calc_spliced_alignments(GthSACollection *sa_collection,
GthChainCollection *chain_collection,
GthCallInfo *call_info,
GthInput *input,
GthStat *stat,
GtUword gen_file_num,
GtUword ref_file_num,
bool directmatches,
GthMatchInfo *match_info,
GthDNACompletePathMatrixJT
dna_complete_path_matrix_jt,
GthProteinCompletePathMatrixJT
protein_complete_path_matrix_jt)
{
const unsigned char *ref_seq_tran, *ref_seq_orig, *ref_seq_tran_rc = NULL,
*ref_seq_orig_rc = NULL;
GtUword chainctr, gen_offset = GT_UNDEF_UWORD, gen_total_length,
ref_total_length;
GtFile *outfp = call_info->out->outfp;
GtRange gen_seq_bounds, gen_seq_bounds_rc;
bool refseqisdna;
GthChain *chain;
GtRange range;
GthSA *saA;
int rval;
gt_assert(sa_collection && chain_collection);
refseqisdna = gth_input_ref_file_is_dna(input, ref_file_num);
for (chainctr = 0;
chainctr < gth_chain_collection_size(chain_collection);
chainctr++) {
chain = gth_chain_collection_get(chain_collection, chainctr);
if (++match_info->call_number > call_info->firstalshown &&
call_info->firstalshown > 0) {
if (!(call_info->out->xmlout || call_info->out->gff3out))
gt_file_xfputc('\n', outfp);
else if (call_info->out->xmlout)
gt_file_xprintf(outfp, "<!--\n");
if (!call_info->out->gff3out) {
gt_file_xprintf(outfp, "Maximal matching %s count (%u) reached.\n",
refseqisdna ? "EST" : "protein",
call_info->firstalshown);
gt_file_xprintf(outfp, "Only the first %u matches will be "
"displayed.\n", call_info->firstalshown);
}
if (!(call_info->out->xmlout || call_info->out->gff3out))
gt_file_xfputc('\n', outfp);
else if (call_info->out->xmlout)
gt_file_xprintf(outfp, "-->\n");
match_info->max_call_number_reached = true;
break; /* break out of loop */
}
/* compute considered genomic regions if not set by -frompos */
if (!gth_input_use_substring_spec(input)) {
gen_seq_bounds = gth_input_get_genomic_range(input, chain->gen_file_num,
chain->gen_seq_num);
gen_total_length = gt_range_length(&gen_seq_bounds);
gen_offset = gen_seq_bounds.start;
gen_seq_bounds_rc = gen_seq_bounds;
}
else {
/* genomic multiseq contains exactly one sequence */
gt_assert(gth_input_num_of_gen_seqs(input, chain->gen_file_num) == 1);
gen_total_length = gth_input_genomic_file_total_length(input,
chain
->gen_file_num);
gen_seq_bounds.start = gth_input_genomic_substring_from(input);
gen_seq_bounds.end = gth_input_genomic_substring_to(input);
gen_offset = 0;
gen_seq_bounds_rc.start = gen_total_length - 1 - gen_seq_bounds.end;
gen_seq_bounds_rc.end = gen_total_length - 1 - gen_seq_bounds.start;
}
/* "retrieving" the reference sequence */
range = gth_input_get_reference_range(input, chain->ref_file_num,
chain->ref_seq_num);
ref_seq_tran = gth_input_current_ref_seq_tran(input) + range.start;
ref_seq_orig = gth_input_current_ref_seq_orig(input) + range.start;
if (refseqisdna) {
ref_seq_tran_rc = gth_input_current_ref_seq_tran_rc(input) + range.start;
ref_seq_orig_rc = gth_input_current_ref_seq_orig_rc(input) + range.start;
}
ref_total_length = range.end - range.start + 1;
/* check if protein sequences have a stop amino acid */
if (!refseqisdna && !match_info->stop_amino_acid_warning &&
ref_seq_orig[ref_total_length - 1] != GT_STOP_AMINO) {
GtStr *ref_id = gt_str_new();
gth_input_save_ref_id(input, ref_id, chain->ref_file_num,
chain->ref_seq_num);
gt_warning("protein sequence '%s' (#" GT_WU " in file %s) does not end "
"with a stop amino acid ('%c'). If it is not a protein "
"fragment you should add a stop amino acid to improve the "
"prediction. For example with `gt seqtransform "
"-addstopaminos` (see http://genometools.org for details).",
gt_str_get(ref_id), chain->ref_seq_num,
gth_input_get_reference_filename(input, chain->ref_file_num),
GT_STOP_AMINO);
match_info->stop_amino_acid_warning = true;
gt_str_delete(ref_id);
}
/* allocating space for alignment */
saA = gth_sa_new_and_set(directmatches, true, input, chain->gen_file_num,
chain->gen_seq_num, chain->ref_file_num,
chain->ref_seq_num, match_info->call_number,
gen_total_length, gen_offset, ref_total_length);
/* extend the DP borders to the left and to the right */
gth_chain_extend_borders(chain, &gen_seq_bounds, &gen_seq_bounds_rc,
gen_total_length, gen_offset);
/* From here on the dp positions always refer to the forward strand of the
genomic DNA. */
/* call the Dynamic Programming */
if (refseqisdna) {
rval = call_dna_DP(directmatches, call_info, input, stat,
sa_collection, saA, gen_file_num, ref_file_num,
gen_total_length, gen_offset, &gen_seq_bounds,
&gen_seq_bounds_rc, ref_total_length, range.start,
chainctr, gth_chain_collection_size(chain_collection),
match_info, ref_seq_tran, ref_seq_orig,
ref_seq_tran_rc, ref_seq_orig_rc, chain,
dna_complete_path_matrix_jt,
protein_complete_path_matrix_jt);
}
else {
rval = call_protein_DP(directmatches, call_info, input,
stat, sa_collection, saA, gen_file_num,
ref_file_num, gen_total_length, gen_offset,
&gen_seq_bounds, &gen_seq_bounds_rc,
ref_total_length, range.start, chainctr,
gth_chain_collection_size(chain_collection),
match_info, ref_seq_tran, ref_seq_orig, chain,
dna_complete_path_matrix_jt,
protein_complete_path_matrix_jt);
}
/* check return value */
if (rval == GTH_ERROR_DP_PARAMETER_ALLOCATION_FAILED) {
/* statistics bookkeeping */
gth_stat_increment_numoffailedDPparameterallocations(stat);
gth_stat_increment_numofundeterminedSAs(stat);
/* free space */
gth_sa_delete(saA);
match_info->call_number--;
continue; /* continue with the next DP range */
}
else if (rval)
return -1;
}
if (!call_info->out->xmlout && !call_info->out->gff3out && !directmatches &&
!match_info->significant_match_found &&
match_info->call_number <= call_info->firstalshown) {
show_no_match_line(gth_input_get_alphatype(input, ref_file_num), outfp);
}
return 0;
}