GtGenomeNode* gt_feature_node_new(GtStr *seqid, const char *type,
GtUword start, GtUword end,
GtStrand strand)
{
GtGenomeNode *gn;
GtFeatureNode *fn;
gt_assert(seqid && type);
gt_assert(start <= end);
gn = gt_genome_node_create(gt_feature_node_class());
fn = gt_feature_node_cast(gn);
fn->seqid = gt_str_ref(seqid);
fn->source = NULL;
fn->type = gt_symbol(type);
fn->score = GT_UNDEF_FLOAT;
fn->range.start = start;
fn->range.end = end;
fn->representative = NULL;
fn->attributes = NULL;
fn->bit_field = 0;
fn->bit_field |= strand << STRAND_OFFSET;
fn->children = NULL; /* the children list is create on demand */
fn->observer = NULL;
gt_feature_node_set_phase(fn, GT_PHASE_UNDEFINED);
set_transcriptfeaturetype(fn, TRANSCRIPT_FEATURE_TYPE_UNDETERMINED);
set_tree_status(&fn->bit_field, IS_TREE);
/* the DFS status is set to DFS_WHITE already */
fn->representative = NULL;
return gn;
}
GtGenomeNode* gt_sequence_node_new(const char *description, GtStr *sequence)
{
GtGenomeNode *gn = gt_genome_node_create(gt_sequence_node_class());
GtSequenceNode *sn = gt_sequence_node_cast(gn);
gt_assert(description && sequence);
sn->description = gt_str_new_cstr(description);
sn->sequence = gt_str_ref(sequence);
return gn;
}
GtGenomeNode* gt_region_node_new(GtStr *seqid, unsigned long start,
unsigned long end)
{
GtGenomeNode *gn = gt_genome_node_create(gt_region_node_class());
GtRegionNode *rn = gt_region_node_cast(gn);
gt_assert(seqid);
gt_assert(start <= end);
rn->seqid = gt_str_ref(seqid);
rn->range.start = start;
rn->range.end = end;
return gn;
}
