const GtCanvasClass* gt_canvas_class_new(size_t size,
GtCanvasVisitLayoutFunc la_visit_pre,
GtCanvasVisitLayoutFunc la_visit_post,
GtCanvasVisitTrackFunc t_visit_pre,
GtCanvasVisitTrackFunc t_visit_post,
GtCanvasVisitLineFunc l_visit_pre,
GtCanvasVisitLineFunc l_visit_post,
GtCanvasVisitBlockFunc b_visit,
GtCanvasVisitElementFunc e_visit,
GtCanvasVisitCustomTrackFunc ct_visit,
GtCanvasDrawRulerFunc draw_ruler_func,
GtCanvasFreeFunc free)
{
GtCanvasClass *c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->visit_layout_pre = la_visit_pre;
c_class->visit_layout_post = la_visit_post;
c_class->visit_track_pre = t_visit_pre;
c_class->visit_track_post = t_visit_post;
c_class->visit_line_pre = l_visit_pre;
c_class->visit_line_post = l_visit_post;
c_class->visit_block = b_visit;
c_class->visit_element = e_visit;
c_class->visit_ct = ct_visit;
c_class->draw_ruler_func = draw_ruler_func;
c_class->free = free;
return c_class;
}
const GtMatchClass* gt_match_class_new(size_t size,
GtMatchFreeFunc free,
GtMatchAcceptFunc accept)
{
GtMatchClass *c_class;
gt_assert(size);
c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->free = free;
c_class->accept = accept;
return c_class;
}
const GtMatchVisitorClass*
gt_match_visitor_class_new(size_t size,
GtMatchVisitorFreeFunc free,
GtMatchVisitorBlastFunc match_blast,
GtMatchVisitorOpenFunc match_open)
{
GtMatchVisitorClass *c_class;
gt_assert(size);
c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->free = free;
c_class->match_blast = match_blast;
c_class->match_open = match_open;
return c_class;
}
const GtClusteredSetClass* gt_clustered_set_class_new(
size_t size,
GtClusteredSetNumberOfClustersFunc number_of_clusters,
GtClusteredSetMergeClustersFunc merge_clusters,
GtClusteredSetFreeFunc free,
GtClusteredSetIteratorFunc iterator,
GtClusteredSetNumberOfElementsFunc number_of_elements,
GtClusteredSetClusterNumFunc cluster_num)
{
GtClusteredSetClass *c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->number_of_clusters = number_of_clusters;
c_class->merge_clusters = merge_clusters;
c_class->free = free;
c_class->iterator = iterator;
c_class->number_of_elements = number_of_elements;
c_class->cluster_num = cluster_num;
return c_class;
}
const GtFeatureIndexClass* gt_feature_index_class_new(size_t size,
GtFeatureIndexAddRegionNodeFunc
add_region_node,
GtFeatureIndexAddFeatureNodeFunc
add_feature_node,
GtFeatureIndexRemoveNodeFunc
remove_node,
GtFeatureIndexGetFeatsForSeqidFunc
get_features_for_seqid,
GtFeatureIndexGetFeatsForRangeFunc
get_features_for_range,
GtFeatureIndexGetFirstSeqidFunc
get_first_seqid,
GtFeatureIndexSaveFunc
save_func,
GtFeatureIndexGetSeqidsFunc
get_seqids,
GtFeatureIndexGetRangeForSeqidFunc
get_range_for_seqid,
GtFeatureIndexGetOrigRangeForSeqidFunc
get_orig_range_for_seqid,
GtFeatureIndexHasSeqidFunc
has_seqid,
GtFeatureIndexFreeFunc
free)
{
GtFeatureIndexClass *c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->add_region_node = add_region_node;
c_class->add_feature_node = add_feature_node;
c_class->remove_node = remove_node;
c_class->get_features_for_seqid = get_features_for_seqid;
c_class->get_features_for_range = get_features_for_range;
c_class->get_first_seqid = get_first_seqid;
c_class->save_func = save_func;
c_class->get_seqids = get_seqids;
c_class->get_range_for_seqid = get_range_for_seqid;
c_class->get_orig_range_for_seqid = get_orig_range_for_seqid;
c_class->has_seqid = has_seqid;
c_class->free = free;
return c_class;
}
GtNodeVisitorClass*
gt_node_visitor_class_new(size_t size,
GtNodeVisitorFreeFunc free,
GtNodeVisitorCommentNodeFunc comment_node,
GtNodeVisitorFeatureNodeFunc feature_node,
GtNodeVisitorRegionNodeFunc region_node,
GtNodeVisitorSequenceNodeFunc sequence_node,
GtNodeVisitorEOFNodeFunc eof_node)
{
GtNodeVisitorClass *c_class;
gt_assert(size);
c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->free = free;
c_class->comment_node = comment_node;
c_class->feature_node = feature_node;
c_class->region_node = region_node;
c_class->sequence_node = sequence_node;
c_class->eof_node = eof_node;
return c_class;
}
const GtSeqColClass* gt_seq_col_class_new(size_t size,
GtSeqColFreeFunc free,
GtSeqColEnableMatchDescStartFunc
enable_match_desc_start,
GtSeqColGrepDescFunc grep_desc,
GtSeqColGrepDescDescFunc
grep_desc_desc,
GtSeqColGrepDescMD5Func grep_desc_md5,
GtSeqColGrepDescSeqlenFunc
grep_desc_seqlen,
GtSeqColMD5ToSeqFunc md5_to_seq,
GtSeqColMD5ToDescFunc md5_to_desc,
GtSeqColMD5ToSeqlenFunc md5_to_seqlen,
GtSeqColNumFilesFunc num_files,
GtSeqColNumSeqsFunc num_seqs,
GtSeqColGetMD5Func get_md5,
GtSeqColGetSeqFunc get_seq,
GtSeqColGetDescFunc get_desc,
GtSeqColGetSeqlenFunc get_seqlen)
{
GtSeqColClass *c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->free = free;
c_class->enable_match_desc_start = enable_match_desc_start;
c_class->grep_desc = grep_desc;
c_class->grep_desc_desc = grep_desc_desc;
c_class->grep_desc_md5 = grep_desc_md5;
c_class->grep_desc_seqlen = grep_desc_seqlen;
c_class->md5_to_desc = md5_to_desc;
c_class->md5_to_seq = md5_to_seq;
c_class->md5_to_seqlen = md5_to_seqlen;
c_class->num_files = num_files;
c_class->num_seqs = num_seqs;
c_class->get_md5 = get_md5;
c_class->get_seq = get_seq;
c_class->get_desc = get_desc;
c_class->get_seqlen = get_seqlen;
return c_class;
}
const GthSeqConClass* gth_seq_con_class_new(size_t size,
GthSeqConDemandOrigSeqFunc
demand_orig_seq,
GthSeqConGetOrigSeqFunc
get_orig_seq,
GthSeqConGetTranSeqFunc
get_tran_seq,
GthSeqConGetOrigSeqRCFunc
get_orig_seq_rc,
GthSeqConGetTranSeqRCFunc
get_tran_seq_rc,
GthSeqConGetDescriptionFunc
get_description,
GthSeqConEchoDescriptionFunc
echo_description,
GthSeqConNumOfSeqsFunc num_of_seqs,
GthSeqConTotalLengthFunc
total_length,
GthSeqConGetRangeFunc get_range,
GthSeqConGetAlphabetFunc
get_alphabet,
GthSeqConFreeFunc free)
{
GthSeqConClass *c_class = gt_class_alloc(sizeof *c_class);
c_class->size = size;
c_class->demand_orig_seq = demand_orig_seq;
c_class->get_orig_seq = get_orig_seq;
c_class->get_tran_seq = get_tran_seq;
c_class->get_orig_seq_rc = get_orig_seq_rc;
c_class->get_tran_seq_rc = get_tran_seq_rc;
c_class->get_description = get_description;
c_class->echo_description = echo_description;
c_class->num_of_seqs = num_of_seqs;
c_class->total_length = total_length;
c_class->get_range = get_range;
c_class->get_alphabet = get_alphabet;
c_class->free = free;
return c_class;
}
gt_assert(cstr_iterator->c_class != NULL);
if (cstr_iterator->c_class->delete_func != NULL)
cstr_iterator->c_class->delete_func(cstr_iterator);
gt_free(cstr_iterator);
}
}
GtCstrIteratorClass *
gt_cstr_iterator_class_new(size_t size,
GtCstrIteratorNextFunc next,
GtCstrIteratorResetFunc reset,
GtCstrIteratorDeleteFunc delete)
{
GtCstrIteratorClass *cstr_iterator_c;
gt_assert(size != 0);
cstr_iterator_c = gt_class_alloc(sizeof (*cstr_iterator_c));
cstr_iterator_c->size = size;
cstr_iterator_c->next_func = next;
cstr_iterator_c->reset_func = reset;
cstr_iterator_c->delete_func = delete;
return cstr_iterator_c;
}
GtCstrIterator *
gt_cstr_iterator_create(const GtCstrIteratorClass *cstr_iterator_c)
{
GtCstrIterator *cstr_iterator;
gt_assert(cstr_iterator_c && cstr_iterator_c->size);
cstr_iterator = gt_calloc((size_t) 1, cstr_iterator_c->size);
cstr_iterator->c_class = cstr_iterator_c;
return cstr_iterator;