def construct_path_ref_placements(path,
segSeqD,
raw_path_length,
prev_seg_index_is_adj,
next_seg_index_is_adj,
cycle_seg_counts,
aln_vect=None):
if aln_vect is None:
aln_vect = []
spacing_bp = seg_spacing * raw_path_length
path_ref_placements = {}
curr_start = 0.0
for ind, i in enumerate(path):
seg_id_count = cycle_seg_counts[i[0]]
seg_len = segSeqD[i[0]][2] - segSeqD[i[0]][1]
seg_end = curr_start + seg_len
padj, nadj = prev_seg_index_is_adj[ind], next_seg_index_is_adj[ind]
curr_obj = vu.CycleVizElemObj(i[0], segSeqD[i[0]][0], segSeqD[i[0]][1],
segSeqD[i[0]][2], i[1], curr_start,
seg_end, seg_id_count, padj, nadj)
path_ref_placements[ind] = curr_obj
next_start = seg_end
mod_ind = (ind + 1) % (len(prev_seg_index_is_adj))
if not prev_seg_index_is_adj[mod_ind]:
next_start += spacing_bp
curr_start = next_start
total_length = next_start
return path_ref_placements, total_length
def construct_cycle_ref_placements(cycle,segSeqD,raw_cycle_length,prev_seg_index_is_adj,isCycle,aln_vect = []):
spacing_bp = seg_spacing*raw_cycle_length
cycle_ref_placements = {}
curr_start = 0.0 if isCycle else spacing_bp
for ind,i in enumerate(cycle):
seg_len = segSeqD[i[0]][2] - segSeqD[i[0]][1]
seg_end = curr_start+seg_len
curr_obj = vu.CycleVizElemObj(i[0],i[1],curr_start,seg_end)
cycle_ref_placements[ind] = curr_obj
next_start = seg_end
mod_ind = (ind+1) % (len(prev_seg_index_is_adj))
if not prev_seg_index_is_adj[mod_ind]:
next_start+=spacing_bp
curr_start = next_start
total_length = next_start
return cycle_ref_placements,total_length