def __init__(self, part, row, col, idnum=0):
self._doc = part.document()
super(VirtualHelix, self).__init__(part)
self._coord = (row, col) # col, row
self._part = part
self._scaf_strandset = StrandSet(StrandType.SCAFFOLD, self)
self._stap_strandset = StrandSet(StrandType.STAPLE, self)
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = None
self.setNumber(idnum)
#Determine position for oligo strands (first oligo: from 1 --> length/2 second oligo: next (length/2)+1 --> length )
oligo_pos.append([1,int(int(i[2])/2),int(int(i[2])/2)+1,int(i[2])])
# Max length of the Strand Set
MAX_LENGTH = 64
offset_idx = 0
# Make the container for the StrandSets
ss_fwd = [None]*vhCounter
ss_rev = [None]*vhCounter
# Create the StrandsSets and fill them with Strands
# The assumption here is that Scaffold is forward strand and that the reverse strands is Staple Strands
try:
for i in range(vhCounter):
ss_fwd[i] = StrandSet(is_fwd=True, id_num=i, part=part, initial_size=MAX_LENGTH)
ss_rev[i] = StrandSet(is_fwd=False, id_num=i, part=part, initial_size=MAX_LENGTH)
ss_fwd[i].createStrand(base_idx_low=offset_idx, base_idx_high=offset_idx+oligo_pos[i][3], color='#0066cc')
ss_rev[i].createStrand(base_idx_low=offset_idx, base_idx_high=offset_idx+oligo_pos[i][1], color='#f44242')
ss_rev[i].createStrand(base_idx_low=offset_idx+oligo_pos[i][2], base_idx_high=offset_idx+oligo_pos[i][3], color='#007200')
part.fwd_strandsets[i] = ss_fwd[i]
part.rev_strandsets[i] = ss_rev[i]
except Exception:
print('Failed to create StrandSet/Strands')
"""
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
