def from_file(cls, f, sequence_id=None):
if sequence_id is None:
sequence_id = os.path.splitext(os.path.basename(f.name))[0]
sequence = []
prediction = []
for line in f:
words = line.split()
if len(words) != 2:
continue
linetype = words[0].lower()
if linetype == 'aa:':
sequence.append(words[1])
elif linetype == 'pred:':
prediction.append(words[1])
regions = make_regions(''.join(prediction), '*')
return cls(sequence_id, sequence=''.join(sequence), regions=regions)
def handle_msa_change(self, msa, change):
if not change.has_changed('sequences'):
return
if msa.ungapped is None:
self.backbones = None
self.gaps = None
return
self.backbones = [ContiguousRegion(make_regions(u, bool)) for u in msa.ungapped]
self.gaps = []
for backbone in self.backbones:
gap_parts = []
previous = None
for part in backbone.parts:
if previous is None:
previous = part
continue
gap_start = previous.start + previous.length
gap_parts.append(Region(gap_start, part.start - gap_start))
self.gaps.append(ContiguousRegion(gap_parts))
self.emit('changed', Change('visualization'))
