def __init__(self, seq, id, extension_handler, rc = None):
# type: (str, str, ExtensionHandler, Optional[NewLine]) -> None
self.extensionHandler = extension_handler
self.seq = seq
self.id = id # type: str
self.circular = False
self.name_printer = None
self.max_extension = False
if rc is None:
self.initial = AlignmentStorage()
self.correct_segments = SegmentStorage()
self.completely_resolved = SegmentStorage()
self.disjointig_alignments = AlignmentStorage()
self.read_alignments = ReadAlignmentStorage()
self.listeners = [self.initial, self.correct_segments, self.completely_resolved, self.disjointig_alignments, self.read_alignments, extension_handler] # type: List[LineListener]
rc = NewLine(basic.RC(seq), basic.Reverse(self.id), extension_handler.rc, self) #type: NewLine
self.rc = rc
self.addListener(ReadAlignmentListener(self))
# self.initial.add(AlignmentPiece.Identical(self.asSegment().asContig().asSegment(), self.asSegment()))
else:
self.initial = rc.initial.rc # type: AlignmentStorage
self.correct_segments = rc.correct_segments.rc # type: SegmentStorage
self.completely_resolved = rc.completely_resolved.rc # type: SegmentStorage
self.disjointig_alignments = rc.disjointig_alignments.rc # type: AlignmentStorage
self.read_alignments = rc.read_alignments.rc # type: ReadAlignmentStorage
self.listeners = [listener.rc for listener in rc.listeners] # type: List[LineListener]
Contig.__init__(self, seq, id, rc)
self.rc = rc #type: NewLine
self.knot = None # type: Knot
def __init__(self, seq, id, rc=None):
# type: (str, str, Optional[Disjointig]) -> None
self.seq = seq
self.id = id
if rc is None:
self.read_alignments = AlignmentStorage() # type: AlignmentStorage
rc = Disjointig(basic.RC(seq), basic.Reverse(id),
self) # type: Disjointig
self.rc = rc
else:
self.rc = rc
self.read_alignments = self.rc.read_alignments.rc # type: AlignmentStorage
Contig.__init__(self, seq, id, rc)
self.rc = rc # type:Disjointig
