def FireMergedLines(self, al1, al2):
# type: (AlignmentPiece, AlignmentPiece) -> None
sys.stdout.trace("Fire merged lines", al1, al2)
new_line = al1.seg_to.contig
line1 = al1.seg_from.contig
line2 = al2.seg_from.contig
sys.stdout.trace(list(self.allInter(line1.asSegment())))
sys.stdout.trace(list(self.allInter(line2.asSegment())))
self.addLine(new_line)
self.auto_alignments[line1.id].setState(-1)
self.auto_alignments[line2.id].setState(-1)
auto1 = AutoAlignmentStorage(new_line).addAll([
al1.composeTargetDifference(al.compose(al1))
for al in self.auto_alignments[line1.id].content
])
auto2 = AutoAlignmentStorage(new_line).addAll([
al2.composeTargetDifference(al.compose(al2))
for al in self.auto_alignments[line2.id].content
])
auto3 = AutoAlignmentStorage(new_line).addAll([
al2.composeTargetDifference(al.compose(al1))
for al in self.getAlignmentsToFrom(line1, line2)
])
self.auto_alignments[new_line.id].addAll(
auto1.merge(auto3).merge(auto2).content)
rc1 = RCAlignmentStorage(new_line).addAll([
al1.rc.composeTargetDifference(al.compose(al1))
for al in self.rc_alignments[line1.id]
])
rc2 = RCAlignmentStorage(new_line).addAll([
al2.rc.composeTargetDifference(al.compose(al2))
for al in self.rc_alignments[line2.id]
])
rc3 = RCAlignmentStorage(new_line).addAll([
al2.rc.composeTargetDifference(al.compose(al1))
for al in self.getAlignmentsToFrom(line1, line2.rc)
])
self.rc_alignments[new_line.id].addAll(rc1.merge(rc3).merge(rc2))
common = set(self.alignmentsToFrom[line1.id].keys()).intersection(
set(self.alignmentsToFrom[line2.id].keys()))
for storage in self.alignmentsToFrom[line1.id].values():
if storage.line_from.id not in common and storage.line_from != line2 and storage.line_from != line2.rc:
self.addTwoLineStorage(new_line, storage.line_from).addAll(
[al.compose(al1) for al in storage])
for storage in self.alignmentsToFrom[line2.id].values():
if storage.line_from.id not in common and storage.line_from != line1 and storage.line_from != line1.rc:
self.addTwoLineStorage(new_line, storage.line_from).addAll(
[al.compose(al2) for al in storage])
for c in common:
storage1 = self.alignmentsToFrom[line1.id][c]
storage2 = self.alignmentsToFrom[line2.id][c]
als1 = AlignmentStorage().addAll(
[al.compose(al1) for al in storage1])
als2 = AlignmentStorage().addAll(
[al.compose(al2) for al in storage2])
self.addTwoLineStorage(new_line,
storage1.line_from).addAll(als1.merge(als2))
self.removeLine(al1.seg_from.contig)
self.removeLine(al2.seg_from.contig)
sys.stdout.trace(list(self.allInter(new_line.asSegment())))
class TwoLineAlignmentStorage(LineListener):
def __init__(self, line_from, line_to, rc = None, reverse = None):
# type: (Contig, Contig, Optional[TwoLineAlignmentStorage], Optional[TwoLineAlignmentStorage]) -> None
assert line_from.id != line_to.id and line_from.rc.id != line_to.id
self.line_from = line_from
self.line_to = line_to
self.reverse = reverse
if rc is None:
self.content = AlignmentStorage()
self.rc = TwoLineAlignmentStorage(line_from.rc, line_to.rc, self, None)
else:
self.rc = rc
self.content = rc.content.rc # type: AlignmentStorage
LineListener.__init__(self, self.rc)
self.rc = self.rc # type: TwoLineAlignmentStorage
if reverse is None and rc is None:
reverse = TwoLineAlignmentStorage(line_to, line_from, None, self)
self.reverse = reverse
self.reverse.reverse = self
self.rc.reverse = self.reverse.rc
self.rc.reverse.reverse = self.rc
def add(self, al):
# type: (AlignmentPiece) -> None
assert al.seg_from.contig == self.line_from
assert al.seg_to.contig == self.line_to
self.content.add(al)
reverse = al.reverse()
self.reverse.content.add(reverse)
def addAll(self, als):
for al in als:
self.add(al)
return self
def __iter__(self):
# type: () -> Generator[AlignmentPiece]
return self.content.__iter__()
def getAlignmentsTo(self, seg):
# type: (Segment) -> Generator[AlignmentPiece]
return self.content.getAlignmentsTo(seg)
def allInter(self, seg):
return self.content.allInter(seg)
def normalizeReverse(self):
self.reverse.content = self.content.reverse()
self.reverse.rc.content = self.reverse.content.rc
def fireBeforeExtendRight(self, line, new_seq, seq):
# type: (Any, Contig, str) -> None
self.content.fireBeforeExtendRight(line, new_seq, seq)
self.normalizeReverse()
def fireBeforeCutRight(self, line, new_seq, pos):
# type: (Any, Contig, int) -> None
self.content.fireBeforeCutRight(line, new_seq, pos)
self.normalizeReverse()
# alignments from new sequence to new sequence
def fireBeforeCorrect(self, alignments):
# type: (Correction) -> None
self.content.fireBeforeCorrect(alignments)
self.normalizeReverse()
def fireAfterExtendRight(self, line, seq, relevant_als = None):
# type: (Any, str, Optional[List[AlignmentPiece]]) -> None
self.content.fireAfterExtendRight(line, seq)
self.normalizeReverse()
def fireAfterCutRight(self, line, pos):
# type: (Any, int) -> None
self.content.fireAfterCutRight(line, pos)
self.normalizeReverse()
def fireAfterCorrect(self, line, alignments):
# type: (Any, Correction) -> None
self.content.fireAfterCorrect(line, alignments)
self.normalizeReverse()
def addAndMergeRight(self, al):
self.content.addAndMergeRight(al)
self.normalizeReverse()
def merge(self, other):
# type: (TwoLineAlignmentStorage) -> TwoLineAlignmentStorage
res = TwoLineAlignmentStorage(self.line_from, self.line_to)
res.content.addAll(self.content.merge(other.content))
res.normalizeReverse()
def save(self, handler):
# type: (TokenWriter) -> None
self.content.save(handler)
def load(self, handler, lines):
# type: (TokenReader, Any) -> None
self.content.load(handler, lines, lines)
self.normalizeReverse()
class RCAlignmentStorage(LineListener):
def __init__(self, line, rc = None):
# type: (Contig, Optional[RCAlignmentStorage]) -> None
self.line = line
if rc is None:
self.content = AlignmentStorage()
rc = RCAlignmentStorage(line.rc, self)
rc.content = self.content.rc
LineListener.__init__(self, rc)
self.rc = rc # type: AutoAlignmentStorage
def __iter__(self):
# type: () -> Generator[AlignmentPiece]
return self.content.__iter__()
def getAlignmentsTo(self, seg):
# type: (Segment) -> Generator[AlignmentPiece]
return self.content.getAlignmentsTo(seg)
def allInter(self, seg):
return self.content.allInter(seg)
def add(self, alignment):
self.content.add(alignment)
self.content.add(alignment.reverse().rc)
def addAndMergeRight(self, al):
# type: (AlignmentPiece) -> None
self.content.addAndMergeRight(al)
self.content.addAndMergeLeft(al.reverse().rc)
def addAll(self, als):
for al in als:
self.add(al)
return self
def fireBeforeExtendRight(self, line, new_seq, seq):
# type: (Any, Contig, str) -> None
self.content.fireBeforeExtendRight(line, new_seq, seq)
self.reverse()
self.content.fireBeforeExtendRight(line, new_seq, seq)
def fireBeforeCutRight(self, line, new_seq, pos):
# type: (Any, Contig, int) -> None
self.content.fireBeforeCutRight(line, new_seq, pos)
self.reverse()
self.content.fireBeforeCutRight(line, new_seq, pos)
# alignments from new sequence to new sequence
def fireBeforeCorrect(self, alignments):
# type: (Correction) -> None
self.content.fireBeforeCorrect(alignments)
self.reverse()
self.content.fireBeforeCorrect(alignments)
def fireAfterExtendRight(self, line, seq, relevant_als = None):
# type: (Any, str, Optional[List[AlignmentPiece]]) -> None
self.content.fireAfterExtendRight(line, seq)
self.reverse()
self.content.fireAfterExtendRight(line, seq)
def fireAfterCutRight(self, line, pos):
# type: (Any, int) -> None
self.content.fireAfterCutRight(line, pos)
self.reverse()
self.content.fireAfterCutRight(line, pos)
def fireAfterCorrect(self, line, alignments):
# type: (Any, Correction) -> None
self.content.fireAfterCorrect(line, alignments)
self.reverse()
self.content.fireAfterCorrect(line, alignments)
# This is CRAAAZY!!! But correct.
def reverse(self):
self.rc.content = self.content.reverse()
self.content = self.rc.content.rc
def merge(self, other):
# type: (RCAlignmentStorage) -> RCAlignmentStorage
res = RCAlignmentStorage(self.line)
res.content.addAll(self.content.merge(other.content))
return res
def save(self, handler):
# type: (TokenWriter) -> None
self.content.save(handler)
def load(self, handler):
# type: (TokenReader) -> None
self.content.load(handler, self.line.rc, self.line)
class AutoAlignmentStorage(LineListener):
def __init__(self, line, rc = None):
# type: (Contig, Optional[AutoAlignmentStorage]) -> None
self.line = line
if rc is None:
self.content = AlignmentStorage()
rc = AutoAlignmentStorage(line.rc, self)
rc.content = self.content.rc
rc.state = -1
LineListener.__init__(self, rc)
self.rc = rc # type: AutoAlignmentStorage
self.state = 1 # from precedes to
def makeCanonical(self, al):
if (self.state == 1) == (al.seg_from.left < al.seg_to.left):
return al
else:
return al.reverse()
def isCanonical(self, al):
return (self.state == 1) == (al.seg_from.left < al.seg_to.left)
def add(self, al):
# type: (AlignmentPiece) -> None
if al.isIdentical():
return
self.content.add(self.makeCanonical(al))
def addAll(self, als):
for al in als:
self.add(al)
return self
def addAndMergeRight(self, al):
if al.isIdentical():
return
if self.isCanonical(al):
self.content.addAndMergeRight(al)
else:
self.content.addAndMergeRight(al.reverse())
def __iter__(self):
# type: () -> Generator[AlignmentPiece]
for al in self.content:
yield al
for al in self.content:
yield al.reverse()
yield AlignmentPiece.Identical(self.line.asSegment())
def getAlignmentsTo(self, seg):
# type: (Segment) -> Generator[AlignmentPiece]
for al in self:
if al.seg_to.contains(seg):
yield al
def allInter(self, seg):
for al in self:
if al.seg_to.inter(seg):
yield al
def fireBeforeExtendRight(self, line, new_seq, seq):
# type: (Any, Contig, str) -> None
self.content.fireBeforeExtendRight(line, new_seq, seq)
self.reverse()
self.content.fireBeforeExtendRight(line, new_seq, seq)
# alignments from new sequence to new sequence
def fireBeforeCutRight(self, line, new_seq, pos):
# type: (Any, Contig, int) -> None
self.content.fireBeforeCutRight(line, new_seq, pos)
self.reverse()
self.content.fireBeforeCutRight(line, new_seq, pos)
def fireBeforeCorrect(self, alignments):
# type: (Correction) -> None
self.content.fireBeforeCorrect(alignments)
self.reverse()
self.content.fireBeforeCorrect(alignments)
def fireAfterExtendRight(self, line, seq, relevant_als = None):
# type: (Any, str, Optional[List[AlignmentPiece]]) -> None
self.content.fireAfterExtendRight(line, seq)
self.reverse()
self.content.fireAfterExtendRight(line, seq)
def fireAfterCutRight(self, line, pos):
# type: (Any, int) -> None
self.content.fireAfterCutRight(line, pos)
self.reverse()
self.content.fireAfterCutRight(line, pos)
def fireAfterCorrect(self, line, alignments):
# type: (Any, Correction) -> None
self.content.fireAfterCorrect(line, alignments)
self.reverse()
self.content.fireAfterCorrect(line, alignments)
def reverse(self):
self.state = -self.state
self.rc.state = -self.rc.state
self.content = self.content.reverse()
self.rc.content = self.content.rc
def merge(self, other):
# type: (AutoAlignmentStorage) -> AutoAlignmentStorage
if self.state != other.state:
self.reverse()
res = AutoAlignmentStorage(self.line)
res.state = self.state
res.content.addAll(self.content.merge(other.content))
return res
def save(self, handler):
# type: (TokenWriter) -> None
self.content.save(handler)
def load(self, handler):
# type: (TokenReader) -> None
self.content.load(handler, self.line, self.line)
def setState(self, state):
assert state in [-1, 1]
if self.state != state:
self.reverse()