def for_interval(cls, interval):
""" Return all snps within an interval """
query = sql.and_(cls.table.c.chromStart >= interval.start,
cls.table.c.chromEnd <= interval.end,
cls.table.c.chrom == interval.chrom,
cls.table.c.bin == bin(interval.start, interval.end))
return session.query(cls).filter(query).all()
def for_interval(cls, interval):
""" Return all snps within an interval """
query = sql.and_(cls.table.c.chromStart>=interval.start,
cls.table.c.chromEnd<=interval.end,
cls.table.c.chrom==interval.chrom,
cls.table.c.bin==bin(interval.start, interval.end)
)
return session.query(cls).filter(query).all()
def clock(self):
"""Executes one clock cycle"""
# choose the device that will write on the bus
eligible = [x for\
x in self.replying\
if len(x) > 0 \
and x not in self.waiting]
eligible += [x for\
x in self.requesting\
if len(x) > 0 \
and (x.read().function != "load"
or x.read().dst not in self.waiting)
]
chosen = self.arbiter.choose(eligible)
if chosen in self.requesting:
# obtain the message to transmit
self.message = chosen.request.read()
# append the address of the device it comes from
src = bin(self.requesting.index(chosen), self.src_len)
for c in reversed(src):
self.message.src.append(c)
# obtain the address of the device that should receive it
self.address = ""
for i in xrange(self.dst_len):
self.address += self.message.dst.pop()
# now that the message is ready, we try to transmit it
try:
self.replying[int(self.address,2)].request.write(message)
except:
return # too bad, try again some other time !
# the message is transmitted, we can update the arbiter and
# add the device to the waiting queue
self.waiting.extend([x for x in self.requesting]) # TODO
else:
# appending
src = bin(self.replying.index(chosen), self.dst_len)
for c in reversed(src):
self.message.dst.append(c)
# obtain the address
for i in xrange(self.dst_len):
self.address += self.message.src.pop()
def for_interval(cls, interval):
""" return all links that overlap the specified interval"""
clause = sql.and_(
cls.bin==bin(interval.start, interval.end),
cls.tStart <= interval.end,
cls.tEnd >= interval.start,
cls.tName == interval.chrom,
)
return session.query(cls).filter(clause).all()
def for_interval(cls, interval):
""" return all links that overlap the specified interval"""
clause = sql.and_(
cls.bin == bin(interval.start, interval.end),
cls.tStart <= interval.end,
cls.tEnd >= interval.start,
cls.tName == interval.chrom,
)
return session.query(cls).filter(clause).all()