def alignment(self):
"""Make self into an alignment, and return it.
If all the sequences are the same length and type, then self,
a sequenceList, could be an Alignment. This method generates
an Alignment instance, runs the Alignment method
checkLengthsAndTypes(), and returns the Alignment.
If you feed p4 a fasta sequence, it makes SequenceList object,
and runs this method on it. If it works then p4 puts the
Alignment object in var.alignments, and if not it puts the
SequenceList object in var.sequenceLists.
It is possible that p4 might think that some short sequences
are DNA when they are really protein. In that case it will
fail to make an alignment, because it will fail the types
check. So what you can do is something like this::
sl = var.sequenceLists[0]
for s in sl.sequences:
s.dataType = 'protein'
a = sl.alignment()
"""
from Alignment import Alignment
a = Alignment()
a.fName = self.fName
import copy
a.sequences = copy.deepcopy(self.sequences) # self will be deleted
a.fName = self.fName
a.checkLengthsAndTypes()
return a
