1.1 --- a/allpy/base.py	Wed May 30 12:43:09 2012 +0400
     1.2 +++ b/allpy/base.py	Wed May 30 13:35:04 2012 +0400
     1.3 @@ -494,24 +494,9 @@
     1.4  
     1.5          This is the same as process(function, False, False)
     1.6          """
     1.7 -        self.verify()
     1.8          new = function(self)
     1.9          self._replace_column_contents(new)
    1.10  
    1.11 -    # Helpers
    1.12 -    # =================================
    1.13 -
    1.14 -    def verify(self):
    1.15 -        """Make sure the alignment is decent. Raise an exception otherwise.
    1.16 -
    1.17 -        I.e.:
    1.18 -
    1.19 -        * it has no sequences with the same seq.name
    1.20 -        """
    1.21 -        seq_names = set(seq.names for seq in self.sequences)
    1.22 -        assert len(seq_names) == len(self.sequences), \
    1.23 -            "Alignment has sequences with the same identifier"
    1.24 -
    1.25  class Column(dict):
    1.26      """Column of alignment.
    1.27  

     2.1 --- a/allpy/processors.py	Wed May 30 12:43:09 2012 +0400
     2.2 +++ b/allpy/processors.py	Wed May 30 13:35:04 2012 +0400
     2.3 @@ -185,6 +185,8 @@
     2.4              (self.id(sequence), sequence)
     2.5              for sequence in out_block.sequences
     2.6          ))
     2.7 +        assert len(sequences) == len(block.sequences), \
     2.8 +            "Sequence identificators must be unique!"
     2.9          out_block.sequences = [
    2.10              sequences[self.id(old_sequence)]
    2.11              for old_sequence in block.sequences

     3.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     3.2 +++ b/test/test_realign.py	Wed May 30 13:35:04 2012 +0400
     3.3 @@ -0,0 +1,17 @@
     3.4 +from nose.tools import raises
     3.5 +from allpy import protein, processors
     3.6 +
     3.7 +example1 = protein.Alignment().\
     3.8 +	append_sequence(protein.Sequence.from_string("mkstf", name="abc")).\
     3.9 +	append_sequence(protein.Sequence.from_string("mstkfff", description="Longer sequence"))
    3.10 +
    3.11 +def test_muscle():
    3.12 +	example1.realign(processors.Muscle())
    3.13 +
    3.14 +example2 = protein.Alignment().\
    3.15 +	append_sequence(protein.Sequence.from_string("mkstf", name="a")).\
    3.16 +	append_sequence(protein.Sequence.from_string("mstkfff", name="a"))
    3.17 +
    3.18 +@raises(AssertionError)
    3.19 +def test_muscle_failure():
    3.20 +	example2.realign(processors.Muscle())