1.1 --- a/allpy/processors.py	Tue May 24 22:12:57 2011 +0400
     1.2 +++ b/allpy/processors.py	Wed May 25 19:46:20 2011 +0400
     1.3 @@ -47,6 +47,14 @@
     1.4          return ExternalCommand.__call__(self, block)
     1.5  
     1.6  def Muscle(remove_gaps=False):
     1.7 +    """"Realign block with Muscle.
     1.8 +
     1.9 +    Accepted arguments:
    1.10 +
    1.11 +    - `remove_gaps` -- make fresh alignment (remove gaps before aligning);
    1.12 +        otherwise, gaps are retained and muscle performs subalignment of
    1.13 +        an existing alignment.
    1.14 +    """
    1.15      return FixOrdering(BypassEmpty(_Muscle()))
    1.16  
    1.17  class _Needle(ExternalCommand):
    1.18 @@ -78,6 +86,10 @@
    1.19              self.command = orig_command
    1.20  
    1.21  def Needle(**kwargs):
    1.22 +    """Realign block with Needle.
    1.23 +
    1.24 +    Arguments are the same as accepted by needle command line program.
    1.25 +    """
    1.26      return FixOrdering(_Needle(**kwargs))
    1.27  
    1.28  class Flush(object):