1.1 --- a/allpy/base.py	Fri Jul 15 16:43:03 2011 +0400
     1.2 +++ b/allpy/base.py	Fri Jul 15 17:02:09 2011 +0400
     1.3 @@ -109,11 +109,13 @@
     1.4          """Hook to be called from __init__ of actual class."""
     1.5          self.markups = {}
     1.6  
     1.7 -    def add_markup(self, name, markup_class=None, **markup_kwargs):
     1.8 +    def add_markup(self, name, markup_class=None, use_existing=False, **kws):
     1.9          """Create a markup object, add to self. Return the created markup.
    1.10  
    1.11          - `name` is name for markup in `self.markups` dictionary
    1.12          - optional `markup_class` is class for created markup
    1.13 +        - if optional `use_existing` is true, it is no error, if same named
    1.14 +          markup already exists (in this case, nothing is changed)
    1.15          - optional keyword arguments are passed on to the markup constructor
    1.16  
    1.17          For user markups you have to specify `name` and `markup_class`,
    1.18 @@ -127,8 +129,11 @@
    1.19          if markup_class is None:
    1.20              kind = self.kind + "_" + "markup"
    1.21              markup_class = markups.by_name[kind, name]
    1.22 +        if use_existing and name in self.markups:
    1.23 +            assert self.markups[name].__class__ is markup_class
    1.24 +            return
    1.25          assert name not in self.markups
    1.26 -        markup = markup_class(self, name, caller='container', **markup_kwargs)
    1.27 +        markup = markup_class(self, name, caller='container', **kws)
    1.28          self.markups[name] = markup
    1.29          return markup
    1.30  

     2.1 --- a/test/test_markups.py	Fri Jul 15 16:43:03 2011 +0400
     2.2 +++ b/test/test_markups.py	Fri Jul 15 17:02:09 2011 +0400
     2.3 @@ -15,6 +15,23 @@
     2.4      assert seq[5].number == 6
     2.5      assert seq.markups["number"][seq[5]] == 6
     2.6  
     2.7 +    try:
     2.8 +        seq.add_markup('number')
     2.9 +    except AssertionError:
    2.10 +        pass
    2.11 +    else:
    2.12 +        raise AssertionError("Silently created same named alignment")
    2.13 +
    2.14 +    seq.add_markup('number', use_existing=True)
    2.15 +
    2.16 +    try:
    2.17 +        other = markups.SequenceIndexMarkup
    2.18 +        seq.add_markup('number', use_existing=True, markup_class=other)
    2.19 +    except AssertionError:
    2.20 +        pass
    2.21 +    else:
    2.22 +        raise AssertionError("Created same named different class alignment")
    2.23 +
    2.24  def test_case():
    2.25      seq = protein.Sequence.from_string('seQVEncE', name='sequence')
    2.26      seq.add_markup('case')