1.1 --- a/allpy/base.py	Wed Jul 20 20:44:59 2011 +0400
     1.2 +++ b/allpy/base.py	Thu Jul 21 13:12:54 2011 +0400
     1.3 @@ -560,7 +560,10 @@
     1.4      """
     1.5  
     1.6      name = None
     1.7 -    """Name of markup elements"""
     1.8 +    """Name of markup elements."""
     1.9 +
    1.10 +    save = True
    1.11 +    """If set to false, fileio should not save this markup."""
    1.12  
    1.13      def __init__(self, container, name, **kwargs):
    1.14          """Markup takes mandatory container and name and optional kwargs.

     2.1 --- a/allpy/fileio.py	Wed Jul 20 20:44:59 2011 +0400
     2.2 +++ b/allpy/fileio.py	Thu Jul 21 13:12:54 2011 +0400
     2.3 @@ -153,6 +153,8 @@
     2.4      def write_markups(self, markups, type, pre_record={}):
     2.5          """Write a dictionary of markups as series of records."""
     2.6          for name, markup in markups.items():
     2.7 +            if not markup.save:
     2.8 +                continue
     2.9              record = markup.to_record()
    2.10              record.update(pre_record)
    2.11              record['type'] = type

     3.1 --- a/test/test_markups.py	Wed Jul 20 20:44:59 2011 +0400
     3.2 +++ b/test/test_markups.py	Thu Jul 21 13:12:54 2011 +0400
     3.3 @@ -82,6 +82,10 @@
     3.4      m2 = aln.add_markup('m2')
     3.5      m2[c[5]] = 5
     3.6      m2[c[6]] = 6
     3.7 +    m3 = aln.add_markup('m3', markup_class=MyAlignmentMarkup)
     3.8 +    m3.save = False
     3.9 +    m3[c[1]] = "hello"
    3.10 +    m4 = aln.add_markup('m4', markup_class=MyAlignmentMarkup)
    3.11  
    3.12      file = StringIO()
    3.13      aln.to_file(file, format='markup')
    3.14 @@ -103,4 +107,7 @@
    3.15      assert s[5].m1 == 5 and s[3].m1 == 3
    3.16      assert out.markups['m2'][c[5]] == 5 and out.markups['m2'][c[6]] == 6
    3.17  
    3.18 +    assert 'm3' not in out.markups
    3.19 +    assert out.markups['m4'].__class__ is MyAlignmentMarkup
    3.20 +
    3.21  # vim: set ts=4 sts=4 sw=4 et: