1.1 --- a/allpy/markups.py	Tue Mar 06 16:08:49 2012 +0400
     1.2 +++ b/allpy/markups.py	Tue Mar 06 20:29:34 2012 +0400
     1.3 @@ -22,10 +22,13 @@
     1.4      global by_name
     1.5      by_name = {}
     1.6      for markup_class in globals().values():
     1.7 -        if hasattr(markup_class, 'name') and hasattr(markup_class, 'kind'):
     1.8 -            fullname = markup_class.kind, markup_class.name
     1.9 -            assert fullname not in by_name, "Samenamed markup already exists!"
    1.10 -            by_name[fullname] = markup_class
    1.11 +        if not hasattr(markup_class, 'name') or not markup_class.name:
    1.12 +            continue
    1.13 +        if not hasattr(markup_class, 'kind') or not markup_class.kind:
    1.14 +            continue
    1.15 +        fullname = markup_class.kind, markup_class.name
    1.16 +        assert fullname not in by_name, "Markup %s already exists!" % (fullname,)
    1.17 +        by_name[fullname] = markup_class
    1.18  
    1.19  class MarkupIOMixin(base.Markup):
    1.20      """Standard helper mixin for creating saveable markups."""
    1.21 @@ -53,16 +56,16 @@
    1.22      def from_record(cls, container, record, name=None):
    1.23          """Read markup from semi-parsed record from 'markup' file."""
    1.24          assert record['io_class'] == cls.io_class
    1.25 -        separator = record.get('separator', cls.separator)
    1.26 -        quotes = record.get('quotes', cls.quotes)
    1.27 -        values = record['markup'].strip(quotes)
    1.28 -        if separator:
    1.29 -            values = values.split(separator)
    1.30          result = container.add_markup(name, markup_class=cls)
    1.31 +        result.separator = record.get('separator', cls.separator)
    1.32 +        result.quotes = record.get('quotes', cls.quotes)
    1.33 +        values = record['markup'].strip(result.quotes)
    1.34 +        if result.separator:
    1.35 +            values = values.split(result.separator)
    1.36          assert len(values) == len(result.sorted_keys())
    1.37          for key, value in zip(result.sorted_keys(), values):
    1.38              if value:
    1.39 -                result[key] = cls.parse_item(key, value)
    1.40 +                result[key] = result.parse_item(key, value)
    1.41          return result
    1.42  
    1.43      def to_record(self):
    1.44 @@ -90,6 +93,31 @@
    1.45      def parse_item(key, value):
    1.46          return int(value)
    1.47  
    1.48 +class FloatMarkupMixin(MarkupIOMixin):
    1.49 +    """Markup that has float values."""
    1.50 +
    1.51 +    io_class = 'FloatMarkup'
    1.52 +
    1.53 +    @staticmethod
    1.54 +    def parse_item(key, value):
    1.55 +        return float(value)
    1.56 +
    1.57 +class BoolMarkupMixin(MarkupIOMixin):
    1.58 +    """Markup that has boolean values."""
    1.59 +
    1.60 +    io_class = 'BoolMarkup'
    1.61 +
    1.62 +    @staticmethod
    1.63 +    def parse_item(key, value):
    1.64 +        return value == '+'
    1.65 +
    1.66 +    @staticmethod
    1.67 +    def repr_item(key, value):
    1.68 +        if value:
    1.69 +            return '+'
    1.70 +        else:
    1.71 +            return '-'
    1.72 +
    1.73  class CharMarkupMixin(MarkupIOMixin):
    1.74      """Markup that has one-letter values."""
    1.75  
    1.76 @@ -105,10 +133,36 @@
    1.77          assert len(str(value)) == 1
    1.78          return str(value)
    1.79  
    1.80 +class StrMarkupMixin(MarkupIOMixin):
    1.81 +    """Markup that is capable of storing ANY strings."""
    1.82 +
    1.83 +    io_class = 'StrMarkup'
    1.84 +
    1.85 +    def parse_item(self, key, value):
    1.86 +        return value.replace("%2C", self.separator).replace("%25", "%")
    1.87 +
    1.88 +    def repr_item(self, key, value):
    1.89 +        return str(value).replace("%", "%25").replace(self.separator, "%2C")
    1.90 +
    1.91 +class SequenceStrMarkup(base.SequenceMarkup, StrMarkupMixin):
    1.92 +    """Generic class for string-based markups."""
    1.93 +    pass
    1.94 +
    1.95  class SequenceCharMarkup(base.SequenceMarkup, CharMarkupMixin):
    1.96      """Generic class for one-letter markups."""
    1.97 +    pass
    1.98  
    1.99 -    name = 'char'
   1.100 +class SequenceIntMarkup(base.SequenceMarkup, IntMarkupMixin):
   1.101 +    """Generic class for integer number markups."""
   1.102 +    pass
   1.103 +
   1.104 +class SequenceFloatMarkup(base.SequenceMarkup, FloatMarkupMixin):
   1.105 +    """Generic class for floating-point number markups."""
   1.106 +    pass
   1.107 +
   1.108 +class SequenceBoolMarkup(base.SequenceMarkup, BoolMarkupMixin):
   1.109 +    """Generic class for boolean markups."""
   1.110 +    pass
   1.111  
   1.112  class SequenceNumberMarkup(base.SequenceMarkup):
   1.113  
   1.114 @@ -126,6 +180,26 @@
   1.115          for index, monomer in enumerate(self.sequence):
   1.116              monomer.index = index
   1.117  
   1.118 +class AlignmentStrMarkup(base.AlignmentMarkup, StrMarkupMixin):
   1.119 +    """Generic class for string-based markups."""
   1.120 +    pass
   1.121 +
   1.122 +class AlignmentCharMarkup(base.AlignmentMarkup, CharMarkupMixin):
   1.123 +    """Generic class for one-letter markups."""
   1.124 +    pass
   1.125 +
   1.126 +class AlignmentIntMarkup(base.AlignmentMarkup, IntMarkupMixin):
   1.127 +    """Generic class for integer number markups."""
   1.128 +    pass
   1.129 +
   1.130 +class AlignmentFloatMarkup(base.AlignmentMarkup, FloatMarkupMixin):
   1.131 +    """Generic class for floating-point number markups."""
   1.132 +    pass
   1.133 +
   1.134 +class AlignmentBoolMarkup(base.AlignmentMarkup, BoolMarkupMixin):
   1.135 +    """Generic class for boolean markups."""
   1.136 +    pass
   1.137 +
   1.138  class AlignmentNumberMarkup(base.AlignmentMarkup):
   1.139  
   1.140      name = 'number'

     2.1 --- a/test/test_markups.py	Tue Mar 06 16:08:49 2012 +0400
     2.2 +++ b/test/test_markups.py	Tue Mar 06 20:29:34 2012 +0400
     2.3 @@ -117,6 +117,57 @@
     2.4      assert s[0].ss == 'H'
     2.5      assert s[5].ss == 'S'
     2.6  
     2.7 +def test_generic():
     2.8 +    aln = (protein.Alignment().
     2.9 +        append_row_from_string('aseq-vence', name='a').
    2.10 +        append_row_from_string('ase-qret--', name='b')
    2.11 +    )
    2.12 +
    2.13 +    s1, s2 = aln.sequences
    2.14 +
    2.15 +    try:
    2.16 +        s1.add_markup(markup_class=markups.SequenceStrMarkup)
    2.17 +    except Exception:
    2.18 +        pass
    2.19 +    else:
    2.20 +        raise AssertionError("Generic markup must not be creatable without name")
    2.21 +
    2.22 +    s1.add_markup("a", markup_class=markups.SequenceStrMarkup)
    2.23 +    s1[6].a = "Q"
    2.24 +
    2.25 +    s1.add_markup("b", markup_class=markups.SequenceStrMarkup)
    2.26 +    s1[5].b = "hello, world %)"
    2.27 +
    2.28 +    s2.add_markup("c", markup_class=markups.SequenceIntMarkup)
    2.29 +    s2[4].c = 42
    2.30 +
    2.31 +    s1.add_markup("d", markup_class=markups.SequenceFloatMarkup)
    2.32 +    s1[3].d = 9000.001
    2.33 +
    2.34 +    s2.add_markup("e", markup_class=markups.SequenceBoolMarkup)
    2.35 +    s2[2].e = "a" is "a"
    2.36 +    s2[6].e = "a" is "b"
    2.37 +
    2.38 +    f = aln.add_markup("f", markup_class=markups.AlignmentBoolMarkup)
    2.39 +    f[aln.columns[3]] = 5
    2.40 +
    2.41 +    file = StringIO()
    2.42 +    aln.to_file(file, format='markup')
    2.43 +
    2.44 +    print file.getvalue()
    2.45 +
    2.46 +    file.seek(0)
    2.47 +    out = protein.Alignment().append_file(file, format='markup')
    2.48 +
    2.49 +    s1, s2 = out.sequences
    2.50 +    assert s1[6].a == "Q"
    2.51 +    assert s1[5].b == "hello, world %)"
    2.52 +    assert s2[4].c == 42
    2.53 +    assert abs(s1[3].d - 9000.001) < 0.001
    2.54 +    assert s2[2].e is True
    2.55 +    assert s2[6].e is False
    2.56 +    assert out.markups["f"][out.columns[3]] is True
    2.57 +
    2.58  def test_ss():
    2.59      seq = protein_pdb.Sequence.from_string('QLSSDAQTANAKADQASNDANAARS', '1jcc_B')
    2.60      seq.auto_pdb()