1.1 --- a/allpy/base.py	Fri Jul 08 16:06:59 2011 +0400
     1.2 +++ b/allpy/base.py	Fri Jul 08 16:20:20 2011 +0400
     1.3 @@ -221,17 +221,13 @@
     1.4          If sequences in file have gaps (detected as characters belonging to
     1.5          `gaps` set), treat them accordingly.
     1.6          """
     1.7 -        sequences = []
     1.8 -        io = fileio.File(file, format)
     1.9 -        for name, description, body in io.read_strings():
    1.10 -            self.append_row_from_string(body, name, description, file.name, gaps)
    1.11 +        fileio.File(file, format, gaps=gaps).read_alignment(self)
    1.12          return self
    1.13  
    1.14      def to_file(self, file, format='fasta', gap='-'):
    1.15          """Write alignment in FASTA file as sequences with gaps."""
    1.16 -        strings = [(s, s.sequence.name, s.sequence.description)
    1.17 -            for s in self.rows_as_strings()]
    1.18 -        fileio.File(file, format).write_strings(strings)
    1.19 +        fileio.File(file, format, gaps=gap).write_alignment(self)
    1.20 +        return self
    1.21  
    1.22      # Data access methods for alignment
    1.23      # =================================
    1.24 @@ -510,11 +506,27 @@
    1.25          return block
    1.26  
    1.27  class Markup(object):
    1.28 +    """Base class for sequence and alignment markups.
    1.29 +
    1.30 +    We shall call either sequence or alignment a container. And we shall call
    1.31 +    either monomers or columns elements respectively.
    1.32 +
    1.33 +    Markup behaves like a dictionary of [element] -> value.
    1.34 +
    1.35 +    Every container has a dictionary of [name] -> markup. It is Markup's
    1.36 +    responsibility to add itself to this dictionary and to avoid collisions
    1.37 +    while doing it.
    1.38 +    """
    1.39  
    1.40      name = None
    1.41      """Name of markup elements"""
    1.42  
    1.43      def _register(self, container, name):
    1.44 +        """Register self within container.
    1.45 +
    1.46 +        Assure the name is not taken before. If name is not given, look in the
    1.47 +        class. Make sure we have some name at all.
    1.48 +        """
    1.49          if name:
    1.50              self.name = name
    1.51          assert self.name is not None
    1.52 @@ -522,37 +534,94 @@
    1.53          container.markups[self.name] = self
    1.54  
    1.55      def refresh(self):
    1.56 +        """Recalculate markup values (if they are generated automatically)."""
    1.57          pass
    1.58  
    1.59 +    @classmethod
    1.60 +    def from_record(cls, container, record, name=None):
    1.61 +        """Restore markup from `record`. (Used for loading from file).
    1.62 +
    1.63 +        `record` is a dict of all metadata and data related to one markup. All
    1.64 +        keys and values in `record` are strings, markup must parse them itself.
    1.65 +
    1.66 +        Markup values should be stored in `record['markup']`, which is a list
    1.67 +        of items separated with either `record['separator']` or a comma.
    1.68 +        """
    1.69 +        return cls(container, name)
    1.70 +
    1.71 +    def to_record(self):
    1.72 +        """Save markup to `record`, for saving to file.
    1.73 +
    1.74 +        For description of `record` see docstring for `from_record` method.
    1.75 +        """
    1.76 +        return {}
    1.77 +
    1.78 +    def sorted_keys(self):
    1.79 +        """Return list of elements in the container in proper order."""
    1.80 +        raise NotImplementedError()
    1.81 +
    1.82 +    def sorted_values(self):
    1.83 +        """Return list of markup values in container."""
    1.84 +        raise NotImplementedError()
    1.85 +
    1.86  class SequenceMarkup(Markup):
    1.87 +    """Markup for sequence.
    1.88 +
    1.89 +    Behaves like a dictionary of [monomer] -> value. Value may be anything
    1.90 +    or something specific, depending on subclass.
    1.91 +
    1.92 +    Actual values are stored in monomers themselves as attributes.
    1.93 +    """
    1.94  
    1.95      def __init__(self, sequence, name=None):
    1.96          self.sequence = sequence
    1.97          self._register(sequence, name)
    1.98          self.refresh()
    1.99  
   1.100 -    def as_list(self):
   1.101 -        for monomer in self.sequence:
   1.102 -            yield self[monomer]
   1.103 +    def sorted_keys(self):
   1.104 +        """Return list of monomers."""
   1.105 +        return self.sequence
   1.106 +
   1.107 +    def sorted_values(self):
   1.108 +        """Return list of markup values, if every monomer is marked up."""
   1.109 +        return (self[monomer] for monomer in self.sequence)
   1.110 +
   1.111 +    def get(self, key, value=None):
   1.112 +        """Part of Mapping collection interface."""
   1.113 +        if key not in self:
   1.114 +            return value
   1.115 +        return self[key]
   1.116  
   1.117      def __contains__(self, monomer):
   1.118 -        return monomer in self.sequence
   1.119 +        """Part of Mapping collection interface."""
   1.120 +        return hasattr(monomer, self.name)
   1.121  
   1.122      def __getitem__(self, monomer):
   1.123 +        """Part of Mapping collection interface."""
   1.124          return getattr(monomer, self.name)
   1.125  
   1.126      def __setitem__(self, monomer, value):
   1.127 +        """Part of Mapping collection interface."""
   1.128          return setattr(monomer, self.name, value)
   1.129  
   1.130  class AlignmentMarkup(dict, Markup):
   1.131 +    """Markupf for alignment.
   1.132 +
   1.133 +    Is a dictionary of [column] -> value. Value may be anything or something
   1.134 +    specific, depending on subclass.
   1.135 +    """
   1.136  
   1.137      def __init__(self, alignment, name=None):
   1.138          self.alignment = alignment
   1.139          self._register(alignment, name)
   1.140          self.refresh()
   1.141  
   1.142 -    def as_list(self):
   1.143 -        for column in self.alignment.columns:
   1.144 -            yield self[column]
   1.145 +    def sorted_keys(self):
   1.146 +        """Return a list of columns."""
   1.147 +        return self.alignment.columns
   1.148 +
   1.149 +    def sorted_values(self):
   1.150 +        """Return a list of makrup values, if every column is marked up."""
   1.151 +        return (self[column] for column in self.alignment.columns)
   1.152  
   1.153  # vim: set ts=4 sts=4 sw=4 et: