1.1 --- a/allpy/base.py	Fri Jul 15 13:57:56 2011 +0400
     1.2 +++ b/allpy/base.py	Fri Jul 15 16:43:03 2011 +0400
     1.3 @@ -101,7 +101,43 @@
     1.4      def __ne__(self, other):
     1.5          return not (self == other)
     1.6  
     1.7 -class Sequence(list):
     1.8 +class MarkupContainerMixin(object):
     1.9 +    """Common functions for alignment and sequence for dealing with markups.
    1.10 +    """
    1.11 +
    1.12 +    def _init(self):
    1.13 +        """Hook to be called from __init__ of actual class."""
    1.14 +        self.markups = {}
    1.15 +
    1.16 +    def add_markup(self, name, markup_class=None, **markup_kwargs):
    1.17 +        """Create a markup object, add to self. Return the created markup.
    1.18 +
    1.19 +        - `name` is name for markup in `self.markups` dictionary
    1.20 +        - optional `markup_class` is class for created markup
    1.21 +        - optional keyword arguments are passed on to the markup constructor
    1.22 +
    1.23 +        For user markups you have to specify `name` and `markup_class`,
    1.24 +        for the standard automatical markups just `name` is enough.
    1.25 +        """
    1.26 +        # We have to import markups here, and not in the module header
    1.27 +        # so as not to create bad import loops.
    1.28 +        # `base` module is used extensively in `markups` for inherinance,
    1.29 +        # so breaking the loop here seems a lot easier.
    1.30 +        import markups
    1.31 +        if markup_class is None:
    1.32 +            kind = self.kind + "_" + "markup"
    1.33 +            markup_class = markups.by_name[kind, name]
    1.34 +        assert name not in self.markups
    1.35 +        markup = markup_class(self, name, caller='container', **markup_kwargs)
    1.36 +        self.markups[name] = markup
    1.37 +        return markup
    1.38 +
    1.39 +    def remove_markup(self, name):
    1.40 +        """Remove markup."""
    1.41 +        self.markups[name].remove()
    1.42 +        del self.markups[name]
    1.43 +
    1.44 +class Sequence(list, MarkupContainerMixin):
    1.45      """Sequence of Monomers.
    1.46  
    1.47      This behaves like list of monomer objects. In addition to standard list
    1.48 @@ -117,13 +153,16 @@
    1.49      types = base
    1.50      """Mapping of related types. SHOULD be redefined in subclasses."""
    1.51  
    1.52 +    kind = 'sequence'
    1.53 +    """Description of object kind."""
    1.54 +
    1.55      name = ''
    1.56      description = ''
    1.57      source = ''
    1.58  
    1.59      def __init__(self, *args):
    1.60 -        self.markups = {}
    1.61          list.__init__(self, *args)
    1.62 +        MarkupContainerMixin._init(self)
    1.63  
    1.64      @classmethod
    1.65      def from_monomers(cls, monomers=[], name=None, description=None, source=None):
    1.66 @@ -158,7 +197,7 @@
    1.67          """Hash sequence by identity."""
    1.68          return id(self)
    1.69  
    1.70 -class Alignment(object):
    1.71 +class Alignment(MarkupContainerMixin):
    1.72      """Alignment. It is a list of Columns."""
    1.73  
    1.74      types = base
    1.75 @@ -167,11 +206,14 @@
    1.76      sequences = None
    1.77      """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
    1.78  
    1.79 +    kind = 'alignment'
    1.80 +    """Description of object kind."""
    1.81 +
    1.82      def __init__(self):
    1.83          """Initialize empty alignment."""
    1.84          self.sequences = []
    1.85          self.columns = []
    1.86 -        self.markups = {}
    1.87 +        MarkupContainerMixin._init(self)
    1.88  
    1.89      # Alignment grow & IO methods
    1.90      # ==============================
    1.91 @@ -507,22 +549,24 @@
    1.92      name = None
    1.93      """Name of markup elements"""
    1.94  
    1.95 -    def _register(self, container, name):
    1.96 -        """Register self within container.
    1.97 +    def __init__(self, container, name, **kwargs):
    1.98 +        """Markup takes mandatory container and name and optional kwargs.
    1.99  
   1.100 -        Assure the name is not taken before. If name is not given, look in the
   1.101 -        class. Make sure we have some name at all.
   1.102 +        Markups should never be created by the user. They are created by
   1.103 +        Sequence or Alignment.
   1.104          """
   1.105 -        if name:
   1.106 -            self.name = name
   1.107 -        assert self.name is not None
   1.108 -        assert self.name not in container.markups
   1.109 -        container.markups[self.name] = self
   1.110 +        self.name = name
   1.111 +        assert kwargs.get('caller') == 'container', "Improper call"
   1.112 +        self.refresh()
   1.113  
   1.114      def refresh(self):
   1.115          """Recalculate markup values (if they are generated automatically)."""
   1.116          pass
   1.117  
   1.118 +    def remove(self):
   1.119 +        """Remove the traces of markup object. Do not call this yourself!"""
   1.120 +        pass
   1.121 +
   1.122      @classmethod
   1.123      def from_record(cls, container, record, name=None):
   1.124          """Restore markup from `record`. (Used for loading from file).
   1.125 @@ -533,7 +577,7 @@
   1.126          Markup values should be stored in `record['markup']`, which is a list
   1.127          of items separated with either `record['separator']` or a comma.
   1.128          """
   1.129 -        return cls(container, name)
   1.130 +        return container.add_markup(name, markup_class=cls)
   1.131  
   1.132      def to_record(self):
   1.133          """Save markup to `record`, for saving to file.
   1.134 @@ -561,10 +605,14 @@
   1.135  
   1.136      kind = 'sequence_markup'
   1.137  
   1.138 -    def __init__(self, sequence, name=None):
   1.139 +    def __init__(self, sequence, name, **kwargs):
   1.140          self.sequence = sequence
   1.141 -        self._register(sequence, name)
   1.142 -        self.refresh()
   1.143 +        Markup.__init__(self, sequence, name, **kwargs)
   1.144 +
   1.145 +    def remove(self):
   1.146 +        """Remove the traces of markup object. Do not call this yourself!"""
   1.147 +        for monomer in self.monomers:
   1.148 +            del self[monomer]
   1.149  
   1.150      def sorted_keys(self):
   1.151          """Return list of monomers."""
   1.152 @@ -592,6 +640,10 @@
   1.153          """Part of Mapping collection interface."""
   1.154          return setattr(monomer, self.name, value)
   1.155  
   1.156 +    def __delitem__(self, monomer):
   1.157 +        """Part of Mapping collection interface."""
   1.158 +        return delattr(monomer, self.name)
   1.159 +
   1.160  class AlignmentMarkup(dict, Markup):
   1.161      """Markupf for alignment.
   1.162  
   1.163 @@ -601,10 +653,9 @@
   1.164  
   1.165      kind = 'alignment_markup'
   1.166  
   1.167 -    def __init__(self, alignment, name=None):
   1.168 +    def __init__(self, alignment, name, **kwargs):
   1.169          self.alignment = alignment
   1.170 -        self._register(alignment, name)
   1.171 -        self.refresh()
   1.172 +        Markup.__init__(self, alignment, name, **kwargs)
   1.173  
   1.174      def sorted_keys(self):
   1.175          """Return a list of columns."""