コード例 #1
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ファイル: distance.py プロジェクト: pycogent/old-cogent
    def __init__(self, data=None, RowOrder=None, ColOrder=None, Default=None,
        Pad=None, RowConstructor=None, info=None):
        """ Init dict with pre-exisitng data: dict of dicts
            Usage:
                data = distance matrix in form acceptable by Dict2D class
                RowOrder = list of 'interesting keys', default is the set of
                    all amino acids
                ColOrder = list of 'interesting keys', default is the set of
                    all amino acids
                Default = value to set padded elements to
                Pad = boolean describing whether to fill object to hold all 
                    possible elements based on RowOrder and ColOrder
                RowConstructor = constructor to use when building inner 
                    objects, default dict
                info = the AAIndexRecord object

            Power = Power the original matrix has been raised to yield current
              matrix
        """
        if RowOrder is not None:
            self.RowOrder = RowOrder
        if ColOrder is not None:
            self.ColOrder = ColOrder
        if Pad is not None:
            self.Pad = Pad
        # Initialize super class attributes
        Dict2D.__init__(self, data=data, RowOrder=self.RowOrder,\
                ColOrder=self.ColOrder, Default=Default, Pad=self.Pad,\
                RowConstructor=RowConstructor)
        Delegator.__init__(self, info)
        
        # The power to which the original data has been raised to give
        # the current data, starts at 1., modified by elementPow()
        # accessed as self.Power
        self.__dict__['Power'] = 1.
コード例 #2
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ファイル: bitvector.py プロジェクト: pombredanne/old-cogent
    def __init__(self, items="", length=None):
        """Initializes the Bitvector class, storing data in long _vector.

        Items can be any sequence with members that evaluate to True or False.

        Private data:
            _vector:     long representing the bitvector
            _string:     string representation of the vector
            _is_current: boolean indicating whether the string is known to
                         match the long data
        """
        Delegator.__init__(self, None)
        self.replace(items, length)
コード例 #3
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ファイル: sequence.py プロジェクト: pombredanne/old-cogent
 def __init__(self, data='', Info=None, **kwargs):
     """Initializes sequence object, bypassing validation.
     
     WARNING: Using this constructor can result in invalid data, though it
     is much faster without doing the validation. If validation is required,
     use the MutableSeq factory function, or one of its relatives (Rna, Dna,
     etc.)
     """
     #ConstrainedContainer, not ConstrainedList, init to bypass validation
     #Note that ConstrainedContainer init ignores data!
     ConstrainedContainer.__init__(self, **kwargs)
     list.__init__(self, data)
     new_info = self._find_info(data, Info)
     Delegator.__init__(self, new_info)
コード例 #4
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ファイル: usage.py プロジェクト: pombredanne/old-cogent
    def __init__(self, data=None, Info=None, **kwargs):
        """Intializes BaseUsage with data, either sequence or dict of freqs.
        
        Ignores additional kwargs (e.g. to support copy).

        Makes the _handler for delegator accessible with the name Info.
        """
        if Info is None:
            if hasattr(data, 'Info'):
                Info = data.Info
            else:
                Info = InfoClass()
        Delegator.__init__(self, Info)
        Freqs.__init__(self, data or [], **kwargs)
コード例 #5
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ファイル: info.py プロジェクト: pombredanne/old-cogent
 def __init__(self, *args, **kwargs):
     """Returns new Info object. Creates DbRefs if necessary."""
     temp = dict(*args, **kwargs)
     if 'Refs' in temp:
         refs = temp['Refs']
         if not isinstance(refs, DbRefs):
             refs = DbRefs(refs)
     else:
         refs = DbRefs()
     #move keys into refs if they belong there: allows init from flat dict 
     for key, val in temp.items():
         if key in KnownDatabases:
             refs[key] = val
             del temp[key]
             
     Delegator.__init__(self, refs)
     self['Refs'] = refs
     MappedRecord.__init__(self, temp)
コード例 #6
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ファイル: tree.py プロジェクト: pombredanne/old-cogent
    def __init__(self, Data=None, Children=None, Parent=None):
        """Returns new TreeNode, intialized with Data and maybe Children/Parent.
        
        Note: Parent is handled automatically when a node is appended to the
        children of another node.

        Desirable input for (phylogenetic) trees:
        - Newick string
        - Nexus block for tree, plus taxon map.
        - another tree object
        """
        #allocate slots for private vars: make sure they don't get captured
        #by self.Data!
        self.__dict__['_data'] = None
        self.__dict__['_parent'] = None
        self.__dict__['_handler'] = None
        Delegator.__init__(self, Data)
        node_checker = ClassChecker(self.__class__)
        ConstrainedList.__init__(self, [], node_checker)
        self.Data = Data
        self.Parent = Parent
        if Children:
            self.extend(Children)
コード例 #7
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ファイル: sequence.py プロジェクト: pombredanne/old-cogent
 def __init__(self, data='', Info=None, **kwargs):
     """Initializes sequence object, with associated Info object."""
     ConstrainedString.__init__(self, data, **kwargs)
     new_info = self._find_info(data, Info)
     Delegator.__init__(self, new_info)
コード例 #8
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ファイル: usage.py プロジェクト: pombredanne/old-cogent
 def __init__(self, First=None, Second=None, Third=None, Info=None):
     """Returns new PositionalBaseUsage with values for the 3 positions."""
     Delegator.__init__(self, Info)
     self.__dict__['First'] = First or BaseUsage()
     self.__dict__['Second'] = Second or BaseUsage()
     self.__dict__['Third'] = Third or BaseUsage()
コード例 #9
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ファイル: test_mage.py プロジェクト: pombredanne/old-cogent
 def __init__(self, data, *args):
     Delegator.__init__(self, *args)
     self.__dict__['Info'] = self._handler
     str.__init__(self, data)