--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corebio/utils/__init__.py	Thu Oct 27 12:09:09 2011 -0400
@@ -0,0 +1,470 @@
+
+ 
+#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
+#
+#  This software is distributed under the MIT Open Source License.
+#  <http://www.opensource.org/licenses/mit-license.html>
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a 
+#  copy of this software and associated documentation files (the "Software"),
+#  to deal in the Software without restriction, including without limitation
+#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+#  and/or sell copies of the Software, and to permit persons to whom the
+#  Software is furnished to do so, subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included
+#  in all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 
+#  THE SOFTWARE.
+#
+
+
+"""Extra utilities and core classes not in standard python.
+"""
+
+
+__all__ = ('isblank', 'isfloat', 'isint', 'fcmp', 'remove_whitespace', 
+            'invert_dict','update', 'stdrepr', 'Token', 'Struct', 'Reiterate',
+             'deoptparse', 'crc32', 'crc64', 'FileIndex', 'find_command',
+             'ArgumentError', 'frozendict')
+
+import os.path
+import math
+
+def isblank( string) :
+    """Is this whitespace or an empty string?"""
+    if string == '' : return True
+    return string.isspace()
+
+def isfloat(s):
+    """Does this object represent a floating point number? """
+    try: 
+        float(s)
+        return True
+    except (ValueError, TypeError): 
+        return False
+
+def isint(s):
+    """Does this object represent an integer?"""
+    try: 
+        int(s)
+        return True
+    except (ValueError, TypeError): 
+        return False
+        
+def fcmp(x, y, precision):
+    """Floating point comparison."""
+    # TODO: Doc string, default precision. Test
+    if math.fabs(x-y) < precision:
+        return 0
+    elif x < y:
+        return -1
+    return 1
+
+def remove_whitespace( astring) :
+    """Remove all whitespace from a string."""
+    # TODO: Is this horrible slow?   
+    return "".join(astring.split())
+
+
+def invert_dict( dictionary) :
+    """Constructs a new dictionary with inverted mappings so that keys become 
+    values and vice versa. If the values of the original dictionary are not
+    unique then only one of the original kesys will be included in the new
+    dictionary.
+    """
+    return dict( [(value, key) for key, value in dictionary.iteritems()] )
+
+
+
+def update(obj, **entries):
+    """Update an instance with new values. 
+
+    >>> update({'a': 1}, a=10, b=20)
+    {'a': 10, 'b': 20}
+    """
+    if hasattr(obj, 'update') :
+        obj.update( entries) 
+    else :
+        for k, v in entries.iteritems() :
+            setattr(obj, k, v)
+    return obj
+
+
+
+def stdrepr( obj,  attributes=None, name=None) :
+    """Create a standard representation of an object."""
+    if name==None : name = obj.__class__.__name__
+    if attributes==None: attributes = obj.__class__.__slots__
+    args = []
+    for a in attributes :
+        args.append( '%s=%s' % ( a, repr( getattr(obj, a) ) ) )
+    args = ',\n'.join(args).replace('\n', '\n    ')
+    return '%s(\n    %s\n)' % (name, args)
+   
+
+class Token(object):
+    """Represents the items returned by a file scanner, normally processed
+    by a parser.
+    
+    Attributes :
+    o typeof    -- a string describing the kind of token
+    o data      -- the value of the token
+    o lineno    -- the line of the file on which the data was found (if known)
+    o offset    -- the offset of the data within the line (if known)
+    """
+    __slots__ = [ 'typeof', 'data', 'lineno', 'offset']
+    def __init__(self, typeof, data=None, lineno=-1, offset=-1) :
+        self.typeof = typeof
+        self.data = data
+        self.lineno = lineno
+        self.offset = offset
+ 
+    def __repr__(self) :
+        return stdrepr( self) 
+
+    def __str__(self):
+        coord = str(self.lineno)
+        if self.offset != -1 : coord += ':'+str(self.offset)
+        coord = coord.ljust(7)
+        return (coord+ '  '+ self.typeof +' : ').ljust(32)+ str(self.data or '')
+
+
+
+def Struct(**kwargs) :
+    """Create a new instance of an anonymous class with the supplied attributes
+    and values.
+    
+    >>> s = Struct(a=3,b=4)
+    >>> s
+    Struct(
+        a=3,
+        b=4
+    )
+    >>> s.a
+    3
+    
+    """
+    name = 'Struct'
+    
+    def _init(obj,  **kwargs) :
+        for k, v in kwargs.iteritems() :
+            setattr( obj, k, v)
+    
+    def _repr(obj) :
+        return stdrepr( obj,  obj.__slots__, name)
+
+    adict = {}
+    adict['__slots__'] = kwargs.keys()
+    adict['__init__'] = _init
+    adict['__repr__'] = _repr
+    
+    return type( name, (object,) , adict)(**kwargs)
+    
+
+class Reiterate(object):
+    """ A flexible wrapper around a simple iterator.    
+    """
+    def __new__(cls, iterator):
+        if isinstance(iterator, cls) : return iterator
+        new = object.__new__(cls)
+        new._iterator = iter(iterator)
+        new._stack = []
+        new._index = 0 
+        return new
+
+    def __init__(self, *args, **kw):
+        pass   
+
+            
+    def __iter__(self):
+        return self
+        
+    def next(self): 
+        """Return the next item in the iteration."""
+        self._index +=1
+        if self._stack : 
+            return self._stack.pop()
+        else: 
+            return self._iterator.next()
+
+    def index(self) :
+        """The number of items returned. Incremented by next(), Decremented
+        by push(), unchanged by peek()  """
+        return self._index
+        
+    def push(self, item) :
+        """Push an item back onto the top of the iterator,"""
+        self._index -=1
+        self._stack.append(item)
+        
+    def peek(self) :
+        """Returns the next item, but does not advance the iteration.
+        Returns None if no more items. (Bit may also return None as the
+        next item.)"""
+        try :
+            item = self.next()
+            self.push(item)
+            return item
+        except StopIteration:
+            return None
+
+    def has_item(self) :
+        """More items to return?"""
+        try :
+            item = self.next()
+            self.push(item)
+            return True
+        except StopIteration:
+            return False    
+            
+    def filter(self, predicate):
+        """Return the next item in the iteration that satisifed the 
+        predicate."""
+        next = self.next()
+        while not predicate(next) : next = self.next()
+        return next
+# End class Reiterate
+
+
+
+
+
+def crc32(string):
+    """Return the standard CRC32 checksum as a hexidecimal string."""
+    import binascii
+    return "%08X"% binascii.crc32(string)
+
+_crc64_table =None
+
+def crc64(string):
+    """ Calculate ISO 3309 standard cyclic redundancy checksum.
+    Used, for example, by SWISS-PROT.
+    
+    Returns : The CRC as a hexadecimal string.
+    
+    Reference: 
+    o W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery,
+     "Numerical recipes in C", 2nd ed., Cambridge University Press. Pages 896ff.
+    """
+    # Adapted from biopython, which was adapted from bioperl
+    global _crc64_table
+    if _crc64_table is None :
+        # Initialisation of CRC64 table
+        table = []
+        for i in range(256):
+            l = i
+            part_h = 0
+            for j in range(8):
+                rflag = l & 1
+                l >>= 1
+                if part_h & 1: l |= (1L << 31)
+                part_h >>= 1L
+                if rflag: part_h ^= 0xd8000000L
+            table.append(part_h)
+        _crc64_table= tuple(table)
+    
+    crcl = 0
+    crch = 0
+    for c in string:
+        shr = (crch & 0xFF) << 24
+        temp1h = crch >> 8
+        temp1l = (crcl >> 8) | shr
+        idx  = (crcl ^ ord(c)) & 0xFF
+        crch = temp1h ^ _crc64_table[idx]
+        crcl = temp1l
+
+    return "%08X%08X" % (crch, crcl)
+# End crc64
+
+
+class FileIndex(object) :
+    """Line based random access to a file. Quickly turn a file into a read-only
+    database.
+    
+    Attr:
+    - indexfile -- The file to be indexed. Can be set to None and latter
+                replaced with a new file handle, for exampel, if you need to
+                close and latter reopen the file. 
+    
+    Bugs:
+        User must set the indexedfile to None before pickling this class.  
+    
+    """
+    __slots__ = [ 'indexedfile', '_parser', '_positions', '_keys', '_key_dict']
+    
+    def __init__(self, indexedfile, linekey = None, parser=None) :
+        """
+            
+        Args:
+        - indexedfile -- The file to index
+        - linekey -- An optional function. keyofline() will be passed each line
+            of the file in turn and should return a string to index the line, 
+            or None. If keyofline() is supplied, then only lines that generate  
+            keys are indexed.
+        - parser -- An optional parser. A function that reads from a file handle
+            positioned at the start of a record and returns an object.   
+        """
+    
+        def default_parser(seekedfile) :
+            return seekedfile.readline()
+            
+        if parser is None : parser = default_parser
+        self._parser = parser
+        
+        indexedfile.seek(0)
+        positions = []
+        keys = []
+        
+        while True :
+            position = indexedfile.tell()
+            line = indexedfile.readline()
+            if line == '' : break    
+            
+            if linekey :
+                k = linekey(line)
+                if k is None: continue
+                keys.append(k)
+
+            positions.append(position)
+        
+        self.indexedfile = indexedfile
+        self._positions = tuple(positions)
+        
+        if linekey :
+            self._keys = tuple(keys)
+            self._key_dict = dict( zip(keys, positions))
+
+        
+    def tell(self, item) :
+        if isinstance(item, str) : 
+            p = self._key_dict[item]
+        else :
+            p = self._positions[item]
+        return p
+        
+    def seek(self, item) :
+        """Seek the indexfile to the position of item."""
+        self.indexedfile.seek(self.tell(item))
+    
+    def __iter__(self) :
+        for i in range(0, len(self)) :
+            yield self[i]
+                
+    def __len__(self) :
+        return len(self._positions)
+         
+    def __getitem__(self, item) :
+        self.indexedfile.seek(self.tell(item))
+        return self._parser(self.indexedfile)
+    
+    def __contains__(self, item) :
+        try:
+            self.tell(item) 
+            return True
+        except KeyError :
+            return False
+        except IndexError :
+            return False            
+            
+# End class FileIndex   
+    
+
+def find_command(command, path=None):
+    """Return the full path to the first match of the given command on
+    the path.
+    
+    Arguments:
+    - command -- is a the name of the executable to search for.
+    - path -- is an optional alternate path list to search. The default it
+        to use the COREBIOPATH environment variable, if it exists, else the 
+        PATH environment variable.
+        
+    Raises:
+    - EnvironmentError -- If no match is found for the command.
+    
+    By default the COREBIO or PATH environment variable is searched (as well
+    as, on Windows, the AppPaths key in the registry), but a specific 'path'
+    list to search may be specified as well.  
+        
+    Author: Adapted from code by Trent Mick (TrentM@ActiveState.com)
+    See: http://trentm.com/projects/which/
+    """
+    import _which
+    if path is None :
+        path = os.environ.get("COREBIOPATH", "").split(os.pathsep)
+        if path==['']: path = None   
+
+    try :
+        match =_which.whichgen(command, path).next()
+    except StopIteration, _which.WhichError:
+        raise EnvironmentError("Could not find '%s' on the path." % command)
+    return match
+
+
+
+class ArgumentError(ValueError) :
+    """ A subclass of ValueError raised when a function receives an argument
+    that has the right type but an inappropriate value, and the situation is not
+    described by a more precise exception such as IndexError. The name of the   
+    argument or component at fault and (optionally) the value are also stored.
+    """
+    
+    def __init__(self, message, key, value=None) :
+        """ Args:
+        - message -- An error message.
+        - key -- The name of the argument or component at fault.
+        - value -- Optional value of the argument.
+        """ 
+        ValueError.__init__(self, message)
+        self.key = key
+        self.value = value
+# end class ArgumentError
+
+
+class frozendict(dict):
+    """A frozendict is a dictionary that cannot be modified after being created
+     -  but it is hashable and may serve as a member of a set or a key in a
+    dictionary.
+    # Author: Adapted from code by Oren Tirosh
+    """
+    # See: http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/414283
+    
+    def _blocked_attribute(obj):
+        raise AttributeError, "A frozendict cannot be modified."
+    _blocked_attribute = property(_blocked_attribute)
+
+    __delitem__ =   _blocked_attribute
+    __setitem__ =   _blocked_attribute
+    clear =         _blocked_attribute
+    pop =           _blocked_attribute
+    popitem =       _blocked_attribute
+    setdefault =    _blocked_attribute
+    update =        _blocked_attribute
+    
+    def __new__(cls, *args, **kw):
+        new = dict.__new__(cls)
+        dict.__init__(new, *args, **kw)
+        return new
+
+    def __init__(self, *args, **kw):
+        pass
+    
+    def __hash__(self):
+        try:
+            return self._cached_hash
+        except AttributeError:
+            # Hash keys, not items, since items can be mutable and unhasahble.
+            h = self._cached_hash = hash(tuple(sorted(self.keys())))
+            return h
+
+    def __repr__(self):
+        return "frozendict(%s)" % dict.__repr__(self)    
+# end class frozendict   
+          
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