annotate OrderedDict.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
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1 # http://code.activestate.com/recipes/576693/
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2 # Backport of OrderedDict() class that runs on Python 2.4, 2.5, 2.6, 2.7 and pypy.
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3 # Passes Python2.7's test suite and incorporates all the latest updates.
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4
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5 try:
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6 from thread import get_ident as _get_ident
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7 except ImportError:
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8 from dummy_thread import get_ident as _get_ident
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9
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10 try:
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11 from _abcoll import KeysView, ValuesView, ItemsView
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12 except ImportError:
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13 pass
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14
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15
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16 class OrderedDict(dict):
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17 'Dictionary that remembers insertion order'
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18 # An inherited dict maps keys to values.
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19 # The inherited dict provides __getitem__, __len__, __contains__, and get.
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20 # The remaining methods are order-aware.
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21 # Big-O running times for all methods are the same as for regular dictionaries.
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22
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23 # The internal self.__map dictionary maps keys to links in a doubly linked list.
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24 # The circular doubly linked list starts and ends with a sentinel element.
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25 # The sentinel element never gets deleted (this simplifies the algorithm).
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26 # Each link is stored as a list of length three: [PREV, NEXT, KEY].
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27
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28 def __init__(self, *args, **kwds):
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29 '''Initialize an ordered dictionary. Signature is the same as for
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30 regular dictionaries, but keyword arguments are not recommended
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31 because their insertion order is arbitrary.
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32
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33 '''
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34 if len(args) > 1:
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35 raise TypeError('expected at most 1 arguments, got %d' % len(args))
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36 try:
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37 self.__root
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38 except AttributeError:
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39 self.__root = root = [] # sentinel node
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40 root[:] = [root, root, None]
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41 self.__map = {}
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42 self.__update(*args, **kwds)
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43
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44 def __setitem__(self, key, value, dict_setitem=dict.__setitem__):
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45 'od.__setitem__(i, y) <==> od[i]=y'
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46 # Setting a new item creates a new link which goes at the end of the linked
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47 # list, and the inherited dictionary is updated with the new key/value pair.
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48 if key not in self:
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49 root = self.__root
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50 last = root[0]
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51 last[1] = root[0] = self.__map[key] = [last, root, key]
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52 dict_setitem(self, key, value)
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53
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54 def __delitem__(self, key, dict_delitem=dict.__delitem__):
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55 'od.__delitem__(y) <==> del od[y]'
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56 # Deleting an existing item uses self.__map to find the link which is
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57 # then removed by updating the links in the predecessor and successor nodes.
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58 dict_delitem(self, key)
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59 link_prev, link_next, key = self.__map.pop(key)
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60 link_prev[1] = link_next
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61 link_next[0] = link_prev
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62
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63 def __iter__(self):
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64 'od.__iter__() <==> iter(od)'
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65 root = self.__root
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66 curr = root[1]
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67 while curr is not root:
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68 yield curr[2]
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69 curr = curr[1]
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70
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71 def __reversed__(self):
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72 'od.__reversed__() <==> reversed(od)'
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73 root = self.__root
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74 curr = root[0]
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75 while curr is not root:
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76 yield curr[2]
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77 curr = curr[0]
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78
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79 def clear(self):
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80 'od.clear() -> None. Remove all items from od.'
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81 try:
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82 for node in self.__map.itervalues():
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83 del node[:]
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84 root = self.__root
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85 root[:] = [root, root, None]
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86 self.__map.clear()
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87 except AttributeError:
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88 pass
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89 dict.clear(self)
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90
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91 def popitem(self, last=True):
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92 '''od.popitem() -> (k, v), return and remove a (key, value) pair.
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93 Pairs are returned in LIFO order if last is true or FIFO order if false.
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94
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95 '''
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96 if not self:
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97 raise KeyError('dictionary is empty')
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98 root = self.__root
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99 if last:
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100 link = root[0]
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101 link_prev = link[0]
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102 link_prev[1] = root
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103 root[0] = link_prev
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104 else:
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105 link = root[1]
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106 link_next = link[1]
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107 root[1] = link_next
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108 link_next[0] = root
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109 key = link[2]
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110 del self.__map[key]
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111 value = dict.pop(self, key)
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112 return key, value
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113
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114 # -- the following methods do not depend on the internal structure --
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115
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116 def keys(self):
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117 'od.keys() -> list of keys in od'
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118 return list(self)
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119
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120 def values(self):
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121 'od.values() -> list of values in od'
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122 return [self[key] for key in self]
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123
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124 def items(self):
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125 'od.items() -> list of (key, value) pairs in od'
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126 return [(key, self[key]) for key in self]
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127
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128 def iterkeys(self):
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129 'od.iterkeys() -> an iterator over the keys in od'
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130 return iter(self)
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131
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132 def itervalues(self):
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133 'od.itervalues -> an iterator over the values in od'
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134 for k in self:
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135 yield self[k]
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136
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137 def iteritems(self):
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138 'od.iteritems -> an iterator over the (key, value) items in od'
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139 for k in self:
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140 yield (k, self[k])
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141
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142 def update(*args, **kwds):
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143 '''od.update(E, **F) -> None. Update od from dict/iterable E and F.
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144
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145 If E is a dict instance, does: for k in E: od[k] = E[k]
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146 If E has a .keys() method, does: for k in E.keys(): od[k] = E[k]
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147 Or if E is an iterable of items, does: for k, v in E: od[k] = v
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148 In either case, this is followed by: for k, v in F.items(): od[k] = v
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149
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150 '''
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151 if len(args) > 2:
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152 raise TypeError('update() takes at most 2 positional '
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153 'arguments (%d given)' % (len(args),))
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154 elif not args:
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155 raise TypeError('update() takes at least 1 argument (0 given)')
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156 self = args[0]
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157 # Make progressively weaker assumptions about "other"
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158 other = ()
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159 if len(args) == 2:
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160 other = args[1]
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161 if isinstance(other, dict):
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162 for key in other:
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163 self[key] = other[key]
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164 elif hasattr(other, 'keys'):
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165 for key in other.keys():
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166 self[key] = other[key]
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167 else:
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168 for key, value in other:
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169 self[key] = value
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170 for key, value in kwds.items():
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171 self[key] = value
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172
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173 __update = update # let subclasses override update without breaking __init__
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174
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175 __marker = object()
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176
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177 def pop(self, key, default=__marker):
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178 '''od.pop(k[,d]) -> v, remove specified key and return the corresponding value.
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179 If key is not found, d is returned if given, otherwise KeyError is raised.
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180
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181 '''
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182 if key in self:
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183 result = self[key]
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184 del self[key]
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185 return result
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186 if default is self.__marker:
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187 raise KeyError(key)
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188 return default
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189
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190 def setdefault(self, key, default=None):
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191 'od.setdefault(k[,d]) -> od.get(k,d), also set od[k]=d if k not in od'
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192 if key in self:
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193 return self[key]
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194 self[key] = default
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195 return default
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196
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197 def __repr__(self, _repr_running={}):
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198 'od.__repr__() <==> repr(od)'
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199 call_key = id(self), _get_ident()
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200 if call_key in _repr_running:
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201 return '...'
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202 _repr_running[call_key] = 1
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203 try:
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204 if not self:
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205 return '%s()' % (self.__class__.__name__,)
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206 return '%s(%r)' % (self.__class__.__name__, self.items())
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207 finally:
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208 del _repr_running[call_key]
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209
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210 def __reduce__(self):
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211 'Return state information for pickling'
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212 items = [[k, self[k]] for k in self]
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213 inst_dict = vars(self).copy()
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214 for k in vars(OrderedDict()):
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215 inst_dict.pop(k, None)
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216 if inst_dict:
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217 return (self.__class__, (items,), inst_dict)
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218 return self.__class__, (items,)
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219
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220 def copy(self):
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221 'od.copy() -> a shallow copy of od'
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222 return self.__class__(self)
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223
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224 @classmethod
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225 def fromkeys(cls, iterable, value=None):
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226 '''OD.fromkeys(S[, v]) -> New ordered dictionary with keys from S
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227 and values equal to v (which defaults to None).
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228
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229 '''
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230 d = cls()
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231 for key in iterable:
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232 d[key] = value
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233 return d
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234
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235 def __eq__(self, other):
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236 '''od.__eq__(y) <==> od==y. Comparison to another OD is order-sensitive
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237 while comparison to a regular mapping is order-insensitive.
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238
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239 '''
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240 if isinstance(other, OrderedDict):
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241 return len(self)==len(other) and self.items() == other.items()
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242 return dict.__eq__(self, other)
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243
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244 def __ne__(self, other):
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245 return not self == other
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246
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247 # -- the following methods are only used in Python 2.7 --
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248
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249 def viewkeys(self):
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250 "od.viewkeys() -> a set-like object providing a view on od's keys"
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251 return KeysView(self)
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252
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253 def viewvalues(self):
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254 "od.viewvalues() -> an object providing a view on od's values"
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255 return ValuesView(self)
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256
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257 def viewitems(self):
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258 "od.viewitems() -> a set-like object providing a view on od's items"
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259 return ItemsView(self)