Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/boltons/mathutils.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """This module provides useful math functions on top of Python's
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2 built-in :mod:`math` module.
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3 """
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4 from __future__ import division
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5
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6 from math import ceil as _ceil, floor as _floor
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7 import bisect
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8 import binascii
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9
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10
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11 def clamp(x, lower=float('-inf'), upper=float('inf')):
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12 """Limit a value to a given range.
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13
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14 Args:
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15 x (int or float): Number to be clamped.
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16 lower (int or float): Minimum value for x.
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17 upper (int or float): Maximum value for x.
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18
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19 The returned value is guaranteed to be between *lower* and
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20 *upper*. Integers, floats, and other comparable types can be
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21 mixed.
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22
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23 >>> clamp(1.0, 0, 5)
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24 1.0
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25 >>> clamp(-1.0, 0, 5)
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26 0
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27 >>> clamp(101.0, 0, 5)
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28 5
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29 >>> clamp(123, upper=5)
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30 5
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31
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32 Similar to `numpy's clip`_ function.
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33
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34 .. _numpy's clip: http://docs.scipy.org/doc/numpy/reference/generated/numpy.clip.html
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35
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36 """
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37 if upper < lower:
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38 raise ValueError('expected upper bound (%r) >= lower bound (%r)'
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39 % (upper, lower))
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40 return min(max(x, lower), upper)
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41
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42
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43 def ceil(x, options=None):
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44 """Return the ceiling of *x*. If *options* is set, return the smallest
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45 integer or float from *options* that is greater than or equal to
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46 *x*.
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47
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48 Args:
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49 x (int or float): Number to be tested.
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50 options (iterable): Optional iterable of arbitrary numbers
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51 (ints or floats).
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52
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53 >>> VALID_CABLE_CSA = [1.5, 2.5, 4, 6, 10, 25, 35, 50]
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54 >>> ceil(3.5, options=VALID_CABLE_CSA)
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55 4
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56 >>> ceil(4, options=VALID_CABLE_CSA)
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57 4
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58 """
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59 if options is None:
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60 return _ceil(x)
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61 options = sorted(options)
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62 i = bisect.bisect_left(options, x)
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63 if i == len(options):
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64 raise ValueError("no ceil options greater than or equal to: %r" % x)
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65 return options[i]
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66
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67
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68 def floor(x, options=None):
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69 """Return the floor of *x*. If *options* is set, return the largest
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70 integer or float from *options* that is less than or equal to
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71 *x*.
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72
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73 Args:
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74 x (int or float): Number to be tested.
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75 options (iterable): Optional iterable of arbitrary numbers
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76 (ints or floats).
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77
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78 >>> VALID_CABLE_CSA = [1.5, 2.5, 4, 6, 10, 25, 35, 50]
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79 >>> floor(3.5, options=VALID_CABLE_CSA)
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80 2.5
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81 >>> floor(2.5, options=VALID_CABLE_CSA)
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82 2.5
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83
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84 """
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85 if options is None:
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86 return _floor(x)
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87 options = sorted(options)
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88
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89 i = bisect.bisect_right(options, x)
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90 if not i:
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91 raise ValueError("no floor options less than or equal to: %r" % x)
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92 return options[i - 1]
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93
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94
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95 try:
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96 _int_types = (int, long)
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97 bytes = str
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98 except NameError:
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99 # py3 has no long
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100 _int_types = (int,)
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101 unicode = str
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102
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103
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104 class Bits(object):
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105 '''
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106 An immutable bit-string or bit-array object.
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107 Provides list-like access to bits as bools,
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108 as well as bitwise masking and shifting operators.
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109 Bits also make it easy to convert between many
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110 different useful representations:
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111
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112 * bytes -- good for serializing raw binary data
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113 * int -- good for incrementing (e.g. to try all possible values)
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114 * list of bools -- good for iterating over or treating as flags
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115 * hex/bin string -- good for human readability
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116
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117 '''
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118 __slots__ = ('val', 'len')
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119
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120 def __init__(self, val=0, len_=None):
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121 if type(val) not in _int_types:
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122 if type(val) is list:
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123 val = ''.join(['1' if e else '0' for e in val])
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124 if type(val) is bytes:
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125 val = val.decode('ascii')
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126 if type(val) is unicode:
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127 if len_ is None:
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128 len_ = len(val)
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129 if val.startswith('0x'):
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130 len_ = (len_ - 2) * 4
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131 if val.startswith('0x'):
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132 val = int(val, 16)
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133 else:
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134 if val:
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135 val = int(val, 2)
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136 else:
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137 val = 0
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138 if type(val) not in _int_types:
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139 raise TypeError('initialized with bad type: {0}'.format(type(val).__name__))
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140 if val < 0:
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141 raise ValueError('Bits cannot represent negative values')
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142 if len_ is None:
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143 len_ = len('{0:b}'.format(val))
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144 if val > 2 ** len_:
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145 raise ValueError('value {0} cannot be represented with {1} bits'.format(val, len_))
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146 self.val = val # data is stored internally as integer
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147 self.len = len_
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148
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149 def __getitem__(self, k):
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150 if type(k) is slice:
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151 return Bits(self.as_bin()[k])
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152 if type(k) is int:
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153 if k >= self.len:
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154 raise IndexError(k)
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155 return bool((1 << (self.len - k - 1)) & self.val)
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156 raise TypeError(type(k))
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157
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158 def __len__(self):
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159 return self.len
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160
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161 def __eq__(self, other):
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162 if type(self) is not type(other):
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163 return NotImplemented
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164 return self.val == other.val and self.len == other.len
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165
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166 def __or__(self, other):
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167 if type(self) is not type(other):
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168 return NotImplemented
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169 return Bits(self.val | other.val, max(self.len, other.len))
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170
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171 def __and__(self, other):
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172 if type(self) is not type(other):
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173 return NotImplemented
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174 return Bits(self.val & other.val, max(self.len, other.len))
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175
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176 def __lshift__(self, other):
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177 return Bits(self.val << other, self.len + other)
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178
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179 def __rshift__(self, other):
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180 return Bits(self.val >> other, self.len - other)
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181
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182 def __hash__(self):
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183 return hash(self.val)
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184
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185 def as_list(self):
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186 return [c == '1' for c in '{0:b}'.format(self.val)]
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187
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188 def as_bin(self):
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189 return '{{0:0{0}b}}'.format(self.len).format(self.val)
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190
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191 def as_hex(self):
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192 # make template to pad out to number of bytes necessary to represent bits
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193 tmpl = '%0{0}X'.format(2 * (self.len // 8 + ((self.len % 8) != 0)))
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194 ret = tmpl % self.val
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195 return ret
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196
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197 def as_int(self):
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198 return self.val
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199
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200 def as_bytes(self):
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201 return binascii.unhexlify(self.as_hex())
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202
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203 @classmethod
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204 def from_list(cls, list_):
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205 return cls(list_)
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206
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207 @classmethod
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208 def from_bin(cls, bin):
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209 return cls(bin)
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210
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211 @classmethod
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212 def from_hex(cls, hex):
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213 if isinstance(hex, bytes):
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214 hex = hex.decode('ascii')
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215 if not hex.startswith('0x'):
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216 hex = '0x' + hex
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217 return cls(hex)
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218
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219 @classmethod
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220 def from_int(cls, int_, len_=None):
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221 return cls(int_, len_)
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222
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223 @classmethod
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224 def from_bytes(cls, bytes_):
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225 return cls.from_hex(binascii.hexlify(bytes_))
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226
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227 def __repr__(self):
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228 cn = self.__class__.__name__
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229 return "{0}('{1}')".format(cn, self.as_bin())