annotate cdblib.py @ 39:e56023008e36 default tip

Changed revision of package_fisher_0_1_4 to be2fc454d121 Changed revision of package_matplotlib_1_2 to a03ee94316b5
author miller-lab
date Mon, 06 Jul 2015 10:32:24 -0400
parents 2c498d40ecde
children
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1 #!/usr/bin/env python
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2
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3 '''
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4 Manipulate DJB's Constant Databases. These are 2 level disk-based hash tables
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5 that efficiently handle many keys, while remaining space-efficient.
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6
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7 http://cr.yp.to/cdb.html
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8
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9 When generated databases are only used with Python code, consider using hash()
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10 rather than djb_hash() for a tidy speedup.
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11 '''
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12
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13 from _struct import Struct
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14 from itertools import chain
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15
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16
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17 def py_djb_hash(s):
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18 '''Return the value of DJB's hash function for the given 8-bit string.'''
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19 h = 5381
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20 for c in s:
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21 h = (((h << 5) + h) ^ ord(c)) & 0xffffffff
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22 return h
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23
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24 try:
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25 from _cdblib import djb_hash
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26 except ImportError:
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27 djb_hash = py_djb_hash
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28
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29 read_2_le4 = Struct('<LL').unpack
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30 write_2_le4 = Struct('<LL').pack
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31
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32
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33 class Reader(object):
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34 '''A dictionary-like object for reading a Constant Database accessed
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35 through a string or string-like sequence, such as mmap.mmap().'''
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36
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37 def __init__(self, data, hashfn=djb_hash):
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38 '''Create an instance reading from a sequence and using hashfn to hash
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39 keys.'''
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40 if len(data) < 2048:
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41 raise IOError('CDB too small')
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42
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43 self.data = data
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44 self.hashfn = hashfn
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45
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46 self.index = [read_2_le4(data[i:i+8]) for i in xrange(0, 2048, 8)]
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47 self.table_start = min(p[0] for p in self.index)
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48 # Assume load load factor is 0.5 like official CDB.
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49 self.length = sum(p[1] >> 1 for p in self.index)
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50
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51 def iteritems(self):
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52 '''Like dict.iteritems(). Items are returned in insertion order.'''
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53 pos = 2048
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54 while pos < self.table_start:
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55 klen, dlen = read_2_le4(self.data[pos:pos+8])
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56 pos += 8
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57
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58 key = self.data[pos:pos+klen]
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59 pos += klen
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60
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61 data = self.data[pos:pos+dlen]
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62 pos += dlen
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63
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64 yield key, data
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65
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66 def items(self):
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67 '''Like dict.items().'''
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68 return list(self.iteritems())
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69
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70 def iterkeys(self):
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71 '''Like dict.iterkeys().'''
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72 return (p[0] for p in self.iteritems())
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73 __iter__ = iterkeys
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74
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75 def itervalues(self):
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76 '''Like dict.itervalues().'''
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77 return (p[1] for p in self.iteritems())
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78
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79 def keys(self):
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80 '''Like dict.keys().'''
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81 return [p[0] for p in self.iteritems()]
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82
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83 def values(self):
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84 '''Like dict.values().'''
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85 return [p[1] for p in self.iteritems()]
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86
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87 def __getitem__(self, key):
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88 '''Like dict.__getitem__().'''
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89 value = self.get(key)
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90 if value is None:
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91 raise KeyError(key)
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92 return value
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93
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94 def has_key(self, key):
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95 '''Return True if key exists in the database.'''
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96 return self.get(key) is not None
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97 __contains__ = has_key
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98
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99 def __len__(self):
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100 '''Return the number of records in the database.'''
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101 return self.length
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102
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103 def gets(self, key):
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104 '''Yield values for key in insertion order.'''
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105 # Truncate to 32 bits and remove sign.
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106 h = self.hashfn(key) & 0xffffffff
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107 start, nslots = self.index[h & 0xff]
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108
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109 if nslots:
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110 end = start + (nslots << 3)
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111 slot_off = start + (((h >> 8) % nslots) << 3)
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112
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113 for pos in chain(xrange(slot_off, end, 8),
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114 xrange(start, slot_off, 8)):
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115 rec_h, rec_pos = read_2_le4(self.data[pos:pos+8])
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116
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117 if not rec_h:
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118 break
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119 elif rec_h == h:
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120 klen, dlen = read_2_le4(self.data[rec_pos:rec_pos+8])
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121 rec_pos += 8
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122
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123 if self.data[rec_pos:rec_pos+klen] == key:
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124 rec_pos += klen
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125 yield self.data[rec_pos:rec_pos+dlen]
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126
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127 def get(self, key, default=None):
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128 '''Get the first value for key, returning default if missing.'''
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129 # Avoid exception catch when handling default case; much faster.
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130 return chain(self.gets(key), (default,)).next()
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131
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132 def getint(self, key, default=None, base=0):
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133 '''Get the first value for key converted it to an int, returning
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134 default if missing.'''
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135 value = self.get(key, default)
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136 if value is not default:
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137 return int(value, base)
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138 return value
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139
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140 def getints(self, key, base=0):
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141 '''Yield values for key in insertion order after converting to int.'''
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142 return (int(v, base) for v in self.gets(key))
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143
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144 def getstring(self, key, default=None, encoding='utf-8'):
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145 '''Get the first value for key decoded as unicode, returning default if
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146 not found.'''
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147 value = self.get(key, default)
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148 if value is not default:
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149 return value.decode(encoding)
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150 return value
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151
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152 def getstrings(self, key, encoding='utf-8'):
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153 '''Yield values for key in insertion order after decoding as
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154 unicode.'''
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155 return (v.decode(encoding) for v in self.gets(key))
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156
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157
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158 class Writer(object):
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159 '''Object for building new Constant Databases, and writing them to a
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160 seekable file-like object.'''
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161
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162 def __init__(self, fp, hashfn=djb_hash):
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163 '''Create an instance writing to a file-like object, using hashfn to
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164 hash keys.'''
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165 self.fp = fp
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166 self.hashfn = hashfn
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167
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168 fp.write('\x00' * 2048)
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169 self._unordered = [[] for i in xrange(256)]
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170
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171 def put(self, key, value=''):
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172 '''Write a string key/value pair to the output file.'''
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173 assert type(key) is str and type(value) is str
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174
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175 pos = self.fp.tell()
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176 self.fp.write(write_2_le4(len(key), len(value)))
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177 self.fp.write(key)
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178 self.fp.write(value)
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179
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180 h = self.hashfn(key) & 0xffffffff
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181 self._unordered[h & 0xff].append((h, pos))
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182
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183 def puts(self, key, values):
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184 '''Write more than one value for the same key to the output file.
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185 Equivalent to calling put() in a loop.'''
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186 for value in values:
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187 self.put(key, value)
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188
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189 def putint(self, key, value):
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190 '''Write an integer as a base-10 string associated with the given key
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191 to the output file.'''
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192 self.put(key, str(value))
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193
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194 def putints(self, key, values):
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195 '''Write zero or more integers for the same key to the output file.
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196 Equivalent to calling putint() in a loop.'''
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197 self.puts(key, (str(value) for value in values))
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198
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199 def putstring(self, key, value, encoding='utf-8'):
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200 '''Write a unicode string associated with the given key to the output
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201 file after encoding it as UTF-8 or the given encoding.'''
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202 self.put(key, unicode.encode(value, encoding))
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203
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204 def putstrings(self, key, values, encoding='utf-8'):
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205 '''Write zero or more unicode strings to the output file. Equivalent to
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206 calling putstring() in a loop.'''
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207 self.puts(key, (unicode.encode(value, encoding) for value in values))
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208
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209 def finalize(self):
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210 '''Write the final hash tables to the output file, and write out its
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211 index. The output file remains open upon return.'''
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212 index = []
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parents:
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213 for tbl in self._unordered:
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parents:
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214 length = len(tbl) << 1
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parents:
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215 ordered = [(0, 0)] * length
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parents:
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216 for pair in tbl:
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parents:
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217 where = (pair[0] >> 8) % length
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parents:
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218 for i in chain(xrange(where, length), xrange(0, where)):
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parents:
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219 if not ordered[i][0]:
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parents:
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220 ordered[i] = pair
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parents:
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221 break
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parents:
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222
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parents:
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223 index.append((self.fp.tell(), length))
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parents:
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224 for pair in ordered:
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parents:
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225 self.fp.write(write_2_le4(*pair))
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226
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227 self.fp.seek(0)
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228 for pair in index:
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229 self.fp.write(write_2_le4(*pair))
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parents:
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230 self.fp = None # prevent double finalize()