annotate commons/core/coord/SetUtils.py @ 57:36eaa579fdb6

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author m-zytnicki
date Fri, 07 Feb 2014 08:29:48 -0500
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31
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32 from commons.core.coord.Set import Set
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33
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34 ## Static methods for the manipulation of Path instances
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35 #
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36 class SetUtils( object ):
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37
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38 ## Change the identifier of each Set instance in the given list
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39 #
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40 # @param lSets list of Set instances
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41 # @param newId new identifier
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42 #
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43 def changeIdInList(lSets, newId):
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44 for iSet in lSets:
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45 iSet.id = newId
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46
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47 changeIdInList = staticmethod( changeIdInList )
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48
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49 ## Return the length of the overlap between two lists of Set instances
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50 #
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51 # @param lSets1 list of Set instances
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52 # @param lSets2 list of Set instances
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53 # @return length of overlap
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54 # @warning sequence names are supposed to be identical
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55 #
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56 def getOverlapLengthBetweenLists(lSets1, lSets2):
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57 lSet1Sorted = SetUtils.getSetListSortedByIncreasingMinThenMax(lSets1)
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58 lSet2Sorted = SetUtils.getSetListSortedByIncreasingMinThenMax(lSets2)
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59 osize = 0
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60 i = 0
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61 j = 0
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62 while i!= len(lSet1Sorted):
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63 while j!= len(lSet2Sorted) and lSet1Sorted[i].getMin()>lSet2Sorted[j].getMax()\
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64 and not(lSet1Sorted[i].isOverlapping(lSet2Sorted[j])):
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65 j+=1
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66 jj=j
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67 while jj!= len(lSet2Sorted) and lSet1Sorted[i].isOverlapping(lSet2Sorted[jj]):
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68 osize+=lSet1Sorted[i].getOverlapLength(lSet2Sorted[jj])
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69 jj+=1
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70 i+=1
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71 return osize
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72
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73 getOverlapLengthBetweenLists = staticmethod( getOverlapLengthBetweenLists )
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74
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75 ## Return True if the two lists of Set instances overlap, False otherwise
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76 #
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77 # @param lSets1 list of Set instances
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78 # @param lSets2 list of Set instances
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79 #
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80 def areSetsOverlappingBetweenLists( lSets1, lSets2 ):
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81 lSet1Sorted = SetUtils.getSetListSortedByIncreasingMinThenMax(lSets1)
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82 lSet2Sorted = SetUtils.getSetListSortedByIncreasingMinThenMax(lSets2)
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83 i=0
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84 j=0
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85 while i!= len(lSet1Sorted):
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86 while j!= len(lSet2Sorted) and lSet1Sorted[i].getMin()>lSet2Sorted[j].getMax()\
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87 and not(lSet1Sorted[i].isOverlapping(lSet2Sorted[j])):
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88 j+=1
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89 if j!= len(lSet2Sorted) and lSet1Sorted[i].isOverlapping(lSet2Sorted[j]):
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90 return True
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91 i+=1
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92 return False
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93
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94 areSetsOverlappingBetweenLists = staticmethod( areSetsOverlappingBetweenLists )
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95
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96 ## Merge all overlapping Set instances between two lists of Set and give the next identifier
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97 #
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98 # @param lSets1 list of Set instances
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99 # @param lSets2 list of Set instances
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100 # @param max_id start id value for inserting new Set
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101 # @return a new list of the merged Set instances and the next identifier
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102 #
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103 def getListOfMergedSetsAndNextId(lSets1, lSets2, max_id=0):
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104 lSets_merged = []
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105 list2merge = SetUtils.getListOfIdListOfOverlappingSets ( lSets1,lSets2 )
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106 idlist1 = SetUtils.getDictOfListsWithIdAsKey(lSets1)
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107 idlist2 = SetUtils.getDictOfListsWithIdAsKey(lSets2)
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108 if max_id == 0:
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109 max_id = max(idlist1.keys()) + 1
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110 for i in list2merge:
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111 if i == []:
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112 continue
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113 l = []
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114 min_id = max(i)
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115 for j in i:
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116 if j>0:
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117 if min_id>j:
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118 min_id=j
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119 l.extend(idlist1[j])
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120 del idlist1[j]
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121 else:
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122 l.extend(idlist2[j*-1])
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123 del idlist2[j*-1]
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124 l = SetUtils.mergeSetsInList(l)
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125 SetUtils.changeIdInList(l, min_id)
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126 lSets_merged.extend(l)
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127 for id, alist in idlist1.items():
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128 lSets_merged.extend(alist)
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129 for id,alist in idlist2.items():
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130 SetUtils.changeIdInList(alist,max_id)
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131 lSets_merged.extend(alist)
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132 max_id+=1
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133 return lSets_merged, max_id
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134
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135 getListOfMergedSetsAndNextId = staticmethod ( getListOfMergedSetsAndNextId )
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136
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137 # ## Concatenate two Set instance lists and give the next identifier
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138 # #
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139 # # @param lSets1 list of Set instances
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140 # # @param lSets2 list of Set instances
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141 # # @param maxId start id value for inserting new Set
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142 # # @return a new list of Set instances and the next identifier
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143 # #
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144 # @staticmethod
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145 # def getSetsListOfTwoConcatenatedSetsListAndNextId(lSets1, lSets2, maxId = 0):
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146 # lOutSets = lSets1
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147 # dId2SetsList2 = SetUtils.getDictOfListsWithIdAsKey(lSets2)
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148 # if maxId == 0:
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149 # dId2SetsList1 = SetUtils.getDictOfListsWithIdAsKey(lSets1)
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150 # maxId = max(dId2SetsList1.keys())
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151 # for lSets in dId2SetsList2.values():
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152 # SetUtils.changeIdInList(lSets, maxId)
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153 # lOutSets.extend(lSets)
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154 # maxId += 1
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155 # return lOutSets, maxId
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156
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157 ## Return the sum of the length of each Set instance in the given list
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158 #
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159 # @param lSets: list of Set instances
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160 #
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161 def getCumulLength(lSets):
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162 length = 0
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163 for i in lSets:
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164 length += i.getLength()
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165 return length
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166
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167 getCumulLength = staticmethod( getCumulLength )
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168
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169 ## Return a tuple with min and max coordinates of Set instances in the given list
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170 #
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171 # @param lSets list of Set instances
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172 #
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173 def getListBoundaries(lSets):
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174 qmin = -1
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175 qmax = -1
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176 for iSet in lSets:
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177 if qmin == -1:
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178 qmin = iSet.start
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179 qmin = min(qmin, iSet.getMin())
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180 qmax = max(qmax, iSet.getMax())
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181 return (qmin, qmax)
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182
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183 getListBoundaries = staticmethod( getListBoundaries )
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184
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185 ## Show Set instances contained in the given list
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186 #
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187 # @param lSets list of Set instances
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188 #
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189 def showList(lSets):
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190 for iSet in lSets:
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191 iSet.show()
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192
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193 showList = staticmethod( showList )
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194
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195 ## Write Set instances contained in the given list
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196 #
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197 # @param lSets list of Set instances
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198 # @param fileName a file name
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199 # @param mode the open mode of the file '"w"' or '"a"'
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200 #
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201 def writeListInFile(lSets, fileName, mode="w"):
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202 fileHandler = open(fileName, mode)
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203 for iSet in lSets:
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204 iSet.write(fileHandler)
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205 fileHandler.close()
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206
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207 writeListInFile = staticmethod( writeListInFile )
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208
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209 ## Split a Set list in several Set lists according to the identifier
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210 #
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211 # @param lSets list of Set instances
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212 # @return a dictionary which keys are identifiers and values Set lists
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213 #
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214 def getDictOfListsWithIdAsKey(lSets):
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215 dId2SetList = {}
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216 for iSet in lSets:
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217 if dId2SetList.has_key(iSet.id):
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218 dId2SetList[iSet.id].append(iSet)
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219 else:
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220 dId2SetList[iSet.id] = [iSet]
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221 return dId2SetList
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222
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223 getDictOfListsWithIdAsKey = staticmethod( getDictOfListsWithIdAsKey )
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224
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225
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226 ## Split a Set list in several Set lists according to the identifier
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227 #
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228 # @param lSets list of Set instances
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229 # @return a dictionary which keys are identifiers and values Set lists
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230 #
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231 def getDictOfListsWithIdAsKeyFromFile( setFile ):
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232 dId2SetList = {}
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233 setFileHandler = open( setFile, "r" )
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234 while True:
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235 line = setFileHandler.readline()
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236 if line == "":
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237 break
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238 iSet = Set()
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239 iSet.setFromTuple( line[:-1].split("\t") )
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240 if not dId2SetList.has_key( iSet.id ):
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241 dId2SetList[ iSet.id ] = []
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242 dId2SetList[ iSet.id ].append( iSet )
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243 setFileHandler.close()
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244 return dId2SetList
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245
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246 getDictOfListsWithIdAsKeyFromFile = staticmethod( getDictOfListsWithIdAsKeyFromFile )
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247
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248
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249 ## Return a Map list from the given Set List
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250 #
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251 # @param lSets list of Set instances
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252 #
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253 def getMapListFromSetList(lSets):
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254 lMaps = []
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255 for iSet in lSets:
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256 lMaps.append(iSet.set2map())
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257 return lMaps
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258
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259 getMapListFromSetList = staticmethod( getMapListFromSetList )
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260
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261 ## Construct a Set list from a Map list
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262 #
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263 # @param lMaps list of Map instances
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264 #
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265 def getSetListFromMapList(lMaps):
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266 lSets = []
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267 c = 0
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268 for iMap in lMaps:
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269 c += 1
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270 lSets.append( Set(c, iMap.name, iMap.seqname, iMap.start, iMap.end) )
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271 return lSets
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272
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273 getSetListFromMapList = staticmethod( getSetListFromMapList )
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274
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275 ## Merge all overlapping Set instances in a list without considering the identifiers.
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276 # Start by sorting Set instances by their increasing Min coordinate.
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277 #
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278 # @return: a new list of the merged Set instances
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279 #
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280 def mergeSetsInList(lSets):
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281 l=[]
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282 if len(lSets)==0:
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283 return l
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284
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285 lSortedSets = SetUtils.getSetListSortedByIncreasingMinThenInvLength( lSets )
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286
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287 prev_count = 0
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288 for iSet in lSortedSets[0:]:
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289 if prev_count != len(lSortedSets):
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290 for i in lSortedSets[ prev_count + 1: ]:
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291 if iSet.isOverlapping( i ):
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292 iSet.merge( i )
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293 IsAlreadyInList = False
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294 for newSet in l:
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295 if newSet.isOverlapping( iSet ):
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296 IsAlreadyInList = True
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297 newSet.merge( iSet )
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298 l [ l.index( newSet ) ] = newSet
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299 if not IsAlreadyInList:
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300 l.append( iSet )
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301 prev_count += 1
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302 return l
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303
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304 mergeSetsInList = staticmethod( mergeSetsInList )
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305
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306 ## Unjoin a Set list according to another
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307 #
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yufei-luo
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308 # @param lToKeep: a list of Set instances to keep
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309 # @param lToUnjoin: a list of Set instances to unjoin
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310 # @return: lToUnjoin split in several list
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311 #
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312 def getSetListUnjoined(lToKeep, lToUnjoin):
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313 lSortedToKeep = SetUtils.getSetListSortedByIncreasingMinThenMax( lToKeep )
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314 lSortedToUnjoin = SetUtils.getSetListSortedByIncreasingMinThenMax( lToUnjoin )
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315 if lSortedToUnjoin == []:
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316 return []
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diff changeset
317 if lSortedToKeep == []:
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318 return [ lSortedToUnjoin ]
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319
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320 i=0
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321 resultListSet=[]
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diff changeset
322 while i<len(lSortedToKeep):
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323 j1=0
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yufei-luo
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diff changeset
324 while j1<len(lSortedToUnjoin) and lSortedToKeep[i].getMin() > lSortedToUnjoin[j1].getMax():
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325 j1+=1
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diff changeset
326 if j1==len(lSortedToUnjoin):
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yufei-luo
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diff changeset
327 break
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diff changeset
328 if j1!=0:
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329 resultListSet.append(lSortedToUnjoin[:j1])
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330 del lSortedToUnjoin[:j1]
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331 j1=0
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diff changeset
332 if i+1==len(lSortedToKeep):
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333 break
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334 j2=j1
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diff changeset
335 if j2<len(lSortedToUnjoin) and lSortedToKeep[i+1].getMin() > lSortedToUnjoin[j2].getMax():
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diff changeset
336 while j2<len(lSortedToUnjoin) and lSortedToKeep[i+1].getMin() > lSortedToUnjoin[j2].getMax():
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337 j2+=1
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338 resultListSet.append(lSortedToUnjoin[j1:j2])
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339 del lSortedToUnjoin[j1:j2]
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340 i+=1
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341
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diff changeset
342 if resultListSet!=[] or i == 0:
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343 resultListSet.append(lSortedToUnjoin)
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344 return resultListSet
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345
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346 getSetListUnjoined = staticmethod(getSetListUnjoined)
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347
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348 ## Return new list of Set instances with no duplicate
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diff changeset
349 #
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diff changeset
350 # @param lSets list of Set instances
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diff changeset
351 #
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diff changeset
352 def getSetListWithoutDuplicates( lSets ):
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diff changeset
353 if len(lSets) < 2:
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354 return lSets
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355 lSortedSet = SetUtils.getSetListSortedByIncreasingMinThenMax( lSets )
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356 lUniqSet = [ lSortedSet[0] ]
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diff changeset
357 for iSet in lSortedSet[1:]:
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yufei-luo
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diff changeset
358 if iSet != lUniqSet[-1]:
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yufei-luo
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diff changeset
359 lUniqSet.append( iSet )
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360 return lUniqSet
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361
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362 getSetListWithoutDuplicates = staticmethod( getSetListWithoutDuplicates )
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363
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364 ## Return a list of Set instances sorted in increasing order according to the Min, then the Max, and finally their initial order
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diff changeset
365 #
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diff changeset
366 # @param lSets: list of Set instances
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diff changeset
367 #
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diff changeset
368 def getSetListSortedByIncreasingMinThenMax( lSets ):
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369 return sorted( lSets, key=lambda iSet: ( iSet.getMin(), iSet.getMax() ) )
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370
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371 getSetListSortedByIncreasingMinThenMax = staticmethod( getSetListSortedByIncreasingMinThenMax )
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372
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373 ## Return a list of Set instances sorted in increasing order according to the min, then the inverse of the length, and finally their initial order
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yufei-luo
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diff changeset
374 #
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yufei-luo
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diff changeset
375 # @param lSets: list of Set instances
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diff changeset
376 #
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parents:
diff changeset
377 def getSetListSortedByIncreasingMinThenInvLength( lSets ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
378 return sorted( lSets, key=lambda iSet: ( iSet.getMin(), 1 / float(iSet.getLength()) ) )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
379
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
380 getSetListSortedByIncreasingMinThenInvLength = staticmethod( getSetListSortedByIncreasingMinThenInvLength )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
381
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
382 ## Return a list of Set instances sorted in increasing order according to the SeqName, then the Name, then the Min, then the Max and finally their initial order
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
383 #
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yufei-luo
parents:
diff changeset
384 # @param lSets: list of Set instances
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yufei-luo
parents:
diff changeset
385 #
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yufei-luo
parents:
diff changeset
386 def getSetListSortedBySeqThenRegionThenMinThenMax(lSets):
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yufei-luo
parents:
diff changeset
387 return sorted(lSets, key=lambda iSet: (iSet.getSeqname(), iSet.getName(), iSet.getMin(), iSet.getMax()))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
388
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
389 getSetListSortedBySeqThenRegionThenMinThenMax = staticmethod(getSetListSortedBySeqThenRegionThenMinThenMax)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
390
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yufei-luo
parents:
diff changeset
391 ## Return a list of identifier lists of overlapping Sets from the subject list, according to the reference list
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yufei-luo
parents:
diff changeset
392 #
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yufei-luo
parents:
diff changeset
393 # @param lRef list of Set instances
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yufei-luo
parents:
diff changeset
394 # @param lSubject list of Set instances
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yufei-luo
parents:
diff changeset
395 #
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yufei-luo
parents:
diff changeset
396 def getListOfIdListOfOverlappingSets(lRef,lSubject):
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yufei-luo
parents:
diff changeset
397 lSortedRef = SetUtils.getSetListSortedByIncreasingMinThenMax( lRef )
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yufei-luo
parents:
diff changeset
398 lSortedSubject = SetUtils.getSetListSortedByIncreasingMinThenMax( lSubject )
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yufei-luo
parents:
diff changeset
399
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yufei-luo
parents:
diff changeset
400 lOverlappingSet = []
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yufei-luo
parents:
diff changeset
401 lOverlappingSetCounter = 0
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yufei-luo
parents:
diff changeset
402
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yufei-luo
parents:
diff changeset
403 id2LOverlappingSet_pos = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
404
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yufei-luo
parents:
diff changeset
405 i = 0
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yufei-luo
parents:
diff changeset
406 j = 0
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
407 while i!= len(lSortedRef):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
408 while j!= len(lSortedSubject) and lSortedRef[i].getMin()>lSortedSubject[j].getMax()\
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
409 and not(lSortedRef[i].isOverlapping(lSortedSubject[j])\
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
410 and lSortedRef[i].isOnDirectStrand()==lSortedSubject[j].isOnDirectStrand()):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
411 j+=1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
412 jj=j
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
413 while jj!= len(lSortedSubject) and lSortedRef[i].isOverlapping(lSortedSubject[jj])\
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
414 and lSortedRef[i].isOnDirectStrand()==lSortedSubject[jj].isOnDirectStrand():
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
415 id1=lSortedRef[i].id
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yufei-luo
parents:
diff changeset
416 id2=lSortedSubject[jj].id*-1
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yufei-luo
parents:
diff changeset
417 if id2LOverlappingSet_pos.has_key(id1) \
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
418 and not id2LOverlappingSet_pos.has_key(id2):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
419 lOverlappingSet[id2LOverlappingSet_pos[id1]].append(id2)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
420 id2LOverlappingSet_pos[id2]=id2LOverlappingSet_pos[id1]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
421 if id2LOverlappingSet_pos.has_key(id2) \
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
422 and not id2LOverlappingSet_pos.has_key(id1):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
423 lOverlappingSet[id2LOverlappingSet_pos[id2]].append(id1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
424 id2LOverlappingSet_pos[id1]=id2LOverlappingSet_pos[id2]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
425 if not id2LOverlappingSet_pos.has_key(id2) \
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
426 and not id2LOverlappingSet_pos.has_key(id1):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
427 lOverlappingSet.append([id1,id2])
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
428 id2LOverlappingSet_pos[id1]=lOverlappingSetCounter
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
429 id2LOverlappingSet_pos[id2]=lOverlappingSetCounter
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
430 lOverlappingSetCounter+=1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
431 jj+=1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
432 i+=1
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
433
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
434 return lOverlappingSet
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
435
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
436 getListOfIdListOfOverlappingSets = staticmethod (getListOfIdListOfOverlappingSets)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
437
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
438 ## Return a list of sets without overlapping between two lists of sets
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
439 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
440 # @param lSet1 and lSet2
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
441 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
442 def getListOfSetWithoutOverlappingBetweenTwoListOfSet(lSet1, lSet2):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
443 for i in lSet1:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
444 for idx,j in enumerate(lSet2):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
445 n=j.diff(i)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
446 if not n.isEmpty() and n.getLength()>=20:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
447 lSet2.append(n)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
448 lSet2WithoutOverlaps=[]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
449 for i in lSet2:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
450 if not i.isEmpty() and i.getLength()>=20:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
451 lSet2WithoutOverlaps.append(i)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
452 return lSet2WithoutOverlaps
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
453
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
454 getListOfSetWithoutOverlappingBetweenTwoListOfSet = staticmethod (getListOfSetWithoutOverlappingBetweenTwoListOfSet)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
455
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
456 ## Return a Set list from a Set file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
457 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
458 # @param setFile string name of a Set file
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
459 # @return a list of Set instances
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
460 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
461 def getSetListFromFile( setFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
462 lSets = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
463 setFileHandler = open( setFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
464 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
465 line = setFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
466 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
467 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
468 iSet = Set()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
469 iSet.setFromString( line )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
470 lSets.append( iSet )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
471 setFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
472 return lSets
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
473
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
474 getSetListFromFile = staticmethod( getSetListFromFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
475
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
476
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
477 def convertSetFileIntoMapFile( setFile, mapFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
478 setFileHandler = open( setFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
479 mapFileHandler = open( mapFile, "w" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
480 iSet = Set()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
481 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
482 line = setFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
483 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
484 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
485 iSet.setFromString( line )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
486 iMap = iSet.getMapInstance()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
487 iMap.write( mapFileHandler )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
488 setFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
489 mapFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
490
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
491 convertSetFileIntoMapFile = staticmethod( convertSetFileIntoMapFile )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
492
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
493
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
494 def getDictOfListsWithSeqnameAsKey( lSets ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
495 dSeqnamesToSetList = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
496 for iSet in lSets:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
497 if not dSeqnamesToSetList.has_key( iSet.seqname ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
498 dSeqnamesToSetList[ iSet.seqname ] = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
499 dSeqnamesToSetList[ iSet.seqname ].append( iSet )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
500 return dSeqnamesToSetList
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
501
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
502 getDictOfListsWithSeqnameAsKey = staticmethod( getDictOfListsWithSeqnameAsKey )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
503
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
504
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
505 def filterOnLength( lSets, minLength=0, maxLength=10000000000 ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
506 if minLength == 0 and maxLength == 0:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
507 return lSets
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
508 lFiltered = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
509 for iSet in lSets:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
510 if minLength <= iSet.getLength() <= maxLength:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
511 lFiltered.append( iSet )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
512 return lFiltered
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
513
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
514 filterOnLength = staticmethod( filterOnLength )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
515
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
516
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
517 def getListOfNames( setFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
518 lNames = []
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
519 setFileHandler = open( setFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
520 iSet = Set()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
521 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
522 line = setFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
523 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
524 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
525 iSet.setFromTuple( line[:-1].split("\t") )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
526 if iSet.name not in lNames:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
527 lNames.append( iSet.name )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
528 setFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
529 return lNames
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
530
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
531 getListOfNames = staticmethod( getListOfNames )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
532
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
533
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
534 def getDictOfDictsWithNamesThenIdAsKeyFromFile( setFile ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
535 dNames2DictsId = {}
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
536 setFileHandler = open( setFile, "r" )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
537 while True:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
538 line = setFileHandler.readline()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
539 if line == "":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
540 break
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
541 iSet = Set()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
542 iSet.setFromTuple( line[:-1].split("\t") )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
543 if not dNames2DictsId.has_key( iSet.name ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
544 dNames2DictsId[ iSet.name ] = { iSet.id: [ iSet ] }
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
545 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
546 if not dNames2DictsId[ iSet.name ].has_key( iSet.id ):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
547 dNames2DictsId[ iSet.name ][ iSet.id ] = [ iSet ]
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
548 else:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
549 dNames2DictsId[ iSet.name ][ iSet.id ].append( iSet )
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
550 setFileHandler.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
551 return dNames2DictsId
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
552
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
553 getDictOfDictsWithNamesThenIdAsKeyFromFile = staticmethod( getDictOfDictsWithNamesThenIdAsKeyFromFile )