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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 ## Interface for TableSetAdaptator
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32 #
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33 class ITableSetAdaptator (object):
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34
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35 ## Insert a set instance
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36 #
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37 # @param obj a set instance
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38 # @param delayed boolean indicating if the insert must be delayed
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39 #
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40 # @warning old name was insASet
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41 #
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42 def insert(self, obj, delayed = False):
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43 pass
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44
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45 ## Insert a list of Set instances
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46 #
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47 # @param l a list of object instances
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48 # @param delayed boolean
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49 #
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50 # @warning old name was insSetList
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51 #
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52 def insertList(self, l, delayed = False):
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53 pass
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54
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55 ## Give a list of identifier numbers contained in the table
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56 #
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57 # @return l integer list
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58 #
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59 # @warning old name was getSet_num
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60 #
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61 def getIdList(self):
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62 pass
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63
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64 ## Give a list of Set instances having a given seq name
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65 #
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66 # @param seqName string seq name
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67 # @return lSets list of instances
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68 #
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69 # @warning old name was get_SetList_from_contig
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70 #
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71 def getSetListFromSeqName(self, seqName):
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72 pass
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73
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74 ## Give a set instances list with a given identifier number
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75 #
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76 # @param id integer identifier number
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77 # @return lSet list of set instances
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78 #
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79 # @warning old name was getSetList_from_num
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80 #
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81 def getSetListFromId(self, id):
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82 pass
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83
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84 ## Give a set instances list with a list of identifier numbers
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85 #
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86 # @param lId integers list identifiers list numbers
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87 # @return lSet list of set instances
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88 #
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89 # @warning old name was getSetList_from_numlist
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90 #
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91 def getSetListFromIdList(self,lId):
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92 pass
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93
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94 ## Return a list of Set instances overlapping a given sequence
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95 #
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96 # @param seqName string sequence name
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97 # @param start integer start coordinate
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98 # @param end integer end coordinate
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99 # @return lSet list of Set instances
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100 #
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101 # @warning old name was getSetList_from_qcoord
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102 #
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103 def getSetListOverlappingCoord( self, seqName, start, end ):
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104 pass
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105
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106 ## Delete set corresponding to a given identifier number
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107 #
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108 # @param id integer identifier number
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109 #
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110 # @warning old name was delSet_from_num
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111 #
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112 def deleteFromId(self, id):
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113 pass
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114
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115 ## Delete set corresponding to a given list of identifier number
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116 #
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117 # @param lId integers list list of identifier number
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118 #
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119 # @warning old name was delSet_from_listnum
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120 #
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121 def deleteFromIdList(self, lId):
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122 pass
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123
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124 ## Join two set by changing id number of id1 and id2 set to the least of id1 and id2
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125 #
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126 # @param id1 integer id path number
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127 # @param id2 integer id path number
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128 #
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129 # @warning old name was joinSet
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130 #
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131 def joinTwoSets(self, id1, id2):
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132 pass
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133
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134 ## Get a new id number
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135 #
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136 # @return new_id integer max_id + 1
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137 #
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138 def getNewId(self):
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139 pass
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140
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141 ## Give the data contained in the table as a list of Sets instances
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142 #
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143 # @return lSets list of set instances
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144 #
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145 def getListOfAllSets( self ):
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146 pass |
