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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 import unittest
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33 from commons.core.coord.Match import Match
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34 from commons.core.coord.Path import Path
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35
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36
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37 class Test_Match( unittest.TestCase ):
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38
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39 def test_eq_match_equals( self ):
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40 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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41 match1 = Match()
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42 match1.setFromTuple(tuple1)
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43 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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44 match2 = Match()
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45 match2.setFromTuple(tuple2)
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46 self.assertEquals( match1, match2 )
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47
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48 def test_eq_match_not_equals_query_name( self ):
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49 tuple1 = ("Name", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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50 match1 = Match()
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51 match1.setFromTuple(tuple1)
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52 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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53 match2 = Match()
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54 match2.setFromTuple(tuple2)
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55 self.assertNotEquals( match1, match2 )
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56
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57 def test_eq_match_not_equals_query_start( self ):
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58 tuple1 = ("QName", 2, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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59 match1 = Match()
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60 match1.setFromTuple(tuple1)
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61 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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62 match2 = Match()
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63 match2.setFromTuple(tuple2)
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64 self.assertNotEquals( match1, match2 )
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65
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66 def test_eq_match_not_equals_query_end( self ):
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67 tuple1 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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68 match1 = Match()
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69 match1.setFromTuple(tuple1)
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70 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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71 match2 = Match()
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72 match2.setFromTuple(tuple2)
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73 self.assertNotEquals( match1, match2 )
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74
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75 def test_eq_match_not_equals_query_length( self ):
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76 tuple1 = ("QName", 1, 5, 6, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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77 match1 = Match()
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78 match1.setFromTuple(tuple1)
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79 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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80 match2 = Match()
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81 match2.setFromTuple(tuple2)
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82 self.assertNotEquals( match1, match2 )
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83
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84 def test_eq_match_not_equals_query_length_perc( self ):
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85 tuple1 = ("QName", 1, 5, 5, 0.15, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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86 match1 = Match()
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87 match1.setFromTuple(tuple1)
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88 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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89 match2 = Match()
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90 match2.setFromTuple(tuple2)
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91 self.assertNotEquals( match1, match2 )
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92
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93 def test_eq_match_not_equals_match_length_perc( self ):
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94 tuple1 = ("QName", 1, 5, 5, 0.1, 0.25, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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95 match1 = Match()
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96 match1.setFromTuple(tuple1)
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97 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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98 match2 = Match()
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99 match2.setFromTuple(tuple2)
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100 self.assertNotEquals( match1, match2 )
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101
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102 def test_eq_match_not_equals_subject_name( self ):
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103 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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104 match1 = Match()
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105 match1.setFromTuple(tuple1)
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106 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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107 match2 = Match()
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108 match2.setFromTuple(tuple2)
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109 self.assertNotEquals( match1, match2 )
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110
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111 def test_eq_match_not_equals_subject_start( self ):
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112 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 6, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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113 match1 = Match()
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114 match1.setFromTuple(tuple1)
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115 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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116 match2 = Match()
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117 match2.setFromTuple(tuple2)
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118 self.assertNotEquals( match1, match2 )
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119
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120 def test_eq_match_not_equals_subject_end( self ):
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121 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 26, 20, 0.15, 1e-20, 15, 87.2, 1)
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122 match1 = Match()
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123 match1.setFromTuple(tuple1)
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124 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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125 match2 = Match()
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126 match2.setFromTuple(tuple2)
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127 self.assertNotEquals( match1, match2 )
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128
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129 def test_eq_match_not_equals_subject_length( self ):
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130 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 21, 0.15, 1e-20, 15, 87.2, 1)
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131 match1 = Match()
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132 match1.setFromTuple(tuple1)
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133 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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134 match2 = Match()
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135 match2.setFromTuple(tuple2)
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136 self.assertNotEquals( match1, match2 )
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137
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138 def test_eq_match_not_equals_subject_length_perc( self ):
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139 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.16, 1e-20, 15, 87.2, 1)
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140 match1 = Match()
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141 match1.setFromTuple(tuple1)
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142 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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143 match2 = Match()
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144 match2.setFromTuple(tuple2)
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145 self.assertNotEquals( match1, match2 )
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146
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147 def test_eq_match_not_equals_subject_e_value( self ):
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148 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-21, 15, 87.2, 1)
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149 match1 = Match()
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150 match1.setFromTuple(tuple1)
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151 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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152 match2 = Match()
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153 match2.setFromTuple(tuple2)
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154 self.assertNotEquals( match1, match2 )
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155
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156 def test_eq_match_not_equals_subject_score( self ):
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157 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 16, 87.2, 1)
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158 match1 = Match()
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159 match1.setFromTuple(tuple1)
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160 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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161 match2 = Match()
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162 match2.setFromTuple(tuple2)
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163 self.assertNotEquals( match1, match2 )
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164
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165 def test_eq_match_not_equals_subject_identity( self ):
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166 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 85.2, 1)
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167 match1 = Match()
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168 match1.setFromTuple(tuple1)
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169 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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170 match2 = Match()
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171 match2.setFromTuple(tuple2)
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172 self.assertNotEquals( match1, match2 )
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173
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174 def test_eq_match_not_equals_subject_id( self ):
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175 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
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176 match1 = Match()
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177 match1.setFromTuple(tuple1)
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178 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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179 match2 = Match()
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180 match2.setFromTuple(tuple2)
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181 self.assertNotEquals( match1, match2 )
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182
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183 def test_setFromTuple_direct_strand( self ):
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184 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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185 obsMatch = Match()
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186 obsMatch.setFromTuple(tuple)
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187 expMatch = Match()
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188 expMatch.range_query.seqname = "QName"
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189 expMatch.range_query.start = 1
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190 expMatch.range_query.end = 5
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191 expMatch.query_length = 5
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192 expMatch.query_length_perc = 0.1
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193 expMatch.match_length_perc = 0.2
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194 expMatch.range_subject.seqname = "SName"
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195 expMatch.range_subject.start = 5
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196 expMatch.range_subject.end = 25
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197 expMatch.subject_length = 20
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198 expMatch.subject_length_perc = 0.15
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199 expMatch.e_value = 1e-20
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200 expMatch.score = 15
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201 expMatch.identity = 87.2
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202 expMatch.id = 1
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203 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
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204 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
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205 self.assertEquals( expMatch, obsMatch )
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206
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207 def test_setFromTuple_reverse_strand_on_subject( self ):
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208 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
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209 obsMatch = Match()
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210 obsMatch.setFromTuple(tuple)
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211 expMatch = Match()
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212 expMatch.range_query.seqname = "QName"
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213 expMatch.range_query.start = 1
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214 expMatch.range_query.end = 5
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215 expMatch.query_length = 5
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216 expMatch.query_length_perc = 0.1
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217 expMatch.match_length_perc = 0.2
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218 expMatch.range_subject.seqname = "SName"
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219 expMatch.range_subject.start = 25
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220 expMatch.range_subject.end = 5
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221 expMatch.subject_length = 20
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222 expMatch.subject_length_perc = 0.15
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223 expMatch.e_value = 1e-20
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224 expMatch.score = 15
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225 expMatch.identity = 87.2
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226 expMatch.id = 1
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227 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
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228 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
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229 self.assertEquals( expMatch, obsMatch )
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230
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231 def test_setFromTuple_reverse_strand_on_query( self ):
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232 tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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233 obsMatch = Match()
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234 obsMatch.setFromTuple(tuple)
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235 expMatch = Match()
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236 expMatch.range_query.seqname = "QName"
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237 expMatch.range_query.start = 1
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238 expMatch.range_query.end = 5
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239 expMatch.query_length = 5
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240 expMatch.query_length_perc = 0.1
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241 expMatch.match_length_perc = 0.2
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242 expMatch.range_subject.seqname = "SName"
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243 expMatch.range_subject.start = 25
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244 expMatch.range_subject.end = 5
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245 expMatch.subject_length = 20
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246 expMatch.subject_length_perc = 0.15
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247 expMatch.e_value = 1e-20
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248 expMatch.score = 15
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249 expMatch.identity = 87.2
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250 expMatch.id = 1
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251 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
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252 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
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253 self.assertEquals( expMatch, obsMatch )
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254
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255 def test_setFromTuple_reverse_strand_on_query_and_subject( self ):
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256 tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
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257 obsMatch = Match()
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258 obsMatch.setFromTuple(tuple)
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259 expMatch = Match()
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260 expMatch.range_query.seqname = "QName"
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261 expMatch.range_query.start = 1
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262 expMatch.range_query.end = 5
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263 expMatch.query_length = 5
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264 expMatch.query_length_perc = 0.1
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265 expMatch.match_length_perc = 0.2
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266 expMatch.range_subject.seqname = "SName"
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267 expMatch.range_subject.start = 5
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268 expMatch.range_subject.end = 25
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269 expMatch.subject_length = 20
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270 expMatch.subject_length_perc = 0.15
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271 expMatch.e_value = 1e-20
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272 expMatch.score = 15
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273 expMatch.identity = 87.2
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274 expMatch.id = 1
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275 expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
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276 expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
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277 self.assertEquals( expMatch, obsMatch )
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278
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279 def test_toString( self ):
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280 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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281 match = Match()
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282 match.setFromTuple(tuple)
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283 expString = "QName\t1\t5\t5\t%f\t%f\tSName\t5\t25\t20\t%f\t%g\t15\t%f\t1" % (0.1,0.2,0.15,1e-20, 87.2)
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284 obsString = match.toString()
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285 self.assertEquals(expString, obsString)
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286
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287 def test_getPathInstance( self ):
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288 tuple = ( "QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1 )
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289 match = Match()
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290 match.setFromTuple( tuple )
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291 tuple = ( 1, "QName", 1, 5, "SName", 5, 25, 1e-20, 15, 87.2 )
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292 exp = Path()
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293 exp.setFromTuple( tuple )
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294 obs = match.getPathInstance()
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295 self.assertEqual( exp, obs )
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296
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297 def test_getQryIsIncluded(self):
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298 tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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299 match = Match()
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300 match.setFromTuple(tuple)
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301 expString = "query QName (50 bp: 1-5) is contained in subject SName (133 bp: 5-25): id=87.20 - 0.100 - 0.200 - 0.150"
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302 obsString = match.getQryIsIncluded()
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303 self.assertEquals(expString, obsString)
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304
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305 def test_isDoublonWith_Matchs_equals(self):
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306 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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307 match1 = Match()
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308 match1.setFromTuple(tuple1)
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309 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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310 match2 = Match()
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311 match2.setFromTuple(tuple2)
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312 self.assertTrue(match1.isDoublonWith(match2))
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313
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314 def test_isDoublonWith_Matchs_unequals_on_MatchNumbers(self):
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315 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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316 match1 = Match()
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317 match1.setFromTuple(tuple1)
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318 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 86.2, 1)
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319 match2 = Match()
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320 match2.setFromTuple(tuple2)
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321 self.assertFalse(match1.isDoublonWith(match2))
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322
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323 def test_isDoublonWith_Matchs_unequals_on_SeqNames(self):
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324 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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325 match1 = Match()
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326 match1.setFromTuple(tuple1)
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327 tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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328 match2 = Match()
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329 match2.setFromTuple(tuple2)
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330 self.assertFalse(match1.isDoublonWith(match2))
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331
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332 def test_isDoublonWith_Matchs_unequals_on_Coordinates(self):
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333 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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334 match1 = Match()
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335 match1.setFromTuple(tuple1)
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336 tuple2 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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337 match2 = Match()
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338 match2.setFromTuple(tuple2)
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339 self.assertFalse(match1.isDoublonWith(match2))
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340
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341 def test_isDoublonWith_Reversed_Matchs_equals(self):
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342 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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343 match1 = Match()
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344 match1.setFromTuple(tuple1)
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345 tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 5, 5, 0.1, 1e-20, 15, 87.2, 1)
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346 match2 = Match()
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347 match2.setFromTuple(tuple2)
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348 self.assertTrue(match1.isDoublonWith(match2))
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349
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350 def test_isDoublonWith_Reversed_Matchs_unequals(self):
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351 tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
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352 match1 = Match()
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353 match1.setFromTuple(tuple1)
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354 tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 6, 5, 0.1, 1e-20, 15, 87.2, 1)
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355 match2 = Match()
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356 match2.setFromTuple(tuple2)
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357 self.assertFalse(match1.isDoublonWith(match2))
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358
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359
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360 test_suite = unittest.TestSuite()
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361 test_suite.addTest( unittest.makeSuite( Test_Match ) )
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362 if __name__ == "__main__":
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363 unittest.TextTestRunner(verbosity=2).run( test_suite )
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