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1 import unittest
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2 from SMART.Java.Python.structure.Interval import Interval
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3 from SMART.Java.Python.structure.SubMapping import SubMapping
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4
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5 class Test_SubMapping(unittest.TestCase):
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6
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7 def test__init__(self):
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8 expEvalue = 0.00
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9 expScore = 0
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10 expIdentity = 0.00
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11 expTargetInterval = Interval()
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12 expQueryInterval = Interval()
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13 expQueryRange = expQueryInterval
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14 expSubjectRange = expTargetInterval
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15 expSize = None
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16 expTags = {}
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17
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18 iSubMapping = SubMapping()
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19 obsQueryRange = iSubMapping.getQueryAsRange()
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20 obsSubjectRange = iSubMapping.getSubjectAsRange()
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21 obsEvalue = iSubMapping.getEvalue()
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22 obsScore = iSubMapping.getScore()
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23 obsIdentity = iSubMapping.getIdentity()
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24 obsTargetInterval = iSubMapping.getTargetInterval()
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25 obsQueryInterval = iSubMapping.getQueryInterval()
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26 obsSize = iSubMapping.getSize()
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27 obsTags = iSubMapping.getTags()
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28
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29 self.assertEquals(expEvalue, obsEvalue)
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30 self.assertEquals(expIdentity, obsIdentity)
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31 self.assertEquals(expQueryInterval, obsQueryInterval)
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32 self.assertEquals(expQueryRange, obsQueryRange)
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33 self.assertEquals(expScore, obsScore)
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34 self.assertEquals(expSize, obsSize)
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35 self.assertEquals(expSubjectRange, obsSubjectRange)
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36 self.assertEquals(expTags, obsTags)
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37 self.assertEquals(expTargetInterval, obsTargetInterval)
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38
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39 def test__init__change_values_by_Interval(self):
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40 iSubMapping = SubMapping()
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41
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42 expSeqName = ""
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43
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44 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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45 obsRangeQuery = iSubMapping.range_query.getSeqname()
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46 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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47 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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48
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49 self.assertEquals(expSeqName, obsRangeSubject)
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50 self.assertEquals(expSeqName, obsRangeQuery)
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51 self.assertEquals(expSeqName, obsIntervalTarget)
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52 self.assertEquals(expSeqName, obsIntervalQuery)
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53
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54 iSubMapping.getTargetInterval().setChromosome("intervalTarget")
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55 iSubMapping.getQueryInterval().setChromosome("intervalQuery")
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56
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57 expTargetSeqName = "intervalTarget"
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58 expQuerySeqName = "intervalQuery"
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59
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60 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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61 obsRangeQuery = iSubMapping.range_query.getSeqname()
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62 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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63 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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64
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65 self.assertEquals(expTargetSeqName, obsRangeSubject)
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66 self.assertEquals(expQuerySeqName, obsRangeQuery)
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67 self.assertEquals(expTargetSeqName, obsIntervalTarget)
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68 self.assertEquals(expQuerySeqName, obsIntervalQuery)
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69
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70 def test__init__change_values_by_Align(self):
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71 iSubMapping = SubMapping()
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72
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73 expSeqName = ""
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74
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75 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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76 obsRangeQuery = iSubMapping.range_query.getSeqname()
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77 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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78 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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79
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80 self.assertEquals(expSeqName, obsRangeSubject)
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81 self.assertEquals(expSeqName, obsRangeQuery)
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82 self.assertEquals(expSeqName, obsIntervalTarget)
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83 self.assertEquals(expSeqName, obsIntervalQuery)
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84
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85 iSubMapping.range_subject.setSeqName("intervalTarget")
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86 iSubMapping.range_query.setSeqName("intervalQuery")
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87
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88 expTargetSeqName = "intervalTarget"
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89 expQuerySeqName = "intervalQuery"
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90
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91 obsRangeSubject = iSubMapping.range_subject.getSeqname()
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92 obsRangeQuery = iSubMapping.range_query.getSeqname()
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93 obsIntervalTarget = iSubMapping.getTargetInterval().getChromosome()
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94 obsIntervalQuery = iSubMapping.getQueryInterval().getChromosome()
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95
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96 self.assertEquals(expTargetSeqName, obsRangeSubject)
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97 self.assertEquals(expQuerySeqName, obsRangeQuery)
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98 self.assertEquals(expTargetSeqName, obsIntervalTarget)
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99 self.assertEquals(expQuerySeqName, obsIntervalQuery)
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100
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101 def test__eq__(self):
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102 iSubMapping1 = SubMapping()
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103 iSubMapping1.setQueryName("Query")
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104 iSubMapping1.setQueryStart(50)
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105 iSubMapping1.setQueryEnd(150)
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106 iSubMapping1.setSubjectName("Subject")
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107 iSubMapping1.setSubjectStart(100)
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108 iSubMapping1.setSubjectEnd(200)
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109 iSubMapping1.e_value = 1e-20
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110 iSubMapping1.score = 30
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111 iSubMapping1.identity = 90.2
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112 iInterval1 = Interval()
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113 iInterval1.setChromosome("chromosome1")
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114 iInterval1.setStart(0)
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115 iInterval1.setEnd(100)
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116 iInterval1.setDirection("+")
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117 iInterval2 = Interval()
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118 iInterval2.setChromosome("chromosome2")
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119 iInterval2.setStart(200)
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120 iInterval2.setEnd(300)
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121 iInterval2.setDirection("+")
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122 iSubMapping1.setTargetInterval(iInterval1)
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123 iSubMapping1.setQueryInterval(iInterval2)
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124 iSubMapping1.setTagValue("name", 50)
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125 iSubMapping1.setSize(100)
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126
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127 iSubMapping2 = SubMapping()
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128 iSubMapping2.setQueryName("Query")
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129 iSubMapping2.setQueryStart(50)
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130 iSubMapping2.setQueryEnd(150)
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131 iSubMapping2.setSubjectName("Subject")
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132 iSubMapping2.setSubjectStart(100)
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133 iSubMapping2.setSubjectEnd(200)
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134 iSubMapping2.e_value = 1e-20
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135 iSubMapping2.score = 30
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136 iSubMapping2.identity = 90.2
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137 iSubMapping2.setTargetInterval(iInterval1)
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138 iSubMapping2.setQueryInterval(iInterval2)
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139 iSubMapping2.setTagValue("name", 50)
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140 iSubMapping2.setSize(100)
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141 self.assertEqual(iSubMapping1, iSubMapping2)
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142
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143
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144 def test__eq__withInitialValue(self):
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145 iSubMapping1 = SubMapping()
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146 iInterval1 = Interval()
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147 iInterval2 = Interval()
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148 iSubMapping1.setTargetInterval(iInterval1)
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149 iSubMapping1.setQueryInterval(iInterval2)
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150 iSubMapping1.setTagValue("name", 50)
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151 iSubMapping1.setSize(100)
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152
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153 iSubMapping2 = SubMapping()
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154 iSubMapping2.setTargetInterval(iInterval1)
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155 iSubMapping2.setQueryInterval(iInterval2)
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156 iSubMapping2.setTagValue("name", 50)
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157 iSubMapping2.setSize(100)
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158 self.assertEqual(iSubMapping1, iSubMapping2)
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159
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160
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161 def test__init__with_copy(self):
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162 iTestSubMapping = SubMapping()
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163 iTestSubMapping.setQueryName("Query")
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164 iTestSubMapping.setQueryStart(50)
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165 iTestSubMapping.setQueryEnd(150)
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166 iTestSubMapping.setSubjectName("Subject")
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167 iTestSubMapping.setSubjectStart(100)
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168 iTestSubMapping.setSubjectEnd(200)
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169 iTestSubMapping.e_value = 1e-20
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170 iTestSubMapping.score = 30
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171 iTestSubMapping.identity = 90.2
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172
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173 iIntervalTarget = Interval()
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174 iIntervalTarget.setChromosome("chromosomeTarget")
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175 iIntervalTarget.setName("sequenceTarget")
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176 iIntervalTarget.setStart(0)
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177 iIntervalTarget.setEnd(123)
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178 iIntervalTarget.setDirection("+")
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179 iIntervalQuery = Interval()
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180 iIntervalQuery.setChromosome("chromosomeQuery")
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181 iIntervalQuery.setName("sequenceQuery")
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182 iIntervalQuery.setStart(200)
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183 iIntervalQuery.setEnd(323)
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184 iIntervalQuery.setDirection("+")
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185
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186 iTestSubMapping.setQueryInterval(iIntervalTarget)
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187 iTestSubMapping.setTargetInterval(iIntervalQuery)
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188 iTestSubMapping.setTagValue("identity", 50)
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189 iTestSubMapping.setSize(10)
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190
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191 iSubMappingWithCopy = SubMapping(iTestSubMapping)
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192 self.assertEquals(iSubMappingWithCopy, iTestSubMapping)
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193
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194
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195 def test_copy(self):
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196 iSubMapping = SubMapping()
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197 iSubMapping.setQueryName("Query")
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198 iSubMapping.setQueryStart(50)
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199 iSubMapping.setQueryEnd(150)
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200 iSubMapping.setSubjectName("Subject")
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201 iSubMapping.setSubjectStart(100)
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202 iSubMapping.setSubjectEnd(200)
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203 iSubMapping.e_value = 1e-20
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204 iSubMapping.score = 30
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205 iSubMapping.identity = 90.2
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206
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207 iInterval1 = Interval()
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208 iInterval1.setChromosome("chromosome1")
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209 iInterval1.setName("sequence1")
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210 iInterval1.setStart(0)
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211 iInterval1.setEnd(123)
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212 iInterval1.setDirection("+")
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213 iInterval2 = Interval()
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214 iInterval2.setChromosome("chromosome2")
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215 iInterval2.setName("sequence2")
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216 iInterval2.setStart(200)
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217 iInterval2.setEnd(300)
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218 iInterval2.setDirection("+")
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219 iSubMapping.setQueryInterval(iInterval1)
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220 iSubMapping.setTargetInterval(iInterval2)
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221 iSubMapping.setTagValue("identity", 50)
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222 iSubMapping.setSize(10)
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223
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224 iSubMappingCopy = SubMapping()
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225 iSubMappingCopy.copy(iSubMapping)
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226 self.assertEqual(iSubMappingCopy, iSubMapping)
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227
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228
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229 def test_setTags(self):
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230 iSubMapping = SubMapping()
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231 iSubMapping.getQueryInterval().setSize(50)
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232 iSubMapping.getTargetInterval().setSize(2)
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233 iSubMapping.setTagValue("identity", 50)
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234 iSubMapping.setSize(10)
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235
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236 expQueryIntervalSize = 50
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237 expTargetIntervalSize = 2
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238 expTags = {"identity" : 50,
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239 "nbMismatches" : 5}
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240
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241 obsTags = iSubMapping.getTags()
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242 self.assertEquals(expTags, obsTags)
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243
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244
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245 def test_setIdentity(self):
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246 iSubMapping = SubMapping()
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247 iSubMapping.setIdentity(10)
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248 expIdentity = 10
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249 expTags = {"identity": 10}
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250
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251 obsIdentity = iSubMapping.getIdentity()
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252 obsTags = iSubMapping.getTags()
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253
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254 self.assertEquals(expIdentity,obsIdentity)
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255 self.assertEquals(expTags,obsTags)
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256
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257
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258 def test_setIdentity_with_size(self):
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259 iSubMapping = SubMapping()
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260 iSubMapping.setSize(10)
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261 iSubMapping.setIdentity(50)
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262
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263 expIdentity = 50
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264 expTags = {"identity" : 50,
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265 "nbMismatches" : 5}
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266
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267 obsIdentity = iSubMapping.getIdentity()
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268 obsTags = iSubMapping.getTags()
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269
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270 self.assertEquals(expIdentity,obsIdentity)
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271 self.assertEquals(expTags,obsTags)
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272
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273
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274 def test_setIdentity_with_sizeAndMismatchTag(self):
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275 iSubMapping = SubMapping()
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276 iSubMapping.setSize(10)
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277 iSubMapping.setTagValue("nbMismatches", 8)
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278 iSubMapping.setIdentity(50)
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279
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280 expIdentity = 50
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281 expTags = {"identity" : 50,
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282 "nbMismatches" : 8}
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283
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284 obsIdentity = iSubMapping.getIdentity()
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285 obsTags = iSubMapping.getTags()
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286
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287 self.assertEquals(expIdentity,obsIdentity)
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288 self.assertEquals(expTags,obsTags)
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289
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290
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291 if __name__ == "__main__":
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292 unittest.main()
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