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1 import os
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2 import unittest
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3 import struct
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4 from SMART.Java.Python.ncList.NCList import NCList
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5 from SMART.Java.Python.misc import Utils
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6 from commons.core.utils.FileUtils import FileUtils
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7 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import *
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8 from commons.core.parsing.GffParser import GffParser
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9 from SMART.Java.Python.ncList.FileSorter import FileSorter
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10
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11 class Test_F_NCList(unittest.TestCase):
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12
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13 def setUp(self):
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14 self._inputGff3FileName = 'sortedFile.gff3'
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15 self._sortedFileName = 'sortedFile.pkl'
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16 self._expHFileName = 'expH.bin'
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17 self._expLFileName = 'expL.bin'
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18 self._obsHFileName = 'H.bin'
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19 self._obsLFileName = 'L.bin'
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20 self._addressFileName = 'address.txt'
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21 self._writeGFF3File(self._inputGff3FileName)
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22 self._ncList = NCList(0)
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23 self._ncList.setChromosome("chr1")
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24
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25 def tearDown(self):
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26 return
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27 for fileName in (self._inputGff3FileName, self._sortedFileName, self._expHFileName, self._expLFileName, self._obsHFileName, self._obsLFileName, self._addressFileName):
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28 if os.path.exists(fileName):
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29 os.remove(fileName)
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30
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31 def _sortAndBuild(self):
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32 parser = GffParser(self._inputGff3FileName)
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33 fs = FileSorter(parser, 0)
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34 fs.setOutputFileName(self._sortedFileName)
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35 fs.sort()
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36 self._ncList.setFileName(self._sortedFileName)
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37 self._ncList.setNbElements(parser.getNbTranscripts())
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38 self._ncList.buildLists()
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39
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40 def test_run_with_one_elementSubList(self):
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41 iMock = MockFindOverlapsWithOneInterval()
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42 iMock.write(self._inputGff3FileName)
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43 self._sortAndBuild()
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44 self._writeExpHFile_one_elementSubList()
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45 self._writeExpLFile_one_elementSubList()
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46 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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47 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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48
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49 def test_case1(self):
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50 iMock = MockFindOverlapsWithServeralIntervals_case1()
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51 iMock.write(self._inputGff3FileName)
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52 self._sortAndBuild()
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53 self._writeExpHFileCase1()
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54 self._writeExpLFileCase1()
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55 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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56 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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57
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58 def test_case2(self):
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59 iMock = MockFindOverlapsWithServeralIntervals_case2()
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60 iMock.write(self._inputGff3FileName)
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61 self._sortAndBuild()
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62 self._writeExpHFileCase2()
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63 self._writeExpLFileCase2()
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64 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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65 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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66
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67 def test_case3(self):
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68 iMock = MockFindOverlapsWithServeralIntervals_case3()
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69 iMock.write(self._inputGff3FileName)
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70 self._sortAndBuild()
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71 self._writeExpHFileCase3()
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72 self._writeExpLFileCase3()
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73 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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74 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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75
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76 def test_case4_5(self):
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77 iMock = MockFindOverlapsWithServeralIntervals_case4_5()
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78 iMock.write(self._inputGff3FileName)
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79 self._sortAndBuild()
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80 self._writeExpHFileCase4_5()
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81 self._writeExpLFileCase4_5()
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82 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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83 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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84
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85 def test_case6_7(self):
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86 iMock = MockFindOverlapsWithServeralIntervals_case6_7()
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87 iMock.write(self._inputGff3FileName)
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88 self._sortAndBuild()
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89 self._writeExpHFileCase6_7()
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90 self._writeExpLFileCase6_7()
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91 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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92 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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93
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94 def test_case8(self):
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95 iMock = MockFindOverlapsWithServeralIntervals_case8()
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96 iMock.write(self._inputGff3FileName)
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97 self._sortAndBuild()
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98 self._writeExpHFileCase8()
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99 self._writeExpLFileCase8()
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100 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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101 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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102
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103 def test_case9(self):
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104 iMock = MockFindOverlapsWithServeralIntervals_case9()
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105 iMock.write(self._inputGff3FileName)
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106 self._sortAndBuild()
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107 self._writeExpHFileCase9()
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108 self._writeExpLFileCase9()
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109 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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110 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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111
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112 def test_case10(self):
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113 iMock = MockFindOverlapsWithServeralIntervals_case10()
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114 iMock.write(self._inputGff3FileName)
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115 self._sortAndBuild()
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116 self._writeExpHFileCase10()
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117 self._writeExpLFileCase10()
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118 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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119 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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120
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121 def test_case11(self):
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122 iMock = MockFindOverlapsWithServeralIntervals_case11()
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123 iMock.write(self._inputGff3FileName)
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124 self._sortAndBuild()
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125 self._writeExpHFileCase11()
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126 self._writeExpLFileCase11()
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127 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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128 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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129
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130 def test_case12(self):
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131 iMock = MockFindOverlapsWithServeralIntervals_case12()
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132 iMock.write(self._inputGff3FileName)
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133 self._sortAndBuild()
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134 self._writeExpHFileCase12()
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135 self._writeExpLFileCase12()
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136 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName))
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137 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName))
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138
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139 def _writeGFF3File(self, fileName):
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140 f = open(fileName, "w")
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141 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n")
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142 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n")
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143 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n")
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144 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n")
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145 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n")
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146 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n")
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147 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n")
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148 f.close()
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149
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150 def _writeBinFile(self, fileName, elements):
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151 handle = open(fileName, "wb")
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152 for element in elements:
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153 handle.write(struct.pack('l', element))
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154 handle.close()
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155
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156 def _writeExpHFile(self, HFileName):
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157 list = [0, 2, 48, 3, -1, -1, -1, -1, 120, 1, 144, 1, -1, -1, -1, -1]
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158 H = open(HFileName, 'wb')
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159
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160 for item in list:
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161 item = struct.pack('l', item)
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162 H.write(item)
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163 H.close()
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164
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165 def _writeExpHFile_with_empty_SubParentDict(self, HFileName):
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166 list = [0, 1, -1, -1]
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167 H = open(HFileName, 'wb')
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168
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169 for item in list:
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170 item = struct.pack('l', item)
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171 H.write(item)
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172 H.close()
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173
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174 def _writeExpHFile_one_elementSubList(self):
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175 elements = [0, 1]
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176 self._writeBinFile(self._expHFileName, elements)
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177
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178 def _writeExpHFileCase1(self):
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179 elements = [0, 2, 2, 3, 5, 1, 6, 1]
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180 self._writeBinFile(self._expHFileName, elements)
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181
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182 def _writeExpHFileCase2(self):
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183 elements = [0, 2, 2, 1, 3, 1, 4, 1]
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184 self._writeBinFile(self._expHFileName, elements)
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185
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186 def _writeExpHFileCase3(self):
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187 elements = [0, 2, 2, 1, 3, 1, 4, 2]
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188 self._writeBinFile(self._expHFileName, elements)
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189
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190 def _writeExpHFileCase4_5(self):
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191 elements = [0, 1, 1, 1, 2, 1]
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192 self._writeBinFile(self._expHFileName, elements)
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193
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194 def _writeExpHFileCase6_7(self):
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195 elements = [0, 1, 1, 4]
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196 self._writeBinFile(self._expHFileName, elements)
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197
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198 def _writeExpHFileCase8(self):
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199 elements = [0, 1, 1, 2]
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200 self._writeBinFile(self._expHFileName, elements)
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201
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202 def _writeExpHFileCase9(self):
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203 elements = [0, 2, 2, 1]
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204 self._writeBinFile(self._expHFileName, elements)
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205
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206 def _writeExpHFileCase10(self):
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207 elements = [0, 3, 3, 3]
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208 self._writeBinFile(self._expHFileName, elements)
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209
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210 def _writeExpHFileCase11(self):
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211 elements = [0, 2, 2, 2, 4, 2]
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212 self._writeBinFile(self._expHFileName, elements)
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213
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214 def _writeExpHFileCase12(self):
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215 elements = [0, 1, 1, 3, 4, 1]
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216 self._writeBinFile(self._expHFileName, elements)
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217
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218 def _writeExpLFile_one_elementSubList(self):
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219 elements = [0, 1000, 0, -1, -1]
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220 self._writeBinFile(self._expLFileName, elements)
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221
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222 def _writeExpLFileCase1(self):
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223 elements = [ 0, 1000, 0, 1, -1, \
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224 1200, 1300, 2345, -1, -1, \
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225 50, 350, 391, -1, 0, \
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226 100, 600, 781, 2, 0, \
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227 700, 950, 1563, 3, 0, \
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228 200, 450, 1172, -1, 3, \
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229 800, 900, 1954, -1, 4]
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230 self._writeBinFile(self._expLFileName, elements)
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231
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232 def _writeExpLFileCase2(self):
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233 elements = [ 0, 500, 0, 1, -1, \
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234 900, 1200, 1561, -1, -1, \
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235 50, 450, 389, 2, 0, \
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236 100, 400, 779, 3, 2, \
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237 100, 200, 1170, -1, 3]
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238 self._writeBinFile(self._expLFileName, elements)
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239
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240 def _writeExpLFileCase3(self):
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241 elements = [ 0, 500, 0, 1, -1, \
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242 800, 1000, 1952, -1, -1, \
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243 50, 450, 389, 2, 0, \
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244 100, 400, 779, 3, 2, \
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245 100, 200, 1170, -1, 3, \
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246 300, 400, 1561, -1, 3]
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247 self._writeBinFile(self._expLFileName, elements)
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248
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249 def _writeExpLFileCase4_5(self):
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250 elements = [ 0, 1000, 0, 1, -1, \
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251 200, 800, 391, 2, 0, \
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252 400, 600, 782, -1, 1]
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253 self._writeBinFile(self._expLFileName, elements)
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254
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255 def _writeExpLFileCase6_7(self):
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256 elements = [ 0, 1000, 0, 1, -1, \
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257 100, 300, 391, -1, 0, \
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258 400, 500, 782, -1, 0, \
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259 510, 520, 1173, -1, 0, \
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260 850, 950, 1563, -1, 0]
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261 self._writeBinFile(self._expLFileName, elements)
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262
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263 def _writeExpLFileCase8(self):
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264 elements = [ 0, 1000, 0, 1, -1, \
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265 100, 200, 391, -1, 0, \
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266 300, 400, 782, -1, 0]
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267 self._writeBinFile(self._expLFileName, elements)
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268
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269 def _writeExpLFileCase9(self):
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270 elements = [ 0, 1000, 0, 1, -1, \
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271 800, 1200, 782, -1, -1, \
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272 600, 700, 391, -1, 0]
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273 self._writeBinFile(self._expLFileName, elements)
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274
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275 def _writeExpLFileCase10(self):
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276 elements = [ 0, 1000, 0, 1, -1, \
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277 1200, 1300, 1576, -1, -1, \
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278 1400, 1500, 1972, -1, -1, \
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279 100, 200, 394, -1, 0, \
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280 300, 400, 788, -1, 0, \
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281 500, 600, 1182, -1, 0]
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282 self._writeBinFile(self._expLFileName, elements)
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283
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284 def _writeExpLFileCase11(self):
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285 elements = [ 0, 500, 0, 1, -1, \
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286 700, 900, 1180, 2, -1, \
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287 100, 200, 392, -1, 0, \
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288 300, 400, 786, -1, 0, \
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289 710, 720, 1574, -1, 1, \
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290 740, 750, 1967, -1, 1]
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291 self._writeBinFile(self._expLFileName, elements)
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292
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293 def _writeExpLFileCase12(self):
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294 elements = [ 0, 1400, 0, 1, -1, \
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295 300, 500, 368, 2, 0, \
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296 800, 1100, 1106, -1, 0, \
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297 1200, 1300, 1476, -1, 0, \
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298 300, 500, 737, -1, 1]
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299 self._writeBinFile(self._expLFileName, elements)
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300
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301 if __name__ == "__main__":
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302 unittest.main()
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