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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 from SMART.Java.Python.structure.Interval import Interval
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31 from commons.core.coord.Align import Align
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32
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33 class SubMapping(Align):
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34 """
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35 A class that represents a part of a mapping, more precisely, a pair (target interval, query interval) that match together
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36 @ivar targetInterval: the target interval
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37 @type targetInterval: class L{Interval<Interval>}
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38 @ivar queryInterval: the query interval
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39 @type queryInterval: class L{Interval<Interval>}
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40 @ivar size: size of this sub-mapping
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41 @type size: int
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42 @ivar tags: various information
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43 @type tags: dict
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44 """
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45
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46 def __init__(self, subMapping = None):
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47 """
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48 Constructor
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49 @param subMapping: a sub-mapping to be copied
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50 @type subMapping: class L{SubMapping<SubMapping>}
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51 """
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52 self.targetInterval = Interval()
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53 self.queryInterval = Interval()
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54 Align.__init__(self, self.queryInterval, self.targetInterval)
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55 self.size = None
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56 self.tags = {}
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57 if subMapping != None:
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58 self.copy(subMapping)
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59
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60 def __eq__(self, o):
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61 if o == None:
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62 return False
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63 areAlignAttributesEquals = Align.__eq__(self, o)
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64 return areAlignAttributesEquals and (self.targetInterval == o.targetInterval) and (self.queryInterval == o.queryInterval) and self.size == o.getSize() and self.tags == o.getTags()
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65
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66 def getSuperAdress(self):
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67 return hex(id(super(Align, self)))
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68
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69 # def setRangesAlignToRangesInterval(self):
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70 # self.range_query = super(Range, self.queryInterval)
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71 # self.range_subject = super(Range, self.targetInterval)
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72
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73 def copy(self, subMapping):
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74 """
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75 Copy method
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76 @param subMapping: a sub-mapping to be copied
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77 @type subMapping: class L{SubMapping<SubMapping>}
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78 """
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79 self.setQueryName(subMapping.getQueryName())
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80 self.setQueryStart(subMapping.getQueryStart())
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81 self.setQueryEnd(subMapping.getQueryEnd())
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82 self.setSubjectName(subMapping.getSubjectName())
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83 self.setSubjectStart(subMapping.getSubjectStart())
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84 self.setSubjectEnd(subMapping.getSubjectEnd())
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85 self.e_value = subMapping.getEvalue()
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86 self.score = subMapping.getScore()
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87 self.identity = subMapping.getIdentity()
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88
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89 self.targetInterval.copy(subMapping.targetInterval)
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90 self.queryInterval.copy(subMapping.queryInterval)
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91 self.size = subMapping.size
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92 for tag in subMapping.tags:
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93 self.tags[tag] = subMapping.tags[tag]
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94
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95
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96 def setTargetInterval(self, interval):
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97 """
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98 Set target interval
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99 @param targetInterval: the target interval of the sub-mapping
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100 @type targetInterval: class L{Interval<Interval>}
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101 """
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102 self.targetInterval.copy(interval)
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103
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104
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105 def setQueryInterval(self, interval):
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106 """
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107 Set query interval
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108 @param queryInterval: the query interval of the sub-mapping
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109 @type queryInterval: class L{Interval<Interval>}
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110 """
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111 self.queryInterval.copy(interval)
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112
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113
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114 def setSize(self, size):
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115 """
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116 Set the size of the sub-mapping
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117 Possibly also target and query interval sizes, as well as number of mismatches
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118 @param size: the size of the sub-mapping
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119 @type size: int
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120 """
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121 self.size = size
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122 if "identity" in self.getTagNames():
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123 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
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124
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125
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126 def getDirection(self):
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127 """
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128 Get the direction of the alignment
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129 """
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130 return self.targetInterval.getDirection()
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131
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132
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133 def setDirection(self, direction):
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134 """
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135 Set the direction of the alignment
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136 @param direction: the directio of the alignment
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137 type direction: int or string
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138 """
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139 return self.targetInterval.setDirection(direction)
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140
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141
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142 def setTagValue(self, name, value):
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143 """
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144 Set the value of a tag
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145 @param name: name of the tag
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146 @type name: string
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147 @param value: value of the tag
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148 @type value: string or int
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149 """
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150 self.tags[name] = value
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151
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152
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153 def getTagValue(self, name):
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154 """
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155 Get the value of a tag
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156 @param name: name of the tag
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157 @type name: string
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158 @return: value of the tag
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159 """
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160 return self.tags[name]
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161
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162
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163 def getTagNames(self):
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164 """
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165 Get all the names of the tags
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166 @return: the names of the tags
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167 """
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168 return self.tags.keys()
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169
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170 def getTargetInterval(self):
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171 return self.targetInterval
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172
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173 def getQueryInterval(self):
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174 return self.queryInterval
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175
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176 def getSize(self):
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177 return self.size
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178
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179 def getTags(self):
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180 return self.tags
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181
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182 def setIdentity(self, identity):
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183 """
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184 Set the percentage of identity of the sub-mapping
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185 Possibly also set number of mismatches
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186 @param identity: the percentage of identity of the sub-mapping
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187 @type identity: float
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188 """
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189 self.identity = identity
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190 self.setTagValue("identity", identity)
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191 if self.size != None and "nbMismatches" not in self.getTagNames():
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192 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
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193
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194
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195 def setNbMismatches(self, nbMismatches):
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196 """
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197 Set the number of mismatches of the sub-mapping
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198 Possibly also set percentage of identity
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199 @param nbMismatches: the number of mismatches of the sub-mapping
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200 @type nbMismatches: int
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201 """
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202 self.nbMismatches = nbMismatches
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203 if self.size != None and "identity" not in self.getTagNames():
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204 self.setTagValue("identity", (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100)
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205
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206
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207 def setNbGaps(self, nbGaps):
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208 """
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209 Set the number of gaps of the sub-mapping
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210 @param nbGaps: the number of gaps of the sub-mapping
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211 @type nbGaps: int
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212 """
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213 self.setTagValue("nbGaps", nbGaps)
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214
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215
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216 def merge(self, subMapping):
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217 """
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218 Merge two subMappings
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219 @param subMapping: another sub-mapping
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220 @type subMapping: class L{SubMapping<SubMapping>}
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221 """
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222 self.targetInterval.merge(subMapping.targetInterval)
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223 self.queryInterval.merge(subMapping.queryInterval)
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224
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225
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226 def printCoordinates(self):
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227 """
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228 Print the coordinates of the sub-mapping (considering the direction)
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229 @return: a string
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230 """
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231 if self.getDirection() == 1:
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232 return "%d-%d" % (self.targetInterval.getStart(), self.targetInterval.getEnd())
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233 else:
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234 return "%d-%d" % (self.targetInterval.getEnd(), self.targetInterval.getStart())
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235
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236
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237 def __str__(self):
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238 """
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239 Return a representation of this object
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240 @return: a string
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241 """
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242
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243 if "match" in self.getTagNames() and not self.getTagValue("match"):
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244 return "%s ---" % self.queryName
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245
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246 direction = "+"
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247 if self.getDirection() == -1:
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248 direction = "-"
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249 string = "%s:%d-%d -- %s:%d-%d (%s)" % (self.targetInterval.getChromosome(), self.targetInterval.getStart(), self.targetInterval.getEnd(), self.queryInterval.name, self.queryInterval.getStart(), self.queryInterval.getEnd(), direction)
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250 if "nbMismatches" in self.getTagNames():
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251 string += "(%i mm)" % (self.getTagValue("nbMismatches"))
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252 if "identity" in self.getTagNames():
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253 string += "(id: %i%%)" % (self.getTagValue("identity"))
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254 if self.targetInterval.getSize() != None and self.queryInterval.getSize() != None and self.size != None:
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255 string += "(sizes: %d, %d -> %d)" % (self.targetInterval.getSize(), self.queryInterval.getSize(), self.size)
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256 return string
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257
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258
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