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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 from commons.core.coord.Map import Map
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33
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34
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35 ## Record a named region on a given sequence with an identifier
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36 #
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37 class Set( Map ):
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38
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39 ## Constructor
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40 #
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41 # @param id identifier
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42 # @param name the name of the region
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43 # @param seqname the name of the sequence
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44 # @param start the start coordinate
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45 # @param end the end coordinate
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46 #
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47 def __init__(self, id=-1, name="", seqname="", start=-1, end=-1):
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48 Map.__init__( self, name, seqname, start, end )
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49 self.id = id
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50
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51 ## Equal operator
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52 #
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53 def __eq__(self, o):
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54 if self.id != o.id:
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55 return False
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56 else:
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57 return Map.__eq__(self, o)
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58
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59 def getId(self):
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60 return self.id
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61
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62 ## Reset
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63 #
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64 def reset(self):
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65 self.setFromTuple([-1, "", "", -1, -1 ])
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66
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67 ## Set attributes from tuple
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68 #
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69 # @param tuple: a tuple with (id, name, seqname, start, end)
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70 #
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71 def setFromTuple(self, tuple):
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72 self.id = int(tuple[0])
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73 Map.setFromTuple(self, tuple[1:])
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74
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75 ## Return the attributes as a formatted string
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76 #
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77 def toString(self):
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78 string = "%i" % (self.id)
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79 string += "\t%s" % (Map.toString(self))
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80 return string
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81
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82 ## Merge the instance with another Set instance
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83 #
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84 # @param o a Set instance
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85 #
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86 def merge(self, o):
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87 if self.seqname == o.seqname:
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88 Map.merge(self, o)
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89 self.id = min(self.id, o.id)
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90
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91 ## Return a Map instance with the attributes
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92 #
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93 def getMap(self):
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94 return Map(self.name, self.seqname, self.start, self.end)
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95
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96 ## Remove in the instance the region overlapping with another Set instance
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97 #
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98 # @param o a Set instance
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99 #
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100 def diff(self, o):
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101 iMap = Map.diff(self, o.getMap())
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102 new = Set()
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103 if not iMap.isEmpty():
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104 new.id = self.id
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105 new.name = self.name
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106 new.seqname = self.seqname
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107 new.start = iMap.start
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108 new.end = iMap.end
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109 return new
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110
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111 ## Return a Map instance with the identifier in the name
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112 #
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113 def set2map(self):
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114 return Map(self.name+"::"+str(self.id),self.seqname,self.start,self.end)
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115
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116
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117 def getMapInstance( self ):
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118 iMap = Map()
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119 lAttributes = []
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120 lAttributes.append( self.name )
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121 lAttributes.append( self.seqname )
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122 lAttributes.append( self.start )
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123 lAttributes.append( self.end )
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124 iMap.setFromTuple( lAttributes )
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125 return iMap
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