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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 ## Interface for TableMapAdaptator
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33 #
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34 class ITableMapAdaptator(object):
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35
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36 ## Insert a map instance
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37 #
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38 # @param obj map or set
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39 # @param delayed boolean must the insert be delayed
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40 #
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41 # @warning old name was insAMap
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42 #
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43 def insert(self, obj, delayed=False):
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44 pass
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45
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46
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47 ## Insert a list of Map or Set or Match instances
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48 #
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49 # @param l a list of object instances
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50 # @param delayed boolean
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51 #
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52 # @warning old name was insMapList
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53 #
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54 def insertList(self, l, delayed = False):
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55 pass
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56
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57 ## Give a list of the distinct seqName/chr present in the table
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58 #
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59 # @return lDistinctContigNames string list
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60 #
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61 # @warning old name was getContig_name
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62 #
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63 def getSeqNameList(self):
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64 pass
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65
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66
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67 ## Give a list of Map instances having a given seq name
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68 #
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69 # @param seqName string seq name
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70 # @return lMap list of instances
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71 #
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72 # @warning old name was get_MapList_from_contig
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73 #
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74 def getMapListFromSeqName(self, seqName):
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75 pass
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76
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77
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78 ## Return a list of Set instances from a given sequence name
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79 #
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80 # @param seqName string sequence name
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81 # @return lSets list of Set instances
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82 #
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83 # @warning old name was getSetList_from_contig
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84 #
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85 def getSetListFromSeqName( self, seqName ):
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86 pass
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87
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88
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89 ## Give a map instances list overlapping a given region
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90 #
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91 # @param seqName string seq name
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92 # @param start integer start coordinate
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93 # @param end integer end coordinate
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94 # @return lMap list of map instances
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95 #
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96 # @warning old name was getMapList_from_qcoord
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97 #
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98 def getMapListOverlappingCoord(self, seqName, start, end):
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99 pass
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100
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101
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102 ## Return a list of Set instances overlapping a given region
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103 #
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104 # @param seqName string sequence name
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105 # @param start integer start coordinate
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106 # @param end integer end coordinate
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107 # @return lSet list of Set instances
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108 #
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109 # @warning old name was getSetList_from_qcoord
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110 #
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111 def getSetListOverlappingCoord( self, seqName, start, end ):
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112 pass
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113 |
