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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.sql.TableAdaptator import TableAdaptator
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33 from commons.core.sql.ITableMatchAdaptator import ITableMatchAdaptator
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34 from commons.core.coord.Match import Match
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35
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36 ## Adaptator for Match table
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37 #
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38 class TableMatchAdaptator( TableAdaptator, ITableMatchAdaptator ):
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39
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40 ## Give a list of Match instances given a query name
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41 #
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42 # @param query string sequence name
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43 # @return lMatches list of Match instances
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44 #
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45 def getMatchListFromQuery( self, query ):
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46 sqlCmd = "SELECT * FROM %s WHERE query_name='%s';" % ( self._table, query )
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47 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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48
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49 ## Give a list of Match instances having the same identifier
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50 #
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51 # @param id integer identifier number
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52 # @return lMatch a list of Match instances
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53 #
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54 def getMatchListFromId( self, id ):
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55 sqlCmd = "SELECT * FROM %s WHERE path='%d';" % ( self._table, id )
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56 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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57 return lMatch
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58
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59 ## Give a list of Match instances according to the given list of identifier numbers
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60 #
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61 # @param lId integer list
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62 # @return lMatch a list of Match instances
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63 #
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64 def getMatchListFromIdList( self, lId ):
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65 lMatch=[]
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66 if lId == []:
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67 return lMatch
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68 sqlCmd = "select * from %s where path=%d" % (self._table, lId[0])
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69 for i in lId[1:]:
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70 sqlCmd += " or path=%d" % (i)
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71 sqlCmd += ";"
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72 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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73 return lMatch
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74
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75 ## Give the data contained in the table as a list of Match instances
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76 #
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77 # @return lMatchs list of match instances
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78 #
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79 def getListOfAllMatches( self ):
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80 sqlCmd = "SELECT * FROM %s" % ( self._table )
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81 lMatches = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
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82 return lMatches
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83
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84 def _getInstanceToAdapt(self):
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85 iMatch = Match()
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86 return iMatch
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87
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88 def _getTypeAndAttr2Insert(self, match):
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89 type2Insert = ("'%s'","'%d'","'%d'","'%d'","'%f'","'%f'","'%s'","'%d'","'%d'","'%d'","'%f'","'%g'","'%d'","'%f'","'%d'")
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90 attr2Insert = ( match.range_query.seqname, match.range_query.start, \
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91 match.range_query.end, match.query_length, match.query_length_perc, \
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92 match.match_length_perc, match.range_subject.seqname, match.range_subject.start,\
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93 match.range_subject.end, match.subject_length, match.subject_length_perc, \
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94 match.e_value, match.score, match.identity, \
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95 match.id)
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96 return type2Insert, attr2Insert
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97
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98 def _escapeAntislash(self, obj):
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99 obj.range_query.seqname = obj.range_query.seqname.replace("\\", "\\\\")
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100 obj.range_subject.seqname = obj.range_subject.seqname.replace("\\", "\\\\")
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