Mercurial > repos > yufei-luo > s_mart
view commons/core/sql/TableMatchAdaptator.py @ 11:2da30502c2f1
Updated CompareOverlappingSmallQuery.xml
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:37:08 -0400 |
parents | 769e306b7933 |
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# Copyright INRA (Institut National de la Recherche Agronomique) # http://www.inra.fr # http://urgi.versailles.inra.fr # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. from commons.core.sql.TableAdaptator import TableAdaptator from commons.core.sql.ITableMatchAdaptator import ITableMatchAdaptator from commons.core.coord.Match import Match ## Adaptator for Match table # class TableMatchAdaptator( TableAdaptator, ITableMatchAdaptator ): ## Give a list of Match instances given a query name # # @param query string sequence name # @return lMatches list of Match instances # def getMatchListFromQuery( self, query ): sqlCmd = "SELECT * FROM %s WHERE query_name='%s';" % ( self._table, query ) return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) ## Give a list of Match instances having the same identifier # # @param id integer identifier number # @return lMatch a list of Match instances # def getMatchListFromId( self, id ): sqlCmd = "SELECT * FROM %s WHERE path='%d';" % ( self._table, id ) lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lMatch ## Give a list of Match instances according to the given list of identifier numbers # # @param lId integer list # @return lMatch a list of Match instances # def getMatchListFromIdList( self, lId ): lMatch=[] if lId == []: return lMatch sqlCmd = "select * from %s where path=%d" % (self._table, lId[0]) for i in lId[1:]: sqlCmd += " or path=%d" % (i) sqlCmd += ";" lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lMatch ## Give the data contained in the table as a list of Match instances # # @return lMatchs list of match instances # def getListOfAllMatches( self ): sqlCmd = "SELECT * FROM %s" % ( self._table ) lMatches = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) return lMatches def _getInstanceToAdapt(self): iMatch = Match() return iMatch def _getTypeAndAttr2Insert(self, match): type2Insert = ("'%s'","'%d'","'%d'","'%d'","'%f'","'%f'","'%s'","'%d'","'%d'","'%d'","'%f'","'%g'","'%d'","'%f'","'%d'") attr2Insert = ( match.range_query.seqname, match.range_query.start, \ match.range_query.end, match.query_length, match.query_length_perc, \ match.match_length_perc, match.range_subject.seqname, match.range_subject.start,\ match.range_subject.end, match.subject_length, match.subject_length_perc, \ match.e_value, match.score, match.identity, \ match.id) return type2Insert, attr2Insert def _escapeAntislash(self, obj): obj.range_query.seqname = obj.range_query.seqname.replace("\\", "\\\\") obj.range_subject.seqname = obj.range_subject.seqname.replace("\\", "\\\\")