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comparison commons/core/sql/TableMatchAdaptator.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30
31
32 from commons.core.sql.TableAdaptator import TableAdaptator
33 from commons.core.sql.ITableMatchAdaptator import ITableMatchAdaptator
34 from commons.core.coord.Match import Match
35
36 ## Adaptator for Match table
37 #
38 class TableMatchAdaptator( TableAdaptator, ITableMatchAdaptator ):
39
40 ## Give a list of Match instances given a query name
41 #
42 # @param query string sequence name
43 # @return lMatches list of Match instances
44 #
45 def getMatchListFromQuery( self, query ):
46 sqlCmd = "SELECT * FROM %s WHERE query_name='%s';" % ( self._table, query )
47 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
48
49 ## Give a list of Match instances having the same identifier
50 #
51 # @param id integer identifier number
52 # @return lMatch a list of Match instances
53 #
54 def getMatchListFromId( self, id ):
55 sqlCmd = "SELECT * FROM %s WHERE path='%d';" % ( self._table, id )
56 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
57 return lMatch
58
59 ## Give a list of Match instances according to the given list of identifier numbers
60 #
61 # @param lId integer list
62 # @return lMatch a list of Match instances
63 #
64 def getMatchListFromIdList( self, lId ):
65 lMatch=[]
66 if lId == []:
67 return lMatch
68 sqlCmd = "select * from %s where path=%d" % (self._table, lId[0])
69 for i in lId[1:]:
70 sqlCmd += " or path=%d" % (i)
71 sqlCmd += ";"
72 lMatch = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
73 return lMatch
74
75 ## Give the data contained in the table as a list of Match instances
76 #
77 # @return lMatchs list of match instances
78 #
79 def getListOfAllMatches( self ):
80 sqlCmd = "SELECT * FROM %s" % ( self._table )
81 lMatches = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt )
82 return lMatches
83
84 def _getInstanceToAdapt(self):
85 iMatch = Match()
86 return iMatch
87
88 def _getTypeAndAttr2Insert(self, match):
89 type2Insert = ("'%s'","'%d'","'%d'","'%d'","'%f'","'%f'","'%s'","'%d'","'%d'","'%d'","'%f'","'%g'","'%d'","'%f'","'%d'")
90 attr2Insert = ( match.range_query.seqname, match.range_query.start, \
91 match.range_query.end, match.query_length, match.query_length_perc, \
92 match.match_length_perc, match.range_subject.seqname, match.range_subject.start,\
93 match.range_subject.end, match.subject_length, match.subject_length_perc, \
94 match.e_value, match.score, match.identity, \
95 match.id)
96 return type2Insert, attr2Insert
97
98 def _escapeAntislash(self, obj):
99 obj.range_query.seqname = obj.range_query.seqname.replace("\\", "\\\\")
100 obj.range_subject.seqname = obj.range_subject.seqname.replace("\\", "\\\\")