Mercurial > repos > yufei-luo > s_mart
comparison commons/core/sql/TableMatchAdaptator.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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("\\", "\\\\") |