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