Mercurial > repos > yufei-luo > s_mart
comparison commons/core/sql/ITableMapAdaptator.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 ## 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 |