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comparison commons/core/sql/ITableSetAdaptator.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 ## Interface for TableSetAdaptator
32 #
33 class ITableSetAdaptator (object):
34
35 ## Insert a set instance
36 #
37 # @param obj a set instance
38 # @param delayed boolean indicating if the insert must be delayed
39 #
40 # @warning old name was insASet
41 #
42 def insert(self, obj, delayed = False):
43 pass
44
45 ## Insert a list of Set instances
46 #
47 # @param l a list of object instances
48 # @param delayed boolean
49 #
50 # @warning old name was insSetList
51 #
52 def insertList(self, l, delayed = False):
53 pass
54
55 ## Give a list of identifier numbers contained in the table
56 #
57 # @return l integer list
58 #
59 # @warning old name was getSet_num
60 #
61 def getIdList(self):
62 pass
63
64 ## Give a list of Set instances having a given seq name
65 #
66 # @param seqName string seq name
67 # @return lSets list of instances
68 #
69 # @warning old name was get_SetList_from_contig
70 #
71 def getSetListFromSeqName(self, seqName):
72 pass
73
74 ## Give a set instances list with a given identifier number
75 #
76 # @param id integer identifier number
77 # @return lSet list of set instances
78 #
79 # @warning old name was getSetList_from_num
80 #
81 def getSetListFromId(self, id):
82 pass
83
84 ## Give a set instances list with a list of identifier numbers
85 #
86 # @param lId integers list identifiers list numbers
87 # @return lSet list of set instances
88 #
89 # @warning old name was getSetList_from_numlist
90 #
91 def getSetListFromIdList(self,lId):
92 pass
93
94 ## Return a list of Set instances overlapping a given sequence
95 #
96 # @param seqName string sequence name
97 # @param start integer start coordinate
98 # @param end integer end coordinate
99 # @return lSet list of Set instances
100 #
101 # @warning old name was getSetList_from_qcoord
102 #
103 def getSetListOverlappingCoord( self, seqName, start, end ):
104 pass
105
106 ## Delete set corresponding to a given identifier number
107 #
108 # @param id integer identifier number
109 #
110 # @warning old name was delSet_from_num
111 #
112 def deleteFromId(self, id):
113 pass
114
115 ## Delete set corresponding to a given list of identifier number
116 #
117 # @param lId integers list list of identifier number
118 #
119 # @warning old name was delSet_from_listnum
120 #
121 def deleteFromIdList(self, lId):
122 pass
123
124 ## Join two set by changing id number of id1 and id2 set to the least of id1 and id2
125 #
126 # @param id1 integer id path number
127 # @param id2 integer id path number
128 #
129 # @warning old name was joinSet
130 #
131 def joinTwoSets(self, id1, id2):
132 pass
133
134 ## Get a new id number
135 #
136 # @return new_id integer max_id + 1
137 #
138 def getNewId(self):
139 pass
140
141 ## Give the data contained in the table as a list of Sets instances
142 #
143 # @return lSets list of set instances
144 #
145 def getListOfAllSets( self ):
146 pass