1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
|
##***********************************************************************
##
## Generic methods
##
##***********************************************************************
## A
setGeneric("activeFilter", function(x, ...) standardGeneric("activeFilter"))
setGeneric("addFilter", function(x, ...) standardGeneric("addFilter"))
## B
setGeneric("buildQuery", function(x, ...)
standardGeneric("buildQuery"))
## C
setGeneric("cleanColumns", function(x, columns, ...)
starndardGeneric("cleanColumns"))
## D
setGeneric("dbSeqlevelsStyle", function(x, ...)
standardGeneric("dbSeqlevelsStyle"))
setGeneric("dropFilter", function(x, ...) standardGeneric("dropFilter"))
## E
setGeneric("ensemblVersion", function(x)
standardGeneric("ensemblVersion"))
setGeneric("ensDbColumn", function(object, ...)
standardGeneric("ensDbColumn"))
setGeneric("ensDbQuery", function(object, ...)
standardGeneric("ensDbQuery"))
## F
## if (!isGeneric("filter"))
## setGeneric("filter", function(x, ...)
## standardGeneric("filter"))
setGeneric("formatSeqnamesForQuery", function(x, sn, ...)
standardGeneric("formatSeqnamesForQuery"))
setGeneric("formatSeqnamesFromQuery", function(x, sn, ...)
standardGeneric("formatSeqnamesFromQuery"))
## G
setGeneric("getGeneRegionTrackForGviz", function(x, ...)
standardGeneric("getGeneRegionTrackForGviz"))
setGeneric("getGenomeFaFile", function(x, ...)
standardGeneric("getGenomeFaFile"))
setGeneric("getGenomeTwoBitFile", function(x, ...)
standardGeneric("getGenomeTwoBitFile"))
setGeneric("getMetadataValue", function(x, name)
standardGeneric("getMetadataValue"))
setGeneric("getProperty", function(x, name=NULL, ...)
standardGeneric("getProperty"))
setGeneric("getWhat", function(x, ...)
standardGeneric("getWhat"))
## H
setGeneric("hasProteinData", function(x)
standardGeneric("hasProteinData"))
## L
setGeneric("lengthOf", function(x, ...)
standardGeneric("lengthOf"))
setGeneric("listColumns", function(x, ...)
standardGeneric("listColumns"))
setGeneric("listGenebiotypes", function(x, ...)
standardGeneric("listGenebiotypes"))
setGeneric("listTables", function(x, ...)
standardGeneric("listTables"))
setGeneric("listTxbiotypes", function(x, ...)
standardGeneric("listTxbiotypes"))
setGeneric("listUniprotDbs", function(object, ...)
standardGeneric("listUniprotDbs"))
setGeneric("listUniprotMappingTypes", function(object, ...)
standardGeneric("listUniprotMappingTypes"))
## O
setGeneric("orderResultsInR", function(x)
standardGeneric("orderResultsInR"))
setGeneric("orderResultsInR<-", function(x, value)
standardGeneric("orderResultsInR<-"))
## P
setGeneric("print", function(x, ...)
standardGeneric("print"))
setGeneric("properties", function(x, ...)
standardGeneric("properties"))
## R
setGeneric("requireTable", function(x, db, ...)
standardGeneric("requireTable"))
setGeneric("returnFilterColumns", function(x)
standardGeneric("returnFilterColumns"))
setGeneric("returnFilterColumns<-", function(x, value)
standardGeneric("returnFilterColumns<-"))
## S
setGeneric("seqinfo", function(x)
standardGeneric("seqinfo"))
setGeneric("setProperty", function(x, value=NULL, ...)
standardGeneric("setProperty"))
## setGeneric("show", function(object, ...)
## standardGeneric("show"))
setGeneric("supportedSeqlevelsStyles", function(x)
standardGeneric("supportedSeqlevelsStyles"))
## T
setGeneric("tablesByDegree", function(x, ...)
standardGeneric("tablesByDegree"))
setGeneric("tablesForColumns", function(x, attributes, ...)
standardGeneric("tablesForColumns"))
setGeneric("toSAF", function(x, ...)
standardGeneric("toSAF"))
## setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
## with.utr5_len=FALSE,
## with.utr3_len=FALSE, ...)
## standardGeneric("transcriptLengths"))
## U
setGeneric("updateEnsDb", function(x, ...)
standardGeneric("updateEnsDb"))
setGeneric("useMySQL", function(x, host = "localhost", port = 3306, user, pass)
standardGeneric("useMySQL"))
|
