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
|
### -----------------------------------------------------------------
### CNE class
### Exported!
setClass(Class="CNE",
slots=c(assembly1Fn="character",
assembly2Fn="character",
axt12Fn="character",
axt21Fn="character",
window="integer",
identity="integer",
CNE12="GRangePairs",
CNE21="GRangePairs",
CNEMerged="GRangePairs",
CNEFinal="GRangePairs",
aligner="character",
cutoffs1="integer",
cutoffs2="integer"
),
prototype=list(assembly1Fn=character(1),
assembly2Fn=character(1),
axt12Fn=character(),
axt21Fn=character(),
window=50L,
identity=50L,
CNE12=GRangePairs(),
CNE21=GRangePairs(),
CNEMerged=GRangePairs(),
CNEFinal=GRangePairs(),
aligner="blat",
cutoffs1=4L,
cutoffs2=4L
)
)
setValidity("CNE",
function(object){
if(length(object@assembly1Fn) != 1L)
return("The filename of `assembly1Fn` must be length 1!")
if(!file.exists(object@assembly1Fn))
return("The file `assembly1Fn` must exist!")
if(length(object@assembly2Fn) != 1L)
return("The filename of `assembly2Fn` must be length 1!")
if(!file.exists(object@assembly2Fn))
return("The file `assembly2Fn` must exist!")
if(!all(file.exists(object@axt12Fn)))
return("The file `axt12Fn` must exist!")
if(!all(file.exists(object@axt21Fn)))
return("The file `axt21Fn` must exist!")
if(length(object@aligner) != 1L)
return("The aligner must be length 1!")
if(object@identity > object@window)
return("The identity must be equal to smaller than window")
return(TRUE)
}
)
### -----------------------------------------------------------------
### CNE class Generics
#setGeneric("assembly1", function(x) standardGeneric("assembly1"))
#setGeneric("assembly2", function(x) standardGeneric("assembly2"))
setGeneric("CNE12", function(x) standardGeneric("CNE12"))
setGeneric("CNE21", function(x) standardGeneric("CNE21"))
setGeneric("thresholds", function(x) standardGeneric("thresholds"))
setGeneric("CNEMerged", function(x) standardGeneric("CNEMerged"))
setGeneric("CNEFinal", function(x) standardGeneric("CNEFinal"))
#setGeneric("saveCNEToSQLite",
# function(CNE, dbName, tableName, overwrite=FALSE)
# standardGeneric("saveCNEToSQLite"))
setGeneric("ceScan",
function(axts, tFilter, qFilter, qSizes, window=50L, identity=50L)
standardGeneric("ceScan"))
### -----------------------------------------------------------------
### CNE Slot getters and setters.
### Exported!
#setMethod("assembly1", "CNE", function(x) x@assembly1)
#setMethod("assembly2", "CNE", function(x) x@assembly2)
setMethod("CNE12", "CNE", function(x) x@CNE12)
setMethod("CNE21", "CNE", function(x) x@CNE21)
setMethod("thresholds", "CNE", function(x)
paste(x@identity, x@window, sep="_"))
setMethod("CNEMerged", "CNE", function(x) x@CNEMerged)
setMethod("CNEFinal", "CNE", function(x) x@CNEFinal)
### -----------------------------------------------------------------
### CNE constructor.
### Exported!
CNE <- function(assembly1Fn=character(1), assembly2Fn=character(1),
axt12Fn=character(), axt21Fn=character(),
window=50L, identity=50L,
CNE12=GRangePairs(), CNE21=GRangePairs(),
CNEMerged=GRangePairs(), CNEFinal=GRangePairs(),
aligner="blat",
cutoffs1=4L, cutoffs2=4L
){
new("CNE", assembly1Fn=assembly1Fn, assembly2Fn=assembly2Fn,
axt12Fn=axt12Fn, axt21Fn=axt21Fn,
window=window, identity=identity, CNE12=CNE12, CNE21=CNE21,
CNEMerged=CNEMerged, CNEFinal=CNEFinal,
aligner=aligner, cutoffs1=cutoffs1, cutoffs2=cutoffs2)
}
|
