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### -----------------------------------------------------------------------
### The "show" method.
###
setMethod("show", "XMatrix",
function(object){
cat("An object of class ", class(object), "\n", sep="")
cat("ID: ", object@ID, "\n", sep="")
cat("Name: ", object@name, "\n", sep="")
cat("Matrix Class: ", object@matrixClass, "\n", sep="")
cat("strand: ", object@strand, "\n", sep="")
if(is(object, "PWMatrix")){
cat("Pseudocounts: ", object@pseudocounts, "\n", sep="")
}
if(is(object, "ICMatrix")){
cat("Schneider correction: ", object@schneider, "\n", sep="")
}
#for(i in 1:length(object@tags)){
# cat(names(object@tags)[i], ": ", object@tags[[i]], "\n", sep="")
#}
cat("Tags: \n")
print(object@tags)
cat("Background: ", "\n", sep="")
print(object@bg)
cat("Matrix: ", "\n", sep="")
# add the tags later and print pretty
print(object@profileMatrix)
}
)
### -----------------------------------------------------------------
### The "show" method.
###
setMethod("show", "TFFM",
function(object){
cat("An object of class ", class(object), "\n", sep="")
cat("ID: ", object@ID, "\n", sep="")
cat("Name: ", object@name, "\n", sep="")
cat("Matrix Class: ", object@matrixClass, "\n", sep="")
cat("strand: ", object@strand, "\n", sep="")
cat("Tags: \n")
print(object@tags)
cat("Background: ", "\n", sep="")
print(object@bg)
cat("Matrix: ", "\n", sep="")
print(object@profileMatrix)
cat("TFFM type: ", "\n", sep="")
print(object@type)
cat("Emission: ", "\n", sep="")
print(object@emission)
cat("Transition: ", "\n", sep="")
print(object@transition)
})
### -----------------------------------------------------------------
### The "show" method
### Perhaps it is not a bad idea to show them in gff format.
setMethod("show", "SiteSet",
function(object){
cat("An object of class", class(object), "with",
length(object), "site",
ifelse(length(object)==1, "sequence", "sequences"))
cat("\n")
if(length(object) > 10000)
object = object[1:10000]
gff = writeGFF3(object)
print(gff)
}
)
### -----------------------------------------------------------------
### The "show" method
### put them in a extended gff. any good idea?
setMethod("show", "SitePairSet",
function(object){
gff1 = writeGFF3(siteset1(object))
gff2 = writeGFF3(siteset2(object))
ans = cbind(gff1, gff2)
cat("An object of class", class(object), "with",
length(object), "site pair set",
ifelse(length(object)==1, "sequence", "sequences"))
cat("\n")
print(ans)
}
)
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