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## -----------------------------------------------------------------
## Axt class
## Exported!
setClass(Class="Axt",
contains="GRangePairs")
setValidity("Axt",
function(object){
if(!isConstant(c(length(targetRanges(object)),
length(targetSeqs(object)),
length(queryRanges(object)),
length(querySeqs(object)),
length(score(object)),
length(symCount(object)))))
return("The lengths of targetRanges, targetSeqs,
queryRanges, querySeqs, score and symCount
must be same!")
if(!(identical(width(targetSeqs(object)), symCount(object)) &&
identical(width(querySeqs(object)), symCount(object))))
return("The widths of targetSeqs, querySeqs and
symCount must be same!")
if(!(all(width(targetRanges(object)) <= symCount(object)) &&
all(width(queryRanges(object)) <= symCount(object))))
return("The widths of targetRanges and queryRanges
must be equal or smaller than symCount.")
## Test the class
if(class(targetRanges(object)) != "GRanges")
return("'x@targetRanges' must be a GRanges instance")
if(class(queryRanges(object)) != "GRanges")
return("'x@queryRanges' must be a GRanges instance")
if(class(targetSeqs(object)) != "DNAStringSet")
return("'x@targetSeqs' must be a DNAStringSet instance")
if(class(querySeqs(object)) != "DNAStringSet")
return("'x@querySeqs' must be a DNAStringSet instance")
return(TRUE)
}
)
### -----------------------------------------------------------------
### Axt Constructor.
### Exported!
Axt <- function(targetRanges=GRanges(), targetSeqs=DNAStringSet(),
queryRanges=GRanges(), querySeqs=DNAStringSet(),
score=integer(0), symCount=integer(0),
names=NULL){
first <- targetRanges
first$seqs <- targetSeqs
last <- queryRanges
last$seqs <- querySeqs
new("Axt", first=first, second=last, NAMES=names,
elementMetadata=DataFrame(score=as.integer(score),
symCount=as.integer(symCount)))
}
### -----------------------------------------------------------------
### Axt class generics
###
setGeneric("targetRanges", function(x) standardGeneric("targetRanges"))
setGeneric("targetSeqs", function(x) standardGeneric("targetSeqs"))
setGeneric("queryRanges", function(x) standardGeneric("queryRanges"))
setGeneric("querySeqs", function(x) standardGeneric("querySeqs"))
setGeneric("symCount", function(x) standardGeneric("symCount"))
setGeneric("subAxt", function(x, chr, start, end,
select=c("target", "query"),
qSize=NULL)
standardGeneric("subAxt")
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Axt Slot getters and setters.
### Exported!
setMethod("targetRanges", "Axt", function(x) first(x))
setMethod("targetSeqs", "Axt", function(x) first(x)$seqs)
setMethod("queryRanges", "Axt", function(x) second(x))
setMethod("querySeqs", "Axt", function(x) second(x)$seqs)
setMethod("score", "Axt", function(x) mcols(x)$score)
setMethod("symCount", "Axt", function(x) mcols(x)$symCount)
setMethod("length", "Axt", function(x) length(targetRanges(x)))
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Subsetting and combining.
### Now it uses the implementation of parent class: GRangePairs
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### "show" method.
###
### 'x' must be an XString or MaskedXString object.
toSeqSnippet <- function(x, width)
{
if (width < 7L)
width <- 7L
seqlen <- length(x)
if (seqlen <= width) {
as.character(x)
} else {
w1 <- (width - 2) %/% 2
w2 <- (width - 3) %/% 2
paste(as.character(subseq(x, start=1, width=w1)),
"...",
as.character(subseq(x, end=seqlen, width=w2)),
sep="")
}
}
.axt.show_frame_line <- function(x, i, iW, tNameW, tStartW, tEndW,
qNameW, qStartW, qEndW, scoreW){
subsetTargetRanges <- targetRanges(x)[i]
subsetQueryRanges <- queryRanges(x)[i]
cat(format(i, width=iW, justify="right"), " ",
format(as.character(seqnames(subsetTargetRanges)),
width=tNameW, justify="right"), " ",
format(start(subsetTargetRanges), width=tStartW, justify="right"), " ",
format(end(subsetTargetRanges), width=tEndW, justify="right"), " ",
format(as.character(seqnames(subsetQueryRanges)),
width=qNameW, justify="right"), " ",
format(start(subsetQueryRanges), width=qStartW, justify="right"), " ",
format(end(subsetQueryRanges), width=qEndW, justify="right"), " ",
format(as.character(strand(subsetQueryRanges)),
width=1, justify="right"), " ",
format(score(x)[i], width=scoreW, justify="right"), " ",
sep=""
)
cat("\n")
snippetWidth <- getOption("width")
seq_snippet <- toSeqSnippet(targetSeqs(x)[[i]], snippetWidth)
cat(seq_snippet)
cat("\n")
seq_snippet <- toSeqSnippet(querySeqs(x)[[i]], snippetWidth)
cat(seq_snippet)
cat("\n")
}
showAxt <- function(x, margin="", half_nrow=5L){
lx <- length(x)
if(is.null((head_nrow = getOption("showHeadLines"))))
head_nrow = half_nrow
if(is.null((tail_nrow = getOption("showTailLines"))))
tail_nrow = half_nrow
iW <- nchar(as.character(lx))
if(lx < (2*half_nrow+1L) | (lx < (head_nrow+tail_nrow+1L))) {
subsetTargetRanges <- targetRanges(x)
subsetQueryRanges <- queryRanges(x)
tNameW <- max(nchar(as.character(seqnames(subsetTargetRanges))))
tStartW <- max(nchar(as.character(start(subsetTargetRanges))))
tEndW <- max(nchar(as.character(end(subsetTargetRanges))))
qNameW <- max(nchar(as.character(seqnames(subsetQueryRanges))))
qStartW <- max(nchar(as.character(start(subsetQueryRanges))))
qEndW <- max(nchar(as.character(end(subsetQueryRanges))))
scoreW <- max(nchar(as.character(score(x))))
for(i in seq_len(lx))
.axt.show_frame_line(x, i, iW, tNameW, tStartW, tEndW,
qNameW, qStartW, qEndW, scoreW)
}else{
subsetTargetRanges <- targetRanges(x)[c(1:head_nrow, (lx-tail_nrow+1L):lx)]
subsetQueryRanges <- queryRanges(x)[c(1:head_nrow, (lx-tail_nrow+1L):lx)]
tNameW <- max(nchar(as.character(seqnames(subsetTargetRanges))))
tStartW <- max(nchar(as.character(start(subsetTargetRanges))))
tEndW <- max(nchar(as.character(end(subsetTargetRanges))))
qNameW <- max(nchar(as.character(seqnames(subsetQueryRanges))))
qStartW <- max(nchar(as.character(start(subsetQueryRanges))))
qEndW <- max(nchar(as.character(end(subsetQueryRanges))))
scoreW <- max(nchar(as.character(score(x)
[c(1:head_nrow, (lx-tail_nrow+1L):lx)])))
if(head_nrow > 0){
for(i in 1:head_nrow)
.axt.show_frame_line(x, i, iW, tNameW, tStartW, tEndW,
qNameW, qStartW, qEndW, scoreW)
}
cat(format("...", width=iW, justify="right"),
format("...", width=tNameW, justify="right"),
format("...", width=tStartW, justify="right"),
format("...", width=tEndW, justify="right"),
format("...", width=qNameW, justify="right"),
format("...", width=qStartW, justify="right"),
format("...", width=qEndW, justify="right"),
format("...", width=scoreW, justify="right")
)
cat("\n")
if(tail_nrow > 0){
for(i in (lx-tail_nrow+1L):lx)
.axt.show_frame_line(x, i, iW, tNameW, tStartW, tEndW,
qNameW, qStartW, qEndW, scoreW)
}
}
}
setMethod("show", "Axt",
function(object){
lx <- length(object)
cat(" A ", class(object), " with ", length(object), " ",
ifelse(lx == 1L, "alignment pair", "alignment pairs"),
":\n", sep="")
if(lx != 0){
showAxt(object, margin=" ")
}
}
)
### -----------------------------------------------------------------
### fixCoordinates: make the coordinates of negative query alignments
### fit the positive strands.
### Exported!
setGeneric("fixCoordinates", function(x) standardGeneric("fixCoordinates"))
setMethod("fixCoordinates", "Axt", function(x){
secondRanges <- queryRanges(x)
querySeqlengths <- seqlengths(secondRanges)
if(any(is.na(querySeqlengths))){
stop("The seqlengths must exist in `x` for this operation!")
}
indexNegative <- as.logical(strand(secondRanges)=="-")
newStart <- start(secondRanges)
newEnd <- end(secondRanges)
newStart[indexNegative] <- querySeqlengths[as.character(seqnames(secondRanges[indexNegative]))] -
end(secondRanges[indexNegative]) + 1
newEnd[indexNegative] <- querySeqlengths[as.character(seqnames(secondRanges[indexNegative]))] -
start(secondRanges[indexNegative]) + 1
ranges(secondRanges) <- IRanges(start=newStart,
end=newEnd)
second(x) <- secondRanges
return(x)
})
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