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as.SparseSimilarityMatrix.matrix <- function(s, lower=-Inf)
{
if (!is(s, "matrix"))
{
s <- try(as(s, "matrix"))
if (is(s, "try-error"))
stop("cannot cast 's' (class '", class(s), "') to class 'matrix'")
}
if (nrow(s) != ncol(s) && ncol(s) != 3)
stop("matrix 's' must be quadratic or have 3 columns")
if (nrow(s) == ncol(s))
{
sel <- which(s > lower, arr.ind=TRUE)
remElem <- which(sel[, 1] == sel[, 2])
if (length(remElem) > 0)
sel <- sel[-remElem, , drop=FALSE]
if (nrow(sel) == 0)
S <- new("dgTMatrix", Dim=dim(s))
else
S <- new("dgTMatrix", Dim=dim(s),
i=as.integer(sel[, 1] - 1),
j=as.integer(sel[, 2] - 1),
x=s[sel])
}
else
{
if (min(s[, 1:2]) <= 0)
stop("indices in 's' must be >= 1")
if (any(s[, 1:2] != floor(s[, 1:2])))
stop("indices in 's' must be natural numbers")
remElem <- which(s[, 1] == s[, 2] | s[, 3] <= lower)
if (length(remElem) > 0)
s <- s[-remElem, , drop=FALSE]
if (nrow(s) == 0)
S <- new("dgTMatrix", Dim=as.integer(c(0, 0)))
else
{
N <- max(s[, 1:2])
S <- new("dgTMatrix", Dim=as.integer(c(N, N)),
i=as.integer(s[, 1] - 1),
j=as.integer(s[, 2] - 1),
x=s[, 3])
}
}
S
}
setMethod("as.SparseSimilarityMatrix", signature(s="matrix"),
as.SparseSimilarityMatrix.matrix)
setMethod("as.SparseSimilarityMatrix", signature(s="Matrix"),
as.SparseSimilarityMatrix.matrix)
as.SparseSimilarityMatrix.sparseMatrix <- function(s, lower=-Inf)
{
if (nrow(s) != ncol(s))
stop("argument 's' must be quadratic similarity matrix")
if (!is(s, "dgTMatrix"))
{
s <- try(as(as(s, "TsparseMatrix"), "dgTMatrix"))
if (is(s, "try-error"))
stop("cannot cast 's' (class '", class(s),
"') to class 'dgTMatrix'")
}
remElem <- which(s@i == s@j | s@x <= lower)
if (length(remElem) > 0)
{
s@i <- s@i[-remElem]
s@j <- s@j[-remElem]
s@x <- s@x[-remElem]
}
s
}
setMethod("as.SparseSimilarityMatrix", signature(s="sparseMatrix"),
as.SparseSimilarityMatrix.sparseMatrix)
as.DenseSimilarityMatrix.matrix <- function(s, fill=-Inf)
{
if (!is(s, "matrix"))
{
s <- try(as(s, "matrix"))
if (is(s, "try-error"))
stop("cannot cast 's' (class '", class(s), "') to class 'matrix'")
}
if (ncol(s) != 3)
stop("'s' must be a matrix with 3 columns")
if (min(s[, 1:2]) <= 0)
stop("indices in 's' must be >= 1")
if (any(s[, 1:2] != floor(s[, 1:2])))
stop("indices in 's' must be natural numbers")
N <- max(s[, 1:2])
S <- matrix(fill, N, N)
S[s[, 1] + N * (s[, 2] - 1)] <- s[, 3]
S
}
setMethod("as.DenseSimilarityMatrix", signature(s="matrix"),
as.DenseSimilarityMatrix.matrix)
setMethod("as.DenseSimilarityMatrix", signature(s="Matrix"),
as.DenseSimilarityMatrix.matrix)
as.DenseSimilarityMatrix.sparseMatrix <- function(s, fill=-Inf)
{
if (nrow(s) != ncol(s))
stop("argument 's' must be quadratic similarity matrix")
if (!is(s, "dgTMatrix"))
{
s <- try(as(as(s, "TsparseMatrix"), "dgTMatrix"))
if (is(s, "try-error"))
stop("cannot cast 's' (class '", class(s),
"') to class 'dgTMatrix'")
}
N <- nrow(s)
S <- matrix(fill, N, N)
S[(s@i + 1) + N * s@j] <- s@x
S
}
setMethod("as.DenseSimilarityMatrix", signature(s="sparseMatrix"),
as.DenseSimilarityMatrix.sparseMatrix)
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