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## apetools.R (2018-06-13)
## APE Tools
## Copyright 2017-2018 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
.file.extensions <-
list(clustal = "aln", fasta = c("fas", "fasta", "fa"),
fastq = c("fq", "fastq"), newick = c("nwk", "newick", "tre", "tree"),
nexus = c("nex", "nexus"), phylip = "phy")
Xplorefiles <- function(from = "HOME", recursive = TRUE, ignore.case = TRUE)
{
if (from == "HOME") from <- Sys.getenv("HOME")
FILES <- list.files(path = from, recursive = recursive, full.names = TRUE)
ext <- if (exists(".file.extensions", envir = .PlotPhyloEnv))
get(".file.extensions", envir = .PlotPhyloEnv)
else .file.extensions
res <- vector("list", length(ext))
names(res) <- names(ext)
for (i in seq_along(res)) {
e <- paste0("\\.", ext[[i]], "$")
if (length(e) > 1) e <- paste(e, collapse = "|")
x <- grep(e, FILES, ignore.case = ignore.case, value = TRUE)
res[[i]] <- data.frame(File = x, Size = file.size(x),
stringsAsFactors = FALSE)
}
res
}
editFileExtensions <- function()
{
foo <- function(x) {
n <- length(x)
if (n < m) x[(n + 1):m] <- NA
x
}
res <- if (exists(".file.extensions", envir = .PlotPhyloEnv))
get(".file.extensions", envir = .PlotPhyloEnv)
else .file.extensions
m <- max(lengths(res, FALSE))
res <- lapply(res, foo)
res <- as.data.frame(res, stringsAsFactors = FALSE)
res <- edit(res)
res <- lapply(res, function(x) x[!is.na(x)])
assign(".file.extensions", res, envir = .PlotPhyloEnv)
}
bydir <- function(x)
{
nofile <- which(sapply(x, nrow) == 0)
if (length(nofile)) x <- x[-nofile]
if (!length(x)) {
cat("No file\n")
return(invisible(NULL))
}
for (i in seq_along(x)) x[[i]]$Type <- names(x)[i]
x <- do.call(rbind, x)
x <- x[order(x$File), ]
SPLIT <- strsplit(x$File, "/")
LL <- lengths(SPLIT)
foo <- function(i, PATH) {
K <- grep(paste0("^", PATH, "/"), x$File)
sel <- intersect(K, which(LL == i + 1L))
if (length(sel)) {
y <- x[sel, ]
y$File <- gsub(".*/", "", y$File)
cat("\n", PATH, "/\n", sep = "")
print(y, row.names = FALSE)
}
if (length(sel) < length(K)) {
d <- setdiff(K, sel)
subdir <- unlist(lapply(SPLIT[d], "[", i + 1L))
for (z in unique(subdir))
foo(i + 1L, paste(PATH, z, sep = "/"))
}
}
top <- unlist(lapply(SPLIT, "[", 1L))
for (z in unique(top)) foo(1L, z)
}
Xplor <- function(from = "HOME")
{
ext <- if (exists(".file.extensions", envir = .PlotPhyloEnv))
get(".file.extensions", envir = .PlotPhyloEnv)
else .file.extensions
OUT <- paste0(tempfile(), ".html")
mycat <- function(...) cat(..., sep = "", file = OUT, append = TRUE)
FILES <- Xplorefiles(from = from)
filetypes <- names(FILES)
## nb of files of each type:
NR <- sapply(FILES, nrow)
## HTML header
mycat('<html><title>Files Sorted by Type</title></head>')
## build the TOC
mycat('<h2>File types searched:</h2>')
mycat('<TABLE border=0>')
mycat('<tr><th align="center"> Type </th><th align="center"> Number of files </th><th align="center"> Extensions* </th></tr>')
for (type in filetypes) {
mycat('<tr><td><a href=#', type, '>', type, '</a></td><td align="center">', NR[type],
'</td><td align="center">', paste(paste0(".", ext[[type]]), collapse = " "), '</td></tr>')
}
mycat('</TABLE>')
mycat('<br>*Case-independent<br>To change the files extensions, type in R: <font face = "courier">editFileExtensions()</font><br>')
if (all(NR == 0)) {
browseURL(OUT)
return(invisible(NULL))
}
OUTBYDIR <- paste0(tempfile(), ".html")
sink(OUTBYDIR)
cat('<html><title>Files Sorted by Directory</title></head>')
.bydir.html(FILES)
cat('</html>')
sink(NULL)
mycat('<br><a target="blank" href=', OUTBYDIR, '><h2>Files sorted by directory (in new tab)</h2></a><br>')
for (type in filetypes) {
nr <- NR[type]
mycat('<a name=', type, '></a><h1>', toupper(type), '</h1>')
if (nr == 0) {
mycat('no file of this type')
next
}
DF <- FILES[[type]]
mycat('<TABLE border=1>')
mycat('<tr><th> File name </th><th align="center"> Size (KB) </th></tr>')
for (i in 1:nr)
mycat('<tr><td><a href="file://', DF[i, 1], '">', DF[i, 1],
'</a></td><td align="right">', round(DF[i, 2]/1000, 1), '</td></tr>')
mycat('</TABLE>')
}
mycat('</html>')
browseURL(OUT)
}
.bydir.html <- function(x)
{
nofile <- which(sapply(x, nrow) == 0)
if (length(nofile)) x <- x[-nofile]
if (!length(x)) return(NULL)
for (i in seq_along(x)) x[[i]]$Type <- names(x)[i]
x <- do.call(rbind, x)
x <- x[order(x$File), ]
SPLIT <- strsplit(x$File, "/")
LL <- lengths(SPLIT)
foo <- function(i, PATH) {
K <- grep(paste0("^", PATH, "/"), x$File)
sel <- intersect(K, which(LL == i + 1L))
if (length(sel)) {
y <- x[sel, ]
y$File <- gsub(".*/", "", y$File)
cat('<h2><a href="file://', PATH, '">', PATH, '/</a></h2>', sep = "")
cat('<TABLE border=1>')
cat('<tr><th> File </th><th align="center"> Size (KB) </th><th align="center"> Type </th></tr>')
for (i in 1:nrow(y))
cat('<tr><td><a href="file://', PATH, '/', y[i, 1], '">', y[i, 1],
'</a></td><td align="right">', round(y[i, 2]/1000, 1),
'</td><td align="right">', y[i, 3], '</td></tr>', sep = "")
cat('</TABLE><br>')
}
if (length(sel) < length(K)) {
d <- setdiff(K, sel)
subdir <- unlist(lapply(SPLIT[d], "[", i + 1L))
for (z in unique(subdir))
foo(i + 1L, paste(PATH, z, sep = "/"))
}
}
top <- unlist(lapply(SPLIT, "[", 1L))
for (z in unique(top)) foo(1L, z)
}
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