From f24f59c93c54ecce1e3d28554476b46966330252 Mon Sep 17 00:00:00 2001
From: junikimm717 <junikimm717@gmail.com>
Date: Mon, 19 Jul 2021 23:20:39 -0400
Subject: [PATCH] added verbose output

---
 README.md        |  7 ++++++-
 src/script.def.R | 33 ++++++++++++++++++++++++++++-----
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index a6db25c..0ab1911 100644
--- a/README.md
+++ b/README.md
@@ -7,12 +7,17 @@ choosing (preferably halogenated compounds).
 ## Installation
 
 The script has the following dependencies:
-- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget) (This should be installed through the devtools package)
+- latest version of the [Nontarget R Package](https://github.com/blosloos/nontarget) 
+(This should be installed
+through the devtools package)
 - [purrr](https://www.rdocumentation.org/packages/purrr/versions/0.2.5)
 - [enviPat](https://rdocumentation.org/packages/enviPat/versions/2.2)
 - [stringr](https://www.rdocumentation.org/packages/stringr/versions/1.4.0)
 - [parallel](https://www.rdocumentation.org/packages/parallel/versions/3.6.2)
 
+Before running/configuring the script, call `make` while in the `/src`
+directory or copy `script.def.R` to `script.R`.
+
 ## Additional Notes
 
 In order to make the search run in linear time, as of right now, the entire
diff --git a/src/script.def.R b/src/script.def.R
index f4e0555..220ba3e 100644
--- a/src/script.def.R
+++ b/src/script.def.R
@@ -31,8 +31,9 @@ columns.spectra <- "Spectra_Number"
 output.intensities <- 5
 
 # Verbose output
-verbose.enable <- TRUE
-verbose.outputdir <- "/output/dir"
+verbose.enable <- FALSE
+# output directory must already exist.
+verbose.outputdir <- "/path/to/directory"
 
 
 # Script #####################################################################
@@ -150,6 +151,14 @@ derive.frame <- function(result) {
     return(res)
 }
 
+verbose.dump <- function(result) {
+    path <- file.path(verbose.outputdir, paste(derive.fragment(result), ".txt",
+                                           sep=""))
+    sink(path)
+    dput(result)
+    sink()
+}
+
 # Execution ##################################################################
 
 ## Set all of the intervals ##################################################
@@ -177,14 +186,28 @@ results <- mclapply(use, diagnostics, mc.cores=use_cores)
 
 results.positive <- Filter(function(x) positive(x), results)
 
+# print to files if verbose output requested
+
+if (verbose.enable) {
+    if (!dir.exists(verbose.outputdir)) {
+        stop(str_interp("Directory $[s]{dir} does not exist", 
+                        list(dir=verbose.outputdir)))
+    }
+    res <- readline(prompt=paste("Are you sure you want to overwrite files in ", 
+                                 verbose.outputdir, "? [y/N] "))
+    if (res != "y") {
+        stop("Process aborted.")
+    }
+    print(paste("printing output to ", verbose.outputdir))
+    mapply(verbose.dump, results.positive)
+}
+
 result.frame <- mapply(derive.frame, results.positive)
 result.fragment <- mapply(derive.fragment, results.positive)
 result.iso <- mapply(derive.iso, results.positive)
 result.intensity <- mapply(derive.intensity, results.positive)
 result.average <- mapply(derive.average, results.positive)
 
-for (x in result.frame) {
-    print(x)
-}
+print(result.fragment)
 
 ##############################################################################