From a6ea1d117f59791e3b7948d462cb6ee7b4999f72 Mon Sep 17 00:00:00 2001
From: junikimm717 <junikimm717@gmail.com>
Date: Wed, 30 Jun 2021 14:03:40 -0400
Subject: [PATCH] began testing

---
 .gitignore       |  2 ++
 specification.md |  3 +++
 src/script.def.R | 31 ++++++++++++++++++++++---------
 3 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3da05d0..2c5219a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
 .DS_Store
 /data
+/.RData
+/.Rhistory
diff --git a/specification.md b/specification.md
index 23cc09c..ddc03f7 100644
--- a/specification.md
+++ b/specification.md
@@ -48,6 +48,8 @@ isotopes.
 - No statistical testing required (check if it is chlorine or bromine)
 
 - Isotopes to check (Carbon, Sulfur, Chlorine, Bromine all have n+2) (check make.isos object)
+
+- Tweak parameters (but also put them into a slideshow/record, see how good the results are).
 - **set all rules to false**
 
 ## Isotopes
@@ -56,3 +58,4 @@ isotopes.
 - Part of the reasoning can be attributed to differences.
 - Forseeable future, adapt to different isotopes.
 - Capture multiple outputs of different isotopes.
+
diff --git a/src/script.def.R b/src/script.def.R
index 5c96dd0..93bf9dd 100644
--- a/src/script.def.R
+++ b/src/script.def.R
@@ -1,32 +1,32 @@
 library("nontarget")
 library("purrr")
-library("funprog")
+#library("funprog")
 library("enviPat")
 library("stringr")
 library("parallel")
 
 # Configurations #############################################################
 # file : decides which file to read in data from #############################
-file <- "/path/to/file"
+file <- "path/to/file"
+
+# check cluster 2846
 
 search_isos <- c("13C", "37Cl")
 
+
 # Minimum size of a cluster
 
 min_cluster_size <- 3
 
 # Number of cores to be used (will be adjusted if not possible)
-used_cores <- 3
-
-##############################################################################
+use_cores <- 6 ##############################################################################
 # Read in the Table ##########################################################
-table <- read.table(file, header=TRUE, sep=",")
+table <- read.table(file, header=TRUE, sep="\t")
 
 # Organize the tables by number ##############################################
 fragments <- max(table[,"Spectra_Number"])
 
 
-
 # The algorithm below guarantees linear complexity of looking up data points.#
 
 # set use_cores to safe amount
@@ -80,7 +80,20 @@ isos <- make.isos(isotopes,use_isotopes=search_isos,
 
 diagnostics <- function(fragment) {
     points <- getdataframe(fragment)
-    ptrn <- pattern.search(points, isos)
+    ptrn <- pattern.search(
+        points,
+        isos,
+        cutint=100000,
+        rttol=c(-0.2,0.2),
+        mztol=1000,
+        mzfrac=1.0,
+        ppm=TRUE,
+        inttol=0.2,
+        # Do not modify anything below.
+        rules=rep(FALSE, 11),
+        deter=FALSE,
+        entry=50
+    );
     return(ptrn)
 }
 
@@ -88,7 +101,7 @@ use <- Filter(function(x) usable[x], 1:fragments)
 
 results <- mclapply(use, diagnostics, mc.cores=use_cores)
 
+
 # Incomplete: Make the analysis more resiliant to different sorting.
-# Incomplete: How to process results. (is it actually supposed to be all negatives?)
 
 ##############################################################################