From 7d6044143bd0d3a31bbbaf8f904b18bdd74da792 Mon Sep 17 00:00:00 2001
From: Taha Ahmed <taha@asks2>
Date: Thu, 16 Feb 2012 22:38:42 +0100
Subject: [PATCH] Implemented a switch (arg) that allows new behaviour
 (optional) ...

without breaking code that relies on old behaviour (default).
---
 ProvideSampleId.R   | 25 +++++++++++++++----------
 ProvideSampleId.tex | 12 +++++++-----
 2 files changed, 22 insertions(+), 15 deletions(-)

diff --git a/ProvideSampleId.R b/ProvideSampleId.R
index b3a9e99..1469185 100644
--- a/ProvideSampleId.R
+++ b/ProvideSampleId.R
@@ -1,16 +1,21 @@
-ProvideSampleId <- function (pathexpfile) {
+ProvideSampleId <- function (pathexpfile, implementation = "filename") {
    # Returns a "unique" sample ID when supplied 
    # with a path to an experimental file.
-   ## Note: the sample ID must derive directly from the file or path.
+   # The second arg is optional, defaults to "old" behaviour, 
+   # but can be set to "dirname" for another behaviour 
+   # The second arg was added so as not to break older code.
+   ## Note to myself: the sample ID must derive directly from the file or path.
    
-   # basename(dirname()) returns the name of the lowest sub-directory
-   # split()[[1]][2] splits the dirname at the hyphen and returns the sampleid
-   sampleid <- strsplit(x = basename(dirname(pathexpfile)),
-                        split = "-")[[1]][2]
-   
-#    # basename() returns the filename sans path
-#    # sub() returns the filename sans extension
-#    sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
+   if (implementation == "dirname") {   
+      # basename(dirname()) returns the name of the lowest sub-directory
+      # split()[[1]][2] splits the dirname at the hyphen and returns the sampleid
+      sampleid <- strsplit(x = basename(dirname(pathexpfile)),
+                           split = "-")[[1]][2]
+   } else {
+      # basename() returns the filename sans path
+      # sub() returns the filename sans extension
+      sampleid <- sub("\\.[\\w]+$", "", basename(pathexpfile), perl = TRUE)
+   }
    
    #### The code below is the old ProvideSampleId() function   
    #  ### OBS! Only very rudimentary error-checking.
diff --git a/ProvideSampleId.tex b/ProvideSampleId.tex
index c7d96c3..6716d20 100644
--- a/ProvideSampleId.tex
+++ b/ProvideSampleId.tex
@@ -1,6 +1,8 @@
-The following function, \Rfun{ProvideSampleId()}, strives to supply a unique sample ID from any path supplied to it. Of course, a certain structure on the part of the path and filename are assumed, namely:
-\begin{itemize}
-\item That the filename (not including the extension) consists of three alphanumeric strings separated by hyphens.
-\item That\ldots
-\end{itemize}
+The aim with \Rfun{ProvideSampleId()} is to supply a unique sample ID from any full path supplied to it.
+
+The function solves this using two approaches:
+\begin{enumerate}
+\item using only the filename,
+\item using only the name of the subdirectory in question.
+\end{enumerate}