Fix trimws generic/methods

o Fix trimws generic/methods with useAsDefault (see issue #75) <2016-02-02 Tue> o add exprs,MSnSet-method alias (since exprs is now exported) <2016-02-02 Tue>
lgatto · Feb 2, 2016 · 3c07de7 · 3c07de7
1 parent f3125a8
commit 3c07de7
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Showing 5 changed files with 24 additions and 6 deletions.
diff --git a/NEWS b/NEWS
@@ -1,6 +1,10 @@
 CHANGES IN VERSION 1.19.11
 --------------------------
-
+ o Fix trimws generic/methods with useAsDefault (see issue #75)
+   <2016-02-02 Tue>
+ o add exprs,MSnSet-method alias (since exprs is now exported)
+   <2016-02-02 Tue>
+
 CHANGES IN VERSION 1.19.10
 --------------------------
  o export exprs, fvarLabels, and sampleNames[<-] <2016-01-30 Sat>

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -122,4 +122,10 @@ setGeneric("fnamesIn", function(x, y, ...) standardGeneric("fnamesIn"))
 ## setGeneric("chromatogram", function(object, ...) standardGeneric("chromatogram"))
 
 ## base::trimws
-setGeneric("trimws", function(x, ...) standardGeneric("trimws"))
+.trimws.useAsDefault <- function (x, which = c("both", "left", "right"), ...)
+    base::trimws(x, which, ...)
+
+setGeneric("trimws", signature = "x",
+    function(x, which = c("both", "left", "right"), ...)
+        standardGeneric("trimws"),
+    useAsDefault=.trimws.useAsDefault)
diff --git a/R/utils.R b/R/utils.R
@@ -876,17 +876,17 @@ utils.colSd <- function(x, na.rm = TRUE) {
 
 
 setMethod("trimws", "data.frame",
-          function(x, ...) {
+          function(x, which, ...) {
               for (i in 1:ncol(x)) {
                   if (inherits(x[, i], "character"))
-                      x[, i] <- base::trimws(x[, i], ...)
+                      x[, i] <- base::trimws(x[, i], which)
               }
               x
           })
 
 setMethod("trimws", "MSnSet",
-          function(x, ...) {
-              fData(x) <- trimws(fData(x), ...)
+          function(x, which, ...) {
+              fData(x) <- trimws(fData(x), which, ...)
               x <- logging(x, "Trimmed featureData white spaces")
               x
           })
diff --git a/man/MSnSet-class.Rd b/man/MSnSet-class.Rd
@@ -6,6 +6,7 @@
 \alias{MSnSet}
 
 %% TODO add methods
+\alias{exprs,MSnSet-method}
 \alias{dim,MSnSet-method}
 \alias{fileNames,MSnSet-method}
 %%\alias{normalise,MSnSet-method}

diff --git a/tests/testthat/test_trimws.R b/tests/testthat/test_trimws.R
@@ -30,3 +30,10 @@ test_that("trimws data.frame vs MSnSet ", {
     dfr2 <- trimws(fData(dunkley2006))
     expect_identical(fData(d2), dfr2)
 })
+
+test_that("check that base:::trimws still works", {
+    expect_equal(trimws("  xx  "), "xx")
+    expect_equal(trimws("  xx  ", "left"), "xx  ")
+    expect_equal(trimws("  xx  ", "right"), "  xx")
+})
+