Merge pull request #28 from VEuPathDB/fix-27-asnumeric-bins

add as.numeric for bins

NAMESPACE

@@ -92,6 +92,7 @@ exportClasses(VariableMetadataList)
 exportClasses(VariableSpec)
 exportClasses(VariableSpecList)
 exportMethods(as.data.table)
+exportMethods(as.numeric)
 exportMethods(asJSON)
 exportMethods(findAllColNames)
 exportMethods(findColNamesByPredicate)

R/methods-Bin.R

@@ -42,4 +42,37 @@ setMethod("whichValuesInBinList", signature("BinList"), function(values, binList
   inBin <- Reduce(`+`, lapply(binList, whichValuesInBin, values = values))
   return (as.logical(inBin))
 
+})
+
+
+#' Convert a Bin with character start and end values to numeric
+#' 
+#' Given a Bin object with binStart and binEnd of class character,
+#' convert both to numeric and return the Bin.
+#' 
+#' @param x Bin
+#' @return Bin
+#' @export 
+setMethod("as.numeric", signature("Bin"), function(x) {
+  binNumeric <- Bin(
+    binStart = as.numeric(x@binStart),
+    binEnd = as.numeric(x@binEnd),
+    binLabel = x@binLabel,
+    value = x@value
+  )
+  return(binNumeric)
+})
+
+
+#' Convert bins in a BinList with character start and end values to numeric
+#' 
+#' Given a BinList object containing Bins that may have a character binStart or binEnd,
+#' convert all binStarts and binEnds to numeric and return the BinList.
+#' 
+#' @param x BinList
+#' @return BinList
+#' @export 
+setMethod("as.numeric", signature("BinList"), function(x) {
+  binListNumeric <-  BinList(lapply(x, as.numeric))
+  return(binListNumeric)
 })

tests/testthat/test-methods-Bin.R

@@ -39,3 +39,38 @@ test_that("whichValuesInBinList works", {
   expect_equal(inBin, c(FALSE, TRUE, FALSE, TRUE, FALSE, FALSE))
 
 })
+
+test_that("converting string bins to numeric bins is successful", {
+
+
+  # Test for regular bins
+  stringBin1 <- Bin(binStart='1', binEnd='2', binLabel='1-2', value = 2)
+
+  numericBin1 <- as.numeric(stringBin1)
+  expect_equal(class(numericBin1@binStart), 'numeric')
+  expect_equal(class(numericBin1@binEnd), 'numeric')
+  expect_equal(numericBin1@binLabel, stringBin1@binLabel)
+  expect_equal(numericBin1@value, stringBin1@value)
+
+
+
+  stringBin2 <- Bin(binStart='2.00001', binEnd='2e10', binLabel='2-2e10')
+
+  numericBin2 <- as.numeric(stringBin2)
+  expect_equal(class(numericBin2@binStart), 'numeric')
+  expect_equal(class(numericBin2@binEnd), 'numeric')
+  expect_equal(numericBin2@binLabel, stringBin2@binLabel)
+  expect_equal(numericBin2@value, stringBin2@value)
+
+
+  # Test for BinLists
+  stringBin3 <- Bin(binStart='2e11', binEnd='2e12', binLabel='2e11-2e12')
+  stringBinList1 <- BinList(S4Vectors::SimpleList(c(stringBin2, stringBin3)))
+
+  numericBinList1 <- as.numeric(stringBinList1)
+  expect_equal(unlist(lapply(numericBinList1, function(x) {class(x@binStart)})), c('numeric','numeric'))
+  expect_equal(unlist(lapply(numericBinList1, function(x) {class(x@binEnd)})), c('numeric','numeric'))
+
+
+})
+