Merge pull request #29 from VEuPathDB/fix-21-lonely-bin-list

allow BinLists to have only one bin
VEuPathDB · Oct 3, 2023 · a6ea003 · a6ea003
2 parents b751b81 + 4f682a1
commit a6ea003
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Showing 5 changed files with 19 additions and 44 deletions.
diff --git a/R/class-Bin.R b/R/class-Bin.R
@@ -97,14 +97,16 @@ check_bin_range_list <- function(object) {
       errors <- c(errors, msg)
     }
 
-    # no overlapping ranges
-    sortOrder <- order(binStarts)
-    binStarts <- binStarts[sortOrder]
-    binEnds <- binEnds[sortOrder]
-    binValues <- binValues[sortOrder]
-    if (any(binStarts[2:length(binStarts)] < binEnds[1:(length(binEnds)-1)], na.rm=TRUE)) {
-      msg <- "Some provided bins overlap."
-      errors <- c(errors, msg) 
+    # no overlapping ranges (only useful when multiple bins in the BinList)
+    if (length(binStarts) > 1) {
+      sortOrder <- order(binStarts)
+      binStarts <- binStarts[sortOrder]
+      binEnds <- binEnds[sortOrder]
+      binValues <- binValues[sortOrder]
+      if (any(binStarts[2:length(binStarts)] < binEnds[1:(length(binEnds)-1)], na.rm=TRUE)) {
+        msg <- "Some provided bins overlap."
+        errors <- c(errors, msg) 
+      }
     }
   }
 

diff --git a/man/as.Date-Bin-method.Rd b/man/as.Date-Bin-method.Rd
diff --git a/man/as.Date-BinList-method.Rd b/man/as.Date-BinList-method.Rd
diff --git a/man/getVariableSpec.Rd b/man/getVariableSpec.Rd
diff --git a/tests/testthat/test-class-Bin.R b/tests/testthat/test-class-Bin.R
@@ -46,4 +46,12 @@ test_that("BinList validation works", {
 
   # none have start or ends or value and thats ok
   expect_equal(length(BinList(S4Vectors::SimpleList(c(bin6, bin7)))), 2)
+})
+
+test_that("BinList can handle a list of one", {
+
+  bin1 <- Bin(binStart=1, binEnd=2, binLabel='1-2')
+  lonelyBinList <- BinList(S4Vectors::SimpleList(c(bin1)))
+  expect_equal(length(lonelyBinList), 1)
+
 })