From 4f682a16729c69fda70648f78e778e6945fa4076 Mon Sep 17 00:00:00 2001
From: asizemore <annsize@seas.upenn.edu>
Date: Tue, 3 Oct 2023 06:24:03 -0400
Subject: [PATCH] allow BinLists to have only one bin

---
 R/class-Bin.R                   | 18 ++++++++++--------
 man/as.Date-Bin-method.Rd       | 18 ------------------
 man/as.Date-BinList-method.Rd   | 17 -----------------
 man/getVariableSpec.Rd          |  2 +-
 tests/testthat/test-class-Bin.R |  8 ++++++++
 5 files changed, 19 insertions(+), 44 deletions(-)
 delete mode 100644 man/as.Date-Bin-method.Rd
 delete mode 100644 man/as.Date-BinList-method.Rd

diff --git a/R/class-Bin.R b/R/class-Bin.R
index 82c65d1..a2302e8 100644
--- 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
deleted file mode 100644
index 6a064aa..0000000
--- a/man/as.Date-Bin-method.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/methods-Bin.R
-\name{as.Date,Bin-method}
-\alias{as.Date,Bin-method}
-\title{Convert a Bin's start and end values to dates}
-\usage{
-\S4method{as.Date}{Bin}(x)
-}
-\arguments{
-\item{x}{Bin}
-}
-\value{
-Bin
-}
-\description{
-Given a Bin object with slots binStart and binEnd, convert
-the binStart and binEnd to dates
-}
diff --git a/man/as.Date-BinList-method.Rd b/man/as.Date-BinList-method.Rd
deleted file mode 100644
index 0d5138c..0000000
--- a/man/as.Date-BinList-method.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/methods-Bin.R
-\name{as.Date,BinList-method}
-\alias{as.Date,BinList-method}
-\title{Convert BinList bin starts and ends to dates}
-\usage{
-\S4method{as.Date}{BinList}(x)
-}
-\arguments{
-\item{x}{BinList}
-}
-\value{
-BinList
-}
-\description{
-Given a BinList object, convert all binStarts and binEnds to dates and return the BinList.
-}
diff --git a/man/getVariableSpec.Rd b/man/getVariableSpec.Rd
index e607e12..a7978f6 100644
--- a/man/getVariableSpec.Rd
+++ b/man/getVariableSpec.Rd
@@ -4,7 +4,7 @@
 \alias{getVariableSpec}
 \title{get a VariableSpec}
 \usage{
-getVariableSpec(object)
+getVariableSpec(object, ...)
 }
 \arguments{
 \item{object}{An object containing a veupathUtils::VariableSpec}
diff --git a/tests/testthat/test-class-Bin.R b/tests/testthat/test-class-Bin.R
index f2b3408..74393c6 100644
--- 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)
+
 })
\ No newline at end of file