Squeeze the IPosRanges class right below IntegerRanges in the class

hierarchy. IRanges, IPos, NCList, and GroupingRanges are now direct subclasses of IPosRanges instead of direct subclasses of IntegerRanges. Views remains a direct subclass of IntegerRanges: Ranges ^ | IntegerRanges ^ ^ | | Views IPosRanges ^ ^ ^ ^ / | | \ / | | \ IRanges IPos NCList GroupingRanges
Bioconductor · Feb 8, 2018 · 62ee74a · 62ee74a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,7 +7,7 @@ Description: Provides efficient low-level and highly reusable S4
 	neighbors. Defines efficient list-like classes for storing,
 	transforming and aggregating large grouped data, i.e., collections
 	of atomic vectors and DataFrames.
-Version: 2.13.22
+Version: 2.13.23
 Encoding: UTF-8
 Author: H. Pagès, P. Aboyoun and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
@@ -28,8 +28,8 @@ Collate: range-squeezers.R
 	AtomicList-class.R
 	AtomicList-utils.R
 	Ranges-and-RangesList-classes.R
-	IntegerRanges-class.R
-	IntegerRanges-comparison.R
+	IPosRanges-class.R
+	IPosRanges-comparison.R
 	IntegerRangesList-class.R
 	IRanges-class.R
 	IRanges-constructor.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -32,12 +32,13 @@ exportClasses(
     FactorList, SimpleFactorList,
 
     ## Ranges-and-RangesList-classes.R:
-    Ranges, Pos,
+    Ranges, IntegerRanges, Pos,
     RangesList, SimpleRangesList,
+    IntegerRangesList, SimpleIntegerRangesList,
     PosList, SimplePosList,
 
-    ## IntegerRanges-class.R:
-    IntegerRanges,
+    ## IPosRanges-class.R:
+    IPosRanges,
 
     ## IntegerRangesList-class.R
     IntegerRangesList, SimpleIntegerRangesList,
@@ -272,7 +273,7 @@ export(
     showAsCell,
     mstack,
 
-    ## IntegerRanges-class.R:
+    ## Ranges-and-RangesList-classes.R:
     mid,
     isNormal, whichFirstNotNormal,
 

diff --git a/R/Grouping-class.R b/R/Grouping-class.R
@@ -424,15 +424,15 @@ setMethod("high2low", "ANY",
 ###
 ### A GroupingRanges object represents a "block-grouping", that is, a
 ### grouping where each group is a block of adjacent elements in the original
-### collection of objects. GroupingRanges objects support the IntegerRanges
+### collection of objects. GroupingRanges objects support the IPosRanges
 ### API (e.g. start/end/width) in addition to the Grouping API.
 ###
 
 setClass("GroupingRanges",
-    ## We put IntegerRanges before Grouping so GroupingRanges objects inherit
-    ## the "show" method for IntegerRanges objects instead of the method for
+    ## We put IPosRanges before Grouping so GroupingRanges objects inherit
+    ## the "show" method for IPosRanges objects instead of the method for
     ## Grouping objects.
-    contains=c("IntegerRanges", "Grouping"),
+    contains=c("IPosRanges", "Grouping"),
     representation("VIRTUAL")
 )
 

diff --git a/R/IPos-class.R b/R/IPos-class.R
@@ -5,7 +5,7 @@
 
 
 setClass("IPos",
-    contains=c("Pos", "IntegerRanges"),
+    contains=c("Pos", "IPosRanges"),
     representation(
         pos_runs="IRanges"
     )

diff --git a/R/IntegerRanges-class.R → R/IPosRanges-class.R b/R/IntegerRanges-class.R → R/IPosRanges-class.R
@@ -1,45 +1,35 @@
 ### =========================================================================
-### IntegerRanges objects
+### IPosRanges objects
 ### -------------------------------------------------------------------------
 ###
-### IntegerRanges is a virtual class that serves as the base for all integer
-### range containers. Conceptually integer ranges are closed, one-dimensional
+### The ranges in an IPosRanges derivative are closed, one-dimensional
 ### intervals with integer end points and on the domain of integers.
 ###
+### The direct IPosRanges subclasses defined in the IRanges package are:
+### IRanges, IPos, NCList, and GroupingRanges.
 
 
-setClass("IntegerRanges",
-    contains="Ranges",
+setClass("IPosRanges",
+    contains="IntegerRanges",
     representation("VIRTUAL")
 )
 
 
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### Getters/setters.
-###
-
-setMethod("update", "IntegerRanges",
-    function(object, ...)
-        as(update(as(object, "IRanges"), ...), class(object))
-)
-
-
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Validity.
 ###
 
 ### The checking of the names(x) is taken care of by the validity method for
 ### Vector objects.
-
-setValidity2("IntegerRanges", validate_Ranges)
+setValidity2("IPosRanges", validate_Ranges)
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### Coercion.
 ###
 
 ### Propagate the names.
-setMethod("as.character", "IntegerRanges",
+setMethod("as.character", "IPosRanges",
     function(x)
     {
         if (length(x) == 0L)
@@ -56,18 +46,18 @@ setMethod("as.character", "IntegerRanges",
 
 ### The as.factor() generic doesn't have the ... argument so this method
 ### cannot support the 'ignore.strand' argument.
-setMethod("as.factor", "IntegerRanges",
+setMethod("as.factor", "IPosRanges",
     function(x)
         factor(as.character(x), levels=as.character(sort(unique(x))))
 )
 
-setMethod("as.matrix", "IntegerRanges",
+setMethod("as.matrix", "IPosRanges",
     function(x, ...)
         matrix(data=c(start(x), width(x)), ncol=2,
                dimnames=list(names(x), NULL))
 )
 
-.as.data.frame.IntegerRanges <- function(x, row.names=NULL, optional=FALSE, ...)
+.as.data.frame.IPosRanges <- function(x, row.names=NULL, optional=FALSE, ...)
 {
     if (!(is.null(row.names) || is.character(row.names)))
         stop("'row.names' must be NULL or a character vector")
@@ -81,14 +71,14 @@ setMethod("as.matrix", "IntegerRanges",
     ans$names <- names(x)
     ans
 }
-setMethod("as.data.frame", "IntegerRanges", .as.data.frame.IntegerRanges)
+setMethod("as.data.frame", "IPosRanges", .as.data.frame.IPosRanges)
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### show()
 ###
 
-.make_naked_matrix_from_IntegerRanges <- function(x)
+.make_naked_matrix_from_IPosRanges <- function(x)
 {
     x_len <- length(x)
     x_mcols <- mcols(x)
@@ -104,7 +94,7 @@ setMethod("as.data.frame", "IntegerRanges", .as.data.frame.IntegerRanges)
     ans
 }
 
-show_IntegerRanges <- function(x, margin="", print.classinfo=FALSE)
+show_IPosRanges <- function(x, margin="", print.classinfo=FALSE)
 {
     x_class <- class(x)
     x_len <- length(x)
@@ -116,14 +106,14 @@ show_IntegerRanges <- function(x, margin="", print.classinfo=FALSE)
         x_nmc, " metadata ", ifelse(x_nmc == 1L, "column", "columns"),
         ":\n", sep="")
     ## S4Vectors:::makePrettyMatrixForCompactPrinting() assumes that 'x' is
-    ## subsettable but not all IntegerRanges objects are (and if they are,
-    ## subsetting them could be costly). However IRanges objects are assumed
-    ## to be subsettable so if 'x' is not one then we turn it into one (this
-    ## coercion is expected to work on any IntegerRanges object).
+    ## subsettable but not all IPosRanges objects necesseraly are (and if they
+    ## are, subsetting them could be costly). However IRanges objects are
+    ## assumed to be subsettable so if 'x' is not one then we turn it into
+    ## one (this coercion is expected to work on any IPosRanges object).
     if (!is(x, "IRanges"))
         x <- as(x, "IRanges", strict=FALSE)
     out <- S4Vectors:::makePrettyMatrixForCompactPrinting(x,
-               .make_naked_matrix_from_IntegerRanges)
+               .make_naked_matrix_from_IPosRanges)
     if (print.classinfo) {
         .COL2CLASS <- c(
             start="integer",
@@ -144,12 +134,12 @@ show_IntegerRanges <- function(x, margin="", print.classinfo=FALSE)
     print(out, quote=FALSE, right=TRUE, max=length(out))
 }
 
-setMethod("show", "IntegerRanges",
+setMethod("show", "IPosRanges",
     function(object)
-        show_IntegerRanges(object, margin="  ", print.classinfo=TRUE)
+        show_IPosRanges(object, margin="  ", print.classinfo=TRUE)
 )
 
-setMethod("showAsCell", "IntegerRanges",
+setMethod("showAsCell", "IPosRanges",
     function(object)
     {
         if (length(object) == 0L)
@@ -159,37 +149,3 @@ setMethod("showAsCell", "IntegerRanges",
     }
 )
 
-
-### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### isEmpty() and isNormal()
-###
-### All of them test an IntegerRanges object as a whole and return a single
-### TRUE or FALSE.
-###
-
-setGeneric("isNormal", function(x, ...) standardGeneric("isNormal"))
-
-setMethod("isNormal", "IntegerRanges",
-    function(x)
-    {
-        all_ok <- all(width(x) >= 1L)
-        if (length(x) >= 2)
-            all_ok <- all_ok && all(start(x)[-1L] - end(x)[-length(x)] >= 2L)
-        all_ok
-    }
-)
-
-setGeneric("whichFirstNotNormal",
-    function(x) standardGeneric("whichFirstNotNormal")
-)
-
-setMethod("whichFirstNotNormal", "IntegerRanges",
-    function(x)
-    {
-        is_ok <- width(x) >= 1L
-        if (length(x) >= 2)
-            is_ok <- is_ok & c(TRUE, start(x)[-1L] - end(x)[-length(x)] >= 2L)
-        which(!is_ok)[1L]
-    }
-)
-
diff --git a/R/IntegerRanges-comparison.R → R/IPosRanges-comparison.R b/R/IntegerRanges-comparison.R → R/IPosRanges-comparison.R
@@ -1,10 +1,10 @@
 ### =========================================================================
-### Comparing and ordering ranges
+### Comparing and ordering the ranges in IPosRanges derivatives
 ### -------------------------------------------------------------------------
 ###
 
 
-setMethod("pcompareRecursively", "IntegerRanges", function(x) FALSE)
+setMethod("pcompareRecursively", "IPosRanges", function(x) FALSE)
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -17,10 +17,10 @@ setMethod("pcompareRecursively", "IntegerRanges", function(x) FALSE)
 ### order.
 ###
 
-setMethod("pcompare", c("IntegerRanges", "IntegerRanges"),
+setMethod("pcompare", c("IPosRanges", "IPosRanges"),
     function(x, y)
     {
-        .Call2("IntegerRanges_pcompare",
+        .Call2("IPosRanges_pcompare",
                start(x), width(x), start(y), width(y),
                PACKAGE="IRanges")
     }
@@ -41,12 +41,12 @@ rangeComparisonCodeToLetter <- function(code)
 ### match()
 ###
 
-setMethod("match", c("IntegerRanges", "IntegerRanges"),
+setMethod("match", c("IPosRanges", "IPosRanges"),
     function(x, table, nomatch=NA_integer_, incomparables=NULL,
                        method=c("auto", "quick", "hash"))
     {
         if (!is.null(incomparables))
-            stop("\"match\" method for IntegerRanges objects ",
+            stop("\"match\" method for IPosRanges objects ",
                  "only accepts 'incomparables=NULL'")
         ## Equivalent to (but faster than):
         ##     findOverlaps(x, table, type="equal", select="first")
@@ -62,7 +62,7 @@ setMethod("match", c("IntegerRanges", "IntegerRanges"),
 ### selfmatch()
 ###
 
-setMethod("selfmatch", "IntegerRanges",
+setMethod("selfmatch", "IPosRanges",
     function(x, method=c("auto", "quick", "hash"))
         selfmatchIntegerPairs(start(x), width(x), method=method)
 )
@@ -71,27 +71,27 @@ setMethod("selfmatch", "IntegerRanges",
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### order() and related methods.
 ###
-### is.unsorted(), order(), sort(), rank() on IntegerRanges derivatives are
+### is.unsorted(), order(), sort(), rank() on IPosRanges derivatives are
 ### consistent with the order implied by pcompare().
-### is.unsorted() is a quick/cheap way of checking whether an IntegerRanges
+### is.unsorted() is a quick/cheap way of checking whether an IPosRanges
 ### derivative is already sorted, e.g., called prior to a costly sort.
-### sort() and rank() will work out-of-the-box on an IntegerRanges derivative
+### sort() and rank() will work out-of-the-box on an IPosRanges derivative
 ### thanks to the method for List objects (which delegates to the method for
 ### Vector objects).
 ###
 
-.IntegerRanges_as_integer_pairs <- function(x)
+.IPosRanges_as_integer_pairs <- function(x)
 {
     a <- start(x)
     b <- width(x)
     list(a, b)
 }
 
-setMethod("is.unsorted", "IntegerRanges",
+setMethod("is.unsorted", "IPosRanges",
     function(x, na.rm=FALSE, strictly=FALSE)
     {
         if (!identical(na.rm, FALSE))
-            warning("\"is.unsorted\" method for IntegerRanges objects ",
+            warning("\"is.unsorted\" method for IPosRanges objects ",
                     "ignores the 'na.rm' argument")
         if (!isTRUEorFALSE(strictly))
             stop("'strictly' must be TRUE of FALSE")
@@ -103,42 +103,42 @@ setMethod("is.unsorted", "IntegerRanges",
         ## full walk on 'x') than when it is unsorted (in which case
         ## S4Vectors:::sortedIntegerPairs() might stop walking on 'x' after
         ## checking its first 2 elements only -- the best-case scenario).
-        pairs <- .IntegerRanges_as_integer_pairs(x)
+        pairs <- .IPosRanges_as_integer_pairs(x)
         !S4Vectors:::sortedIntegerPairs(pairs[[1L]], pairs[[2L]],
                                         strictly=strictly)
     }
 )
 
-.order_IntegerRanges <- function(x, decreasing=FALSE)
+.order_IPosRanges <- function(x, decreasing=FALSE)
 {
     if (!isTRUEorFALSE(decreasing))
         stop("'decreasing' must be TRUE or FALSE")
-    pairs <- .IntegerRanges_as_integer_pairs(x)
+    pairs <- .IPosRanges_as_integer_pairs(x)
     orderIntegerPairs(pairs[[1L]], pairs[[2L]], decreasing=decreasing)
 }
 
-### 'na.last' is pointless (IntegerRanges objects don't contain NAs) so is
+### 'na.last' is pointless (IPosRanges derivatives don't contain NAs) so is
 ### ignored.
 ### 'method' is also ignored at the moment.
-setMethod("order", "IntegerRanges",
+setMethod("order", "IPosRanges",
     function(..., na.last=TRUE, decreasing=FALSE,
                   method=c("auto", "shell", "radix"))
     {
         ## Turn off this warning for now since it triggers spurious warnings
-        ## when calling sort() on an IntegerRangesList object. The root of the
-        ## problem is inconsistent defaults for 'na.last' between order() and
-        ## sort(), as reported here:
+        ## when calling sort() on an IPosRangesList derivative. The root of
+        ## the problem is inconsistent defaults for 'na.last' between order()
+        ## and sort(), as reported here:
         ##   https://stat.ethz.ch/pipermail/r-devel/2015-November/072012.html
         #if (!identical(na.last, TRUE))
-        #    warning("\"order\" method for IntegerRanges objects ",
+        #    warning("\"order\" method for IPosRanges objects ",
         #            "ignores the 'na.last' argument")
         if (!isTRUEorFALSE(decreasing))
             stop("'decreasing' must be TRUE or FALSE")
-        ## All arguments in '...' are guaranteed to be IntegerRanges objects.
+        ## All arguments in '...' are guaranteed to be IPosRanges derivatives.
         args <- list(...)
         if (length(args) == 1L)
-            return(.order_IntegerRanges(args[[1L]], decreasing))
-        order_args <- c(unlist(lapply(args, .IntegerRanges_as_integer_pairs),
+            return(.order_IPosRanges(args[[1L]], decreasing))
+        order_args <- c(unlist(lapply(args, .IPosRanges_as_integer_pairs),
                                recursive=FALSE, use.names=FALSE),
                         list(na.last=na.last, decreasing=decreasing))
         do.call(order, order_args)