Remove stuff that was defunct in BioC 3.0:

- "map" and "splitAsListReturnedClass" methods, - argument 'with.mapping' in "reduce" method, - makeSeqnameIds() function. git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@95799 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Oct 20, 2014 · c413930 · c413930
1 parent 2d5c74b
commit c413930
Show file tree

Hide file tree

Showing 10 changed files with 14 additions and 134 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,7 +13,7 @@ Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,
         GenomeAnnotation
 Depends: R (>= 2.10), methods, BiocGenerics (>= 0.11.3), S4Vectors (>=
-        0.2.3), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.1.20)
+        0.2.3), IRanges (>= 2.1.2), GenomeInfoDb (>= 1.1.20)
 Imports: utils, stats, XVector
 LinkingTo: S4Vectors, IRanges
 Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome,
@@ -27,7 +27,7 @@ Suggests: AnnotationDbi (>= 1.21.1), AnnotationHub, BSgenome,
         pasillaBamSubset, RUnit, digest, BiocStyle
 License: Artistic-2.0
 Collate: utils.R phicoef.R transcript-utils.R constraint.R
-        makeSeqnameIds.R strand-utils.R range-squeezers.R
+        strand-utils.R range-squeezers.R
         GenomicRanges-class.R GRanges-class.R
         DelegatingGenomicRanges-class.R GIntervalTree-class.R
         GenomicRanges-comparison.R GenomicRangesList-class.R

diff --git a/NAMESPACE b/NAMESPACE
@@ -74,7 +74,7 @@ exportMethods(
     elementMetadata, "elementMetadata<-",
     mcols, "mcols<-",
     values, "values<-",
-    relistToClass, splitAsListReturnedClass,
+    relistToClass,
     compare,
     ranges, "ranges<-", trim,
     ngap,
@@ -85,7 +85,7 @@ exportMethods(
     punion, pintersect, psetdiff, pgap,
     findOverlaps, countOverlaps, overlapsAny, subsetByOverlaps,
     precede, follow, nearest, distance, distanceToNearest,
-    map, mapCoords,
+    mapCoords,
     tile,
     subset,
     subjectHits, queryHits,
@@ -103,7 +103,6 @@ exportMethods(
 export(
     phicoef,
 
-    makeSeqnameIds,
     GRanges, GRangesList, GenomicRangesList, GIntervalTree, 
     .DollarNames.GenomicRanges,
     makeGRangesFromDataFrame,

diff --git a/R/GRangesList-class.R b/R/GRangesList-class.R
@@ -492,10 +492,6 @@ setReplaceMethod("[[", "GRangesList", .dBracketReplaceGRList)
 
 setMethod("relistToClass", "GRanges", function(x) "GRangesList")
 
-setMethod("splitAsListReturnedClass", "GRanges",
-    function(x) {.Defunct("relistToClass"); "GRangesList"}
-)
-
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### show method.

diff --git a/R/inter-range-methods.R b/R/inter-range-methods.R
@@ -42,17 +42,15 @@
 }
 
 .interIntervalGenomicRanges2 <- function(x, FUN,
-                                         with.revmap=FALSE, with.mapping=FALSE,
+                                         with.revmap=FALSE,
                                          ignore.strand=FALSE, ...)
 {
     x <- clone(x)
     mcols(x) <- NULL
     f <- .interIntervalSplitVariable(x, ignore.strand=ignore.strand)
     xIRangesList <- split(unname(ranges(x)), f)
-    if (with.revmap || with.mapping) {
-        ansIRangesList <- FUN(xIRangesList,
-                              with.revmap=with.revmap,
-                              with.mapping=with.mapping, ...)
+    if (with.revmap) {
+        ansIRangesList <- FUN(xIRangesList, with.revmap=with.revmap, ...)
     } else {
         ansIRangesList <- FUN(xIRangesList, ...)
     }
@@ -74,19 +72,14 @@
         ans_mcols <- new("DataFrame", nrows=length(ans_seqnames))
     } else {
         mcols(ans_ranges) <- NULL
-        if (with.revmap || with.mapping) {
-            if (with.revmap) {
-                revmap_colname <- "revmap"
-            } else {
-                revmap_colname <- "mapping"
-            }
-            revmap_unlisted <- ans_mcols[[revmap_colname]]
+        if (with.revmap) {
+            revmap_unlisted <- ans_mcols[["revmap"]]
             revmap_partitioning <- PartitioningByEnd(ansIRangesList)
             old2new <- splitAsList(seq_along(x), f)
             revmap_unlisted2 <- .translateRevmap(revmap_unlisted,
                                                  revmap_partitioning,
                                                  old2new)
-            ans_mcols[[revmap_colname]] <- revmap_unlisted2
+            ans_mcols[["revmap"]] <- revmap_unlisted2
         }
     }
     if (length(extraColumnSlotNames(x)) > 0L)
@@ -152,7 +145,7 @@ setMethod("range", "GRangesList",
 
 setMethod("reduce", "GenomicRanges",
     function(x, drop.empty.ranges=FALSE, min.gapwidth=1L,
-                with.revmap=FALSE, with.mapping=FALSE,
+                with.revmap=FALSE,
                 with.inframe.attrib=FALSE, ignore.strand=FALSE)
     {
         if (!identical(with.inframe.attrib, FALSE))
@@ -165,8 +158,7 @@ setMethod("reduce", "GenomicRanges",
         .interIntervalGenomicRanges2(x, reduce,
                                      drop.empty.ranges=drop.empty.ranges,
                                      min.gapwidth=min.gapwidth,
-                                     with.revmap=with.revmap,
-                                     with.mapping=with.mapping)
+                                     with.revmap=with.revmap)
     }
 )
 

diff --git a/R/makeSeqnameIds.R b/R/makeSeqnameIds.R
diff --git a/R/mapCoords-methods.R b/R/mapCoords-methods.R
@@ -31,10 +31,6 @@
   relist(gr[ord], x)
 }
 
-setMethod("map", c("GenomicRanges", "GRangesList"), function(from, to) {
-  .Defunct(msg="map() is defunct. Use mapCoords() instead.")
-})
-
 setMethod("mapCoords", c("GenomicRanges", "GRangesList"), 
   function(x, to, ..., ignore.strand = FALSE, elt.loc = FALSE,
            elt.hits = FALSE) {

diff --git a/man/GRangesList-class.Rd b/man/GRangesList-class.Rd
@@ -45,7 +45,6 @@
 
 % extractList() and family:
 \alias{relistToClass,GRanges-method}
-\alias{splitAsListReturnedClass,GRanges-method}
 
 % show method:
 \alias{show,GRangesList-method}

diff --git a/man/deprecated.Rd b/man/deprecated.Rd
diff --git a/man/inter-range-methods.Rd b/man/inter-range-methods.Rd
@@ -46,7 +46,7 @@
 \S4method{range}{GRangesList}(x, ..., na.rm=FALSE)
 
 \S4method{reduce}{GenomicRanges}(x, drop.empty.ranges=FALSE, min.gapwidth=1L,
-       with.revmap=FALSE, with.mapping=FALSE, with.inframe.attrib=FALSE,
+       with.revmap=FALSE, with.inframe.attrib=FALSE,
        ignore.strand=FALSE)
 \S4method{reduce}{GRangesList}(x, drop.empty.ranges=FALSE, min.gapwidth=1L,
        with.inframe.attrib=FALSE)
@@ -64,7 +64,7 @@
 
 \arguments{
   \item{x}{A \link{GenomicRanges} object.}
-  \item{drop.empty.ranges, min.gapwidth, with.revmap, with.mapping, with.inframe.attrib, start, end}{
+  \item{drop.empty.ranges, min.gapwidth, with.revmap, with.inframe.attrib, start, end}{
     See \code{?`\link[IRanges]{inter-range-methods}`} in the IRanges package.
   } 
   \item{ignore.strand}{

diff --git a/man/map-methods.Rd b/man/map-methods.Rd