1. gmapR
  2. R
  3. GmapBamReader-class.R
Browse code

follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12

Hervé Pagès authored on 22/01/2018 00:24:43
Showing 1 changed files
R/GmapBamReader-class.R
History View file @ c087114
... ... 
@@ -19,15 +19,15 @@ setMethod("path", "GmapBamReader", function(object) object@path)
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 ## setReplaceMethod("bamWhich", c("GmapBamReader", "ANY"),
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 ##                  function(object, value) {
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-##                    bamWhich(object) <- as(value, "RangesList")
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+##                    bamWhich(object) <- as(value, "IntegerRangesList")
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 ##                    object
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 ##                  })
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-## setReplaceMethod("bamWhich", c("GmapBamReader", "RangesList"),
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+## setReplaceMethod("bamWhich", c("GmapBamReader", "IntegerRangesList"),
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 ##                  function(object, value) {
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 ##                    if (length(value) != 1L || length(value[[1]]) != 1L)
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-##                      stop("'value' must be a RangesList with a single, ",
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-##                           "length-one element")
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+##                      stop("'value' must be an IntegerRangesList with a ",
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+##                           "single, length-one element")
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 ##                    .Call(R_Bamread_limit_region, object, names(value),
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 ##                          start(value[[1]]), end(value[[1]]))
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 ##                  })
Browse code

resync with stuff moving from IRanges to S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89179 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 18/04/2014 15:04:25
Showing 1 changed files
R/GmapBamReader-class.R
History View file @ f7ab666
... ... 
@@ -44,7 +44,7 @@ setMethod("path", "GmapBamReader", function(object) object@path)
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 GmapBamReader <- function(path, which = NULL) {
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   if (is(path, "BamFile"))
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     path <- path(path)
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-  if (!IRanges:::isSingleString(path))
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+  if (!isSingleString(path))
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     stop("'path' must be a single, non-NA string")
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   path <- path.expand(path)
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   obj <- new("GmapBamReader", .extptr = .Call(R_Bamread_new, path), path = path)
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
R/GmapBamReader-class.R
History View file @ b22faf0
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new file mode 100644
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@@ -0,0 +1,75 @@
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+### =========================================================================
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+### GmapBamReader class
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+### -------------------------------------------------------------------------
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+###
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+### The C-level BAM file iterator used by BAM processors in gmap/gstruct.
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+###
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+### This is very similar to BamFile from Rsamtools, but it iterates
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+### line-by-line, not by chunk.
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+###
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+
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+setClass("GmapBamReader",
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+         representation(.extptr = "externalptr", path = "character"))
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Accessors
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+###
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+
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+setMethod("path", "GmapBamReader", function(object) object@path)
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+
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+## setReplaceMethod("bamWhich", c("GmapBamReader", "ANY"),
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+##                  function(object, value) {
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+##                    bamWhich(object) <- as(value, "RangesList")
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+##                    object
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+##                  })
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+
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+## setReplaceMethod("bamWhich", c("GmapBamReader", "RangesList"),
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+##                  function(object, value) {
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+##                    if (length(value) != 1L || length(value[[1]]) != 1L)
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+##                      stop("'value' must be a RangesList with a single, ",
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+##                           "length-one element")
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+##                    .Call(R_Bamread_limit_region, object, names(value),
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+##                          start(value[[1]]), end(value[[1]]))
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+##                  })
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+
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+## setReplaceMethod("bamWhich", c("GmapBamReader", "NULL"),
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+##                  function(object, value) {
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+##                    .Call(R_Bamread_unlimit_region, object)
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+##                  })
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Constructor
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+###
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+
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+GmapBamReader <- function(path, which = NULL) {
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+  if (is(path, "BamFile"))
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+    path <- path(path)
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+  if (!IRanges:::isSingleString(path))
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+    stop("'path' must be a single, non-NA string")
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+  path <- path.expand(path)
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+  obj <- new("GmapBamReader", .extptr = .Call(R_Bamread_new, path), path = path)
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+### TODO:
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+  ##  bamWhich(obj) <- which
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+  obj
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+}
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Coercion
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+###
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+
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+setAs("BamFile", "GmapBamReader", function(from) {
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+  GmapBamReader(from)
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+})
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+
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+setAs("GmapBamReader", "BamFile", function(from) {
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+  BamFile(path(from))
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+})
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+
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Show
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+###
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+
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+setMethod("show", "GmapBamReader", function(object) {
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+  cat("GmapBamReader object\npath:", path(object), "\n")
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+})