Browse code

follow renaming of union classes in S4Vectors

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@126394 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 01/02/2017 13:23:02
Showing9 changed files

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@@ -9,10 +9,10 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.17.1
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+Version: 1.17.2
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12), Rsamtools (>= 1.17.8)
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-Imports: S4Vectors (>= 0.9.25), IRanges, 
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+Imports: S4Vectors (>= 0.13.13), IRanges, 
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         rtracklayer (>= 1.31.2), GenomicFeatures (>= 1.17.13), Biostrings,
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         VariantAnnotation (>= 1.11.4), tools, Biobase, BSgenome,
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         GenomicAlignments (>= 1.1.9), BiocParallel
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@@ -9,7 +9,7 @@
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 setClass("BamTallyParam",
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          representation(genome = "GmapGenome",
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                         which = "GenomicRanges",
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-                        desired_read_group = "characterORNULL",
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+                        desired_read_group = "character_OR_NULL",
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                         minimum_mapq = "integer",
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                         concordant_only = "logical",
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                         unique_only = "logical",
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@@ -20,7 +20,7 @@ setClass("BamTallyParam",
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                         ignore_query_Ns = "logical",
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                         indels = "logical",
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                         include_soft_clips = "integer",
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-                        exon_iit = "characterORNULL",
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+                        exon_iit = "character_OR_NULL",
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                         xs = "logical",
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                         read_pos = "logical",
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                         min_base_quality = "integer",
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@@ -7,8 +7,8 @@
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 ### unique directory.
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 ###
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-setClassUnion("GmapParamORNULL", c("GmapParam", "NULL"))
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-setIs("GmapParamORNULL", "GmapAlignerParamORNULL")
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+setClassUnion("GmapParam_OR_NULL", c("GmapParam", "NULL"))
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+setIs("GmapParam_OR_NULL", "GmapAlignerParam_OR_NULL")
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 .valid_GmapOutput <- function(object) {
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     if (length(paths(object)) == 0L)
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@@ -17,8 +17,8 @@ setIs("GmapParamORNULL", "GmapAlignerParamORNULL")
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 setClass("GmapOutput",
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          representation(path = "character",
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-                        param = "GmapParamORNULL",
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-                        version = "POSIXltORNULL"),
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+                        param = "GmapParam_OR_NULL",
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+                        version = "POSIXlt_OR_NULL"),
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          contains="GmapAlignerOutput",
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          validity = .valid_GmapOutput)
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@@ -5,13 +5,13 @@
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 ### High-level interface to gmap.
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 ###
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-setClassUnion("GmapSnpsORNULL", c("GmapSnps", "NULL"))
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+setClassUnion("GmapSnps_OR_NULL", c("GmapSnps", "NULL"))
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 setClass("GmapAlignerParam",
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          representation(genome = "GmapGenome",
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-                        part = "characterORNULL",
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+                        part = "character_OR_NULL",
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                         batch = "character",
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-                        snps = "GmapSnpsORNULL",
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+                        snps = "GmapSnps_OR_NULL",
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                         mode = "character",
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                         nthreads = "integer",
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                         npaths = "integer",
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@@ -7,25 +7,25 @@
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 ### unique directory.
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 ###
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-setClassUnion("POSIXltORNULL", c("POSIXlt", "NULL"))
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+setClassUnion("POSIXlt_OR_NULL", c("POSIXlt", "NULL"))
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 .valid_GsnapOutput <- function(object) {
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   if (length(samPaths(object)) == 0L && length(bamPaths(object)) == 0L)
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     paste0("No GSNAP output at '", object@path, "'")
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 }
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-setClassUnion("GmapAlignerParamORNULL", c("GmapAlignerParam", "NULL"))
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+setClassUnion("GmapAlignerParam_OR_NULL", c("GmapAlignerParam", "NULL"))
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-setClassUnion("GsnapParamORNULL", c("GsnapParam", "NULL"))
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-setIs("GsnapParamORNULL", "GmapAlignerParamORNULL")
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+setClassUnion("GsnapParam_OR_NULL", c("GsnapParam", "NULL"))
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+setIs("GsnapParam_OR_NULL", "GmapAlignerParam_OR_NULL")
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 setClass("GmapAlignerOutput",
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          representation(path = "character",
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-                        param = "GmapAlignerParamORNULL",
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-                        version = "POSIXltORNULL"))
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+                        param = "GmapAlignerParam_OR_NULL",
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+                        version = "POSIXlt_OR_NULL"))
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 setClass("GsnapOutput",
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-         representation(param = "GsnapParamORNULL"),
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+         representation(param = "GsnapParam_OR_NULL"),
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          contains="GmapAlignerOutput",
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          validity = .valid_GsnapOutput)
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@@ -114,7 +114,7 @@ setMethod("bamPaths", "GmapAlignerOutput", function(x) {
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 newGmapAlignerOutput <- function(Class, path, param = NULL, version = NULL) {
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     if (!is.character(path) || any(is.na(path)))
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         stop("'path' must be a character vector without any NA's")
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-    if (!is(version, "POSIXltORNULL")) {
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+    if (!is(version, "POSIXlt_OR_NULL")) {
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         if (is.character(version))
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             version <- parseGsnapVersion(version)
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         else stop("'version' must be a version string, POSIXlt object or NULL")
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@@ -8,13 +8,13 @@
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 ### list.
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 ###
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-setClassUnion("integerORNULL", c("integer", "NULL"))
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+setClassUnion("integer_OR_NULL", c("integer", "NULL"))
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 setClass("GsnapParam",
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-         representation(max_mismatches = "integerORNULL",
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+         representation(max_mismatches = "integer_OR_NULL",
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                         suboptimal_levels = "integer",
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                         novelsplicing = "logical",
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-                        splicing = "characterORNULL",
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+                        splicing = "character_OR_NULL",
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                         terminal_threshold = "integer",
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                         gmap_mode = "character",
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                         clip_overlap = "logical"),
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@@ -205,12 +205,12 @@ setAs("GsnapParam", "list", function(from) {
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 as.list.GmapAlignerParam <- function(x, ...) as(x, "list")
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-setAs("ANY", "characterORNULL", function(from) {
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+setAs("ANY", "character_OR_NULL", function(from) {
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   if (is.null(from))
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     NULL
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   else as.character(from)
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 })
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-setAs("ANY", "integerORNULL", function(from) {
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+setAs("ANY", "integer_OR_NULL", function(from) {
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   if (is.null(from))
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     NULL
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   else as.integer(from)
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@@ -9,7 +9,7 @@
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 setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)
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            standardGeneric("gsnap"))
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-setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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+setMethod("gsnap", c("character", "character_OR_NULL", "GsnapParam"),
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           function(input_a, input_b, params,
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                    output = file.path(getwd(),
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                      file_path_sans_ext(basename(input_a), TRUE)),
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@@ -11,10 +11,10 @@
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 ###
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 setClass("IIT", representation(ptr = "externalptr"))
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-setClassUnion("IITORNULL", c("IIT", "NULL"))
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+setClassUnion("IIT_OR_NULL", c("IIT", "NULL"))
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 setRefClass("IITFile",
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-            fields=c(iit="IITORNULL"),
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+            fields=c(iit="IIT_OR_NULL"),
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             contains="RTLFile")
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 IITFile <- function(resource) {
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@@ -1,7 +1,7 @@
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 \name{gsnap-methods}
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 \docType{methods}
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 \alias{gsnap-methods}
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-\alias{gsnap,character,characterORNULL,GsnapParam-method}
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+\alias{gsnap,character,character_OR_NULL,GsnapParam-method}
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 \alias{gsnap}
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 \title{Align a Set of Reads Using the GSNAP Aligner}
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@@ -15,7 +15,7 @@
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 }
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 \usage{
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-\S4method{gsnap}{character,characterORNULL,GsnapParam}(input_a, input_b, params,
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+\S4method{gsnap}{character,character_OR_NULL,GsnapParam}(input_a, input_b, params,
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                    output = file.path(getwd(),
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                                       file_path_sans_ext(basename(input_a),
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                                                          TRUE)),