@@ -1,12 +1,3 @@

-

-### =========================================================================

-### CharOrGRangesList

-### -------------------------------------------------------------------------

-###

-### Unifies the two ways we can represent the genome IIT BamTally now expects

-### (specifying CDS regions)

-setClassUnion("CharOrGRangesList", c("character", "GRangesList", "NULL"))

-

 ### =========================================================================

 ### BamTallyParam class

 ### -------------------------------------------------------------------------

@@ -44,11 +35,13 @@ normArgWhich <- function(x, genome) {

   x

 }

-setGeneric("normArgCdsIIT", function(exon_iit, genome, ...) standardGeneric("normArgCdsIIT"))

+setGeneric("normArgCdsIIT", function(exon_iit, genome, ...)

+           standardGeneric("normArgCdsIIT"))

 setMethod("normArgCdsIIT", "ANY", function(exon_iit, genome, BPPARAM) {

-    if(!is.null(exon_iit) && (!is(exon_iit, "character") || length(exon_iit) > 1))

-        stop("Invalid exon_iit value. Accepted values types are: single character value (file location), GRangesList of exons, a TxDb object (use the exons in the TxDb),  a GmapGenome (use the genome gene map iit), or NULL")

+    if(!is.null(exon_iit)

+       && (!is(exon_iit, "character") || length(exon_iit) > 1))

+      stop("Invalid exon_iit value. See ?BamTallyParam for acceptable values")

     if(!is.null(exon_iit) && (nchar(exon_iit) && !file.exists(exon_iit)))

         stop("exon_iit is non-empty and does not point to an existing file")

     exon_iit

@@ -56,18 +49,14 @@ setMethod("normArgCdsIIT", "ANY", function(exon_iit, genome, BPPARAM) {

 })

 setMethod("normArgCdsIIT", "TxDb", function(exon_iit, genome, BPPARAM) {

-    exon_iit = iit_store(exonsBy(exon_iit, "gene"), dest = tempfile(pattern = "cds", fileext = ".iit"), BPPARAM = BPPARAM)

+    exon_iit = iit_store(exonsBy(exon_iit, "gene"),

+      dest = tempfile(pattern = "cds", fileext = ".iit"), BPPARAM = BPPARAM)

     normArgCdsIIT(exon_iit)

 })

 setMethod("normArgCdsIIT", "GRangesList", function(exon_iit, genome, BPPARAM) {

-    exon_iit = iit_store(exon_iit, dest = tempfile(pattern = "cds", fileext = ".iit"), BPPARAM = BPPARAM)

-    normArgCdsIIT(exon_iit)

-})

-

-

-setMethod("normArgCdsIIT", "GRanges", function(exon_iit, genome, BPPARAM) {

-    exon_iit = iit_store(GRangesList( exon_iit), dest = tempfile(pattern = "cds", fileext = ".iit"), BPPARAM = BPPARAM)

+    exon_iit = iit_store(exon_iit, dest = tempfile(pattern = "cds",

+                                     fileext = ".iit"), BPPARAM = BPPARAM)

     normArgCdsIIT(exon_iit)

 })

@@ -82,7 +71,9 @@ setMethod("normArgCdsIIT", "GmapGenome", function(exon_iit, genome, BPPARAM) {

     normArgsCdsIIT(exon_iit)

 })

-.makeCdsIIT= function(exons, filename = tempfile(pattern="exon_iit", fileext=".iit")) {

+.makeCdsIIT <- function(exons,

+                        filename = tempfile(pattern="exon_iit", fileext=".iit"))

+{

     exonsFlat <- unlist(exons, use.names=FALSE)

     exonsPart <- PartitioningByWidth(exons)

     exonsHead <- exonsFlat[-end(exonsPart)]