@@ -86,7 +86,6 @@ importFrom(utils, "modifyList", "type.convert")

 export(".chrName",

        ".doCache",

-       "AlignedReadTrack",

        "AlignmentsTrack",

        "AnnotationTrack",

        "DetailsAnnotationTrack",

@@ -1994,13 +1994,6 @@ UcscTrack <- function(track, table = NULL, trackType = c(

 }

-

-## AlignedReadTrack ----------------------------------------------------------------------------------------------------

-AlignedReadTrack <- function() {

-    .Defunct("AlignmentsTrack")

-}

-

-

 ## SequenceTrack -------------------------------------------------------------------------------------------------------

 ##

 ## SequenceTrack: A generic track to visualize nucleotide sequences. This class is virtual.

@@ -319,7 +319,7 @@ allDisplayParsDoc <- function(details) {

     require(Gviz)

     text <- indent(c("\\section{Display Parameters}{", "\\describe{"), level=0:1)

     for(cl in c("GenomeAxisTrack", "DataTrack", "IdeogramTrack",

-         "AnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", "AlignmentsTrack", "AlignedReadTrack"))

+         "AnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", "AlignmentsTrack"))

     {

         parents <- names(getClassDef(cl)@contains)

         pars <- sapply(c(cl, parents), function(x) as.list(getClassDef(x)@prototype@dp), simplify=FALSE)

@@ -703,16 +703,6 @@ details <- list(

                                          "verbose"="Logical scalar. Report data loading events from Bioamart or retrieval from cache."

                                          ),

-                AlignedReadTrack=c(

-

-                                   collapse="collapse overlapping ranges and aggregate the underlying data.",

-                                   detail="the amount of detail to plot the data. Either \\code{coverage} to show the coverage only, or \\code{reads} to show individual reads. For large data sets the latter can be very inefficient. Please note that \\code{reads} is only available when the object has been created with option \\code{coverageOnly=FALSE}.",

-                                   fill="the fill color for the coverage indicator.",

-                                   size="the relative size of the track. Defaults to size selection based on the underlying data. Can be overridden in the \\code{\\link{plotTracks}} function.",

-                                   type="the plot type, one or several in \\code{c(\"p\",\"l\", \"b\", \"a\", \"s\", \"g\", \"r\", \"S\", \"smooth\", \"histogram\", \"mountain\", \"polygon\", \"h\", \"boxplot\", \"gradient\", \"heatmap\", \"horizon\")}. See the 'Details' section in \\code{\\linkS4class{DataTrack}} for more information on the individual plotting types."

-

-                                   ),

-

                 SequenceTrack=c(

                                 add53="Logical scalar. Add a direction indicator.",

@@ -815,7 +805,7 @@ updateDocumentation <- function(outdir="~/Rpacks/Gviz/man")

     library(AnnotationDbi)

     ##source(file.path(dirname(outdir), "inst/scripts/sourcePackage.R"))

     dps <- sapply(c("GdObject", "GenomeAxisTrack", "RangeTrack", "NumericTrack", "DataTrack", "IdeogramTrack", "StackedTrack",

-                    "AnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", "AlignedReadTrack", "AlignmentsTrack"),

+                    "AnnotationTrack", "GeneRegionTrack", "BiomartGeneRegionTrack", "AlignmentsTrack"),

                   updateRdFile, outdir)

     settings <- updateSettingsFile(outdir)

     links <- updateLinks(outdir)

@@ -1,9 +1,8 @@

 \name{Gviz-defunct}

-\alias{AlignedReadTrack}

 \title{Defunct functions in package \sQuote{Gviz}}

 \description{These functions are defunct and no longer available.}

 \details{

-  Defunct functions are: \code{AlignedReadTrack}

+  Defunct functions are:

 }