Fixed documentation warnings

Author: FelixErnst

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Structstrings
 Title: Implementation of the dot bracket annotations with Biostrings
-Version: 1.25.2
+Version: 1.25.3
 Date: 2025-09-22
 Authors@R: person("Felix G.M.","Ernst",
                   email = "felix.gm.ernst@outlook.com",
@@ -43,7 +43,7 @@ Suggests:
     tRNAscanImport,
     BiocStyle
 VignetteBuilder: knitr
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate: 
     'Structstrings.R'
     'AllGenerics.R'

R/Structstrings-DotBracketDataFrame.R

@@ -445,7 +445,7 @@ SDBDFL <- function(..., compress = TRUE, cbindArgs = FALSE)
 
 setMethod("classNameForDisplay", "DotBracketDFrame",
           function(x) {
-            if (class(x) == "DotBracketDFrame") 
+            if (is(x, "DotBracketDFrame")) 
               "DotBracketDataFrame" 
             else 
               class(x)
@@ -454,7 +454,7 @@ setMethod("classNameForDisplay", "DotBracketDFrame",
 
 setMethod("classNameForDisplay", "DotBracketDFrameList",
           function(x) {
-            if (class(x) == "DotBracketDFrameList") 
+            if (is(x, "DotBracketDFrameList"))
               "DotBracketDataFrameList" 
             else 
               class(x)

R/Structstrings.R

@@ -12,11 +12,11 @@
 #' \code{Structstrings} uses the infrastructure provided by the
 #' \code{Biostrings} package and derives the class
 #' \code{\link{DotBracketString}} and such from the equivalent
-#' \code{\link{BString}} class. From these base pair table can be produced for
+#' \code{\link[Biostrings:XStringSet-class]{BString}} class. From these base pair table can be produced for
 #' in depth analysis. For this purpose the \code{\link{DotBracketDataFrame}}
-#' class is derived from the \code{\link{DataFrame}} class. In addition the loop
+#' class is derived from the \code{\link[S4Vectors:DataFrame-class]{DataFrame}} class. In addition the loop
 #' IDs of the base pairs can be retrieved as a \code{\link{LoopIndexList}}, a
-#' derivate if the \code{\link{IntegerList}}. Generally, it checks automatically
+#' derivate if the \code{\link[IRanges:AtomicList]{IntegerList}}. Generally, it checks automatically
 #' for the validity of the dot bracket annotation.
 #'
 #' The conversion of the \code{\link{DotBracketString}} to the base pair table
@@ -131,7 +131,7 @@ STRUCTURE_CLOSE_CHR <- c("\\)",">","\\]","\\}")
 #' is part of the \code{tRNAscanImport} package.
 #' @docType data
 #' @format object of class \code{\link{DotBracketStringSet}} and 
-#' \code{\link{DNAStringSet}}
+#' \code{\link[Biostrings:XStringSet-class]{DNAStringSet}}
 #' 
 #' @usage data(dbs)
 #' @keywords datasets