Biostrings 2.79.3: Repair compatible_seqtypes/get_seqtype_conversion_lookup

Repair low-level utilities Biostrings:::compatible_seqtypes() and
get_seqtype_conversion_lookup() when at least one of the supplied
sequence type is "ModDNA" or "ModRNA".

This regression was introduced in previous commit (commit b15bffb,
Biostrings 2.79.2) and was breaking the Modstrings package. See
#132

Author: hpages

DESCRIPTION

@@ -7,7 +7,7 @@ biocViews: SequenceMatching, Alignment, Sequencing, Genetics,
 	DataImport, DataRepresentation, Infrastructure
 URL: https://bioconductor.org/packages/Biostrings
 BugReports: https://github.com/Bioconductor/Biostrings/issues
-Version: 2.79.2
+Version: 2.79.3
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(

R/seqtype.R

@@ -3,7 +3,8 @@
 ### -------------------------------------------------------------------------
 ###
 ### Most sequence containers in Biostrings have a "sequence type" that
-### indicates the nature of the sequence(s) that the container can store:
+### reflects the type of sequences that it represents as well as the
+### encoding that is used to store the sequence internally:
 ###
 ###   sequence  |                           |              |
 ###   type      | description               | alphabet     | encoded
@@ -13,8 +14,14 @@
 ###   "RNA"     | RNA sequence(s)           | RNA_ALPHABET | yes
 ###   "AA"      | amino acid sequence(s)    | AA_ALPHABET  | yes
 ###
-### seqtype() returns that sequence type. For example 'seqtype(AAString())'
-### returns "AA".
+### The seqtype() function returns the sequence type. For
+### example 'seqtype(AAString())' returns "AA".
+###
+### The ModString package by Felix Ernst introduces two additional sequence
+### types, "ModDNA" and "ModRNA", that are treated as sequence type "B" by
+### compatible_seqtypes(), get_seqtype_conversion_lookup(), and
+### get_seqtype_switches_before_binary_op() below.
+###
 ### Unless specified otherwise, things in this file are not exported.
 
 
@@ -96,10 +103,18 @@ xs_dec_lkup <- function(x)
 ### determine those restrictions.
 ###
 
+### Note that sequence types "ModDNA" and "ModRNA" are treated as sequence
+### type "B" by compatible_seqtypes(), get_seqtype_conversion_lookup(), and
+### get_seqtype_switches_before_binary_op() below.
+.SUPPORTED_SEQTYPES <- c("B", "DNA", "RNA", "AA", "ModDNA", "ModRNA")
+
 compatible_seqtypes <- function(seqtype1, seqtype2)
 {
-    stopifnot(isSingleString(seqtype1), isSingleString(seqtype2))
-    if (seqtype1 == seqtype2 || seqtype1 == "B" || seqtype2 == "B")
+    stopifnot(isSingleString(seqtype1), seqtype1 %in% .SUPPORTED_SEQTYPES,
+              isSingleString(seqtype2), seqtype2 %in% .SUPPORTED_SEQTYPES)
+    if (seqtype1 == seqtype2 ||
+        seqtype1 %in% c("B", "ModDNA", "ModRNA") ||
+        seqtype2 %in% c("B", "ModDNA", "ModRNA"))
         return(TRUE)
     is_nucleo1 <- seqtype1 %in% c("DNA", "RNA")
     is_nucleo2 <- seqtype2 %in% c("DNA", "RNA")
@@ -112,6 +127,10 @@ get_seqtype_conversion_lookup <- function(from_seqtype, to_seqtype)
     if (!compatible_seqtypes(from_seqtype, to_seqtype))
         stop("incompatible sequence types \"",
              from_seqtype, "\" and \"", to_seqtype, "\"")
+    if (from_seqtype %in% c("ModDNA", "ModRNA"))
+        from_seqtype <- "B"
+    if (to_seqtype %in% c("ModDNA", "ModRNA"))
+        to_seqtype <- "B"
     if (from_seqtype == to_seqtype)
         return(NULL)
     from_is_nucleo <- from_seqtype %in% c("DNA", "RNA")
@@ -130,7 +149,7 @@ get_seqtype_conversion_lookup <- function(from_seqtype, to_seqtype)
         return(AA_STRING_CODEC@enc_lkup)
     if (from_seqtype == "AA")
         return(AA_STRING_CODEC@dec_lkup)
-    stop("Biostrings internal error, please report") # should never happen
+    stop("Biostrings internal error, please report")  # should never happen
 }
 
 ### Returns a character vector of length 2 indicating the 2 target seqtypes
@@ -140,6 +159,10 @@ get_seqtype_conversion_lookup <- function(from_seqtype, to_seqtype)
                                                    what_op, class1, class2)
 {
     stopifnot(isSingleString(seqtype1), isSingleString(seqtype2))
+    if (seqtype1 %in% c("ModDNA", "ModRNA"))
+        seqtype1 <- "B"
+    if (seqtype2 %in% c("ModDNA", "ModRNA"))
+        seqtype2 <- "B"
     if (seqtype1 == seqtype2)
         return(c(seqtype1, seqtype2))
     if (!compatible_seqtypes(seqtype1, seqtype2))

tests/testthat/test-seqtype.R

@@ -0,0 +1,16 @@
+
+test_that("compatible_seqtypes()", {
+    compatible_seqtypes <- Biostrings:::compatible_seqtypes
+    SUPPORTED_SEQTYPES <- Biostrings:::.SUPPORTED_SEQTYPES
+    target <- matrix(TRUE,
+                     nrow=length(SUPPORTED_SEQTYPES),
+                     ncol=length(SUPPORTED_SEQTYPES),
+                     dimnames=list(SUPPORTED_SEQTYPES, SUPPORTED_SEQTYPES))
+    target[c("DNA", "RNA"), "AA"] <- target["AA", c("DNA", "RNA")] <- FALSE
+    current <- sapply(SUPPORTED_SEQTYPES,
+        function(seqtype1) sapply(SUPPORTED_SEQTYPES,
+            function(seqtype2) compatible_seqtypes(seqtype1, seqtype2))
+    )
+    expect_identical(current, target)
+})
+