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Add "DotBracket" seqtype as compatible "B" seqtype #134

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Merged
hpages merged 2 commits into from
Jan 6, 2026
Merged

Add "DotBracket" seqtype as compatible "B" seqtype #134

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eb1586f
Add "DotBracket" seqtype as compatible "B" seqtype
FelixErnst Dec 26, 2025
2fa620a
Fixed typos in comments
FelixErnst Dec 26, 2025
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28 changes: 17 additions & 11 deletions R/seqtype.R
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,16 @@
### The seqtype() function returns the sequence type. For
### example 'seqtype(AAString())' returns "AA".
###
### The ModString package by Felix Ernst introduces two additional sequence
### The Modstrings 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.
###
### The Structstrings package by Felix Ernst introduces one additional sequence
### type, "DotBracket", which is 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.


Expand Down Expand Up @@ -103,18 +108,19 @@ 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")
### Note that sequence types "ModDNA", "ModRNA" and "DotBracket" 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",
"DotBracket")

compatible_seqtypes <- function(seqtype1, seqtype2)
{
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"))
seqtype1 %in% c("B", "ModDNA", "ModRNA", "DotBracket") ||
seqtype2 %in% c("B", "ModDNA", "ModRNA", "DotBracket"))
return(TRUE)
is_nucleo1 <- seqtype1 %in% c("DNA", "RNA")
is_nucleo2 <- seqtype2 %in% c("DNA", "RNA")
Expand All @@ -127,9 +133,9 @@ 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"))
if (from_seqtype %in% c("ModDNA", "ModRNA", "DotBracket"))
from_seqtype <- "B"
if (to_seqtype %in% c("ModDNA", "ModRNA"))
if (to_seqtype %in% c("ModDNA", "ModRNA", "DotBracket"))
to_seqtype <- "B"
if (from_seqtype == to_seqtype)
return(NULL)
Expand Down Expand Up @@ -159,9 +165,9 @@ get_seqtype_conversion_lookup <- function(from_seqtype, to_seqtype)
what_op, class1, class2)
{
stopifnot(isSingleString(seqtype1), isSingleString(seqtype2))
if (seqtype1 %in% c("ModDNA", "ModRNA"))
if (seqtype1 %in% c("ModDNA", "ModRNA", "DotBracket"))
seqtype1 <- "B"
if (seqtype2 %in% c("ModDNA", "ModRNA"))
if (seqtype2 %in% c("ModDNA", "ModRNA", "DotBracket"))
seqtype2 <- "B"
if (seqtype1 == seqtype2)
return(c(seqtype1, seqtype2))
Expand Down