Biostrings 2.79.1: Post-release cleanup

Remove all the functions that went to the pwalign package in BioC 3.19,
that is: writePairwiseAlignments(), nucleotideSubstitutionMatrix(),
errorSubstitutionMatrices(), qualitySubstitutionMatrices(),
insertion(), deletion(), unaligned(), aligned(), indel(), nindel(),
PairwiseAlignments(), pattern(), alignedPattern(), alignedSubject(),
PairwiseAlignmentsSingleSubject, nedit(), mismatchTable(),
mismatchSummary(), compareStrings(), pid(), pairwiseAlignment(),
stringDist().

Note that these functions got formally deprecated in Biostrings in
BioC 3.21 and defunct in BioC 3.22.

Additionally, the XStringPartialMatches class and following functions
are now gone after being defunct in BioC 3.22 or non-functional for
years: matchprobes(), subpatterns(), pmatchPattern(), lcsubstr().

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: 2.79.0
+Version: 2.79.1
 License: Artistic-2.0
 Encoding: UTF-8
 Authors@R: c(
@@ -33,7 +33,7 @@ Authors@R: c(
 	person("Jen", "Wokaty", role="ctb",
 	       comment="Converted 'matchprobes' vignette from Sweave to RMarkdown"),
 	person("Erik", "Wright", role="ctb"))
-Depends: R (>= 4.0.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12),
+Depends: R (>= 4.1.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12),
 	IRanges (>= 2.31.2), XVector (>= 0.37.1), Seqinfo
 Imports: methods, utils, grDevices, stats, crayon
 LinkingTo: S4Vectors, IRanges, XVector
@@ -89,11 +89,10 @@ Collate: utils.R
 	findPalindromes.R
 	PDict-class.R
 	matchPDict.R
-	XStringPartialMatches-class.R
 	XStringQuality-class.R
 	QualityScaledXStringSet.R
-	pmatchPattern.R
+	lcsuffix.R
 	MultipleAlignment.R
-	matchprobes.R
-	moved_to_pwalign.R
+	longestConsecutive.R
+	predefined_scoring_matrices.R
 	zzz.R

NAMESPACE

@@ -104,6 +104,7 @@ exportMethods(
 ###   getSeq.R
 ###   letterFrequency.R
 ###   dinucleotideFrequencyTest.R
+###   lcsuffix.R
 ###   chartr.R
 ###   reverse.R
 ###   translate.R
@@ -140,12 +141,15 @@ export(
     oligonucleotideTransitions,
     twoWayAlphabetFrequency,
 
-    ## chartr.R:
-    replaceAmbiguities,
-
     ## dinucleotideFrequencyTest.R
     dinucleotideFrequencyTest,
 
+    ## lcsuffix.R:
+    lcprefix, lcsuffix,
+
+    ## chartr.R:
+    replaceAmbiguities,
+
     ## reverseComplement.R:
     complement, reverseComplement,
 
@@ -188,6 +192,7 @@ exportMethods(
     oligonucleotideFrequency,
     nucleotideFrequencyAt,
     dinucleotideFrequencyTest,
+    lcprefix, lcsuffix,
     chartr,
     reverse, complement, reverseComplement,
     codons, translate,
@@ -294,14 +299,11 @@ exportMethods(
 ### ==========================================================================
 ### STRING ALIGNMENT
 ### --------------------------------------------------------------------------
-###   XStringPartialMatches-class.R
 ###   XStringQuality-class.R
 ###   QualityScaledXStringSet.R
-###   pmatchPattern.R
 ###   MultipleAlignment.R
 
 exportClasses(
-    XStringPartialMatches,
     XStringQuality, PhredQuality, SolexaQuality, IlluminaQuality,
     QualityScaledXStringSet,
     QualityScaledBStringSet, QualityScaledDNAStringSet,
@@ -311,9 +313,6 @@ exportClasses(
 )
 
 export(
-    ## XStringPartialMatches-class.R:
-    subpatterns,
-
     ## XStringQuality-class.R:
     PhredQuality, SolexaQuality, IlluminaQuality,
     encoding,
@@ -324,9 +323,6 @@ export(
     QualityScaledRNAStringSet, QualityScaledAAStringSet,
     readQualityScaledDNAStringSet, writeQualityScaledXStringSet,
 
-    ## pmatchPattern.R:
-    lcprefix, lcsuffix, pmatchPattern, lcsubstr,
-
     ## MultipleAlignment.R:
     DNAMultipleAlignment,
     RNAMultipleAlignment,
@@ -349,11 +345,9 @@ exportMethods(
     show, summary,
     start, end, width,
     Views,
-    subpatterns,
     quality, encoding,
     parallel_slot_names,
     parallelVectorNames,
-    lcprefix, lcsuffix, pmatchPattern, lcsubstr,
     nchar, names, "names<-", "[[", windows,
     consensusMatrix, consensusString,
     alphabetFrequency, as.list,
@@ -367,39 +361,18 @@ exportMethods(
 
 
 ### ==========================================================================
-### STUFF THAT BELONGED ORIGINALLY TO OLD matchprobes PACKAGE AND IS NOW
-### SUPERSEDED BY SOME NATIVE Biostrings FUNCTIONALITY
+### MISCELLANEOUS
 ### --------------------------------------------------------------------------
-###   matchprobes.R
+###   longestConsecutive.R
 
 export(
-    longestConsecutive,
-    matchprobes
+    longestConsecutive
 )
 
 
 ### ==========================================================================
 ### STUFF THAT HAS MOVED TO THE pwalign PACKAGE
 ### --------------------------------------------------------------------------
 
-export(
-    writePairwiseAlignments,
-    nucleotideSubstitutionMatrix,
-    errorSubstitutionMatrices,
-    qualitySubstitutionMatrices,
-
-    insertion, deletion,
-    unaligned, aligned, indel, nindel,
-    PairwiseAlignments, pattern, alignedPattern, alignedSubject,
-    PairwiseAlignmentsSingleSubject,
-    nedit,
-    mismatchTable, mismatchSummary,
-    compareStrings,
-    pid,
-    pairwiseAlignment,
-    stringDist,
-    print.moved_to_pwalign_pkg
-)
-
 S3method(print, moved_to_pwalign_pkg)
 

R/XStringPartialMatches-class.R

@@ -0,0 +1,82 @@
+### =========================================================================
+### Find Longest Common Prefix/Suffix
+### -------------------------------------------------------------------------
+
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### Longest Common Prefix
+###
+
+### 's1' and 's2' must be XString objects containing sequences of the same
+### type. Return the length (integer) of the Longest Common Prefix.
+XString.lcprefix <- function(s1, s2)
+{
+    .Call2("lcprefix", s1@shared@xp, s1@offset, s1@length,
+                      s2@shared@xp, s2@offset, s2@length,
+                      PACKAGE="Biostrings")
+}
+
+setGeneric("lcprefix", signature=c("s1", "s2"),
+    function(s1, s2) standardGeneric("lcprefix")
+)
+setMethod("lcprefix", signature(s1="character", s2="character"),
+    function(s1, s2)
+        XString.lcprefix(BString(s1), BString(s2))
+)
+setMethod("lcprefix", signature(s1="character", s2="XString"),
+    function(s1, s2)
+        XString.lcprefix(XString(seqtype(s2), s1), s2)
+)
+setMethod("lcprefix", signature(s1="XString", s2="character"),
+    function(s1, s2)
+        XString.lcprefix(s1, XString(seqtype(s1), s2))
+)
+setMethod("lcprefix", signature(s1="XString", s2="XString"),
+    function(s1, s2)
+    {
+        if (seqtype(s1) != seqtype(s2))
+            stop("'s1' and 's2' must be XString objects containing ",
+                 "sequences of the same type")
+        XString.lcprefix(s1, s2)
+    }
+)
+
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### Longest Common Suffix
+###
+
+### 's1' and 's2' must be XString objects containing sequences of the same
+### type. Return the length (integer) of the Longest Common Suffix.
+XString.lcsuffix <- function(s1, s2)
+{
+    .Call2("lcsuffix", s1@shared@xp, s1@offset, s1@length,
+                      s2@shared@xp, s2@offset, s2@length,
+                      PACKAGE="Biostrings")
+}
+
+setGeneric("lcsuffix", signature=c("s1", "s2"),
+    function(s1, s2) standardGeneric("lcsuffix")
+)
+setMethod("lcsuffix", signature(s1="character", s2="character"),
+    function(s1, s2)
+        XString.lcsuffix(BString(s1), BString(s2))
+)
+setMethod("lcsuffix", signature(s1="character", s2="XString"),
+    function(s1, s2)
+        XString.lcsuffix(XString(seqtype(s2), s1), s2)
+)
+setMethod("lcsuffix", signature(s1="XString", s2="character"),
+    function(s1, s2)
+        XString.lcsuffix(s1, XString(seqtype(s1), s2))
+)
+setMethod("lcsuffix", signature(s1="XString", s2="XString"),
+    function(s1, s2)
+    {
+        if (seqtype(s1) != seqtype(s2))
+            stop("'s1' and 's2' must be XString objects containing ",
+                 "sequences of the same type")
+        XString.lcsuffix(s1, s2)
+    }
+)
+

R/lcsuffix.R

@@ -0,0 +1,4 @@
+longestConsecutive <- function(seq, letter) {
+  .Call2("MP_longestConsecutive", seq, letter, PACKAGE="Biostrings")
+}
+