[med-svn] [r-bioc-biostrings] 02/04: New upstream version 2.46.0
Andreas Tille
tille at debian.org
Wed Nov 8 11:06:27 UTC 2017
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tille pushed a commit to branch master
in repository r-bioc-biostrings.
commit 869824fb87cd1d53c9c8ce604d2e9fcb6fcc7fea
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 8 12:02:59 2017 +0100
New upstream version 2.46.0
---
DESCRIPTION | 7 +++---
R/MultipleAlignment.R | 44 +++++++++++------------------------
build/vignette.rds | Bin 455 -> 455 bytes
inst/doc/Biostrings2Classes.pdf | Bin 162098 -> 162402 bytes
inst/doc/BiostringsQuickOverview.pdf | Bin 112955 -> 113097 bytes
inst/doc/MultipleAlignments.pdf | Bin 157335 -> 157479 bytes
inst/doc/PairwiseAlignments.pdf | Bin 288462 -> 288684 bytes
inst/doc/matchprobes.pdf | Bin 245608 -> 245737 bytes
man/MultipleAlignment-class.Rd | 2 --
9 files changed, 17 insertions(+), 36 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index c1645a5..ac79b85 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,9 @@
Package: Biostrings
-Title: String objects representing biological sequences, and matching
- algorithms
+Title: Efficient manipulation of biological strings
Description: Memory efficient string containers, string matching
algorithms, and other utilities, for fast manipulation of large
biological sequences or sets of sequences.
-Version: 2.44.2
+Version: 2.46.0
Encoding: UTF-8
Author: H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy
Maintainer: H. Pagès <hpages at fredhutch.org>
@@ -40,4 +39,4 @@ Collate: 00datacache.R utils.R IUPAC_CODE_MAP.R AMINO_ACID_CODE.R
align-utils.R pmatchPattern.R pairwiseAlignment.R stringDist.R
needwunsQS.R MultipleAlignment.R matchprobes.R zzz.R
NeedsCompilation: yes
-Packaged: 2017-07-20 22:18:22 UTC; biocbuild
+Packaged: 2017-10-30 22:39:11 UTC; biocbuild
diff --git a/R/MultipleAlignment.R b/R/MultipleAlignment.R
index 879c4bf..feeedec 100644
--- a/R/MultipleAlignment.R
+++ b/R/MultipleAlignment.R
@@ -88,25 +88,17 @@ setReplaceMethod("rownames", "MultipleAlignment",
setGeneric("rowmask", signature="x", function(x) standardGeneric("rowmask"))
setMethod("rowmask", "MultipleAlignment", function(x) x at rowmask)
-.appendMask <- function(mask, append, value){
- append <- match.arg(append, choices=c("union", "replace", "intersect"))
- switch(append,
- "union" = return(union(mask, value)),
- "replace" = return(value),
- "intersect" = return(intersect(mask, value)))
-}
.setMask <- function(mask, append, invert, length, value){
if (!isTRUEorFALSE(invert))
stop("'invert' must be TRUE or FALSE")
- if(invert==TRUE){
- ## 1st invert value using gaps()
- value <- gaps(value, start=1, end=length)
- value <- .appendMask(mask=mask, append=append, value=value)
- }
- if(invert==FALSE){
- value <- .appendMask(mask=mask, append=append, value=value)
- }
- value
+ if (invert)
+ value <- gaps(value, start=1L, end=length)
+ append <- match.arg(append, choices=c("union", "replace", "intersect"))
+ value <- switch(append,
+ "union"=union(mask, value),
+ "replace"=value,
+ "intersect"=intersect(mask, value))
+ as(value, "NormalIRanges")
}
setGeneric("rowmask<-", signature=c("x", "value"),
function(x, append="union", invert=FALSE, value)
@@ -119,20 +111,16 @@ setReplaceMethod("rowmask", signature(x="MultipleAlignment", value="NULL"),
value=new("NormalIRanges"))
)
setReplaceMethod("rowmask",
- signature(x="MultipleAlignment", value="NormalIRanges"),
+ signature(x="MultipleAlignment", value="ANY"),
function(x, append="union", invert=FALSE, value)
{
+ if (!is(value, "IRanges"))
+ value <- as(value, "IRanges")
value <- .setMask(mask=rowmask(x), append=append, invert=invert,
length=dim(x)[1], value=value)
initialize(x, rowmask = value)
}
)
-setReplaceMethod("rowmask",
- signature(x="MultipleAlignment", value="ANY"),
- function(x, append="union", invert=FALSE, value)
- callGeneric(x, append=append, invert=invert,
- value=as(value, "NormalIRanges"))
-)
setGeneric("colmask", signature="x", function(x) standardGeneric("colmask"))
setMethod("colmask", "MultipleAlignment", function(x) x at colmask)
@@ -147,20 +135,16 @@ setReplaceMethod("colmask", signature(x="MultipleAlignment", value="NULL"),
value=new("NormalIRanges"))
)
setReplaceMethod("colmask",
- signature(x="MultipleAlignment", value="NormalIRanges"),
+ signature(x="MultipleAlignment", value="ANY"),
function(x, append="union", invert=FALSE, value)
{
+ if (!is(value, "IRanges"))
+ value <- as(value, "IRanges")
value <- .setMask(mask=colmask(x), append=append, invert=invert,
length=dim(x)[2], value=value)
initialize(x, colmask = value)
}
)
-setReplaceMethod("colmask",
- signature(x="MultipleAlignment", value="ANY"),
- function(x, append="union",invert=FALSE, value)
- callGeneric(x, append=append, invert=invert,
- value=as(value, "NormalIRanges"))
-)
setMethod("maskMotif", signature(x="MultipleAlignment", motif="ANY"),
function(x, motif, min.block.width=1, ...)
diff --git a/build/vignette.rds b/build/vignette.rds
index ef2b588..7779998 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/Biostrings2Classes.pdf b/inst/doc/Biostrings2Classes.pdf
index 4d1736a..4c95336 100644
Binary files a/inst/doc/Biostrings2Classes.pdf and b/inst/doc/Biostrings2Classes.pdf differ
diff --git a/inst/doc/BiostringsQuickOverview.pdf b/inst/doc/BiostringsQuickOverview.pdf
index 91ee8e8..570d7ab 100644
Binary files a/inst/doc/BiostringsQuickOverview.pdf and b/inst/doc/BiostringsQuickOverview.pdf differ
diff --git a/inst/doc/MultipleAlignments.pdf b/inst/doc/MultipleAlignments.pdf
index c63b3ba..9df9460 100644
Binary files a/inst/doc/MultipleAlignments.pdf and b/inst/doc/MultipleAlignments.pdf differ
diff --git a/inst/doc/PairwiseAlignments.pdf b/inst/doc/PairwiseAlignments.pdf
index 2f09b0d..d7f3355 100644
Binary files a/inst/doc/PairwiseAlignments.pdf and b/inst/doc/PairwiseAlignments.pdf differ
diff --git a/inst/doc/matchprobes.pdf b/inst/doc/matchprobes.pdf
index a5858ad..14d49d5 100644
Binary files a/inst/doc/matchprobes.pdf and b/inst/doc/matchprobes.pdf differ
diff --git a/man/MultipleAlignment-class.Rd b/man/MultipleAlignment-class.Rd
index ba37a35..50a50e5 100644
--- a/man/MultipleAlignment-class.Rd
+++ b/man/MultipleAlignment-class.Rd
@@ -23,13 +23,11 @@
\alias{rowmask,MultipleAlignment-method}
\alias{rowmask<-}
\alias{rowmask<-,MultipleAlignment,NULL-method}
-\alias{rowmask<-,MultipleAlignment,NormalIRanges-method}
\alias{rowmask<-,MultipleAlignment,ANY-method}
\alias{colmask}
\alias{colmask,MultipleAlignment-method}
\alias{colmask<-}
\alias{colmask<-,MultipleAlignment,NULL-method}
-\alias{colmask<-,MultipleAlignment,NormalIRanges-method}
\alias{colmask<-,MultipleAlignment,ANY-method}
\alias{maskMotif,MultipleAlignment,ANY-method}
\alias{maskGaps}
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