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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@114013 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 25/02/2016 15:24:31
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+msaConvert <- function(x, type=c("seqinr::alignment",
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+                                 "bios2mds::align"))
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+{
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+    type <- match.arg(type)
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+
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+    if (!is(x, "MultipleAlignment"))
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+        stop("x must be a 'MultipleAlignment' object")
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+
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+    x <- as.character(unmasked(x))
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+
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+    if (type == "seqinr::alignment")
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+    {
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+        out <- list(nb=length(x),
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+                    nam=names(x),
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+                    seq=unname(x),
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+                    com=NA)
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+
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+        class(out) <- "alignment"
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+    }
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+    else if (type == "bios2mds::align")
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+    {
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+        out <- .Call("SplitCharVector2List", x)
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+        names(out) <- names(x)
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+        class(out) <- "align"
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+    }
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+
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+    out
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+}