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Remove C function getXStringSetClass()

C function getXStringSetClass() was a wrapper around C function
get_XStringSet_xsbaseclassname() defined in the Biostrings package,
which is itself a wrapper around C function get_List_elementType()
defined in the S4Vectors package. However, get_XStringSet_xsbaseclassname()
is about to be removed from Biostrings so any call to it should be replaced
with a call to get_List_elementType(). But since getXStringSetClass() is
not used, I removed it instead of fixing it (the fix would have been to
make it a wrapper around get_List_elementType() instead of around
get_XStringSet_xsbaseclassname()).

Hervé Pagès authored on 16/03/2018 02:31:17
Showing1 changed files
... ...
@@ -54,11 +54,6 @@ ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
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     return(result);
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 }
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-const char * getXStringSetClass(SEXP xR)
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-{
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-    return get_XStringSet_xsbaseclassname(xR);
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-}
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-
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 char DNAorRNAdecode(int c, int decodeType)
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 {
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     if (decodeType == DT_RNA_BIOSTRING)
Browse code

fix to adapt to changed Biostrings/S4Vectors API

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@97254 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 01/12/2014 18:20:14
Showing1 changed files
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@@ -42,7 +42,7 @@ ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
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         {
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             Chars_holder s = get_elt_from_XStringSet_holder(&holder, i);
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             result.nchar[i] = s.length;
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-            result.ptr[i] = (char *)s.seq;
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+            result.ptr[i] = (char *)s.ptr;
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         }
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     }
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     else
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Update to version 1.1.2; see inst/NEWS for details

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@97200 bc3139a8-67e5-0310-9ffc-ced21a209358

Ulrich Bodenhofer authored on 28/11/2014 12:49:36
Showing1 changed files
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@@ -42,7 +42,7 @@ ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
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         {
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             Chars_holder s = get_elt_from_XStringSet_holder(&holder, i);
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             result.nchar[i] = s.length;
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-            result.ptr[i] = (char *)s.ptr;
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+            result.ptr[i] = (char *)s.seq;
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         }
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     }
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     else
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'seq' member was renamed 'ptr' in data structs Chars_holder, Ints_holder, and Doubles_holder.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@97101 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 25/11/2014 10:46:00
Showing1 changed files
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@@ -42,7 +42,7 @@ ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
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         {
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             Chars_holder s = get_elt_from_XStringSet_holder(&holder, i);
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             result.nchar[i] = s.length;
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-            result.ptr[i] = (char *)s.seq;
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+            result.ptr[i] = (char *)s.ptr;
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         }
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     }
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     else
Browse code

Adds facopy/ IMPCdata/ kebabs/ ToPASeq/ tracktables/ to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/kebabs@95191 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 08/10/2014 23:11:31
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1 1
new file mode 100644
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@@ -0,0 +1,76 @@
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+#include "ByteStringVector.h"
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+#include "IRanges_interface.h"
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+#include "Biostrings_interface.h"
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+
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+ByteStringVector charVector2ByteStringVec(SEXP cvR)
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+{
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+    ByteStringVector result;
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+    result.length = LENGTH(cvR);
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+
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+    if (result.length > 0)
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+    {
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+        result.nchar = (int *)R_alloc(result.length, sizeof(int));
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+        result.ptr   = (char **)R_alloc(result.length, sizeof(char *));
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+
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+        for (R_len_t i = 0; i < result.length; i++)
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+        {
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+            result.ptr[i] = (char *)CHAR(STRING_ELT(cvR, i));
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+            result.nchar[i] = strlen(result.ptr[i]);
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+        }
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+    }
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+    else
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+    {
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+        result.nchar = NULL;
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+        result.ptr = NULL;
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+    }
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+
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+    return(result);
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+}
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+
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+ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
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+{
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+    ByteStringVector result;
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+    XStringSet_holder holder = hold_XStringSet(xssR);
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+    result.length = get_XStringSet_length(xssR);
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+
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+    if (result.length > 0)
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+    {
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+        result.nchar = (int *)R_alloc(result.length, sizeof(int));
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+        result.ptr   = (char **)R_alloc(result.length, sizeof(char *));
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+
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+        for (int i = 0; i < result.length; i++)
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+        {
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+            Chars_holder s = get_elt_from_XStringSet_holder(&holder, i);
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+            result.nchar[i] = s.length;
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+            result.ptr[i] = (char *)s.seq;
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+        }
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+    }
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+    else
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+    {
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+        result.nchar = NULL;
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+        result.ptr = NULL;
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+    }
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+
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+    return(result);
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+}
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+
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+const char * getXStringSetClass(SEXP xR)
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+{
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+    return get_XStringSet_xsbaseclassname(xR);
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+}
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+
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+char DNAorRNAdecode(int c, int decodeType)
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+{
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+    if (decodeType == DT_RNA_BIOSTRING)
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+        return RNAdecode((char) c);
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+    else
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+        return DNAdecode((char) c);
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+}
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+
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+char DNAorRNAencode(int c, int encodeType)
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+{
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+    if (encodeType == DT_RNA_BIOSTRING)
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+        return RNAencode((char) c);
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+    else
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+        return DNAencode((char) c);
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+}