#include "ByteStringVector.h"
 #include "IRanges_interface.h"
 #include "Biostrings_interface.h"
 
 ByteStringVector charVector2ByteStringVec(SEXP cvR)
 {
     ByteStringVector result;
     result.length = LENGTH(cvR);
 
     if (result.length > 0)
     {
         result.nchar = (int *)R_alloc(result.length, sizeof(int));
         result.ptr   = (char **)R_alloc(result.length, sizeof(char *));
 
         for (R_len_t i = 0; i < result.length; i++)
         {
             result.ptr[i] = (char *)CHAR(STRING_ELT(cvR, i));
             result.nchar[i] = strlen(result.ptr[i]);
         }
     }
     else
     {
         result.nchar = NULL;
         result.ptr = NULL;
     }
 
     return(result);
 }
 
 ByteStringVector XStringSet2ByteStringVec(SEXP xssR)
 {
     ByteStringVector result;
     XStringSet_holder holder = hold_XStringSet(xssR);
     result.length = get_XStringSet_length(xssR);
 
     if (result.length > 0)
     {
         result.nchar = (int *)R_alloc(result.length, sizeof(int));
         result.ptr   = (char **)R_alloc(result.length, sizeof(char *));
 
         for (int i = 0; i < result.length; i++)
         {
             Chars_holder s = get_elt_from_XStringSet_holder(&holder, i);
             result.nchar[i] = s.length;

             result.ptr[i] = (char *)s.ptr;

         }
     }
     else
     {
         result.nchar = NULL;
         result.ptr = NULL;
     }
 
     return(result);
 }
 
 char DNAorRNAdecode(int c, int decodeType)
 {
     if (decodeType == DT_RNA_BIOSTRING)
         return RNAdecode((char) c);
     else
         return DNAdecode((char) c);
 }
 
 char DNAorRNAencode(int c, int encodeType)
 {
     if (encodeType == DT_RNA_BIOSTRING)
         return RNAencode((char) c);
     else
         return DNAencode((char) c);
 }