--- /dev/null
+/* read_dna.c 2012-12-27 */
+
+/* Copyright 2008-2012 Emmanuel Paradis */
+
+/* This file is part of the R-package `ape'. */
+/* See the file ../COPYING for licensing issues. */
+
+#include <R.h>
+#include <Rinternals.h>
+
+// The initial code defining and initialising the translation table:
+//
+// for (i = 0; i < 122; i++) tab_trans[i] = 0x00;
+//
+// tab_trans[65] = 0x88; /* A */
+// tab_trans[71] = 0x48; /* G */
+// tab_trans[67] = 0x28; /* C */
+// tab_trans[84] = 0x18; /* T */
+// tab_trans[82] = 0xc0; /* R */
+// tab_trans[77] = 0xa0; /* M */
+// tab_trans[87] = 0x90; /* W */
+// tab_trans[83] = 0x60; /* S */
+// tab_trans[75] = 0x50; /* K */
+// tab_trans[89] = 0x30; /* Y */
+// tab_trans[86] = 0xe0; /* V */
+// tab_trans[72] = 0xb0; /* H */
+// tab_trans[68] = 0xd0; /* D */
+// tab_trans[66] = 0x70; /* B */
+// tab_trans[78] = 0xf0; /* N */
+//
+// tab_trans[97] = 0x88; /* a */
+// tab_trans[103] = 0x48; /* g */
+// tab_trans[99] = 0x28; /* c */
+// tab_trans[116] = 0x18; /* t */
+// tab_trans[114] = 0xc0; /* r */
+// tab_trans[109] = 0xa0; /* m */
+// tab_trans[119] = 0x90; /* w */
+// tab_trans[115] = 0x60; /* s */
+// tab_trans[107] = 0x50; /* k */
+// tab_trans[121] = 0x30; /* y */
+// tab_trans[118] = 0xe0; /* v */
+// tab_trans[104] = 0xb0; /* h */
+// tab_trans[100] = 0xd0; /* d */
+// tab_trans[98] = 0x70; /* b */
+// tab_trans[110] = 0xf0; /* n */
+//
+// tab_trans[45] = 0x04; /* - */
+// tab_trans[63] = 0x02; /* ? */
+
+static const unsigned char tab_trans[] = {
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 0-9 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 10-19 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 20-29 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 30-39 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x04, 0x00, 0x00, 0x00, 0x00, /* 40-49 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 50-59 */
+ 0x00, 0x00, 0x00, 0x02, 0x00, 0x88, 0x70, 0x28, 0xd0, 0x00, /* 60-69 */
+ 0x48, 0x00, 0xb0, 0x00, 0x00, 0x50, 0x00, 0xa0, 0xf0, 0x00, /* 70-79 */
+ 0x00, 0x00, 0xc0, 0x60, 0x18, 0x00, 0xe0, 0x90, 0x00, 0x30, /* 80-89 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x88, 0x70, 0x28, /* 90-99 */
+ 0xd0, 0x00, 0x00, 0x48, 0xb0, 0x00, 0x00, 0x50, 0x00, 0xa0, /* 100-109 */
+ 0xf0, 0x00, 0x00, 0x00, 0xc0, 0x60, 0x18, 0x00, 0xe0, 0x90, /* 110-119 */
+ 0x00, 0x30, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 120-129 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 130-139 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 140-149 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 150-159 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 160-169 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 170-179 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 180-189 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 190-199 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 200-209 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 210-219 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 220-229 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 230-239 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, /* 240-249 */
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00}; /* 250-255 */
+
+static const unsigned char hook = 0x3e;
+static const unsigned char lineFeed = 0x0a;
+/* static const unsigned char space = 0x20; */
+
+SEXP rawStreamToDNAbin(SEXP x)
+{
+ int N, i, j, k, n;
+ unsigned char *xr, *rseq, *buffer, tmp;
+ SEXP obj, nms, seq;
+
+ PROTECT(x = coerceVector(x, RAWSXP));
+ N = LENGTH(x);
+ xr = RAW(x);
+
+/* do a 1st pass to find the number of sequences */
+
+ n = 0;
+ j = 0; /* use j as a flag */
+ for (i = 0; i < N; i++) {
+ if (j && xr[i] == lineFeed) {
+ n++;
+ j = 0;
+ } else if (xr[i] == hook) j = 1;
+ }
+
+ PROTECT(obj = allocVector(VECSXP, n));
+ PROTECT(nms = allocVector(STRSXP, n));
+
+/* Refine the way the size of the buffer is set? */
+ buffer = (unsigned char *)R_alloc(N, sizeof(unsigned char *));
+
+ i = j = 0;
+ while (i < N) {
+ /* 1st read the label... */
+ if (xr[i] == hook) {
+ i++;
+ k = 0;
+ while (xr[i] != lineFeed) buffer[k++] = xr[i++];
+ buffer[k] = '\0';
+ SET_STRING_ELT(nms, j, mkChar(buffer));
+ }
+ /* ... then read the sequence */
+ n = 0;
+ while (xr[i] != hook && i < N) {
+ tmp = tab_trans[xr[i++]];
+/* If we are sure that the FASTA file is correct (ie, the sequence on
+ a single line and only the IUAPC code (plus '-' and '?') is used,
+ then the following check would not be needed; additionally the size
+ of tab_trans could be restriced to 0-121. This check has the
+ advantage that all invalid characters are simply ignored without
+ causing error. */
+ if (tmp) buffer[n++] = tmp;
+ }
+ PROTECT(seq = allocVector(RAWSXP, n));
+ rseq = RAW(seq);
+ for (k = 0; k < n; k++) rseq[k] = buffer[k];
+ SET_VECTOR_ELT(obj, j, seq);
+ UNPROTECT(1);
+ j++;
+ }
+ setAttrib(obj, R_NamesSymbol, nms);
+ UNPROTECT(3);
+ return obj;
+}
projects / ape.git / blobdiff