new chronos files and a bunch of various improvements

[ape.git] / src / read_dna.c

diff --git a/src/read_dna.c b/src/read_dna.c
index 6d44c6665603d19c0bcd0f6c8aea2409c94e671b..01a4db32c5d2b1de517d2f659496a73c1d1b9c13 100644 (file)
--- a/src/read_dna.c
+++ b/src/read_dna.c
@@ -1,6 +1,6 @@
-/* read_dna.c       2012-12-27 */
+/* read_dna.c       2013-01-04 */
 
-/* Copyright 2008-2012 Emmanuel Paradis */
+/* Copyright 2013 Emmanuel Paradis */
 
 /* This file is part of the R-package `ape'. */
 /* See the file ../COPYING for licensing issues. */
@@ -81,7 +81,7 @@ static const unsigned char lineFeed = 0x0a;
 
 SEXP rawStreamToDNAbin(SEXP x)
 {
-       int N, i, j, k, n;
+       int N, i, j, k, n, startOfSeq;
        unsigned char *xr, *rseq, *buffer, tmp;
        SEXP obj, nms, seq;
 
@@ -89,15 +89,25 @@ SEXP rawStreamToDNAbin(SEXP x)
        N = LENGTH(x);
        xr = RAW(x);
 
-/* do a 1st pass to find the number of sequences */
+/* 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++) {
+   this code should be robust to '>' present inside
+   a label or in the header text before the sequences */
+
+       n = j = 0; /* use j as a flag */
+       if (xr[0] == hook) {
+               j = 1;
+               startOfSeq = 0;
+       }
+       i = 1;
+       for (i = 1; i < N; i++) {
                if (j && xr[i] == lineFeed) {
                        n++;
                        j = 0;
-               } else if (xr[i] == hook) j = 1;
+               } else if (xr[i] == hook) {
+                       if (!n) startOfSeq = i;
+                       j = 1;
+               }
        }
 
        PROTECT(obj = allocVector(VECSXP, n));
@@ -106,16 +116,15 @@ SEXP rawStreamToDNAbin(SEXP x)
 /* Refine the way the size of the buffer is set? */
        buffer = (unsigned char *)R_alloc(N, sizeof(unsigned char *));
 
-       i = j = 0;
+       i = startOfSeq;
+       j = 0; /* gives the index of the sequence */
        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));
-               }
+               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) {
@@ -125,7 +134,7 @@ SEXP rawStreamToDNAbin(SEXP x)
    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. */
+   causing error -- except if '>' occurs in the middle of a sequence. */
                        if (tmp) buffer[n++] = tmp;
                }
                PROTECT(seq = allocVector(RAWSXP, n));