ARB
seqio.cxx
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1 // ============================================================= //
2 // //
3 // File : seqio.cxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // ============================================================= //
10 
11 #include "seqio.hxx"
12 
13 #include <arbdb.h>
14 
15 #define sio_assert(cond) arb_assert(cond)
16 
17 namespace SEQIO {
18 
19  char *fgets_smartLF(char *s, int size, FILE *stream) {
20  // same as fgets but also works with file in MacOS format
21  int i;
22  for (i = 0; i<(size-1); ++i) {
23  int byte = fgetc(stream);
24  if (byte == EOF) {
25  if (i == 0) return NULp;
26  break;
27  }
28 
29  s[i] = byte;
30  if (byte == '\n' || byte == '\r') break;
31  }
32  s[i] = 0;
33 
34  return s;
35  }
36 
37  bool read_string_pair(FILE *in, char *&s1, char *&s2, size_t& lineNr) {
38  // helper function to read import/export filters.
39  // returns true if successfully read
40  //
41  // 's1' is set to a heap-copy of the first token on line
42  // 's2' is set to a heap-copy of the rest of the line (or NULp if only one token is present)
43  // 'lineNr' is incremented with each line read
44 
45  s1 = NULp;
46  s2 = NULp;
47 
48  const int BUFSIZE = 8000;
49  char buffer[BUFSIZE];
50  char *res;
51 
52  do {
53  res = fgets_smartLF(&buffer[0], BUFSIZE-1, in);
54  if (res) {
55  char *p = buffer;
56 
57  lineNr++;
58 
59  while (*p == ' ' || *p == '\t') p++;
60  if (*p != '#') {
61  int len = strlen(p)-1;
62  while (len >= 0 && strchr("\t \n\r", p[len])) {
63  p[len--] = 0;
64  }
65 
66  if (*p) {
67  char *e = strpbrk(p, " \t");
68 
69  if (e) {
70  *(e++) = 0;
71  s1 = strdup(p);
72 
73  e += strspn(e, " \t"); // skip whitespace
74 
75  if (*e == '"') {
76  char *k = strrchr(e, '"');
77  if (k!=e) {
78  e++;
79  *k=0;
80  }
81  }
82  s2 = strdup(e);
83  }
84  else {
85  s1 = strdup(p);
86  }
87  }
88  }
89  }
90  } while (res && !s1); // read until EOF or something found
91 
92  sio_assert(correlated(res, s1));
93 
94  return res;
95  }
96 
97 };
bool read_string_pair(FILE *in, char *&s1, char *&s2, size_t &lineNr)
Definition: seqio.cxx:37
char buffer[MESSAGE_BUFFERSIZE]
Definition: seq_search.cxx:34
#define sio_assert(cond)
Definition: seqio.cxx:15
#define NULp
Definition: cxxforward.h:97
#define BUFSIZE
char * fgets_smartLF(char *s, int size, FILE *stream)
Definition: seqio.cxx:19
GB_write_int const char s
Definition: AW_awar.cxx:156