seqio.cxx

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// ============================================================= //
//                                                               //
//   File      : seqio.cxx                                       //
//   Purpose   :                                                 //
//                                                               //
//   Institute of Microbiology (Technical University Munich)     //
//   http://www.arb-home.de/                                     //
//                                                               //
// ============================================================= //

#include "seqio.hxx"

#include <arbdb.h>

#define sio_assert(cond) arb_assert(cond)

namespace SEQIO {

    char *fgets_smartLF(char *s, int size, FILE *stream) {
        // same as fgets but also works with file in MacOS format
        int i;
        for (i = 0; i<(size-1); ++i) {
            int byte = fgetc(stream);
            if (byte == EOF) {
                if (i == 0) return NULp;
                break;
            }

            s[i] = byte;
            if (byte == '\n' || byte == '\r') break;
        }
        s[i] = 0;

        return s;
    }

    bool read_string_pair(FILE *in, char *&s1, char *&s2, size_t& lineNr) {
        // helper function to read import/export filters.
        // returns true if successfully read
        //
        // 's1' is set to a heap-copy of the first token on line
        // 's2' is set to a heap-copy of the rest of the line (or NULp if only one token is present)
        // 'lineNr' is incremented with each line read

        s1 = NULp;
        s2 = NULp;

        const int  BUFSIZE = 8000;
        char       buffer[BUFSIZE];
        char      *res;

        do {
            res = fgets_smartLF(&buffer[0], BUFSIZE-1, in);
            if (res) {
                char *p = buffer;

                lineNr++;

                while (*p == ' ' || *p == '\t') p++;
                if (*p != '#') {
                    int len = strlen(p)-1;
                    while  (len >= 0 && strchr("\t \n\r", p[len])) {
                        p[len--] = 0;
                    }

                    if (*p) {
                        char *e = strpbrk(p, " \t");

                        if (e) {
                            *(e++) = 0;
                            s1     = strdup(p);

                            e += strspn(e, " \t"); // skip whitespace

                            if (*e == '"') {
                                char *k = strrchr(e, '"');
                                if (k!=e) {
                                    e++;
                                    *k=0;
                                }
                            }
                            s2 = strdup(e);
                        }
                        else {
                            s1 = strdup(p);
                        }
                    }
                }
            }
        } while (res && !s1);                           // read until EOF or something found

        sio_assert(correlated(res, s1));

        return res;
    }

};