source: branches/port5/PROBE/PT_io.cxx

#include <stdio.h>
#include <stdlib.h>
// #include <malloc.h>
#include <memory.h>
#include <string.h>
#include <stdint.h>

#include <PT_server.h>
#include "probe.h"
#include <arbdbt.h>
#include <BI_helix.hxx>

#include <inline.h>

extern "C" { char *gbs_malloc_copy(char *,long); }


/* change a sequence with normal bases the PT_? format and delete all other signs */
int compress_data(char *probestring)
{
    char    c;
    char    *src,
        *dest;
    dest = src = probestring;

    while((c=*(src++)))
    {
        switch (c) {
            case 'A':
            case 'a': *(dest++) = PT_A;break;
            case 'C':
            case 'c': *(dest++) = PT_C;break;
            case 'G':
            case 'g': *(dest++) = PT_G;break;
            case 'U':
            case 'u':
            case 'T':
            case 't': *(dest++) = PT_T;break;
            case 'N':
            case 'n': *(dest++) = PT_N;break;
            default: break;
        }

    }
    *dest = PT_QU;
    return 0;
}

/* get a string with readable bases from a string with PT_? */
void PT_base_2_string(char *id_string, long len)
{
    char    c;
    char    *src,
        *dest;
    if (!len) len = strlen(id_string);
    dest = src = id_string;

    while((len--)>0){
        c=*(src++);
        switch (c) {
            case PT_A: *(dest++)  = 'A';break;
            case PT_C: *(dest++)  = 'C';break;
            case PT_G: *(dest++)  = 'G';break;
            case PT_T: *(dest++)  = 'U';break;
            case PT_N: *(dest++)  = 'N';break;
            case 0: *(dest++)     = '0'; break;
            default: *(dest++)    = c;break;
        }

    }
    *dest = '\0';
}

void probe_read_data_base(char *name)
{
    GBDATA *gb_main;
    GBDATA *gb_species_data;

    GB_set_verbose();
#if defined(DEVEL_RALF)
#warning gb_main should be closed    
#endif // DEVEL_RALF
    gb_main = GB_open(name,"r");
    if (!gb_main) {
        printf("Error reading file %s\n",name);
        exit(EXIT_FAILURE);
    }
    GB_begin_transaction(gb_main);
    gb_species_data = GB_entry(gb_main,"species_data");
    if (!gb_species_data){
        printf("Database %s is empty\n",name);
        exit(EXIT_FAILURE);
    }
    psg.gb_main         = gb_main;
    psg.gb_species_data = gb_species_data;
    psg.gb_sai_data     = GBT_get_SAI_data(gb_main);

    GB_commit_transaction(gb_main);
}

inline size_t count_uint_32(uint32_t *seq, size_t seqsize, uint32_t cmp) {
    size_t count = 0;
    while (count<seqsize && seq[count] == cmp) count++;
    return count*4;
}

inline size_t count_char(const char *seq, size_t seqsize, char c, uint32_t c4) {
    if (seq[0] == c) {
        size_t count = 1+count_uint_32((uint32_t*)(seq+1), (seqsize-1)/4, c4);
        for (; count<seqsize && seq[count] == c; ++count) ;
        return count;
    }
    return 0;
}

inline size_t count_dots(const char *seq, int seqsize) { return count_char(seq, seqsize, '.', 0x2E2E2E2E); }
inline size_t count_gaps(const char *seq, int seqsize) { return count_char(seq, seqsize, '-', 0x2D2D2D2D); }

inline size_t count_gaps_and_dots(const char *seq, int seqsize) {
    size_t count = 0;
    size_t count2;
    size_t count3;

    do {
        count2  = count_dots(seq+count, seqsize-count);
        count  += count2;
        count3  = count_gaps(seq+count, seqsize-count);
        count  += count3;
    }
    while (count2 || count3);
    return count;
}

int probe_compress_sequence(char *seq, int seqsize)
{
    static uchar *tab = 0;
    if (!tab) {
        tab = (uchar *)malloc(256);
        memset(tab,PT_N,256);
        
        tab['A'] = tab['a'] = PT_A;
        tab['C'] = tab['c'] = PT_C;
        tab['G'] = tab['g'] = PT_G;
        tab['T'] = tab['t'] = PT_T;
        tab['U'] = tab['u'] = PT_T;
        tab['.'] = PT_QU;
        tab[0]   = PT_B_UNDEF;
    }

    char   *dest   = seq;
    size_t  offset = 0;

    while (seq[offset]) {
        offset += count_gaps(seq+offset, seqsize-offset); // skip over gaps

        uchar c = tab[safeCharIndex(seq[offset++])];
        if (c == PT_B_UNDEF) break;                 // already seen terminal zerobyte

        *dest++ = c;
        if (c == PT_QU) {                           // TODO: *seq = '.' ???
            offset += count_gaps_and_dots(seq+offset, seqsize-offset); // skip over gaps and dots
            // dest[-1] = PT_N; // @@@ uncomment this to handle '.' like 'N' (experimental!!!)
        }
    }

    if (dest[-1] != PT_QU) {
        *dest++ = PT_QU;
    }

#ifdef ARB_64
    arb_assert(!((dest - seq) & 0xffffffff00000000));    // must fit into 32 bit
#endif    

    return dest-seq;
}

static char *probe_read_string_append_point(GBDATA *gb_data, int *psize) {
    long  len  = GB_read_string_count(gb_data);
    char *data = GB_read_string(gb_data);

    if (data) {
        if (data[len - 1] != '.') {
            char *buffer = (char *) malloc(len + 2);
            strcpy(buffer, data);
            buffer[len++] = '.';
            buffer[len] = 0;
            freeset(data, buffer);
        }
        *psize = len;
    }
    else {
        *psize = 0;
    }
    return data;
}

char *probe_read_alignment(int j, int *psize) {
    char   *buffer = 0;
    GBDATA *gb_ali = GB_entry(psg.data[j].gbd, psg.alignment_name);
    
    if (gb_ali) {
        GBDATA *gb_data = GB_entry(gb_ali, "data");
        if (gb_data) buffer = probe_read_string_append_point(gb_data, psize);
    }
    return buffer;
}

void probe_read_alignments() {
    // reads sequence data into psg.data

    GB_begin_transaction(psg.gb_main);

    // read ref SAI (e.g. ecoli)
    {
        char   *def_ref = GBT_get_default_ref(psg.gb_main);
        GBDATA *gb_ref  = GBT_find_SAI_rel_SAI_data(psg.gb_sai_data, def_ref);

        psg.ecoli = 0;
        if (gb_ref) {
            GBDATA *gb_data = GBT_read_sequence(gb_ref, psg.alignment_name);
            if (gb_data) {
                psg.ecoli = GB_read_string(gb_data);
            }
        }
        free(def_ref);
    }

    int count = GB_number_of_subentries(psg.gb_species_data);

    psg.data       = (probe_input_data *)calloc(sizeof(probe_input_data), count);
    psg.data_count = 0;
    
    printf("Database contains %i species.\nPreparing sequence data:\n", count);

    int data_missing  = 0;
    int species_count = count;

    count = 0;

    for (GBDATA *gb_species = GBT_first_species_rel_species_data(psg.gb_species_data);
         gb_species;
         gb_species = GBT_next_species(gb_species) )
    {
        probe_input_data& pid = psg.data[count];

        pid.name     = strdup(GBT_read_name(gb_species));
        pid.fullname = GBT_read_string(gb_species, "full_name");

        if (!pid.fullname) pid.fullname = strdup("");

        pid.is_group = 1;
        pid.gbd      = gb_species;
        
        GBDATA *gb_ali = GB_entry(gb_species, psg.alignment_name);
        if (gb_ali) {
            GBDATA *gb_data = GB_entry(gb_ali,"data");
            if (!gb_data) {
                fprintf(stderr,"Species '%s' has no data in '%s'\n", pid.name, psg.alignment_name);
                data_missing++;
            }
            else {
                int   hsize;
                char *data = probe_read_string_append_point(gb_data, &hsize);

                if (!data) {
                    GB_ERROR error = GB_await_error();
                    fprintf(stderr, "Could not read data in '%s' for species '%s'\n(Reason: %s)\n",
                            psg.alignment_name, pid.name, error);
                    data_missing++;
                }
                else {
                    pid.checksum = GB_checksum(data, hsize, 1, ".-");
                    int size     = probe_compress_sequence(data, hsize);

                    pid.data = (char *)gbs_malloc_copy(data, size);
                    pid.size = size;
                    
                    count ++;
                    if (count%10 == 0) {
                        if (count%500) fputc('.', stdout);
                        else printf(".%6i (%5.1f%%)\n", count, ((double)count/species_count)*100);
                        fflush(stdout);
                    }
                }
                free(data);
            }
        }
    }

    psg.data_count = count;
    GB_commit_transaction(psg.gb_main);
    
    if (data_missing) {
        printf("\n%i species were ignored because of missing data.\n", data_missing);
    }
    else {
        printf("\nAll species contain data in alignment '%s'.\n", psg.alignment_name);
    }
    fflush(stdout);
}

void PT_build_species_hash(void){
    long i;
    psg.namehash = GBS_create_hash(PT_NAME_HASH_SIZE, GB_MIND_CASE);
    for (i=0;i<psg.data_count;i++){
        GBS_write_hash(psg.namehash, psg.data[i].name,i+1);
    }
    unsigned int    max_size;
    max_size = 0;
    for (i = 0; i < psg.data_count; i++){   /* get max sequence len */
        max_size = max(max_size, (unsigned)(psg.data[i].size));
        psg.char_count += psg.data[i].size;
    }
    psg.max_size = max_size;

    if ( psg.ecoli){
        BI_ecoli_ref *ref = new BI_ecoli_ref;
        const char *error = ref->init(psg.ecoli,strlen(psg.ecoli));
        if (error) {
            delete psg.ecoli;
            psg.ecoli = 0;
        }else{
            psg.bi_ecoli = ref;
        }
    }
}


long PT_abs_2_rel(long pos) {
    if (!psg.ecoli) return pos;
    return psg.bi_ecoli->abs_2_rel(pos);
}

long PT_rel_2_abs(long pos) {
    if (!psg.ecoli) return pos;
    return psg.bi_ecoli->rel_2_abs(pos);
}