probe_match_parser.cxx

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//  ==================================================================== //
//                                                                       //
//    File      : probe_match_parser.cxx                                 //
//    Purpose   : parse the results of a probe match                     //
//                                                                       //
//                                                                       //
//  Coded by Ralf Westram (coder@reallysoft.de) in June 2004             //
//  Copyright Department of Microbiology (Technical University Munich)   //
//                                                                       //
//  Visit our web site at: http://www.arb-home.de/                       //
//                                                                       //
//  ==================================================================== //

#include "probe_match_parser.hxx"

#include <arbdbt.h>
#include <arb_defs.h>

#include <cctype>
#include <map>

#define pm_assert(cond) arb_assert(cond)

using namespace std;

// ----------------
//      column

struct column {
    const char *title;          // column title (pointer into ProbeMatch_impl::headline)
    int         start_column, end_column;

    column() : title(NULp), start_column(-1), end_column(-1) {}
    column(const char *t, int sc, int ec) : title(t), start_column(sc), end_column(ec) {}
};

// -------------------------
//      ProbeMatch_impl

typedef map<const char*, column, charpLess> ColumnMap;

class ProbeMatch_impl : virtual Noncopyable {
    char      *headline;
    ColumnMap  columns;
    int probe_region_offset;    // left index of probe region


public:
    ProbeMatch_impl(const char *headline_, char **errPtr) :
        headline(NULp),
        probe_region_offset(-1)
    {
        pm_assert(headline_);
        headline = ARB_strdup(headline_);

        for (char *tok_start = strtok(headline, " "); tok_start; tok_start = strtok(NULp, " ")) {
            char *tok_end = strchr(tok_start, 0)-1;

            int startPos = tok_start-headline;
            int endPos   = tok_end-headline;

            while (tok_end >= tok_start && tok_end[0] == '-') --tok_end;
            while (tok_start <= tok_end && tok_start[0] == '-') ++tok_start;
            pm_assert(tok_start <= tok_end); // otherwise column only contained '-'
            tok_end[1] = 0;

            columns[tok_start] = column(tok_start, startPos-2, endPos-2); // -2 because headline is 2 shorter than other lines
        }

        if (columns.empty()) *errPtr = ARB_strdup("No columns found");
    }

    ~ProbeMatch_impl() {
        free(headline);
    }

    column *findColumn(const char *columntitle) {
        ColumnMap::iterator ci = columns.find(columntitle);
        if (ci == columns.end()) return NULp;
        return &(ci->second);
    }

    void set_probe_region_offset(int offset) { probe_region_offset = offset; }
    int get_probe_region_offset() const { return probe_region_offset; }
};

// --------------------------
//      ProbeMatchParser

ProbeMatchParser::ProbeMatchParser(const char *probe_target, const char *headline) :
    pimpl(NULp),
    init_error(NULp)
{
    if (!headline) {
        init_error = ARB_strdup("No headline given");
    }
    else if (!probe_target) {
        init_error = ARB_strdup("No probe target given.");
    }
    else {
        pimpl = new ProbeMatch_impl(headline, &init_error);
        if (!init_error) {
            // modify target, so that it matches the target string in headline
            char *probe_target_copy = GBS_global_string_copy("'%s'", probe_target); // add single quotes
            for (int i = 0; probe_target_copy[i]; ++i) {
                probe_target_copy[i] = toupper(probe_target_copy[i]);
                if (probe_target_copy[i] == 'T') { // replace 'T' by 'U'
                    probe_target_copy[i] = 'U';
                }
            }

            // find that column and
            column *target_found = pimpl->findColumn(probe_target_copy);
            if (!target_found) {
                char *probe_rev_compl = ARB_strdup(probe_target_copy);
                GBT_reverseComplementNucSequence(probe_rev_compl, strlen(probe_rev_compl), 'U');
                target_found          = pimpl->findColumn(probe_rev_compl);
                free(probe_rev_compl);
            }

            if (target_found) {
                int probe_region_offset = target_found->start_column - 9;
                pimpl->set_probe_region_offset(probe_region_offset);
            }
            else {
                init_error = GBS_global_string_copy("Probe match parser failed (Could not find target '%s' in headline)", probe_target_copy);
            }
            free(probe_target_copy);
        }
    }
}

ProbeMatchParser::~ProbeMatchParser() {
    free(init_error);
    delete pimpl;
}

bool ProbeMatchParser::getColumnRange(const char *columnName, int *startCol, int *endCol) const {
    pm_assert(!init_error);
    column *col = pimpl->findColumn(columnName);
    if (!col) return false;

    *startCol = col->start_column;
    *endCol   = col->end_column;
    return true;
}

bool ProbeMatchParser::is_gene_result() const {
    pm_assert(!init_error);
    return pimpl->findColumn("organism") && pimpl->findColumn("genename");
}

int ProbeMatchParser::get_probe_region_offset() const {
    pm_assert(!init_error);
    return pimpl->get_probe_region_offset();
}

// --------------------------
//      ParsedProbeMatch

ParsedProbeMatch::ParsedProbeMatch(const char *match_, const ProbeMatchParser& parser_) :
    parser(parser_),
    match(NULp),
    error(NULp)
{
    if (match_) match = ARB_strdup(match_);
    else error = "No match given";
}

ParsedProbeMatch::~ParsedProbeMatch() {
    free(match);
}

inline char *strpartdup(const char *str, int c1, int c2) {
    int len = c2-c1+1;

    pm_assert(str);
    pm_assert(c1 <= c2);
    pm_assert((int)strlen(str) > c2);

    return ARB_strndup(str+c1, len);
}

int ParsedProbeMatch::get_position() const {
    pm_assert(!error);
    int c1, c2;
    if (parser.getColumnRange("pos", &c1, &c2)) {
        char *content = strpartdup(match, c1, c2);
        int   pos     = bio2info(atoi(content));
        free(content);
        return pos;
    }
    error = "no such column: 'pos'";
    return -1;
}

const char *ParsedProbeMatch::get_probe_region() const {
    pm_assert(!error);
    int pro      = parser.pimpl->get_probe_region_offset();
    int matchlen = strlen(match);

    if (pro<matchlen) {
        return match+pro;
    }

    error = GBS_global_string("can't parse match info '%s'", match);
    return NULp;
}

char *ParsedProbeMatch::get_column_content(const char *columnName, bool chop_spaces) const {
    pm_assert(!error);
    int sc, ec;
    if (parser.getColumnRange(columnName, &sc, &ec)) {
        if (chop_spaces) {
            while (sc<ec && match[sc] == ' ') ++sc;
            while (sc<ec && match[ec] == ' ') --ec;
        }
        return strpartdup(match, sc, ec);
    }
    return NULp;
}