arb_string.cxx

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// ================================================================ //
//                                                                  //
//   File      : arb_string.cxx                                     //
//   Purpose   :                                                    //
//                                                                  //
//   Coded by Ralf Westram (coder@reallysoft.de) in November 2010   //
//   Institute of Microbiology (Technical University Munich)        //
//   http://www.arb-home.de/                                        //
//                                                                  //
// ================================================================ //

#include "arb_string.h"

#include <ctime>
#include <sys/time.h>
#include <Keeper.h>

inline tm *get_current_time() {
    timeval  date;
    tm      *p;

    gettimeofday(&date, NULp);

#if defined(DARWIN)
    struct timespec local;
    TIMEVAL_TO_TIMESPEC(&date, &local); // not avail in time.h of Linux gcc 2.95.3
    p = localtime(&local.tv_sec);
#else
    p = localtime(&date.tv_sec);
#endif // DARWIN

    return p;
}

const char *ARB_date_string() {
    const char *date_string = NULp;
#if defined(UNIT_TESTS)
    if (RUNNING_TEST()) {
        date_string = "Thu Nov 29 22:33:09 1973"; // timestamp used in unittests (=@123456789 CET)
    }
    else
#endif
    {
        tm   *p        = get_current_time();
        char *readable = asctime(p);          // points to a static buffer
        char *cr       = strchr(readable, '\n');
        arb_assert(cr);
        cr[0]          = 0;                   // cut of \n
        date_string    = readable;
    }
    return date_string;
}

const char *ARB_dateTime_suffix() {
    const  unsigned  SUFFIXLEN = 8+1+6;
    static char      buffer[SUFFIXLEN+1];
    tm              *p         = get_current_time();

#if defined(ASSERTION_USED)
    size_t printed =
#endif
        strftime(buffer, SUFFIXLEN+1, "%Y%m%d_%H%M%S", p);
    arb_assert(printed == SUFFIXLEN);
    buffer[SUFFIXLEN] = 0;

    return buffer;
}

// --------------------------------------------------------------------------------

const char *ARB_keep_string(char *str) {
    static Keeper<char*> stringKeeper;
    stringKeeper.keep(str);
    return str;
}


// --------------------------------------------------------------------------------


#ifdef UNIT_TESTS

#include <string>
#include <climits>

#ifndef TEST_UNIT_H
#include <test_unit.h>
#endif

using namespace std;

// ----------------------------------------------
//      some tests for unit-test-code itself

#define TEST_EXPECT_HEAPCOPY_EQUAL(copy,expected) do {  \
        char *theCopy = (copy);                         \
        TEST_EXPECT_EQUAL(theCopy, expected);           \
        free(theCopy);                                  \
    } while(0)

void TEST_arbtest_strf() {
    // tests string formatter from test_unit.h
    using namespace arb_test;
    TEST_EXPECT_HEAPCOPY_EQUAL(StaticCode::strf("<%i>", 7), "<7>");
    TEST_EXPECT_HEAPCOPY_EQUAL(StaticCode::strf("<%0*i>", 3, 7), "<007>");
}

void TEST_arbtest_readable() {
    using namespace arb_test;

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy('x')), "'x' (=0x78)");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(static_cast<unsigned char>('x'))), "'x' (=0x78)");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(static_cast<signed char>('x'))), "'x' (=0x78)");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(true)), "true");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(false)), "false");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(1)), "1");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2hex(make_copy(2)), "0x2");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(3L)), "3");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2hex(make_copy(4L)), "0x4");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(5U)), "5");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2hex(make_copy(6U)), "0x6");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy("some\ntext\twhich\"special\\chars")), "\"some\\ntext\\twhich\\\"special\\\\chars\"");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy("a\x01\x02\x07\x08\x09\x0b\x0c\x0d\x1a\x22\x27\x5c\x7e\x7f\x80\xfe\xff")),
                               /*                  */ "\"a\\1\\2\\a\\b\\t\\v\\f\\r\\x1a\\\"'\\\\~\\x7f\\x80\\xfe\\xff\"");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy((const char *)NULp)), "(null)");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy((const unsigned char *)NULp)), "(null)");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy((const signed char *)NULp)), "(null)");

    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(1.7)), "1.700000");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(177.0e20)),  "17699999999999998951424.000000");
    TEST_EXPECT_HEAPCOPY_EQUAL(val2readable(make_copy(177.0e20F)), "17699999967695435988992.000000");
}

void TEST_arbtest_copyable() {
    using namespace arb_test;

    int         i = 7;
    const char *s = "servas";

    TEST_EXPECT(make_copy(i) == make_copy(7));
    TEST_EXPECT_ZERO(strcmp(make_copy(s), make_copy("servas")));
}

#define TEST_DESCRIPTIONS(d, tt, tf, ft, ff) do {        \
        TEST_EXPECT_EQUAL((d).make(true, true), (tt));   \
        TEST_EXPECT_EQUAL((d).make(true, false), (tf));  \
        TEST_EXPECT_EQUAL((d).make(false, true), (ft));  \
        TEST_EXPECT_EQUAL((d).make(false, false), (ff)); \
    } while(0)

#define TEST_SIMPLE_DESCRIPTIONS(d, ae, nae) TEST_DESCRIPTIONS(d, ae, nae, ae, nae)

void TEST_arbtest_predicate_description() {
    TEST_SIMPLE_DESCRIPTIONS(predicate_description("similar"), "is similar", "isnt similar");
    TEST_SIMPLE_DESCRIPTIONS(predicate_description("repairs"), "repairs", "doesnt repair");

    TEST_DESCRIPTIONS(predicate_description("equals", "differs"),
                      "equals", "doesnt equal",
                      "doesnt differ", "differs");

    TEST_DESCRIPTIONS(predicate_description("less_than", "more_than"),
                      "is less_than", "isnt less_than",
                      "isnt more_than", "is more_than");
}

void TEST_arbtest_expectations() {
    // used to TDD expectations
    using namespace arb_test;

    string apple       = "Apfel";
    string pear        = "Birne";
    string boskop      = apple;
    string pomegranate = "Granatapfel";

    TEST_EXPECTATION(that(apple).is_equal_to("Apfel"));

    TEST_EXPECTATION(that(apple).does_differ_from(pear));
    TEST_EXPECTATION(that(apple).is_equal_to(boskop));
    TEST_EXPECTATION(wrong(that(pomegranate).is_equal_to(apple)));

    match_expectation ff1 = that(1.0).is_equal_to(2-1);
    match_expectation ff2 = that(boskop).is_equal_to(apple);
    match_expectation ff3 = that(apple).is_equal_to(apple);

    match_expectation nf1 = that(apple).is_equal_to(pear);
    match_expectation nf2 = that(pomegranate).is_equal_to(apple);
    match_expectation nf3 = that(apple).does_differ_from(boskop);

    match_expectation a1 = all().of(ff1);
    match_expectation a2 = all().of(ff1, ff2);
    match_expectation a3 = all().of(ff1, ff2, ff3);

    TEST_EXPECTATION(a1);
    TEST_EXPECTATION(a2);
    TEST_EXPECTATION(a3);

    match_expectation n1 = none().of(ff1);
    match_expectation n2 = none().of(ff1, ff2);
    match_expectation n3 = none().of(ff1, ff2, ff3);

    TEST_EXPECTATION(wrong(none().of(that(boskop).is_equal_to(apple))));
    TEST_EXPECTATION(wrong(n1));
    TEST_EXPECTATION(wrong(n2));
    TEST_EXPECTATION(wrong(n3));

    TEST_EXPECTATION(atleast(1).of(a1));
    TEST_EXPECTATION(atleast(1).of(a1, n1));
    TEST_EXPECTATION(atleast(1).of(n2, a1, n1));

    TEST_EXPECTATION(wrong(atleast(2).of(a1, n1, n2)));
    TEST_EXPECTATION(wrong(atleast(2).of(a1, n1)));
    TEST_EXPECTATION(wrong(atleast(2).of(a1))); // impossible

    TEST_EXPECTATION(atmost(2).of(a1));
    TEST_EXPECTATION(atmost(2).of(a1, a2));
    TEST_EXPECTATION(atmost(2).of(a1, a2, n1));
    TEST_EXPECTATION(atmost(2).of(a1, n1, n2));
    TEST_EXPECTATION(atmost(2).of(n1, n2));
    TEST_EXPECTATION(wrong(atmost(2).of(a1, a2, a3)));

    TEST_EXPECTATION(exactly(1).of(ff1, nf1, nf2));
    TEST_EXPECTATION(wrong(exactly(1).of(nf1, nf2)));
    TEST_EXPECTATION(wrong(exactly(1).of(nf1, nf2, nf3)));
    TEST_EXPECTATION(wrong(exactly(1).of(ff1, ff2, nf2)));
    TEST_EXPECTATION(wrong(exactly(1).of(ff1, ff2, ff3)));

}

void TEST_expectation_groups() {
    using namespace arb_test;

    expectation_group no_expectations;
    TEST_EXPECTATION(all().ofgroup(no_expectations));
    TEST_EXPECTATION(none().ofgroup(no_expectations));

    expectation_group fulfilled_expectation  (that(1).is_equal_to(1));
    expectation_group unfulfilled_expectation(that(1).is_equal_to(0));
    expectation_group some_fulfilled_expectations(that(1).is_equal_to(0), that(1).is_equal_to(1));

    TEST_EXPECTATION(all().ofgroup(fulfilled_expectation));
    TEST_EXPECTATION(none().ofgroup(unfulfilled_expectation));

    TEST_EXPECT(none().ofgroup(fulfilled_expectation).unfulfilled());
    TEST_EXPECT(all().ofgroup(unfulfilled_expectation).unfulfilled());

    TEST_EXPECT(all().ofgroup(some_fulfilled_expectations).unfulfilled());
    TEST_EXPECT(none().ofgroup(some_fulfilled_expectations).unfulfilled());
}

void TEST_replace_old_TEST_EXPECTS_by_expectations() {
    // test various string-types are matchable (w/o casts)
    {
        const char *car_ccp = "Alfa";
        char       *car_cp  = ARB_strdup("Alfa");
        string      car_str("Alfa");

        TEST_EXPECT_EQUAL(car_ccp, "Alfa");
        TEST_EXPECT_EQUAL(car_cp, "Alfa");
        TEST_EXPECT_EQUAL(car_str, "Alfa");

        TEST_EXPECT_EQUAL("Alfa", car_ccp);
        TEST_EXPECT_EQUAL("Alfa", car_cp);
        TEST_EXPECT_EQUAL("Alfa", car_str);

        TEST_EXPECT_EQUAL(car_cp, car_ccp);
        TEST_EXPECT_EQUAL(car_cp, car_str);
        TEST_EXPECT_EQUAL(car_ccp, car_cp);
        TEST_EXPECT_EQUAL(car_ccp, car_str);
        TEST_EXPECT_EQUAL(car_str, car_cp);
        TEST_EXPECT_EQUAL(car_str, car_ccp);

        char *null = NULp;
        TEST_EXPECT_NULL((void*)NULp);
        TEST_EXPECT_NULL(null);

        TEST_EXPECT_CONTAINS(car_ccp, "lf");
        TEST_EXPECT_CONTAINS(car_cp, "fa");
        TEST_EXPECT_CONTAINS(car_str, "Al");

        free(car_cp);
    }

    // test various numeric types are matchable

    {
        short unsigned su = 7;
        short          s  = -su;

        unsigned iu = su;
        int      i  = -iu;

        long unsigned lu = (long unsigned)INT_MAX+3;
        long          l  = -lu;

        float  f = s;
        double d = i;

        TEST_EXPECT_EQUAL(s, -7);
        TEST_EXPECT_EQUAL(i, -7);

        TEST_EXPECT_EQUAL(su, 7);  TEST_EXPECT_EQUAL(iu, 7);
        TEST_EXPECT_EQUAL(su, 7U); TEST_EXPECT_EQUAL(iu, 7U);
        TEST_EXPECT_EQUAL(su, 7L); TEST_EXPECT_EQUAL(iu, 7L);

        TEST_EXPECT_EQUAL(s, -su); TEST_EXPECT_EQUAL(s, -iu);
        TEST_EXPECT_EQUAL(i, -iu); TEST_EXPECT_EQUAL(i, -su);
        TEST_EXPECT_EQUAL(l, -lu);

        TEST_EXPECT_EQUAL(f, d);
        TEST_EXPECT_EQUAL(d, f);
    }

    TEST_EXPECT_ZERO(7-7);
}

// --- simulate user_type (which may be defined anywhere) ---
class user_type {
    int x, y;
public:
    user_type(int X, int Y) : x(X), y(Y) {}

    int get_x() const { return x; }
    int get_y() const { return y; }

    user_type flipped() const { return user_type(y,x); }

    int quadrant() const {
        if (x == 0 || y == 0) return 0; // on axis
        if (y>0) return x<0 ? 2 : 1;
        return x<0 ? 3 : 4;
    }
};
// --- end of user_type ---

// helpers needed for tests:
inline bool operator == (const user_type& u1, const user_type& u2) { return u1.get_x() == u2.get_x() && u1.get_y() == u2.get_y(); }
inline char *val2readable(const user_type& u) { return arb_test::StaticCode::strf("user_type(%i,%i)", u.get_x(), u.get_y()); }
inline bool in_same_quadrant(const user_type& u1, const user_type& u2) { return u1.quadrant() == u2.quadrant(); }

void TEST_user_type_with_expectations() {
    user_type ut1(3, 4);
    user_type ut12(4, 4);
    user_type ut2(-4, 4);
    user_type ut3(-4, -8);
    user_type ut4(4, -8);

    TEST_EXPECTATION(that(ut1).does_differ_from(ut12));
    TEST_EXPECTATION(that(ut12).is_equal_to(ut12.flipped()));
    TEST_EXPECTATION(that(ut1).does_differ_from(ut1.flipped()));

    TEST_EXPECTATION(that(ut1).fulfills(in_same_quadrant, ut12));
    TEST_EXPECTATION(none().of(that(ut1).fulfills(in_same_quadrant, ut2),
                          that(ut2).fulfills(in_same_quadrant, ut3),
                          that(ut3).fulfills(in_same_quadrant, ut4)));
}
TEST_PUBLISH(TEST_user_type_with_expectations);

void TEST_similarity() {
    double d1      = 0.7531;
    double epsilon = 0.00001;
    double d2      = d1-epsilon*0.6;
    double d3      = d1+epsilon*0.6;

    TEST_EXPECTATION(that(d1).fulfills(epsilon_similar(epsilon), d2));
    TEST_EXPECTATION(that(d1).fulfills(epsilon_similar(epsilon), d3));
    TEST_EXPECTATION(that(d2).contradicts(epsilon_similar(epsilon), d3));

    TEST_EXPECT_SIMILAR(d1, d2, epsilon);
    TEST_EXPECT_SIMILAR(d1, d3, epsilon);
}

void TEST_less_equal() {
    int x = 7;
    int y = 8;
    int z = 9;

    // less/more etc

    TEST_EXPECTATION(that(x).is_less_than(y));
    TEST_EXPECTATION(that(x).is_less_or_equal(y));
    TEST_EXPECTATION(that(x).is_less_or_equal(x));

    TEST_EXPECTATION(that(y).is_more_than(x));
    TEST_EXPECTATION(that(y).is_more_or_equal(x));
    TEST_EXPECTATION(that(y).is_more_or_equal(y));

    TEST_EXPECT_LESS_EQUAL(x, y);
    TEST_EXPECT_LESS_EQUAL(x, x);
    TEST_EXPECT_LESS(x, y);
    TEST_EXPECT_IN_RANGE(y, x, z);
}
TEST_PUBLISH(TEST_less_equal);

class readModified { // modifies on "read" (used to test unwanted double-evaluation)
    int val;
public:
    readModified(int v) : val(v) {}
    void set(int n) { val = n; }
    int getAndMod(int n) {
        int v = val;
        set(n);
        return v;
    }
};

#if !defined(__clang__)
// TEST_DISABLED_CLANG: evaluation order differs under clang
void TEST_single_eval() {
    readModified mod(5);
    TEST_EXPECT_EQUAL__BROKEN(mod.getAndMod(2), 2, 5); // now succeeds (this is no broken test; it tests behavior of TEST_EXPECT_EQUAL__BROKEN!)

    mod.set(5);
    TEST_EXPECT_IN_RANGE(mod.getAndMod(10), 4, 6);
    TEST_EXPECT_EQUAL(mod.getAndMod(10), 10);
    TEST_EXPECT_IN_RANGE__BROKEN(mod.getAndMod(2), 8, 12); // @@@ tested expression is evaluated twice
    TEST_EXPECT_EQUAL(mod.getAndMod(2), 2);
    TEST_EXPECT_IN_RANGE(mod.getAndMod(33), 1, 3);
    TEST_EXPECT_EQUAL(mod.getAndMod(33), 33);
    TEST_EXPECT_IN_RANGE__BROKEN(mod.getAndMod(20), 32, 34); // @@@ tested expression is evaluated twice
    TEST_EXPECT_EQUAL(mod.getAndMod(20), 20);
}
#endif

enum MyEnum {
    MY_UNKNOWN,
    MY_RNA,
    MY_DNA,
    MY_AA,
};

void TEST_MyEnum_loop() {
    int loops_performed = 0;
    const char *db_name[]=  { NULp, "TEST_trees.arb", "TEST_realign.arb", "TEST_realign.arb", NULp };
    for (int iat = MY_RNA; iat<=MY_AA; ++iat) {
        MyEnum at = MyEnum(iat);
        TEST_EXPECT(at>=1 && at<=3);
        fprintf(stderr, "at=%i db_name[%i]='%s'\n", at, at, db_name[at]);
        TEST_REJECT_NULL(db_name[at]);
        loops_performed++;
    }
    TEST_EXPECT_EQUAL(loops_performed, 3);
}


void TEST_ARB_strchrnul() {
    const char *check = "check";

    TEST_EXPECT_EQUAL(ARB_strchrnul("check", 'c'),  "check");
    TEST_EXPECT_EQUAL(ARB_strchrnul("check", 'e'),  "eck");
    TEST_EXPECT_EQUAL(ARB_strchrnul("check", 'i'),  "");
    TEST_EXPECT_EQUAL(ARB_strchrnul("check", '\0'), "");

    TEST_EXPECT_EQUAL(ARB_strchrnul(check, 'c'),  "check");
    TEST_EXPECT_EQUAL(ARB_strchrnul(check, 'e'),  "eck");
    TEST_EXPECT_EQUAL(ARB_strchrnul(check, 'i'),  "");
    TEST_EXPECT_EQUAL(ARB_strchrnul(check, '\0'), "");

    TEST_EXPECT(ARB_strchrnul(check, 'c')  == check);
    TEST_EXPECT(ARB_strchrnul(check, 'e')  == (check+2));
    TEST_EXPECT(ARB_strchrnul(check, 'i')  == (check+5));
    TEST_EXPECT(ARB_strchrnul(check, '\0') == (check+5));
}

static const char *keepOne(char *s) {
    static char *s2 = NULp;
    reassign(s2, s);
    return s2;
}

#define TEST_EXPECT_STRPARTDUP_TO(start,end,expected) TEST_EXPECT_EQUAL(keepOne(ARB_strpartdup(start,end)),expected)
#define TEST_EXPECT_STRNDUP_TO(start,len,expected)    TEST_EXPECT_EQUAL(keepOne(ARB_strndup(start,len)),expected)

void TEST_string_duppers() {
    const char *text  = "text";
    const char *empty = "";

    TEST_EXPECT_STRPARTDUP_TO(text, text+4, text); // dup with 0-byte
    TEST_EXPECT_STRPARTDUP_TO(text, text+3, text); // dup w/o 0-byte (afterwards append 0-byte)
    TEST_EXPECT_STRPARTDUP_TO(text, text,   "t");
    TEST_EXPECT_STRPARTDUP_TO(text, text-1, empty);

    // copy whole string
    TEST_EXPECT_STRPARTDUP_TO(text,  NULp, text);
    TEST_EXPECT_STRPARTDUP_TO(empty, NULp, empty);

    TEST_EXPECT_STRNDUP_TO(text, 5, text); // dup with 0-byte
    TEST_EXPECT_STRNDUP_TO(text, 4, text); // dup w/o 0-byte (afterwards append 0-byte)
    TEST_EXPECT_STRNDUP_TO(text, 1, "t");
    TEST_EXPECT_STRNDUP_TO(text, 0, empty);

    // error cases:
    // a. "less" than empty string
    TEST_EXPECT_NULL(ARB_strpartdup(text, text-2));
    TEST_EXPECT_NULL(ARB_strpartdup(text, text-200));

    TEST_EXPECT_NULL(ARB_strndup(text, -1));
    TEST_EXPECT_NULL(ARB_strndup(text, -1000));

    // b. no source -> no result
    TEST_EXPECT_STRPARTDUP_TO(NULp, empty, NULp);
    TEST_EXPECT_STRPARTDUP_TO(NULp, text,  NULp);
    TEST_EXPECT_STRPARTDUP_TO(NULp, NULp,  NULp);

    keepOne(NULp); // =free
}
TEST_PUBLISH(TEST_string_duppers);

#endif // UNIT_TESTS

// --------------------------------------------------------------------------------