source: branches/lib/GDE/SINA/builddir/src/unit_tests/cseq_test.cpp

/*
Copyright (c) 2012-2013 Arne Boeckman
Copyright (c) 2012-2013 Elmar Pruesse

This file is part of SINA.

SINA is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

#include <vector>
#include <algorithm> 
#include <fstream>

#define BOOST_TEST_MODULE cseq_module
#include <boost/test/unit_test.hpp>

#include <boost/algorithm/string.hpp>

#include "../cseq.h"
#include "../aligned_base.h"
using sina::cseq;
using sina::cseq_base;
using sina::aligned_base;

#include <string>
using std::string;

#include <iostream>

#define CASE BOOST_AUTO_TEST_CASE
#define FIXTURE_CASE BOOST_FIXTURE_TEST_CASE
#define EQUAL BOOST_CHECK_EQUAL
#define EQUAL_COLLECTIONS BOOST_CHECK_EQUAL_COLLECTIONS
#define THROW BOOST_CHECK_THROW

BOOST_AUTO_TEST_SUITE(cseq_test);

const string rna = "AGCURYKMSWBDHVN";
const string rna_aligned = "--A-G---CUR-YKM-S---WBD-HVN---";
const string rna_aligned_complemented = "--T-C---GAR-YKM-S---WBD-HVN---";
const string rna_aligned_dots = "..A-G---CUR-YKM-S---WBD-HVN...";

#define test_empty(cs)                         \
    EQUAL((cs).size(), 0u);                    \
    EQUAL((cs).getWidth(), 0u);                \
    EQUAL((cs).getBases(), string());          \
    EQUAL((cs).getAligned(true), string());    \
    EQUAL((cs).end() - c.begin(), 0);          \
    EQUAL((cs).rend() - c.rbegin(), 0);        \
    EQUAL((cs).getName(), string());


#define test_data(cs, name, _aligned)                               \
    {                                                               \
        string aligned = (_aligned);                                \
        string unaligned = aligned;                                 \
        boost::erase_all(unaligned, "-");                           \
        EQUAL((cs).size(), unaligned.size());                       \
        EQUAL((cs).getWidth(), aligned.size());                     \
        EQUAL((cs).getBases(), unaligned);                          \
        EQUAL((cs).getAligned(true), aligned);                      \
        EQUAL((cs).end() - (cs).begin(), (long)unaligned.size());   \
        EQUAL((cs).rend() - (cs).rbegin(), (long)unaligned.size()); \
        EQUAL((cs).getName(), name);                                \
    }


CASE(test_constructor_empty) {
    cseq c;

    test_empty(c);
}

CASE(test_constructur_normal) {
    const string name("thename");
    cseq c(name.c_str(), rna.c_str());

    test_data(c, name, rna);
}

CASE(test_constructor_copy) {
    cseq c("", rna.c_str());
    cseq d = c;

    test_data(d, "", rna);
}

CASE(test_append,
     *boost::unit_test::expected_failures(1)) {
    cseq c;

    c.append(rna);
    test_data(c, "", rna);
    c.append("");
    test_data(c, "", rna);
    c.append(rna);
    test_data(c, "", rna+rna);
    c.clearSequence();
    test_empty(c);
    c.append(rna_aligned);
    test_data(c, "", rna_aligned);
    c.append(rna);
    test_data(c, "", rna_aligned+rna);
    c.append(rna_aligned);
    test_data(c, "", rna_aligned+rna+rna_aligned);


    aligned_base b(0,'A');
    std::cerr << "==================" << std::endl
              << "Triggering 1 message: "
              << "\"$ cseq::append(): wrong order! A(0<75)\""
              << std::endl;
    c.append(b);
    std::cerr << "Triggering 1 error: "
              << "c.getWidth() == 75 and aligned.size() == 76"
              << std::endl;
    test_data(c, "", rna_aligned+rna+rna_aligned + "A");
    std::cerr << "==================" << std::endl << std::endl;

}


CASE(test_setWidth) {
    cseq c;
    string twentygaps="--------------------";

    c.setWidth(20);
    test_data(c, "", twentygaps);
    c.setWidth(40);
    test_data(c, "", twentygaps + twentygaps);
    c.setWidth(20);
    test_data(c, "", twentygaps);

    c.setWidth(0);
    test_data(c, "", "");

    c.append(rna_aligned);
    c.setWidth(rna_aligned.size() + 20);
    test_data(c, "", rna_aligned + twentygaps);
    c.setWidth(rna_aligned.size());
    test_data(c, "", rna_aligned);
    c.setWidth(27);
    test_data(c, "", "--A-G---CUR-YKM-S---WBD-HVN");
    c.setWidth(26);
    test_data(c, "", "--A-G---CUR-YKM-S---WBDHVN");
    c.setWidth(25);
    test_data(c, "", "--A-G---CUR-YKM-S--WBDHVN");
    c.setWidth(23);
    test_data(c, "", "--A-G---CUR-YKM-SWBDHVN");
    c.setWidth(22);
    test_data(c, "", "--A-G---CUR-YKMSWBDHVN");
    c.setWidth(21);
    test_data(c, "", "--A-G---CURYKMSWBDHVN");
    c.setWidth(20);
    test_data(c, "", "--A-G--CURYKMSWBDHVN");
    c.setWidth(19);
    test_data(c, "", "--A-G-CURYKMSWBDHVN");
    c.setWidth(18);
    test_data(c, "", "--A-GCURYKMSWBDHVN");
    c.setWidth(17);
    test_data(c, "", "--AGCURYKMSWBDHVN");
    c.setWidth(16);
    test_data(c, "", "-AGCURYKMSWBDHVN");
    c.setWidth(15);
    test_data(c, "", "AGCURYKMSWBDHVN");
}

CASE(test_setWidth_throw) {
    cseq c("", rna_aligned.c_str());
    THROW(c.setWidth(14), std::runtime_error);
}

CASE(test_dna) {
    string rna = boost::to_lower_copy(rna_aligned);
    string dna = boost::replace_all_copy(rna, "u", "t");
    string DNA = boost::replace_all_copy(rna_aligned, "U", "T");
    string RNA = rna_aligned;
    cseq c("", rna.c_str());
    cseq d("", dna.c_str());
    EQUAL(c.getAligned(true, true), dna);
    EQUAL(c.getAligned(true, false), rna);
    EQUAL(d.getAligned(true, true), dna);
    EQUAL(d.getAligned(true, false), rna);
    c.upperCaseAll();
    d.upperCaseAll();
    EQUAL(c.getAligned(true, true), DNA);
    EQUAL(c.getAligned(true, false), RNA);
    EQUAL(d.getAligned(true, true), DNA);
    EQUAL(d.getAligned(true, false), RNA);
}

CASE(test_operator_access) {
    cseq c("", rna_aligned.c_str());
    for (unsigned int i = 0; i < c.size(); ++i) {
        EQUAL(rna_aligned[i], c[i]);
    }
}

CASE(test_reverse) {
    string name("testtt");
    cseq c(name.c_str(), rna_aligned.c_str());
    string reversed = rna_aligned;
    std::reverse(reversed.begin(), reversed.end());

    c.reverse();
    test_data(c, name, reversed);
    c.reverse();
    test_data(c, name, rna_aligned);
}

CASE(test_lowercase) {
    string rna_aligned_lower = boost::to_lower_copy(rna_aligned);
    string rna_lower = boost::to_lower_copy(rna);
    cseq c("", rna_lower.c_str());
    EQUAL(c.getAligned(true), rna_lower);
}

CASE(test_uppercase){
    string rna_aligned_lower = boost::to_lower_copy(rna_aligned);
    string rna_lower = boost::to_lower_copy(rna);
    cseq c("", rna_lower.c_str());
    c.upperCaseAll();
    EQUAL(c.getAligned(true), rna);
    c.append(rna_aligned_lower);
    c.upperCaseAll();
    EQUAL(c.getAligned(true), rna + rna_aligned);
}

CASE(test_complement)
{
    //reference for complements:
    //http://www.animalgenome.org/edu/gene/genetic-code.html
    cseq c("", rna.c_str());
    c.complement();
    EQUAL(c.size(),rna.length());
    EQUAL(c.getBases(),"UCGAYRMKSWVHDBN");
}

class compression_data {
public:
    const cseq c_alig; 
    const cseq c_unalig;
    static const unsigned char c_alig_compr[];
    static const unsigned char c_unalig_compr[];

    compression_data() 
        : c_alig("", rna_aligned.c_str()),
          c_unalig("", rna.c_str())
    {
    }
};

const unsigned char
compression_data::c_alig_compr[] = {
    0x23, 0x00, 0x80, 0x00, 0x78, 0xda, 0x73, 0x74, 
    0x77, 0x0e, 0x0d, 0x8a, 0xf4, 0xf6, 0x0d, 0x0e,
    0x77, 0x72, 0xf1, 0x08, 0xf3, 0xd3, 0x63, 0x62, 
    0x62, 0x61, 0x64, 0x64, 0x02, 0x22, 0x08, 0xc5,
    0xc2, 0x40, 0x63, 0x00, 0x00, 0x40, 0xd5, 0x04,
    0xcc
        /* (used this to generate verification data)
        std::ofstream of("/tmp/thefile1");
        of << std::string((char*)&data.front(), data.size());
        */
};

const unsigned char
compression_data::c_unalig_compr[] = {
    0x23, 0x00, 0x80, 0x00, 0x78, 0xda, 0x73, 0x74, 
    0x77, 0x0e, 0x0d, 0x8a, 0xf4, 0xf6, 0x0d, 0x0e,
    0x77, 0x72, 0xf1, 0x08, 0xf3, 0xd3, 0x63, 0x60, 
    0x44, 0x05, 0x0c, 0x34, 0x06, 0x00, 0x3a, 0xad,
    0x04, 0xbd
};

FIXTURE_CASE(test_compress_unaligned, compression_data) {
    std::vector<unsigned char> data;
    cseq c = c_unalig;
    c.compressAligned(data);
    EQUAL_COLLECTIONS(data.begin(), data.end(), c_unalig_compr, 
                      c_unalig_compr + sizeof(c_unalig_compr));
}

FIXTURE_CASE(test_compress_aligned, compression_data) {
    std::vector<unsigned char> data;
    cseq c = c_alig;
    c.compressAligned(data);
    EQUAL_COLLECTIONS(data.begin(), data.end(), c_alig_compr, 
                      c_alig_compr + sizeof(c_alig_compr));
}

FIXTURE_CASE(test_decompress_unaligned, compression_data) {
    cseq c;
    c.assignFromCompressed(c_unalig_compr, sizeof(c_unalig_compr));
    test_data(c, "", rna);
}

FIXTURE_CASE(test_decompress_aligned, compression_data) {
    cseq c;
    c.assignFromCompressed(c_alig_compr, sizeof(c_alig_compr));
    test_data(c, "", rna_aligned);
}


CASE(test_dots) {
    cseq c("", rna_aligned.c_str());
    EQUAL(c.getAligned(false),rna_aligned_dots);
}


CASE(test_write_alignment) {
    std::stringstream out;
    std::vector<cseq> vs{
        {"1", rna_aligned.c_str()},
        {"2", rna_aligned.c_str()}
    };
    std::vector<const cseq_base*> vsp;
    for (auto& i : vs) {
        vsp.push_back(&i);
    }
    cseq::write_alignment(out, vsp, 0, rna_aligned.size()-1, false);
    EQUAL(out.str(),
          "Dumping pos 0 through 29:\n"
          "AGCURYKMSWBDHVN-  0-1 <---(## NEW ##)  <---(%% ORIG %%) \n\n"
        );

    out.str(std::string());
    cseq::write_alignment(out, vsp, 0, rna_aligned.size()-1, true);
    EQUAL(out.str(),
          "Dumping pos 0 through 29:\n"
          "\033[34mA"
          "\033[35mG"
          "\033[32mC"
          "\033[33mU"
          "\033[0mR"
          "YKMSWBDHVN-  0-1 <---(## NEW ##)  <---(%% ORIG %%) \n\n"
        );

    out.str(std::string());
    cseq::write_alignment(out, vsp, 0, rna_aligned.size(), false);
    EQUAL(out.str(), "cseq::write_alignment(): range out of bounds!\n");

    out.str(std::string());
    vs = std::vector<cseq>{{"1", "ACGU"}};
    vsp.clear();
    vsp.push_back(&vs[0]);
    cseq::write_alignment(out, vsp, 0, 3, true);
    EQUAL(out.str(),
          "Dumping pos 0 through 3:\n"
          "\033[34mA"
          "\033[32mC"
          "\033[35mG"
          "\033[33mU"
          "\033[0m"
          "  0 <---(## NEW ##) \n\n");
}

CASE(test_write_alignment_empty) {
    std::stringstream out;
    std::vector<const cseq_base*> vsp;
    cseq::write_alignment(out, vsp, 0, 0, false);
    EQUAL(out.str(), "cseq::write_alignment(): no sequences?\n");
}

CASE(test_ostream_operator) {
    const char* name = "test_name";
    cseq c(name);
    std::stringstream out;
    out << c << "";
    EQUAL(out.str(), name);
}

CASE(test_attr) {
    const char* name = "test_name";
    cseq c(name);
    c.set_attr("test", 123);
    EQUAL(c.get_attr<int>("test"), 123);
    EQUAL(c.get_attr<std::string>("test"), "123");
    c.set_attr("test", "hello");
    EQUAL(c.get_attr<std::string>("test"), "hello");
    c.set_attr("test", 2.3f);
    EQUAL(c.get_attr<float>("test"), 2.3f);
}

BOOST_AUTO_TEST_SUITE_END(); // cseq_test

/*
  Local Variables:
  mode:c++
  c-file-style:"stroustrup"
  c-file-offsets:((innamespace . 0)(inline-open . 0)(case-label . +))
  indent-tabs-mode:nil
  fill-column:99
  End:
*/
// vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=99 :