//***************************************************************************
//* Copyright (c) 2015 Saint Petersburg State University
//* Copyright (c) 2011-2014 Saint Petersburg Academic University
//* All Rights Reserved
//* See file LICENSE for details.
//***************************************************************************

#include "cute.h"
#include "seq.hpp"
#include "nucl.hpp"
#include "constructHashTable.hpp"
#include "pipeline/graphio.hpp"

void TestEmptyDecompress() {
    ASSERT_EQUAL(decompress(0, 0), "");
}

void TestSingleNucleotideDecompress() {
    ASSERT_EQUAL("A", decompress(0, 1));
    ASSERT_EQUAL("C", decompress(1, 1));
    ASSERT_EQUAL("G", decompress(2, 1));
    ASSERT_EQUAL("T", decompress(3, 1));
}

void TestDoubleNucleotideDecompress() {
    ASSERT_EQUAL("AA", decompress(0, 2));
    ASSERT_EQUAL("AC", decompress(1, 2));
    ASSERT_EQUAL("AG", decompress(2, 2));
    ASSERT_EQUAL("AT", decompress(3, 2));
    ASSERT_EQUAL("CA", decompress(4 + 0, 2));
    ASSERT_EQUAL("CC", decompress(4 + 1, 2));
    ASSERT_EQUAL("CG", decompress(4 + 2, 2));
    ASSERT_EQUAL("CT", decompress(4 + 3, 2));
    ASSERT_EQUAL("GA", decompress(8 + 0, 2));
    ASSERT_EQUAL("GC", decompress(8 + 1, 2));
    ASSERT_EQUAL("GG", decompress(8 + 2, 2));
    ASSERT_EQUAL("GT", decompress(8 + 3, 2));
    ASSERT_EQUAL("TA", decompress(12 + 0, 2));
    ASSERT_EQUAL("TC", decompress(12 + 1, 2));
    ASSERT_EQUAL("TG", decompress(12 + 2, 2));
    ASSERT_EQUAL("TT", decompress(12 + 3, 2));
}

void TestMultyNucleotideDecompress() {
    ASSERT_EQUAL("CATGCA", decompress(124132, 6));
}

template<typename tType>
void checkArraysEqual(tType *a, tType *b, int length) {
    for (int i = 0; i < length; i++) {
        ASSERT_EQUAL(a[i], b[i]);
    }
}

void TestCodeReadAllA() {
    char *code = new char[readLength + 1];
    char *input = new char[readLength + 1];
    char *result = new char[readLength + 1];
    fill_n(input, readLength, 'A');
    fill_n(result, readLength, 0);
    codeRead(input, code);
    checkArraysEqual<char> (result, code, readLength);
    delete[] input;
    delete[] code;
}

void TestCodeReadAllACGT() {
    char *code = new char[readLength + 1];
    char *input = new char[readLength + 1];
    char *result = new char[readLength + 1];
    for (int i = 0; i < readLength; i++)
        if (i % 4 == 0) {
            input[i] = 'A';
            result[i] = 0;
        } else if (i % 4 == 1) {
            input[i] = 'C';
            result[i] = 1;
        } else if (i % 4 == 2) {
            input[i] = 'G';
            result[i] = 2;
        } else if (i % 4 == 3) {
            input[i] = 'T';
            result[i] = 3;
        }
    codeRead(input, code);
    checkArraysEqual<char> (result, code, readLength);
    delete[] input;
    delete[] code;
}

void TestExtractMerLen2() {
    char *input = new char[2];
    for (input[0] = 0; input[0] < 4; input[0]++)
        for (input[1] = 0; input[1] < 4; input[1]++)
            ASSERT_EQUAL(input[0] * 4 + input[1], extractMer(input, 0, 2));
    delete[] input;
}

void TestExtractMerLen3FromLen20() {
    int length = 20;
    char *input = new char[length];
    for (int i = 0; i < length; i++)
        input[i] = (100l << i) % 101 % 4;
    for (int i = 0; i + 2 < length; i++)
        ASSERT_EQUAL(input[i] * 16 + input[i + 1] * 4 + input[i + 2], extractMer(input, i, 3));
    delete[] input;
}

void TestExtractMerAllA() {
    char *input = new char[100];
    fill_n(input, readLength, 0);
    for (int merLength = 1; merLength < 100; merLength++) {
        for (int shift = 0; shift + merLength < 100; shift++) {
            ll result = extractMer(input, shift, merLength);
            ASSERT_EQUAL(0l, result);
        }
    }
    delete[] input;
}

void TestAddPairToTableSingleEntry() {
    myMap map;
    addPairToTable(map, 1, 2);
    ASSERT_EQUAL(1u, map.size());
    for (myMap::iterator it = map.begin(); it != map.end(); ++it) {
        ASSERT_EQUAL(1, it->first);
        ASSERT_EQUAL(1u, it->second.size());
        ASSERT_EQUAL(2, it->second[0]);
    }
}

void TestAddPairToTableTwoEntries() {
    myMap map;
    addPairToTable(map, 1, 2);
    addPairToTable(map, 3, 4);
    ASSERT_EQUAL(2u, map.size());
    ASSERT_EQUAL(1u, map[1].size());
    ASSERT_EQUAL(1u, map[3].size());
    ASSERT_EQUAL(2, map[1][0]);
    ASSERT_EQUAL(4, map[3][0]);
}

void TestAddPairToTableCoinsidingEntries() {
    myMap map;
    for(int i = 0; i < 10; i++)
        addPairToTable(map, 1, i);
    ASSERT_EQUAL(1u, map.size());
    for(int i = 0; i < 10; i++)
        ASSERT_EQUAL(i, map[1][i]);
}

cute::suite HashTableSuite() {
    cute::suite s;
    s.push_back(CUTE(TestEmptyDecompress));
    s.push_back(CUTE(TestSingleNucleotideDecompress));
    s.push_back(CUTE(TestDoubleNucleotideDecompress));
    s.push_back(CUTE(TestMultyNucleotideDecompress));
    s.push_back(CUTE(TestCodeReadAllA));
    s.push_back(CUTE(TestCodeReadAllACGT));
    s.push_back(CUTE(TestExtractMerLen2));
    s.push_back(CUTE(TestExtractMerLen3FromLen20));
    s.push_back(CUTE(TestExtractMerAllA));
    s.push_back(CUTE(TestAddPairToTableSingleEntry));
    s.push_back(CUTE(TestAddPairToTableTwoEntries));
    s.push_back(CUTE(TestAddPairToTableCoinsidingEntries));
    return s;
}