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

#pragma once

#include <boost/test/unit_test.hpp>

#include "test_utils.hpp"

namespace debruijn_graph {

BOOST_FIXTURE_TEST_SUITE(basic_debruijn_graph_tests, fs::TmpFolderFixture)

BOOST_AUTO_TEST_CASE( EmptyGraphTest ) {
    Graph g(11);
    BOOST_CHECK_EQUAL(11u, g.k());
    BOOST_CHECK_EQUAL(0u, g.size());
}

BOOST_AUTO_TEST_CASE( OneVertexGraphTest ) {
    Graph g(11);
    g.AddVertex();
    BOOST_CHECK_EQUAL(2u, g.size());
    VertexId v = *(g.begin());
    VertexId rcv = g.conjugate(v);
    BOOST_CHECK(v != rcv);
    BOOST_CHECK_EQUAL(v, g.conjugate(rcv));
}

pair<vector<VertexId> , vector<EdgeId> > createGraph(Graph &graph,
        int edgeNumber) {
    vector<VertexId> v;
    vector<EdgeId> e;
    v.push_back(graph.AddVertex());
    for (int i = 0; i < edgeNumber; i++) {
        v.push_back(graph.AddVertex());
        e.push_back(
                graph.AddEdge(v[v.size() - 2], v[v.size() - 1],
                        Sequence("AAAAAAAAAAAAAAAAA")));
    }
    return make_pair(v, e);
}

BOOST_AUTO_TEST_CASE( OneEdgeGraphTest ) {
    Graph g(11);
    pair<vector<VertexId> , vector<EdgeId> > data = createGraph(g, 1);
    BOOST_CHECK_EQUAL(1u, g.OutgoingEdgeCount(data.first[0]));
    BOOST_CHECK_EQUAL(0u, g.OutgoingEdgeCount(data.first[1]));
    BOOST_CHECK_EQUAL(data.second[0], g.GetUniqueOutgoingEdge(data.first[0]));
    BOOST_CHECK_EQUAL(g.conjugate(data.second[0]),
            g.GetUniqueOutgoingEdge(g.conjugate(data.first[1])));
    BOOST_CHECK_EQUAL(data.second[0],
            g.conjugate(g.conjugate(data.second[0])));
    BOOST_CHECK_EQUAL(!(g.EdgeNucls(data.second[0])),
            g.EdgeNucls(g.conjugate(data.second[0])));
}

/*void EdgeMethodsSimpleTest() {
    Graph g(11);
    pair<vector<VertexId> , vector<EdgeId> > data = createGraph(g, 2);
//    ASSERT_EQUAL(data.second[0], &g.GetData(data.second[0]));
    ASSERT_EQUAL(
            true,
            g.AreLinkable(data.first[0], data.first[1],
                    Sequence("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")));
    ASSERT_EQUAL(
            false,
            g.AreLinkable(data.first[0], data.first[1],
                    Sequence("CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC")));
}*/

BOOST_AUTO_TEST_CASE( VertexMethodsSimpleTest ) {
    Graph g(11);
    pair<vector<VertexId> , vector<EdgeId> > data = createGraph(g, 2);
    BOOST_CHECK_EQUAL(data.second[0], g.GetUniqueIncomingEdge(data.first[1]));
    BOOST_CHECK_EQUAL(data.second[0], g.GetUniqueOutgoingEdge(data.first[0]));
    BOOST_CHECK_EQUAL(false, g.CanCompressVertex(data.first[0]));
    BOOST_CHECK_EQUAL(true, g.CanCompressVertex(data.first[1]));
    BOOST_CHECK_EQUAL(false, g.CheckUniqueIncomingEdge(data.first[0]));
    BOOST_CHECK_EQUAL(true, g.CheckUniqueIncomingEdge(data.first[1]));
    BOOST_CHECK_EQUAL(false, g.CheckUniqueOutgoingEdge(data.first[2]));
    BOOST_CHECK_EQUAL(true, g.CheckUniqueOutgoingEdge(data.first[1]));
    BOOST_CHECK_EQUAL(true, g.IsDeadEnd(data.first[2]));
    BOOST_CHECK_EQUAL(false, g.IsDeadEnd(data.first[1]));
    BOOST_CHECK_EQUAL(true, g.IsDeadStart(data.first[0]));
    BOOST_CHECK_EQUAL(false, g.IsDeadStart(data.first[1]));
}

//void GraphMethodsSimpleTest() {
//    EdgeGraph g(11);
//    pair<vector<VertexId> , vector<EdgeId> > data = createGraph(g, 2);
//    ASSERT_EQUAL(vector<ActionHandler*> (), g.GetHandlers());
//    ActionHandler* handler = new ActionHandler();
//    g.AddActionHandler(handler);
//    vector<ActionHandler*> handlers = g.GetHandlers();
//    ASSERT_EQUAL(1u, handlers.size());
//    ASSERT_EQUAL(handler, handlers[0]);
//    g.RemoveActionHandler(handler);
//    ASSERT_EQUAL(vector<ActionHandler*> (), g.GetHandlers());
//}

BOOST_AUTO_TEST_CASE( SmartIteratorTest ) {
    Graph g(11);
    pair<vector<VertexId> , vector<EdgeId> > data = createGraph(g, 4);
    size_t num = 0;
    set<VertexId> visited;
//    std::less<VertexId> comp;
//    auto it = g.SmartVertexBegin(comp);
    for (auto it = g.SmartVertexBegin(); !it.IsEnd(); ++it) {
        num++;
        DEBUG( "with seq in vert" << g.VertexNucls(*it).str());
        visited.insert(*it);
    }
    BOOST_CHECK_EQUAL(num, data.first.size() * 2);
    for (size_t i = 0; i < data.first.size(); i++) {
        BOOST_CHECK(visited.find(data.first[i]) != visited.end());
        BOOST_CHECK(visited.find(g.conjugate(data.first[i])) != visited.end());
    }
}

//todo rename tests

BOOST_AUTO_TEST_CASE( TestSimpleThread ) {
    vector<string> reads = { "ACAAACCACCA" };
//    vector<string> edges = { "ACAAACCACCA" };
    AssertGraph (5, reads, reads);
}

BOOST_AUTO_TEST_CASE( TestSimpleThread2 ) {
    vector<string> reads = { "ACAAACCACCC", "AAACCACCCAC" };
    vector<string> edges = { "ACAAACCACCCAC" };
    AssertGraph (5, reads, edges);
}

BOOST_AUTO_TEST_CASE( TestSplitThread ) {
    vector<string> reads = { "ACAAACCACCA", "ACAAACAACCC" };
    vector<string> edges = { "ACAAAC", "CAAACCACCA", "CAAACAACCC" };
    AssertGraph (5, reads, edges);
}

BOOST_AUTO_TEST_CASE( TestSplitThread2 ) {
    vector<string> reads = { "ACAAACCACCA", "ACAAACAACCA" };
    vector<string> edges = { "AACCACCA", "ACAAAC", "CAAACCA", "CAAACAACCA" };
    AssertGraph (5, reads, edges);
}

BOOST_AUTO_TEST_CASE( TestBuldge ) {
    vector<string> reads = { "ACAAAACACCA", "ACAAACCACCA" };
//    vector<string> edges = { "ACAAAACACCA", "ACAAACCACCA" };
    AssertGraph (5, reads, reads);
}

BOOST_AUTO_TEST_CASE( TestCondenseSimple ) {
    vector<string> reads = { "CGAAACCAC", "CGAAAACAC", "AACCACACC", "AAACACACC" };
    vector<string> edges = { "CGAAAACACAC", "CACACC", "CGAAACCACAC" };
    AssertGraph (5, reads, edges);
}

BOOST_AUTO_TEST_CASE( TestKmerStoringIndex ) {
    vector<string> reads = { "CGAAACCAC", "CGAAAACAC", "AACCACACC", "AAACACACC" };
    CheckIndex<graph_pack<Graph>>(reads, 5);
}

BOOST_AUTO_TEST_CASE( TestKmerFreeIndex ) {
    vector<string> reads = { "CGAAACCAC", "CGAAAACAC", "AACCACACC", "AAACACACC" };
    CheckIndex<conj_graph_pack>(reads, 5);
}

//BOOST_AUTO_TEST_CASE( TestStrange ) {
//    vector<string> reads = {"TTCTGCATGGTTATGCATAACCATGCAGAA", "ACACACACTGGGGGTCCCTTTTGGGGGGGGTTTTTTTTG"};
//    typedef VectorStream<SingleRead> RawStream;
//    typedef io::RCReaderWrapper<SingleRead> Stream;
//    RawStream raw_stream(MakeReads(reads));
//    Stream read_stream(raw_stream);
//    Graph g(27);
//    EdgeIndex<28, Graph> index(g);
//
//    ConstructGraph<27, Stream>(g, index, read_stream);
//    EdgeId e = index.get(Seq<28>("TTCTGCATGGTTATGCATAACCATGCAG")).first;
//    VertexId start = g.EdgeEnd(e);
//    vector<EdgeId> edgeIds[2];
//    edgeIds[0] = g.OutgoingEdges(start);
//    edgeIds[1] = g.IncomingEdges(start);
//    for(int ii = 0; ii < 2; ii++)
//        for(auto e_iter = edgeIds[ii].begin(), end_iter = edgeIds[ii].end(); e_iter != end_iter; e_iter++) {
//            g.DeleteEdge(*e_iter);
//        }
//    g.DeleteVertex(start);
//
////        g.DeleteEdge(e);
////
////
////
////    g.DeleteEdge(r_e);
////    g.DeleteVertex(start);
//
//    INFO("FINISH");
//
////    AssertEdges(g, AddComplement(Edges(etalon_edges.begin(), etalon_edges.end())));
//
//}

BOOST_AUTO_TEST_CASE( SimpleTestEarlyPairedInfo ) {
    vector<MyPairedRead> paired_reads = {{"CCCAC", "CCACG"}, {"ACCAC", "CCACA"}};
    vector<MyEdge> edges = {"CCCA", "ACCA", "CCAC", "CACG", "CACA"};
    CoverageInfo coverage_info = {{"CCCA", 1}, {"ACCA", 1}, {"CCAC", 4}, {"CACG", 1}, {"CACA", 1}};
    EdgePairInfo edge_pair_info = {{{"CCCA", "CACG"}, {2, 1.0}}, {{"ACCA", "CACA"}, {2, 1.0}}
        , {{"CCCA", "CCAC"}, {1, 1.0}}, {{"ACCA", "CCAC"}, {1, 1.0}}
        , {{"CCAC", "CACG"}, {1, 1.0}}, {{"CCAC", "CACA"}, {1, 1.0}}};

    AssertGraph(3, paired_reads, 5, 6, edges, coverage_info, edge_pair_info);
}

BOOST_AUTO_TEST_CASE( TestSelfRCEdgeMerge ) {
    Graph g(5);
    VertexId v1 = g.AddVertex();
    VertexId v2 = g.AddVertex();
    EdgeId edge1 = g.AddEdge(v1, v2, Sequence("AACGCTATT"));
    EdgeId edge2 = g.AddEdge(v2, g.conjugate(v2), Sequence("CTATTCACGTGAATAG"));
    vector<EdgeId> path = {edge1, edge2};
    g.MergePath(path);
    BOOST_CHECK_EQUAL(2u, g.size());
    BOOST_CHECK_EQUAL(1u, g.OutgoingEdgeCount(v1));
    BOOST_CHECK_EQUAL(Sequence("AACGCTATTCACGTGAATAGCGTT"), g.EdgeNucls(g.GetUniqueOutgoingEdge(v1)));
}

BOOST_AUTO_TEST_SUITE_END()

}