// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
// All rights reserved.
//
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// modification, are permitted provided that the following conditions are met:
//
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//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
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//       its contributors may be used to endorse or promote products derived
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//
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#ifndef SEQAN_HEADER_TEST_GRAPH_ALGORITHMS_H
#define SEQAN_HEADER_TEST_GRAPH_ALGORITHMS_H

#include <random>
#include <seqan/misc/union_find.h>

namespace seqan
{

template<typename TGraph>
inline void
_createRandomGraph(TGraph& g)
{
    int const SEED = 0;
    std::mt19937 rng(SEED);
    std::uniform_int_distribution<int> vertexPdf(0, 49);
    std::uniform_int_distribution<int> edgePdf(0, 99);

    clear(g);
    unsigned int nVertices = vertexPdf(rng) + 10;
    std::uniform_int_distribution<int> stPdf(0, nVertices - 1);
    for(unsigned int i=0; i<nVertices; ++i) addVertex(g);
    unsigned int maxEdges = edgePdf(rng) + 2 * nVertices;
    unsigned int nEdges = 0;
    for(unsigned int i=0; i<maxEdges; ++i) {
        unsigned int source = 0;
        unsigned int target = 0;
        do {
            source = stPdf(rng);
            target = stPdf(rng);
        } while (source == target);
        if (findEdge(g, source, target) == 0) {
            ++nEdges;
            addEdge(g, source, target);
        }
    }
}


//////////////////////////////////////////////////////////////////////////////
void Test_HeapTree() {
    // Keyless heap
    String<int> test;
    appendValue(test, 4);appendValue(test, 1);appendValue(test, 3);
    appendValue(test, 2);appendValue(test, 16);appendValue(test, 9);
    appendValue(test, 10);appendValue(test, 14);
    appendValue(test, 8);appendValue(test, 7);

    HeapTree<int, std::greater<int> > firstHeap;
    SEQAN_ASSERT(empty(firstHeap) == true);
    SEQAN_ASSERT(length(firstHeap) == 0);
    buildHeap(firstHeap, begin(test), end(test));
    HeapTree<int, std::greater<int> > firstHeapTest(firstHeap);
    SEQAN_ASSERT(length(firstHeapTest) == length(firstHeap));
    clear(firstHeapTest);
    firstHeapTest = firstHeap;
    SEQAN_ASSERT(length(firstHeapTest) == length(firstHeap));
    SEQAN_ASSERT(empty(firstHeap) == false);
    SEQAN_ASSERT(length(firstHeap) == 10);
    clear(firstHeap);
    SEQAN_ASSERT(empty(firstHeap) == true);
    SEQAN_ASSERT(length(firstHeap) == 0);
    buildHeap(firstHeap, begin(test), end(test));
    SEQAN_ASSERT(empty(firstHeap) == false);
    SEQAN_ASSERT(length(firstHeap) == 10);
    SEQAN_ASSERT(heapRoot(firstHeap) == 16);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 16);
    SEQAN_ASSERT(heapRoot(firstHeap) == 14);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 14);
    SEQAN_ASSERT(heapRoot(firstHeap) == 10);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 10);
    SEQAN_ASSERT(heapRoot(firstHeap) == 9);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 9);
    SEQAN_ASSERT(heapRoot(firstHeap) == 8);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 8);
    SEQAN_ASSERT(heapRoot(firstHeap) == 7);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 7);
    SEQAN_ASSERT(heapRoot(firstHeap) == 4);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 4);
    SEQAN_ASSERT(heapRoot(firstHeap) == 3);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 3);
    SEQAN_ASSERT(heapRoot(firstHeap) == 2);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 2);
    SEQAN_ASSERT(heapRoot(firstHeap) == 1);
    SEQAN_ASSERT(heapExtractRoot(firstHeap) == 1);
    SEQAN_ASSERT(empty(firstHeap) == true);
    SEQAN_ASSERT(length(firstHeap) == 0);


    // Keyed Heap
    typedef Pair<char, int> TKeyValue;
    typedef HeapTree<TKeyValue, std::greater<int>, KeyedHeap<> > TKeyedHeap;
    TKeyedHeap keyedHeap;
    String<TKeyValue> keyedTest;
    appendValue(keyedTest, TKeyValue('i', 4));appendValue(keyedTest, TKeyValue('a', 1));
    appendValue(keyedTest, TKeyValue('b', 3));appendValue(keyedTest, TKeyValue('c', 2));
    appendValue(keyedTest, TKeyValue('j', 16));appendValue(keyedTest, TKeyValue('m', 9));
    appendValue(keyedTest, TKeyValue('o', 10));appendValue(keyedTest, TKeyValue('p', 14));
    appendValue(keyedTest, TKeyValue('h', 8));appendValue(keyedTest, TKeyValue('z', 7));

    TKeyedHeap firstKeyedHeap;
    SEQAN_ASSERT(empty(firstKeyedHeap) == true);
    SEQAN_ASSERT(length(firstKeyedHeap) == 0);
    buildHeap(firstKeyedHeap, begin(keyedTest), end(keyedTest));
    TKeyedHeap firstKeyedHeapTest(firstKeyedHeap);
    SEQAN_ASSERT(length(firstKeyedHeapTest) == length(firstKeyedHeap));
    clear(firstKeyedHeapTest);
    firstKeyedHeapTest = firstKeyedHeap;
    SEQAN_ASSERT(length(firstKeyedHeapTest) == length(firstKeyedHeap));

    SEQAN_ASSERT(empty(firstKeyedHeap) == false);
    SEQAN_ASSERT(length(firstKeyedHeap) == 10);
    clear(firstKeyedHeap);
    SEQAN_ASSERT(empty(firstKeyedHeap) == true);
    SEQAN_ASSERT(length(firstKeyedHeap) == 0);
    buildHeap(firstKeyedHeap, begin(keyedTest), end(keyedTest));
    SEQAN_ASSERT(empty(firstKeyedHeap) == false);
    SEQAN_ASSERT(length(firstKeyedHeap) == 10);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'j');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 16);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 16);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'p');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 14);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 14);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'o');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 10);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 10);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 9);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 9);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 8);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 8);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 7);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 7);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 4);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 4);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 3);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 3);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 2);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 2);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 1);
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 1);
    SEQAN_ASSERT(empty(firstKeyedHeap) == true);
    SEQAN_ASSERT(length(firstKeyedHeap) == 0);

    // Change value only for keyed heaps
    buildHeap(firstKeyedHeap, begin(keyedTest), end(keyedTest));
    heapChangeValue(firstKeyedHeap, 'c', 20);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'c');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 20);
    heapChangeValue(firstKeyedHeap, 'c', 2);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'j');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 16);
    heapInsert(firstKeyedHeap, TKeyValue('x', 100));
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'x');
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i2 == 100);
    heapChangeValue(firstKeyedHeap, 'c', 200);
    SEQAN_ASSERT(heapRoot(firstKeyedHeap).i1 == 'c');
    SEQAN_ASSERT(heapExtractRoot(firstKeyedHeap).i2 == 200);

    // Test Heap Sort
    typedef int TValue;
    String<TValue> result1;
    String<TValue> result2;

    int const SEED = 0;
    std::mt19937 rng(SEED);
    std::uniform_int_distribution<int> uniformDist(0, 9999);

    for(unsigned int i=0; i<1000; ++i) {

        TValue val = uniformDist(rng) - 5000;
        appendValue(result1, val);
        appendValue(result2, val);
    }
    std::sort(begin(result1, Standard()), end(result1, Standard()));
    heapSort(begin(result2, Standard()), end(result2, Standard()));
    if (result1 != result2) {
        for(unsigned int i=0; i<length(result1);++i) std::cout << value(result1, i) << ',';
        std::cout << std::endl;
        for(unsigned int i=0; i<length(result2);++i) std::cout << value(result2, i) << ',';
        std::cout << std::endl;
        std::cout << "Error" << std::endl;
        exit(0);
    }

    // Test Heap Sort
    typedef int TValue;
    clear(result1);
    clear(result2);

    for(unsigned int i=0; i<1000; ++i) {
        TValue val = uniformDist(rng) - 5000;
        appendValue(result1, val);
        appendValue(result2, val);
    }
    std::sort(begin(result1, Standard()), end(result1, Standard()), std::greater<TValue>());
    heapSort(begin(result2, Standard()), end(result2, Standard()), std::greater<TValue>());
    if (result1 != result2) {
        for(unsigned int i=0; i<length(result1);++i) std::cout << value(result1, i) << ',';
        std::cout << std::endl;
        for(unsigned int i=0; i<length(result2);++i) std::cout << value(result2, i) << ',';
        std::cout << std::endl;
        std::cout << "Error" << std::endl;
        exit(0);
    }
}

//////////////////////////////////////////////////////////////////////////////
void Test_BreadthFirstSearch() {
//____________________________________________________________________________
// Breadth-First Search
    typedef Graph<Undirected<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 10;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,4, 1,5, 2,5, 2,6, 2,3, 3,6, 3,7, 5,6, 6,7};

    //Create the graph
    TGraph g;
    addEdges(g, edges, numEdges);

    // Predecessor and distance map
    String<TVertexDescriptor> predMap;
    String<TVertexDescriptor> distMap;

    // Bfs
    breadthFirstSearch(predMap, distMap, g, 1);

    SEQAN_ASSERT(getProperty(distMap, 0) == 1);
    SEQAN_ASSERT(getProperty(distMap, 1) == 0);
    SEQAN_ASSERT(getProperty(distMap, 2) == 2);
    SEQAN_ASSERT(getProperty(distMap, 3) == 3);
    SEQAN_ASSERT(getProperty(distMap, 4) == 2);
    SEQAN_ASSERT(getProperty(distMap, 5) == 1);
    SEQAN_ASSERT(getProperty(distMap, 6) == 2);
    SEQAN_ASSERT(getProperty(distMap, 7) == 3);
    SEQAN_ASSERT(getProperty(predMap, 0) == 1);
    SEQAN_ASSERT(getProperty(predMap, 1) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 2) == 5);
    SEQAN_ASSERT(getProperty(predMap, 3) == 6);
    SEQAN_ASSERT(getProperty(predMap, 4) == 0);
    SEQAN_ASSERT(getProperty(predMap, 5) == 1);
    SEQAN_ASSERT(getProperty(predMap, 6) == 5);
    SEQAN_ASSERT(getProperty(predMap, 7) == 6);
}

//////////////////////////////////////////////////////////////////////////////

void Test_DepthFirstSearch() {
//____________________________________________________________________________
// Depth-First Search
    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 8;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,3, 0,1, 1,4, 2,4, 2,5, 3,1, 4,3, 5,5};

    //Create the graph
    Graph<> g;
    addEdges(g, edges, numEdges);

    // Predecessor and distance map
    String<unsigned int> predMap;
    String<unsigned int> discoveryTimeMap;
    String<unsigned int> finishingTimeMap;

    // Dfs
    depthFirstSearch(predMap, discoveryTimeMap, finishingTimeMap, g);

    SEQAN_ASSERT(getProperty(discoveryTimeMap, 0) == 1);
    SEQAN_ASSERT(getProperty(discoveryTimeMap, 1) == 2);
    SEQAN_ASSERT(getProperty(discoveryTimeMap, 2) == 9);
    SEQAN_ASSERT(getProperty(discoveryTimeMap, 3) == 4);
    SEQAN_ASSERT(getProperty(discoveryTimeMap, 4) == 3);
    SEQAN_ASSERT(getProperty(discoveryTimeMap, 5) == 10);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 0) == 8);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 1) == 7);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 2) == 12);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 3) == 5);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 4) == 6);
    SEQAN_ASSERT(getProperty(finishingTimeMap, 5) == 11);
    SEQAN_ASSERT(getProperty(predMap, 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 1) == 0);
    SEQAN_ASSERT(getProperty(predMap, 2) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 3) == 4);
    SEQAN_ASSERT(getProperty(predMap, 4) == 1);
    SEQAN_ASSERT(getProperty(predMap, 5) == 2);
}

//////////////////////////////////////////////////////////////////////////////

void Test_TopologicalSort() {
//____________________________________________________________________________
// Topological Sort
    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 9;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,3, 0,1, 1,2, 3,2, 5,7, 5,6, 6,7, 6,3, 8,7};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    // Predecessor and distance map
    String<TVertexDescriptor> order;

    // Topological sort
    topologicalSort(order, g);

    SEQAN_ASSERT(getValue(order, 0) == 8);
    SEQAN_ASSERT(getValue(order, 1) == 5);
    SEQAN_ASSERT(getValue(order, 2) == 6);
    SEQAN_ASSERT(getValue(order, 3) == 7);
    SEQAN_ASSERT(getValue(order, 4) == 4);
    SEQAN_ASSERT(getValue(order, 5) == 0);
    SEQAN_ASSERT(getValue(order, 6) == 3);
    SEQAN_ASSERT(getValue(order, 7) == 1);
    SEQAN_ASSERT(getValue(order, 8) == 2);
}

//////////////////////////////////////////////////////////////////////////////

void Test_StronglyConnectedComponents() {
//____________________________________________________________________________
// Strongly-Connected-Components

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 14;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {1,0, 0,4, 2,1, 4,1, 5,1, 6,2, 3,2, 2,3, 7,3, 5,4, 6,5, 5,6, 7,6, 7,7};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    // Predecessor and distance map
    String<unsigned int> component;

    // Strongly Connected Components
    stronglyConnectedComponents(component, g);

    SEQAN_ASSERT(getValue(component, 0) == 3);
    SEQAN_ASSERT(getValue(component, 1) == 3);
    SEQAN_ASSERT(getValue(component, 2) == 2);
    SEQAN_ASSERT(getValue(component, 3) == 2);
    SEQAN_ASSERT(getValue(component, 4) == 3);
    SEQAN_ASSERT(getValue(component, 5) == 1);
    SEQAN_ASSERT(getValue(component, 6) == 1);
    SEQAN_ASSERT(getValue(component, 7) == 0);
}

//////////////////////////////////////////////////////////////////////////////

void Test_ConnectedComponents() {
//____________________________________________________________________________
// Connected-Components

    typedef Graph<Undirected<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 3;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 2,3, 3,4};

    //Create the graph
    TGraph g;
    addEdges(g,edges, numEdges);

    //Components
    String<unsigned int> component;

    //Connected Components
    connectedComponents(component, g);

    SEQAN_ASSERT(getValue(component, 0) == 0);
    SEQAN_ASSERT(getValue(component, 1) == 0);
    SEQAN_ASSERT(getValue(component, 2) == 1);
    SEQAN_ASSERT(getValue(component, 3) == 1);
    SEQAN_ASSERT(getValue(component, 4) == 1);
}


//////////////////////////////////////////////////////////////////////////////

void Test_PrimsAlgorithm() {
//____________________________________________________________________________
// Prim's algorithm
    typedef Graph<Undirected<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 14;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,6, 1,2, 1,6, 2,3, 2,4, 2,8, 3,5, 3,8, 4,6, 4,7, 5,8, 6,7, 7,8};
    unsigned int weights[] =    {4,   8,   8,   11,  7,   2,   4,   9,   14,  7,   6,   10,  1,   2  };

    //Create the graph
    TGraph g;
    addEdges(g,edges, numEdges);
    String<unsigned int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Tree and predecessor map
    String<TVertexDescriptor> predMap;

    primsAlgorithm(predMap, g, 0, weightMap);

    SEQAN_ASSERT(getProperty(predMap, 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 1) == 0);
    SEQAN_ASSERT(getProperty(predMap, 2) == 1);
    SEQAN_ASSERT(getProperty(predMap, 3) == 2);
    SEQAN_ASSERT(getProperty(predMap, 4) == 2);
    SEQAN_ASSERT(getProperty(predMap, 5) == 3);
    SEQAN_ASSERT(getProperty(predMap, 6) == 7);
    SEQAN_ASSERT(getProperty(predMap, 7) == 8);
    SEQAN_ASSERT(getProperty(predMap, 8) == 2);
}


//////////////////////////////////////////////////////////////////////////////

void Test_KruskalsAlgorithm() {
//____________________________________________________________________________
// Kruskal's algorithm
    typedef Graph<Undirected<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 14;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,6, 1,2, 1,6, 2,3, 2,4, 2,8, 3,5, 3,8, 4,6, 4,7, 5,8, 6,7, 7,8};
    unsigned int weights[] =    {4,   8,   8,   11,  7,   2,   4,   9,   14,  7,   6,   10,  1,   2  };

    //Create the graph
    TGraph g;
    addEdges(g,edges, numEdges);
    String<unsigned int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Tree edges
    String<TVertexDescriptor> treeEdges;
    kruskalsAlgorithm(treeEdges, g, 0, weightMap);

    SEQAN_ASSERT_EQ(length(treeEdges), 16u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 0), 6u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 1), 7u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 2), 2u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 3), 4u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 4), 7u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 5), 8u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 6), 0u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 7), 1u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 8), 2u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 9), 8u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 10), 2u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 11), 3u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 12), 0u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 13), 6u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 14), 3u);
    SEQAN_ASSERT_EQ(getValue(treeEdges, 15), 5u);
}

//////////////////////////////////////////////////////////////////////////////

void Test_MST_All() {
    int const SEED = 0;
    std::mt19937 rng(SEED);

    //while (true) {
        Graph<Undirected<> > myGraph;
        _createRandomGraph(myGraph);
        String<unsigned int> initialWeights;
        for(unsigned int i = 0; i<numEdges(myGraph); ++i)
            appendValue(initialWeights, std::uniform_int_distribution<int>(0, 999)(rng));
        String<unsigned int> weightMapInput;
        assignEdgeMap(weightMapInput, myGraph, initialWeights);
        clear(initialWeights);

        // Prim1
        String<unsigned int> predMapOut;
        primsAlgorithmSpaceEfficient(predMapOut, myGraph, 0, weightMapInput);
        typedef std::set<EdgeDescriptor<Graph<Undirected<> > >::Type> TEdgeSet;
        TEdgeSet edgeSet1;
        _collectEdges(myGraph,predMapOut,0,edgeSet1);
        unsigned int sum1 = 0;
        for(TEdgeSet::const_iterator pos = edgeSet1.begin(); pos != edgeSet1.end(); ++pos) {
            sum1 += getProperty(weightMapInput, *pos);
        }

        // Prim2
        String<unsigned int> predMapOut2;
        primsAlgorithm(predMapOut2, myGraph, 0, weightMapInput);
        TEdgeSet edgeSet2;
        _collectEdges(myGraph,predMapOut2,0,edgeSet2);
        unsigned int sum2 = 0;
        for(TEdgeSet::const_iterator pos = edgeSet2.begin(); pos != edgeSet2.end(); ++pos) {
            sum2 += getProperty(weightMapInput, *pos);
        }

        unsigned int sum3 = 0;
        if (sum1 != 0) {
            // Kruskal
            String<unsigned int> treeEdges;
            kruskalsAlgorithm(treeEdges, myGraph, 0, weightMapInput);
            for(unsigned int i = 0; i < length(treeEdges); i = i + 2) {
                sum3 += getProperty(weightMapInput, findEdge(myGraph, value(treeEdges, i), value(treeEdges, i + 1)));
            }
        }

        //std::cout << sum1 << ',';
    SEQAN_ASSERT(sum1 == sum2);
    SEQAN_ASSERT(sum2 == sum3);
    //}

}

//////////////////////////////////////////////////////////////////////////////

void Test_DagShortestPath() {
//____________________________________________________________________________
// DAG-Shortest Paths
    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 10;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,2, 0,1, 1,3, 1,2, 2,5, 2,4, 2,3, 3,5, 3,4, 4,5};
    int weights[] =             {3,   5,   6,   2,   2,   4,   7,   1,   -1,  -2};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    String<int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Predecessor map and distance map
    String<unsigned int> predMap;
    String<unsigned int> distMap;

    // DAG-Shortest path(Graph, sourceVertex_vertex, weightMap, predMap, distMap)
    dagShortestPath(predMap, distMap, g, 1, weightMap);

    SEQAN_ASSERT(getProperty(distMap, 1) == 0);
    SEQAN_ASSERT(getProperty(distMap, 2) == 2);
    SEQAN_ASSERT(getProperty(distMap, 3) == 6);
    SEQAN_ASSERT(getProperty(distMap, 4) == 5);
    SEQAN_ASSERT(getProperty(distMap, 5) == 3);
    SEQAN_ASSERT(getProperty(predMap, 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 1) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 2) == 1);
    SEQAN_ASSERT(getProperty(predMap, 3) == 1);
    SEQAN_ASSERT(getProperty(predMap, 4) == 3);
    SEQAN_ASSERT(getProperty(predMap, 5) == 4);
}

//////////////////////////////////////////////////////////////////////////////

void Test_BellmanFord() {
//____________________________________________________________________________
// Bellman-Ford

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 10;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,3, 1,2, 1,3, 2,4, 3,1, 3,2, 3,4, 4,0, 4,2};
    unsigned int weights[] =    {10,  5,   1,   2,   4,   3,   9,   2,   7,   6};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    String<unsigned int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Out parameters of Bellman-Ford: Predecessor map and distance map
    String<unsigned int> predMap;
    String<unsigned int> distMap;

    // Bellman-Ford
    bool noNegativeCycle = bellmanFordAlgorithm(predMap, distMap, g, 0, weightMap);

    SEQAN_ASSERT(getProperty(distMap, 0) == 0);
    SEQAN_ASSERT(getProperty(distMap, 1) == 8);
    SEQAN_ASSERT(getProperty(distMap, 2) == 9);
    SEQAN_ASSERT(getProperty(distMap, 3) == 5);
    SEQAN_ASSERT(getProperty(distMap, 4) == 7);
    SEQAN_ASSERT(getProperty(predMap, 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 1) == 3);
    SEQAN_ASSERT(getProperty(predMap, 2) == 1);
    SEQAN_ASSERT(getProperty(predMap, 3) == 0);
    SEQAN_ASSERT(getProperty(predMap, 4) == 3);
    SEQAN_ASSERT(noNegativeCycle == true);
}

//////////////////////////////////////////////////////////////////////////////

void Test_Dijkstra() {
//____________________________________________________________________________
// Dijkstra

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 10;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,3, 1,2, 1,3, 2,4, 3,1, 3,2, 3,4, 4,0, 4,2};
    unsigned int weights[] =    {10,  5,   1,   2,   4,   3,   9,   2,   7,   6};

    //Create the graph
    Graph<> g;
    addEdges(g, edges, numEdges);

    String<unsigned int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Out parameters of Dijkstra: Predecessor map and distance map
    String<unsigned int> predMap;
    String<unsigned int> distMap;

    // Dijkstra
    dijkstra(predMap, distMap, g, 0, weightMap);

    SEQAN_ASSERT(getProperty(distMap, 0) == 0);
    SEQAN_ASSERT(getProperty(distMap, 1) == 8);
    SEQAN_ASSERT(getProperty(distMap, 2) == 9);
    SEQAN_ASSERT(getProperty(distMap, 3) == 5);
    SEQAN_ASSERT(getProperty(distMap, 4) == 7);
    SEQAN_ASSERT(getProperty(predMap, 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getProperty(predMap, 1) == 3);
    SEQAN_ASSERT(getProperty(predMap, 2) == 1);
    SEQAN_ASSERT(getProperty(predMap, 3) == 0);
    SEQAN_ASSERT(getProperty(predMap, 4) == 3);
}

//////////////////////////////////////////////////////////////////////////////

void Test_AllPairsShortestPath() {
//____________________________________________________________________________
// All-Pairs Shortest Path

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 9;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,2, 0,4, 1,3, 1,4, 2,1, 3,0, 3,2, 4,3};
    int weights[] =    {3,   8,   -4,  1,   7,   4,   2,   -5,  6};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    String<int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Out parameter
    String<int> distMat;
    String<TVertexDescriptor> predMat;

    // All-Pairs shortest path
    allPairsShortestPath(distMat, predMat, g, weightMap);

    unsigned int len = (unsigned int) sqrt((double) length(distMat));
    SEQAN_ASSERT(getValue(distMat, 0*len + 0) == 0);
    SEQAN_ASSERT(getValue(distMat, 0*len + 1) == 1);
    SEQAN_ASSERT(getValue(distMat, 0*len + 2) == -3);
    SEQAN_ASSERT(getValue(distMat, 0*len + 3) == 2);
    SEQAN_ASSERT(getValue(distMat, 0*len + 4) == -4);
    SEQAN_ASSERT(getValue(distMat, 1*len + 0) == 3);
    SEQAN_ASSERT(getValue(distMat, 1*len + 1) == 0);
    SEQAN_ASSERT(getValue(distMat, 1*len + 2) == -4);
    SEQAN_ASSERT(getValue(distMat, 1*len + 3) == 1);
    SEQAN_ASSERT(getValue(distMat, 1*len + 4) == -1);
    SEQAN_ASSERT(getValue(distMat, 2*len + 0) == 7);
    SEQAN_ASSERT(getValue(distMat, 2*len + 1) == 4);
    SEQAN_ASSERT(getValue(distMat, 2*len + 2) == 0);
    SEQAN_ASSERT(getValue(distMat, 2*len + 3) == 5);
    SEQAN_ASSERT(getValue(distMat, 2*len + 4) == 3);
    SEQAN_ASSERT(getValue(distMat, 3*len + 0) == 2);
    SEQAN_ASSERT(getValue(distMat, 3*len + 1) == -1);
    SEQAN_ASSERT(getValue(distMat, 3*len + 2) == -5);
    SEQAN_ASSERT(getValue(distMat, 3*len + 3) == 0);
    SEQAN_ASSERT(getValue(distMat, 3*len + 4) == -2);
    SEQAN_ASSERT(getValue(distMat, 4*len + 0) == 8);
    SEQAN_ASSERT(getValue(distMat, 4*len + 1) == 5);
    SEQAN_ASSERT(getValue(distMat, 4*len + 2) == 1);
    SEQAN_ASSERT(getValue(distMat, 4*len + 3) == 6);
    SEQAN_ASSERT(getValue(distMat, 4*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 0*len + 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 0*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 0*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 0*len + 3) == 4);
    SEQAN_ASSERT(getValue(predMat, 0*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 1*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 1*len + 1) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 1*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 1*len + 3) == 1);
    SEQAN_ASSERT(getValue(predMat, 1*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 2*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 2*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 2*len + 2) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 2*len + 3) == 1);
    SEQAN_ASSERT(getValue(predMat, 2*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 3*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 3*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 3*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 3*len + 3) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 3*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 4*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 4*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 4*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 4*len + 3) == 4);
    SEQAN_ASSERT(getValue(predMat, 4*len + 4) == getNil<TVertexDescriptor>());
}

//////////////////////////////////////////////////////////////////////////////

void Test_FloydWarshall() {
//____________________________________________________________________________
// Floyd Warshall

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 9;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,2, 0,4, 1,3, 1,4, 2,1, 3,0, 3,2, 4,3};
    int weights[] =    {3,   8,   -4,  1,   7,   4,   2,   -5,  6};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    String<int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Out parameter
    String<int> distMat;
    String<TVertexDescriptor> predMat;

    // Floyd-Warshall
    floydWarshallAlgorithm(distMat, predMat, g, weightMap);

    unsigned int len = (unsigned int) sqrt((double) length(distMat));
    SEQAN_ASSERT(getValue(distMat, 0*len + 0) == 0);
    SEQAN_ASSERT(getValue(distMat, 0*len + 1) == 1);
    SEQAN_ASSERT(getValue(distMat, 0*len + 2) == -3);
    SEQAN_ASSERT(getValue(distMat, 0*len + 3) == 2);
    SEQAN_ASSERT(getValue(distMat, 0*len + 4) == -4);
    SEQAN_ASSERT(getValue(distMat, 1*len + 0) == 3);
    SEQAN_ASSERT(getValue(distMat, 1*len + 1) == 0);
    SEQAN_ASSERT(getValue(distMat, 1*len + 2) == -4);
    SEQAN_ASSERT(getValue(distMat, 1*len + 3) == 1);
    SEQAN_ASSERT(getValue(distMat, 1*len + 4) == -1);
    SEQAN_ASSERT(getValue(distMat, 2*len + 0) == 7);
    SEQAN_ASSERT(getValue(distMat, 2*len + 1) == 4);
    SEQAN_ASSERT(getValue(distMat, 2*len + 2) == 0);
    SEQAN_ASSERT(getValue(distMat, 2*len + 3) == 5);
    SEQAN_ASSERT(getValue(distMat, 2*len + 4) == 3);
    SEQAN_ASSERT(getValue(distMat, 3*len + 0) == 2);
    SEQAN_ASSERT(getValue(distMat, 3*len + 1) == -1);
    SEQAN_ASSERT(getValue(distMat, 3*len + 2) == -5);
    SEQAN_ASSERT(getValue(distMat, 3*len + 3) == 0);
    SEQAN_ASSERT(getValue(distMat, 3*len + 4) == -2);
    SEQAN_ASSERT(getValue(distMat, 4*len + 0) == 8);
    SEQAN_ASSERT(getValue(distMat, 4*len + 1) == 5);
    SEQAN_ASSERT(getValue(distMat, 4*len + 2) == 1);
    SEQAN_ASSERT(getValue(distMat, 4*len + 3) == 6);
    SEQAN_ASSERT(getValue(distMat, 4*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 0*len + 0) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 0*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 0*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 0*len + 3) == 4);
    SEQAN_ASSERT(getValue(predMat, 0*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 1*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 1*len + 1) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 1*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 1*len + 3) == 1);
    SEQAN_ASSERT(getValue(predMat, 1*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 2*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 2*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 2*len + 2) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 2*len + 3) == 1);
    SEQAN_ASSERT(getValue(predMat, 2*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 3*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 3*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 3*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 3*len + 3) == getNil<TVertexDescriptor>());
    SEQAN_ASSERT(getValue(predMat, 3*len + 4) == 0);
    SEQAN_ASSERT(getValue(predMat, 4*len + 0) == 3);
    SEQAN_ASSERT(getValue(predMat, 4*len + 1) == 2);
    SEQAN_ASSERT(getValue(predMat, 4*len + 2) == 3);
    SEQAN_ASSERT(getValue(predMat, 4*len + 3) == 4);
    SEQAN_ASSERT(getValue(predMat, 4*len + 4) == getNil<TVertexDescriptor>());
}


//////////////////////////////////////////////////////////////////////////////

void Test_TransitiveClosure() {
//____________________________________________________________________________
// Transitive Closure

    typedef VertexDescriptor<Graph<> >::Type TVertexDescriptor;
    //typedef EdgeDescriptor<Graph<> >::Type TEdgeDescriptor;
    typedef Size<Graph<> >::Type TSize;

    //Number of edges
    TSize numEdges = 5;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {3,0, 1,2, 2,1, 1,3, 3,2};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);

    // Transitive-Closure
    String<bool> closure;
    transitiveClosure(closure, g);

    unsigned int len = (unsigned int) sqrt((double) length(closure));
    SEQAN_ASSERT(getValue(closure, 0*len + 0) == 1);
    SEQAN_ASSERT(getValue(closure, 0*len + 1) == 0);
    SEQAN_ASSERT(getValue(closure, 0*len + 2) == 0);
    SEQAN_ASSERT(getValue(closure, 0*len + 3) == 0);
    SEQAN_ASSERT(getValue(closure, 1*len + 0) == 1);
    SEQAN_ASSERT(getValue(closure, 1*len + 1) == 1);
    SEQAN_ASSERT(getValue(closure, 1*len + 2) == 1);
    SEQAN_ASSERT(getValue(closure, 1*len + 3) == 1);
    SEQAN_ASSERT(getValue(closure, 2*len + 0) == 1);
    SEQAN_ASSERT(getValue(closure, 2*len + 1) == 1);
    SEQAN_ASSERT(getValue(closure, 2*len + 2) == 1);
    SEQAN_ASSERT(getValue(closure, 2*len + 3) == 1);
    SEQAN_ASSERT(getValue(closure, 3*len + 0) == 1);
    SEQAN_ASSERT(getValue(closure, 3*len + 1) == 1);
    SEQAN_ASSERT(getValue(closure, 3*len + 2) == 1);
    SEQAN_ASSERT(getValue(closure, 3*len + 3) == 1);
}

//////////////////////////////////////////////////////////////////////////////

void Test_FordFulkerson() {
//____________________________________________________________________________
// Ford-Fulkerson
    typedef Graph<Directed<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    typedef Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 10;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,1, 0,4, 1,2, 1,4, 2,3, 2,4, 4,1, 4,5, 5,2, 5,3};
    unsigned int capacity[] =    {16,  13,  12,  10,  20,  9,   4,   14,  7,   4};

    //Create the graph
    Graph<> g;
    addEdges(g,edges, numEdges);
    String<unsigned int> capMap;
    assignEdgeMap(capMap, g, capacity);

    // Out-parameter
    String<unsigned int> flow;
    unsigned int valF = fordFulkersonAlgorithm(flow, g, 0, 3, capMap);

    SEQAN_ASSERT(valF == 23);
    TEdgeIterator itEdge(g);
    for(;!atEnd(itEdge);goNext(itEdge)) {
        SEQAN_ASSERT(getProperty(flow, getValue(itEdge)) <= getProperty(capMap, getValue(itEdge)));
    }
}

//////////////////////////////////////////////////////////////////////////////

void Test_PathGrowingAlgorithm() {
//____________________________________________________________________________
// Path growing algorithm
    typedef Graph<Undirected<> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<TGraph>::Type TEdgeDescriptor;
    //typedef Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
    typedef Size<TGraph>::Type TSize;

    //Number of edges
    TSize numEdges = 14;
    //Source, Target, Source, Target, Source, ...
    TVertexDescriptor edges[] = {0,7, 0,5, 0,8, 1,5, 1,6, 2,6, 2,5, 2,8, 3,8, 3,4, 4,5, 4,6, 4,7, 4,8};
    unsigned int weights[] =    {20,  5,   19,  6,   7,   10,  3,   9,   12,  11,  13,  12,  9,   12};

    //Create the graph
    TGraph g;
    addEdges(g,edges, numEdges);
    String<unsigned int> weightMap;
    assignEdgeMap(weightMap, g, weights);

    // Path growing algorithm
    String<bool> edgeMap;

    // EdgeMap indicates whether an edge is selected or not
    unsigned int weight = pathGrowingAlgorithm(edgeMap, g, weightMap);

    SEQAN_ASSERT(weight == 49);
    SEQAN_ASSERT(getProperty(edgeMap, findEdge(g, 0, 7)) == true);
    SEQAN_ASSERT(getProperty(edgeMap, findEdge(g, 1, 6)) == true);
    SEQAN_ASSERT(getProperty(edgeMap, findEdge(g, 2, 8)) == true);
    SEQAN_ASSERT(getProperty(edgeMap, findEdge(g, 4, 5)) == true);
}


//////////////////////////////////////////////////////////////////////////////

void Test_LongestIncreasingSubsequence() {
    typedef Position<String<char> >::Type TPosition;

    String<char> seq1("zeitgeist");
    String<TPosition, Block<> > pos1;
    longestIncreasingSubsequence(seq1,pos1);
    // Trace is backwards
    SEQAN_ASSERT(seq1[pos1[4]] == 'e');
    SEQAN_ASSERT(seq1[pos1[3]] == 'g');
    SEQAN_ASSERT(seq1[pos1[2]] == 'i');
    SEQAN_ASSERT(seq1[pos1[1]] == 's');
    SEQAN_ASSERT(seq1[pos1[0]] == 't');

    String<TPosition> seq;
    appendValue(seq, 5); appendValue(seq, 3); appendValue(seq, 4);
    appendValue(seq, 9); appendValue(seq, 6); appendValue(seq, 2);
    appendValue(seq, 1); appendValue(seq, 8); appendValue(seq, 7);
    appendValue(seq, 10);
    String<TPosition, Block<> > pos;
    longestIncreasingSubsequence(seq,pos);
    SEQAN_ASSERT(seq[pos[4]] == 3);
    SEQAN_ASSERT(seq[pos[3]] == 4);
    SEQAN_ASSERT(seq[pos[2]] == 6);
    SEQAN_ASSERT(seq[pos[1]] == 7);
    SEQAN_ASSERT(seq[pos[0]] == 10);
}

//////////////////////////////////////////////////////////////////////////////

void Test_LongestCommonSubsequence() {
    typedef Position<String<char> >::Type TPosition;

    String<char> seq1("abacx");
    String<char> seq2("baabca");
    String<std::pair<TPosition, TPosition> > pos;
    longestCommonSubsequence(seq1, seq2, 100, pos);
    SEQAN_ASSERT(seq1[pos[2].first] == 'b');
    SEQAN_ASSERT(seq2[pos[2].second] == 'b');
    SEQAN_ASSERT(seq1[pos[1].first] == 'a');
    SEQAN_ASSERT(seq2[pos[1].second] == 'a');
    SEQAN_ASSERT(seq1[pos[0].first] == 'c');
    SEQAN_ASSERT(seq2[pos[0].second] == 'c');
}


//////////////////////////////////////////////////////////////////////////////

void Test_HeaviestIncreasingSubsequence() {
    typedef Position<String<char> >::Type TPosition;

    String<char> seq1("zeitgeist");
    String<unsigned int> weights1;
    String<TPosition> pos1;
    resize(weights1, length(seq1), 1);
    unsigned int w = heaviestIncreasingSubsequence(seq1, weights1, pos1);
    // Trace is backwards
    SEQAN_ASSERT(w == 5);
    SEQAN_ASSERT(seq1[pos1[4]] == 'e');
    SEQAN_ASSERT(seq1[pos1[3]] == 'g');
    SEQAN_ASSERT(seq1[pos1[2]] == 'i');
    SEQAN_ASSERT(seq1[pos1[1]] == 's');
    SEQAN_ASSERT(seq1[pos1[0]] == 't');
    //// Output
    //for(int i = length(pos1)-1; i>=0; --i) {
    //    std::cout << seq1[pos1[i]] <<  ',';
    //}
    //std::cout << std::endl;

    // Alter weights
    clear(pos1);
    assignProperty(weights1, 2, 10);
    w = heaviestIncreasingSubsequence(seq1, weights1, pos1);
    SEQAN_ASSERT(w == 13);
    SEQAN_ASSERT(seq1[pos1[3]] == 'e');
    SEQAN_ASSERT(seq1[pos1[2]] == 'i');
    SEQAN_ASSERT(seq1[pos1[1]] == 's');
    SEQAN_ASSERT(seq1[pos1[0]] == 't');
    //// Output
    //for(int i = length(pos1)-1; i>=0; --i) {
    //    std::cout << seq1[pos1[i]] <<  ',';
    //}
    //std::cout << std::endl;

    String<unsigned int> seq;
    appendValue(seq, 1); appendValue(seq, 0);
    appendValue(seq, 1); appendValue(seq, 0);
    appendValue(seq, 1); appendValue(seq, 0);
    String<unsigned int> weights;
    appendValue(weights, 15); appendValue(weights, 10);
    appendValue(weights, 10); appendValue(weights, 10);
    appendValue(weights, 10); appendValue(weights, 15);
    String<TPosition> pos;
    w = heaviestIncreasingSubsequence(seq, weights, pos);
    SEQAN_ASSERT(w == 20);
    SEQAN_ASSERT(seq[pos[1]] == 0);
    SEQAN_ASSERT(seq[pos[0]] == 1);
    //// Output
    //for(int i = length(pos)-1; i>=0; --i) {
    //    std::cout << seq[pos[i]] <<  ',';
    //}
    //std::cout << std::endl;
}


//////////////////////////////////////////////////////////////////////////////

void Test_HmmAlgorithms() {
    typedef double TProbability;
    typedef Dna TAlphabet;
    typedef Size<TAlphabet>::Type TSize;
    typedef Graph<Hmm<TAlphabet, TProbability> > THmm;
    typedef VertexDescriptor<THmm>::Type TVertexDescriptor;
    //typedef EdgeDescriptor<THmm>::Type TEdgeDescriptor;
    TSize alph_size = ValueSize<TAlphabet>::VALUE;

    Dna dnaA = Dna('A');
    Dna dnaC = Dna('C');
    Dna dnaG = Dna('G');
    Dna dnaT = Dna('T');

    THmm hmm;
    TVertexDescriptor state1 = addVertex(hmm);
    emissionProbability(hmm, state1, dnaA) = 0.2;
    emissionProbability(hmm, state1, dnaC) = 0.2;
    emissionProbability(hmm, state1, dnaG) = 0.3;
    emissionProbability(hmm, state1, dnaT) = 0.3;
    String<TProbability> emis;
    resize(emis, alph_size);
    value(emis, ordValue(dnaA)) = 0.5;
    value(emis, ordValue(dnaC)) = 0.5;
    value(emis, ordValue(dnaG)) = 0.0;
    value(emis, ordValue(dnaT)) = 0.0;
    TVertexDescriptor state2 = addVertex(hmm, emis);
    TVertexDescriptor state3 = addVertex(hmm, emis);
    assignEmissionProbability(hmm, state3, dnaA, 0.3);
    assignEmissionProbability(hmm, state3, dnaC, 0.3);
    assignEmissionProbability(hmm, state3, dnaG, 0.2);
    assignEmissionProbability(hmm, state3, dnaT, 0.2);
    addEdge(hmm, state1, state1, 0.95);
    addEdge(hmm, state1, state3, 0.05);
    TVertexDescriptor begState = addVertex(hmm);
    TVertexDescriptor eState = addVertex(hmm);
    addEdge(hmm, begState, state1, 1.0);
    addEdge(hmm, state3, eState, 0.5);
    addEdge(hmm, eState, eState, 1.0);
    assignBeginState(hmm, begState);
    assignEndState(hmm, eState);
    removeVertex(hmm, state2);

    // Algorithms
    String<Dna> sequence = "AC";
    String<TVertexDescriptor> path;
    viterbiAlgorithm(path, hmm, sequence);
    forwardAlgorithm(hmm, sequence);
    backwardAlgorithm(hmm, sequence);
}


//////////////////////////////////////////////////////////////////////////////

SEQAN_DEFINE_TEST(test_union_find)
{
    {
        UnionFind<int> uf;

        resize(uf, 3);
        SEQAN_ASSERT_EQ(uf._values[0], -1);
        SEQAN_ASSERT_EQ(uf._values[1], -1);
        SEQAN_ASSERT_EQ(uf._values[2], -1);

        SEQAN_ASSERT_EQ(findSet(uf, 0), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 1), 1);
        SEQAN_ASSERT_EQ(findSet(uf, 2), 2);

        joinSets(uf, 0, 1);
        SEQAN_ASSERT_EQ(findSet(uf, 0), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 1), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 2), 2);

        joinSets(uf, 0, 1);
        SEQAN_ASSERT_EQ(findSet(uf, 0), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 1), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 2), 2);

        joinSets(uf, 0, 2);
        SEQAN_ASSERT_EQ(findSet(uf, 0), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 1), 0);
        SEQAN_ASSERT_EQ(findSet(uf, 2), 0);
    }
}

SEQAN_DEFINE_TEST(test_heap_tree)
{
    Test_HeapTree();
}
    // Elementary graph algorithms
SEQAN_DEFINE_TEST(test_breadth_first_search)
{
    Test_BreadthFirstSearch();
}
SEQAN_DEFINE_TEST(test_depth_first_search)
{
    Test_DepthFirstSearch();
}
SEQAN_DEFINE_TEST(test_topological_sort)
{
    Test_TopologicalSort();
}
SEQAN_DEFINE_TEST(test_strongly_connected_components)
{
    Test_StronglyConnectedComponents();
}
SEQAN_DEFINE_TEST(test_connected_components)
{
    Test_ConnectedComponents();
}
    // Minimum Spanning Trees
SEQAN_DEFINE_TEST(test_prims_algorithm)
{
    Test_PrimsAlgorithm();
}
SEQAN_DEFINE_TEST(test_kruskals_algorithm)
{
    Test_KruskalsAlgorithm();
}
SEQAN_DEFINE_TEST(test_mst_all)
{
    Test_MST_All();
}
    // Single-Source shortest paths
SEQAN_DEFINE_TEST(test_dag_shortest_path)
{
    Test_DagShortestPath();
}
SEQAN_DEFINE_TEST(test_bellmann_ford)
{
    Test_BellmanFord();
}
SEQAN_DEFINE_TEST(test_dijkstra)
{
    Test_Dijkstra();
}
    // All-Pairs Shortest paths
SEQAN_DEFINE_TEST(test_all_pairs_shortest_path)
{
    Test_AllPairsShortestPath();
}
SEQAN_DEFINE_TEST(test_floyd_warshall)
{
    Test_FloydWarshall();
}
SEQAN_DEFINE_TEST(test_transitive_closure)
{
    Test_TransitiveClosure();
}
    //Maximum Flow
SEQAN_DEFINE_TEST(test_ford_fulkerson)
{
    Test_FordFulkerson();
}
    //Matching
SEQAN_DEFINE_TEST(test_path_growing_algorithm)
{
    Test_PathGrowingAlgorithm();
}
    // Lis, lcs, his, hcs
SEQAN_DEFINE_TEST(test_longest_increasing_subsequence)
{
    Test_LongestIncreasingSubsequence();
}
SEQAN_DEFINE_TEST(test_longest_common_subsequence)
{
    Test_LongestCommonSubsequence();
}
SEQAN_DEFINE_TEST(test_heaviest_increasing_subsequence)
{
    Test_HeaviestIncreasingSubsequence();
}
    // ToDo: Generic heaviest common subsequence

    // Hmm algorithms
SEQAN_DEFINE_TEST(test_hmm_algorithm)
{
    Test_HmmAlgorithms();
}


}

#endif

