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NCBI C++ ToolKit: src/algo/cobalt/unit_test/clusterer_unit_test.cpp Source File

BOOST_CHECK_EQUAL((

)cluster.

(), 0);

BOOST_CHECK_EQUAL((

)clusterer.

().size(), 0);

BOOST_CHECK_EQUAL((

)clusterer.

().size(), 1);

dmat(1, 0) = dmat(0, 1);

BOOST_CHECK_EQUAL((

)clusterer.

().size(), 1);

BOOST_CHECK_EQUAL((

)clusterer.

().size(), 2);

dmat(0, 1) = dmat(1, 0) = 0.1;

dmat(0, 2) = dmat(2, 0) = 0.3;

dmat(0, 3) = dmat(3, 0) = 0.2;

dmat(1, 2) = dmat(2, 1) = 0.5;

dmat(1, 3) = dmat(3, 1) = 0.2;

dmat(2, 3) = dmat(3, 2) = 0.1;

BOOST_CHECK((

)clusterer.

().size() > 1);

vector<double> dists;

(!istr.eof()) {

= DBL_MAX;

(

!= DBL_MAX) {

dists.push_back(

);

num_elements = (

)sqrt((

)dists.size());

BOOST_REQUIRE_EQUAL(num_elements * num_elements, (

)dists.size());

dmat.

(num_elements, num_elements, 0.0);

(

=0;

< num_elements;

++) {

(

j=0;j < num_elements;j++) {

dmat(

, j) = dists[

*num_elements + j];

= node->

().GetId();

BOOST_REQUIRE(

< (

)elems.size());

BOOST_REQUIRE(!elems[

]);

BOOST_REQUIRE(

);

BOOST_REQUIRE(cluster.

() > 0);

max_elem = cluster[0];

(

=1;

< (

)cluster.

();

++) {

(cluster[

] > max_elem) {

max_elem = cluster[

];

vector<bool> elems(max_elem + 1,

);

elems[*elem] =

;

(vector<bool>, it, elems) {

& ref_filename =

)

BOOST_REQUIRE(clusterer.

().size() > 0);

vector<bool> check_elems(num_elems,

);

vector<TPhyTreeNode*>& trees = clusterer.

();

num_elements = 0;

BOOST_REQUIRE(*elem < num_elems);

BOOST_REQUIRE(!check_elems[*elem]);

check_elems[*elem] =

;

(vector<bool>, it, check_elems) {

BOOST_REQUIRE_EQUAL(clusters.size(), trees.size());

(

=0;

< clusters.size();

++) {

(!ref_filename.empty()) {

BOOST_REQUIRE(ref_istr);

vector<int> ref_clust_elems;

ref_num_clusters = 0;

ref_num_elems = 0;

* buff =

[256];

(ref_istr.peek() == (

)

) {

ref_istr.getline(buff, 256);

ref_istr >> ref_num_clusters;

BOOST_REQUIRE_EQUAL((

)clusters.size(), ref_num_clusters);

(

=0;

< ref_num_clusters;

++) {

BOOST_REQUIRE(!ref_istr.eof());

ref_istr >> ref_size;

BOOST_REQUIRE_EQUAL((

)clusters[ind++].

(), ref_size);

ref_num_elems += ref_size;

zero_found =

;

(

=0;

< ref_num_elems;

++) {

BOOST_REQUIRE(!ref_istr.eof());

ref_istr >> ref_elem;

ref_clust_elems.push_back(ref_elem);

BOOST_REQUIRE((!zero_found && ref_elem >= 0)

|| (zero_found && ref_elem > 0));

BOOST_REQUIRE_EQUAL(*elem, ref_clust_elems[ind++]);

num_elements = 5;

num_elements = 1;

num_elements = 2;

num_elements = 2;

num_elements = (

)dmat.

();

max_distance = 0.8;

(

=0;

< dmat.

() - 1;

++) {

(

j=

+1;j < dmat.

();j++) {

(dmat(

, j) < max_distance) {

links->

((

)

, (

)j, dmat(

, j));

pre_clusters[0].AddElement(0);

pre_clusters[0].AddElement(1);

pre_clusters[0].AddElement(2);

pre_clusters[1].AddElement(3);

BOOST_REQUIRE_EQUAL(clusters.size(), 3u);

elem = *clust->begin();

(elem == 5 || elem == 3) {

BOOST_REQUIRE_EQUAL(clust->size(), 1u);

BOOST_REQUIRE(!presence[elem]);

presence[elem] =

;

BOOST_REQUIRE_EQUAL(clust->size(), 4u);

BOOST_REQUIRE(!presence[*it]);

presence[*it] =

;

(vector<bool>, it, presence) {

kNumElements = 10;

unique_ptr<CClusterer> clusterer(

(links));

clusterer->SetReportSingletons(

);

clusters.swap(clusterer->SetClusters());

clusterer->SetClusters().swap(clusters);

vector<size_t> sizes(kNumElements, 0);

vector< set<int> > reference(kNumElements);

reference[0].insert(0);

reference[0].insert(1);

reference[0].insert(2);

reference[3].insert(3);

reference[4].insert(4);

reference[5].insert(5);

reference[5].insert(6);

reference[7].insert(7);

reference[8].insert(8);

reference[9].insert(9);

(cluster->begin(), cluster->end());

cl_index = *cluster->begin();

BOOST_REQUIRE_EQUAL(cluster->size(), sizes[cl_index]);

BOOST_REQUIRE(it != reference[cl_index].end());

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

Exceptions for CClusterer class.

int FindCenterElement(const TDistMatrix &dmatrix) const

Find element that is closest to the center of the cluster.

int GetPrototype(void) const

Get cluster prototype.

size_t size(void) const

Get cluster size.

Interface for CClusterer class used for clustering any type of data based on distance matrix.

void GetTrees(vector< TPhyTreeNode * > &trees) const

Get list of trees for clusters.

const TSingleCluster & GetSingleCluster(size_t index) const

Get list of elements of a specified cluster.

void SetMakeTrees(bool trees)

Set make cluster tree/dendrogram option.

void SetDistMatrix(const TDistMatrix &dmat)

Set new distance matrix.

const TDistMatrix & GetDistMatrix(void) const

Get distance matrix.

void SetLinks(CRef< CLinks > links)

Set distance links.

void Run(void)

Cluster elements.

const TClusters & GetClusters(void) const

Get clusters.

void ComputeClusters(double max_diam, EDistMethod dist_method=eCompleteLinkage, bool do_trees=true, double infinity=-1.0)

Compute clusters.

vector< TSingleCluster > TClusters

TClusters & SetClusters(void)

Set clusters.

void PurgeDistMatrix(void)

Delete distance matrix.

void GetClusterDistMatrix(int index, TDistMatrix &mat) const

Get distance matrix for elements of a selected cluster.

Set of edges with weights between nodes represented by zero-based positive integers.

void AddLink(int first, int second, double weight)

Add link.

Uint4 GetNumElements(void) const

Get number of nodes.

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

size_t GetRows() const

get the number of rows in this matrix

size_t GetCols() const

get the number of columns in this matrix

definition of a Culling tree

const_iterator find(const key_type &key) const

static void s_ReadDistMatrix(const string &filename, CClusterer::TDistMatrix &dmat)

Read distance matrix from file.

BOOST_AUTO_TEST_CASE(TestSingleCluster)

static void s_TestClusterTree(const CClusterer::TSingleCluster &cluster, const TPhyTreeNode *tree)

static void s_TestTree(vector< bool > &elems, const TPhyTreeNode *node)

static void s_TestClustersAndTrees(int num_elems, CClusterer &clusterer, const string &ref_filename="")

Check clusters.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void Reset(void)

Reset reference object.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList::const_iterator TNodeList_CI

bool IsLeaf() const

Report whether this is a leaf node.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

const TValue & GetValue(void) const

Return node's value.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

Utility stuff for more convenient using of Boost.Test library.

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