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NCBI C++ ToolKit: src/algo/phy_tree/unit_test/phytree_calc_unit_test.cpp Source File

54 #ifndef SKIP_DOXYGEN_PROCESSING 56 #ifdef NCBI_COMPILER_MSVC 57 # define isfinite _finite 58 #elif defined(NCBI_COMPILER_WORKSHOP) && !defined(__builtin_isfinite) 60 # define isfinite finite 79

vector<bool>& leaves);

118 const int

kNumSeqs = 12;

121

vector<string> labels = calc.

SetLabels

();

122 for

(

int i

=1;

<= kNumSeqs;

++) {

131 "((4:0.474, (1:0.814, ((2:0.092, 3:0.060):0.586, " 132 "(((9:0.044, ((7:0.012, 8:0.020):0.045, 6:0.044)" 133 ":0.018):0.070, 10:0.000):0.390, (0:0.000, 5:0.034)" 134 ":0.393):0.078):0.072):0.474):x)"

);

150 const int

kNumSeqs = 12;

153

vector<string> labels = calc.

SetLabels

();

154 for

(

int i

=1;

<= kNumSeqs;

++) {

163 "((4:0.449, ((1:0.699, (2:0.061, 3:0.062):0.440)" 164 ":0.070, (((9:0.038, ((7:0.005, 8:0.017):0.044, " 165 "6:0.037):0.017):0.050, 10:0.000):0.403, (0:0.000, " 166 "5:0.034):0.360):0.104):0.449):x)"

);

187 "(((5:0.000, 9:0.000):0.002, (7:0.000, (3:0.000, " 188 "(4:0.001, (1:0.000, (0:0.000, ((6:0.000, 8:0.000)" 189 ":0.000, 2:0.000):0.000):0.000):0.001):0.000):0.000)" 213 "(((5:0.000, 9:0.000):0.002, (7:0.000, (3:0.000, " 214 "(4:0.001, (1:0.000, (0:0.000, ((6:0.000, 8:0.000)" 215 ":0.000, 2:0.000):0.000):0.000):0.001):0.000):0.000)" 231

vector<string>& labels = calc.

SetLabels

();

232

labels.push_back(

"label1"

);

233

labels.push_back(

"label2"

);

378 #if NCBI_PLATFORM_BITS == 64 381 const string

kSeq1 =

"A--"

;

382 const string

kSeq2 =

"-A-"

;

385

BOOST_REQUIRE_EQUAL(kSeq1.length(), kSeq2.length());

387 for

(

size_t i

=0;

< kSeq1.length();

++) {

388

BOOST_REQUIRE(kSeq1[

] ==

'-'

|| kSeq2[

] ==

'-'

);

405

dmat(0, 1) = dmat(1, 0) = -1.0;

410 #if NCBI_PLATFORM_BITS == 64 420

dmat(0, 1) = dmat(1, 0) = numeric_limits<double>::quiet_NaN();

425

dmat(0, 1) = dmat(1, 0) = numeric_limits<double>::signaling_NaN();

436 const int

num_seqs = 2;

443

denseg.

SetDim

(num_seqs);

445

denseg.

SetIds

().push_back(

id

);

446

denseg.

SetIds

().push_back(

id

);

453

denseg.

SetLens

().push_back(10);

454

denseg.

SetLens

().push_back(10);

459 const

vector<int>& starts = denseg.

GetStarts

();

460 for

(

size_t i

=0;

< starts.size();

+=num_seqs) {

461

BOOST_REQUIRE(starts[

] < 0 || starts[

+1] < 0);

465

vector<int> included_inds;

470

BOOST_REQUIRE_EQUAL(valid,

false

);

474

BOOST_REQUIRE_EQUAL(included_inds.size(), 1u);

477

BOOST_REQUIRE_EQUAL(included_inds[0], 0);

494

BOOST_REQUIRE_EQUAL((

int

)seg_info.size(), seq_align.

GetDim

());

496

BOOST_REQUIRE(!seq->empty());

497 ITERATE

(vector<CPhyTreeCalc::TRange>, it, *seq) {

498

BOOST_REQUIRE(it->NotEmpty());

514

BOOST_REQUIRE(instream);

522 while

(!line_reader.

AtEOF

()) {

528 "Could not retrieve seq entry"

);

550

BOOST_REQUIRE(!

label

.empty());

554

BOOST_REQUIRE(

id

>= 0 &&

id

< (

int

)leaves.size());

557

BOOST_REQUIRE(!leaves[

id

]);

573

vector<bool> leaves(num_sequences,

false

);

577 ITERATE

(vector<bool>, it, leaves) {

621

vector<bool>& leaves)

623 if

(node->IsLeaf()) {

625 string label

= node->GetFeature(

"label"

);

628

BOOST_REQUIRE(!

label

.empty());

632

BOOST_REQUIRE(

id

>= 0 &&

id

< (

int

)leaves.size());

635

BOOST_REQUIRE(!leaves[

id

]);

641

CBioTreeDynamic::CBioNode::TParent::TNodeList_CI child

642

= node->SubNodeBegin();

644 while

(child != node->SubNodeEnd()) {

658

vector<bool> leaves(num_sequences,

false

);

662 ITERATE

(vector<bool>, it, leaves) {

674 const int

kNumInputSequences = seq_align.

GetDim

();

675 const int

kNumUsedSequences = calc.

GetSeqIds

().size();

680

BOOST_REQUIRE_EQUAL(kNumUsedSequences, diverg.

GetNumElements

());

683

BOOST_REQUIRE(diverg(

, j) >= 0.0 && diverg(

, j) <= 1.0);

691

BOOST_REQUIRE_EQUAL(kNumUsedSequences, diverg.

GetNumElements

());

694

BOOST_REQUIRE(dist(

, j) >= 0.0);

703

BOOST_REQUIRE_EQUAL(kNumInputSequences,

708 const

vector< CRef<CSeq_id> > input_seq_ids

711 const

vector< CRef<CSeq_id> > used_seq_ids

714

vector<bool> found(used_seq_ids.size(),

false

);

715 for

(

size_t i

=0;

< used_seq_ids.size();

++) {

716 for

(

size_t

j=0;j < input_seq_ids.size();j++) {

717 if

(used_seq_ids[

]->Match(*input_seq_ids[j])) {

723 ITERATE

(vector<bool>, it, found) {

739

vector< CRef<CSeq_id> > input_seq_ids;

740

input_seq_ids.reserve(seq_align_set.

Get

().size());

741

input_seq_ids.push_back(

742

(*seq_align_set.

Get

().begin())->GetSegs().GetDenseg().GetIds()[0]);

745

BOOST_REQUIRE_EQUAL((*it)->GetSegs().GetDenseg().GetDim(), 2);

746 int i

= (

int

)input_seq_ids.size() - 1;

747 while

(

>= 0 && !(*it)->GetSegs().GetDenseg().GetIds()[1]->Match(

748

*input_seq_ids[

])) {

752

input_seq_ids.push_back((*it)->GetSegs().GetDenseg().GetIds()[1]);

756 const int

kNumInputSequences = (

int

)input_seq_ids.size();

757 const int

kNumUsedSequences = calc.

GetSeqIds

().size();

760

BOOST_REQUIRE_EQUAL(kNumUsedSequences, diverg.

GetNumElements

());

763

BOOST_REQUIRE(diverg(

, j) >= 0.0 && diverg(

, j) <= 1.0);

771

BOOST_REQUIRE(dist(

, j) >= 0.0);

778

BOOST_REQUIRE_EQUAL(kNumInputSequences,

783 const

vector< CRef<CSeq_id> > used_seq_ids

786

vector<bool> found(used_seq_ids.size(),

false

);

787 for

(

size_t i

=0;

< used_seq_ids.size();

++) {

788 for

(

size_t

j=0;j < input_seq_ids.size();j++) {

789 if

(used_seq_ids[

]->Match(*input_seq_ids[j])) {

795 ITERATE

(vector<bool>, it, found) {

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

void Validate(bool full_test=false) const

static TTree * NjTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >())

Compute a tree by neighbor joining; as per Hillis et al.

static double Divergence(const string &seq1, const string &seq2)

Calculate pairwise fractions of non-identity.

static TTree * FastMeTree(const TMatrix &dist_mat, const vector< string > &labels=vector< string >(), EFastMePar btype=eOls, EFastMePar wtype=eOls, EFastMePar ntype=eBalanced)

Compute a tree using the fast minimum evolution algorithm.

Base class for reading FASTA sequences.

Guide tree calc exceptions.

Distance matrix (square, symmetric with zeros on diagnol)

int GetNumElements(void) const

Get number of rows/columns.

Computaion of distance-based phylognetic tree.

void SetTreeMethod(ETreeMethod method)

Set algorithm for phylogenetic tree computation.

vector< string > & SetLabels(void)

Set labels for tree leaves.

CRef< CSeq_align > GetSeqAlign(void) const

Get seq_align that corresponds to current tree.

CRef< CBioTreeContainer > GetSerialTree(void) const

Get serial tree.

void SetMaxDivergence(double div)

Set maximum allowed divergence between sequences included in tree.

void SetCalcAlnSegInfo(bool s)

Calculate summarized segment positions in mutliple alignment.

bool CalcBioTree(void)

Compute bio tree for the current alignment in a black box manner.

const vector< string > & GetMessages(void) const

Get error/warning messages.

const vector< string > & GetRemovedSeqIds(void) const

Get ids of sequences excluded from tree computation.

const vector< CRef< CSeq_id > > & GetSeqIds(void) const

Get seq-ids of sequences used in tree construction.

@ eFastME

Fast Minumum Evolution.

const CDistMatrix & GetDivergenceMatrix(void) const

Get divergence matrix.

bool x_CalcDivergenceMatrix(vector< int > &used_indices)

Compute divergence matrix and find sequences to exclude from tree reconstruction.

void SetDistMethod(EDistMethod method)

Set evolutionary correction method for computing distance between sequences.

TPhyTreeNode * GetTree(void)

Get computed tree.

vector< vector< TRange > > TSegInfo

const CDistMatrix & GetDistanceMatrix(void) const

Get distance matrix.

const TSegInfo & GetAlnSegInfo(void) const

Get simplified segment positions in multiple or query anchored alignment.

Simple implementation of ILineReader for i(o)streams.

Test class for accessing CPhyTreeCalc private methods and attributes.

static bool CalcDivergenceMatrix(CPhyTreeCalc &calc, vector< int > &included)

definition of a Culling tree

Template class for iteration on objects of class C (non-medifiable version)

Operators to edit gaps in sequences.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

#define MSerial_AsnText

I/O stream manipulators â.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

@ fNoParseID

Generate an ID (whole defline -> title)

@ fForceType

Force specified type regardless of accession.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

void BioTreeConvertContainer2Dynamic(TDynamicTree &dyn_tree, const TBioTreeContainer &tree_container, bool preserve_node_ids=false)

Convert ASN.1 BioTree container to dynamic tree.

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 TBioTreeNode * GetTreeNode() const

const TValue & GetValue(void) const

Return node's value.

const TTreeType * GetParent(void) const

Get node's parent.

static const char label[]

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

TLens & SetLens(void)

Assign a value to Lens data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

TDim GetDim(void) const

Get the Dim member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetDim(TDim value)

Assign a value to Dim data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CSeq_align > > Tdata

TIds & SetIds(void)

Assign a value to Ids data member.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TAlign & GetAlign(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

unsigned int

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

BOOST_AUTO_TEST_CASE(TestProteinSeqAlign)

static void s_TraverseDynTree(const CBioTreeDynamic::CBioNode *node, vector< bool > &leaves)

static CRef< CScope > s_CreateScope(const string &filename)

static void s_TraverseTree(const TPhyTreeNode *node, vector< bool > &leaves)

static string s_GetNewickLike(const TPhyTreeNode *tree)

static bool s_TestTree(int num_sequences, const TPhyTreeNode *tree)

static bool s_TestTreeContainer(int num_sequences, const CBioTreeContainer &tree)

static bool s_TestCalc(const CSeq_align &seq_align, const CPhyTreeCalc &calc)

static void s_GetNewick(const TPhyTreeNode *node, string &result)

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

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

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phytree__calc__unit__test_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/phy_tree/unit_test/phytree_calc_unit_test.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/phytreecalcunit__test_8cpp_source.html below: