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

(it->seq1_start, it->seq1_stop),

(it->seq2_start, it->seq2_stop),

* sequence = it->GetSequence();

(

=0;

< it->GetLength();

++) {

);

);

(*it >= (

)

.size() || *it < 0) {

);

(*it >= (

)

.size() || *it < 0) {

);

);

(from1 > to1 || from2 > to2) {

);

);

(queries.size() < 2) {

);

(queries.size() < 2) {

);

= objects::CObjectManager::GetInstance();

vector<objects::CBioseq_Handle> bioseq_handles;

bioseq_handles.push_back(

->AddBioseq(**it));

(vector<objects::CBioseq_Handle>, it, bioseq_handles) {

seq_loc(

objects::CSeq_loc(objects::CSeq_loc::e_Whole));

seq_loc->SetId(*it->GetSeqId());

(objects::CObjMgrException e) {

(

)

+ e.

());

(queries.size() < 2) {

);

(

=0;

< queries.size();

++) {

->AddScope(*queries[

].scope);

objects::CSeq_align& msa2,

(objects::CDense_seg::TIds, it,

msa1.GetSegs().GetDenseg().GetIds()) {

objects::CSeq_loc(objects::CSeq_loc::e_Whole)));

(objects::CDense_seg::TIds, it,

msa2.GetSegs().GetDenseg().GetIds()) {

objects::CSeq_loc(objects::CSeq_loc::e_Whole)));

(!repr1.

()) {

(!repr2.

()) {

);

(

(matrix_name,

) == 0)

(

(matrix_name,

) == 0)

(

(matrix_name,

) == 0)

(

(matrix_name,

) == 0)

(

(matrix_name,

) == 0)

(

(matrix_name,

) == 0)

\

);

kGapOpen = 11;

kGapExtend = 1;

(blast::CBlastException, eInvalidArgument,

);

dmat.

(clusters.size(), clusters.size(), 0.0);

(

=0;

< clusters.size() - 1;

++) {

(

j=

+1;j < clusters.size();j++) {

dmat(

, j) = bigmat(clusters[

].GetPrototype(),

clusters[j].GetPrototype());

dmat(j,

) = dmat(

, j);

printf(

);

(

= matrix.

() - 1;

> 0;

--)

printf(

,

);

printf(

,

);

(

j = matrix.

() - 1; j >

; j--) {

printf(

, matrix(

, j));

);

vector<CTree::STreeLeaf> node_list1;

vector<CTree::STreeLeaf> node_list2;

vector<int> compress_inds;

compress_inds.push_back(

);

compress_inds.clear();

compress_inds.push_back(

);

vector<const CSequence*> pattern_queries;

(

= 0;

< pair_info.

();

++) {

(

j = 0; j < pair_info.

(); j++) {

pair_info(

, j).ResetList();

(

)

is_cluster_found =

;

vector<TPhyTreeNode*> cluster_trees;

);

vector<const CSequence*> pattern_queries;

(is_cluster_found) {

);

(blast::CBlastException e) {

blast::CBlastException::EErrCode err_code

= (blast::CBlastException::EErrCode)e.

();

status = (err_code == blast::CBlastException::eInvalidArgument

(std::exception e) {

vector<TKmerCounts> kmer_counts;

shared_ptr<CClusterer::TDistMatrix> dmat

(

=0;

< dmat->GetRows();

++) {

(*dmat)(center,

) = 0.0;

(*dmat)(

, center) = 0.0;

(

=0;

< (

)dmat->GetCols() - 1;

++) {

(!constr_q.

() && constr_q.

(

) != constr_q.

()) {

(

j=

+1;j < (

)dmat->GetCols();j++) {

(!constr_q.

() && constr_q.

(j) != constr_q.

()) {

links->

(

, j, (*dmat)(

, j));

kMaxDistance = 1.5;

(

=0;

< (

)dmat->GetRows();

++) {

(*dmat)(

, *it) = kMaxDistance;

(*dmat)(*it,

) = kMaxDistance;

printf(

);

(

=dmat->GetCols() - 1;

> 0;

--) {

printf(

, (

)

);

(

=0;

< dmat->GetRows() - 1;

++) {

printf(

, (

)

);

(

j=dmat->GetCols() - 1;j >

;j--) {

printf(

, (*dmat)(

, j));

printf(

);

printf(

);

printf(

);

(it->size() == 1) {

it->SetPrototype(*it->begin());

}

(it->size() == 2) {

= (len1 > len2) ? (*it)[0] : (*it)[1];

it->SetPrototype(

);

vector< CRef<objects::CSeq_loc> > cluster_prototypes;

cluster_prototypes.push_back(

[cluster_it->GetPrototype()]);

vector<CSequence>& q =

printf(

);

num_in_clusters = 0;

printf(

, cluster_idx++);

printf(

, it_cl->GetPrototype());

printf(

, *it_el, q[*it_el].

());

(it_cl->size() > 1) {

num_in_clusters += it_cl->size();

gain =

.size() - clusters.size();

printf(

,

(

)num_in_clusters /

.size() * 100.0);

printf(

, gain,

printf(

);

(

cluster_idx=0;cluster_idx < clusters.size();

(cluster.

() == 1) {

printf(

, (

)cluster_idx);

(cluster.

() == 2) {

printf(

, d(cluster[0], cluster[1]));

(

= cluster.

() - 1;

> 0;

--) {

printf(

, (

)cluster[

]);

(

=0;

< cluster.

() - 1;

++) {

printf(

, (

)cluster[

]);

(

j=cluster.

() - 1;j >

;j--) {

printf(

, d(cluster[

], cluster[j]));

printf(

);

(it->size() == 1) {

(*el == cl->GetPrototype()) {

printf(

, *elem, *el, d(*elem, *el));

(

cluster_idx=0;cluster_idx < clusters.size();cluster_idx++) {

(clusters[cluster_idx].

() > 1) {

is_gap_in_prototype =

;

(len1 > 1.2 * len2 || len2 > 1.2 * len1) {

(

j=0;j <

.size();j++) {

is_gap_in_prototype =

;

(!is_gap_in_prototype) {

(it=clusters[cluster_idx].begin();it != seq_idx;++it) {

printf(

, (

)cluster_idx);

printf(

, *elem);

);

printf(

, (

)

);

(clusters.size() == 1) {

it->insert =

;

it->letters.resize(

);

(

=0;

<

;

++) {

it->letters[

] = -1;

vector<CMultiAligner::SColumn>::iterator& it,

,

num,

cluster)

it->letters.resize(

);

(

=0;

<

;

++) {

it->letters[

] = -1;

it->cluster = cluster;

seq_length =

[0].GetLength();

vector<int> letter_inds(clusters.size());

vector<SColumn>

(seq_length);

(

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

it->letters[clusters[j].GetPrototype()] = letter_inds[j]++;

new_length = seq_length;

(

cluster_idx=0;cluster_idx < clusters.size();cluster_idx++) {

vector<SColumn>::iterator it =

.begin();

prototype_idx = clusters[cluster_idx].GetPrototype();

&& (it->insert || it->letters[prototype_idx] < (

)

)) {

);

it->Reset(new_length);

vector<int> gap_offsets(clusters.size());

(

=0;

< clusters.size();

++) {

prototype_idx = clusters[

].GetPrototype();

= it->letters[prototype_idx];

[*elem].SetLetter(col,

(

=0;

< it->number;

++) {

[*elem].SetLetter(col +

,

);

printf(

);

printf(

);

(

=0;

< (

)clusters.size();

++) {

(clusters[

].

() > 1) {

printf(

,

);

(

j=0;j < seq.

();j++) {

printf(

);

(

cluster_idx=0;cluster_idx < clusters.size();cluster_idx++) {

(cluster.

() == 1) {

freqs(

, k) += matrix(

+

, k);

);

vector<int>& indices)

queries.push_back(sl);

indices.push_back(*it);

queries.push_back(sl);

indices.push_back((

)

.size() + *it);

blast::SSeqLoc sl(**it, *

);

queries.push_back(sl);

index = it->GetPrototype();

queries.push_back(sl);

indices.push_back(index);

);

vector<int>& indices)

indices[

] = (

)

;

queries.resize(clusters.size());

indices.resize(clusters.size());

(

=0;

< clusters.size();

++) {

index = clusters[

].GetPrototype();

indices[

] = index;

);

node_dist = distance / 2.0;

(node_dist <= 0.0) {

node->

().SetDist(node_dist);

node->

().SetDist(node_dist);

= ids[node->

().GetId()];

(trees.size() == clusters.size());

(

=0;

< trees.size();

++) {

(clusters[

].

() == 1) {

trees.resize(clusters.size());

(

clust_idx=0;clust_idx < (

)clusters.size();clust_idx++) {

(cluster.

() == 1) {

trees[clust_idx] =

;

(cluster.

() == 2) {

single_tree(mat,

trees[clust_idx] = root;

(

=0;

< trees.size();

++) {

printf(

, (

)

);

vector<double>& leaf_dists,

vector<TPhyTreeNode*>& leaf_nodes,

last_edge_only =

)

(

->IsLeaf()) {

=

->GetValue().GetId();

dist =

->GetValue().GetDist();

(!last_edge_only) {

dist += dist_from_root;

(

< (

)leaf_dists.size());

leaf_dists[id] = dist;

(

< (

)leaf_nodes.size() && !leaf_nodes[

]);

leaf_nodes[id] =

;

(

->GetParent() &&

->GetValue().IsSetDist() && !last_edge_only) {

dist =

->GetValue().GetDist();

(it !=

->SubNodeEnd()) {

dist_from_root)

(node->

().GetId() ==

) {

dist_from_root + node->

().GetDist();

dist = node->

().GetDist();

(curr_dist > 0.0) {

scale = dist / curr_dist;

vector<TPhyTreeNode*>& cluster_trees,

vector<TPhyTreeNode*>& cluster_leaves)

(vector<TPhyTreeNode*>, it, cluster_leaves) {

cluster_id = node->

().GetId();

seq_id = cluster[0];

vector<TPhyTreeNode*> children;

children.push_back(*child);

(vector<TPhyTreeNode*>, it, children) {

(cluster_trees.size() == clusters.size());

vector<double> cluster_dists(clusters.size(), 0.0);

vector<TPhyTreeNode*> cluster_leaves(clusters.size(),

);

vector<TPhyTreeNode*> dummy_vect(clusters.size(),

);

vector<double>d(cluster_dists.size());

(

=0;

< d.size();

++) {

printf(

, (

)

, d[

]);

(

=0;

< cluster_trees.size();

++) {

(!cluster_trees[

]) {

(cluster_dists[

] <= 0.0) {

cluster_dists[

] = 1e-5;

cluster_dists[

]);

(

=0;

< cluster_dists.size();

++) {

printf(

, (

)

, cluster_dists[

]);

printf(

);

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

Declares the BLAST exception class.

Int2 Blast_KarlinBlkGappedLoadFromTables(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, const char *matrix_name, Boolean standard_only)

Attempts to fill KarlinBlk for given gap opening, extensions etc.

int GetPrototype(void) const

Get cluster prototype.

size_t size(void) const

Get cluster size.

vector< int >::const_iterator const_iterator

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

void ReleaseTrees(vector< TPhyTreeNode * > &trees)

Get list of trees for clusters and release ownership to caller.

@ eClique

Clusters can be joined if there is a link between all pairs of their elements.

@ eCompleteLinkage

Maximum distance between elements.

TPhyTreeNode * ReleaseTree(int index=0)

Get cluster tree and release ownership to caller.

void Reset(void)

Clear clusters and distance matrix.

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.

void SetClustMethod(EClustMethod method)

Set clustering method for links.

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.

Representation of pairwise distances, intended for use in multiple sequence alignment applications.

const CDistMethods::TMatrix & GetMatrix() const

Access the current distance matrix.

Interface for the traceback from blast hits.

An ordered collection of CHit objects.

int Size() const

Retrieve number of hits in list.

void PurgeAllHits()

Delete all hits unconditionally.

CHit * GetHit(int index)

Retrieve a hit from the hitlist.

void AddToHitList(CHit *hit)

Append a hit to the hitlist.

A generalized representation of a pairwise alignment.

int m_SeqIndex1

Numerical identifier for first sequence in alignment.

int m_SeqIndex2

Numerical identifier for second sequence in alignment.

TRange m_SeqRange1

The range of offsets on the first sequence.

TRange m_SeqRange2

The range of offsets on the second sequence.

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

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

Add link.

void Sort(void)

Sort links according to weights in ascending order.

Options and parameters for multiple alignement.

@ eFastME

Fast Minimum Evolution.

@ eClusters

Clustering dendrogram.

TScore GetEndGapExtendPenalty(void) const

Get gap extension penalty for end gaps in pairwise global alignment of profiles.

double GetMaxInClusterDist(void) const

Get maximum allowed distance between sequences in a cluster.

string GetScoreMatrixName(void) const

Get alignment score matrix name.

TKMethods::EDistMeasures GetKmerDistMeasure(void) const

Get method for computing distance between word count vectors.

int GetCentralSeq(void) const

Get central sequence.

EInClustAlnMethod GetInClustAlnMethod(void) const

TScore GetGapExtendPenalty(void) const

Get gap extension penlaty for middle gaps in pairwise global alignment of profiles.

const TConstraints & GetUserConstraints(void) const

Get user constraints.

TScore GetGapOpenPenalty(void) const

Get gap opening penalty for middle gaps in pairwise global alignment of profiles.

TScore GetEndGapOpenPenalty(void) const

Get gap opening penalty for end gaps in pairwise global alignment of profiles.

TKMethods::ECompressedAlphabet GetKmerAlphabet(void) const

Get alphabet used for creating word count vectors.

ETreeMethod GetTreeMethod(void) const

Get method for creating tree that guides progressive alignment.

vector< SConstraint > TConstraints

bool GetUseQueryClusters(void) const

Check if query clustering option is on.

@ eToPrototype

All cluster elements are aligner to cluster prototype.

@ eMulti

Alignment guide tree for each cluster is attached to the main alignment guide tree.

int GetKmerLength(void) const

Get word size for creating word count vectors.

int GetUserConstraintsScore(void) const

Get score for user alignment constraints.

bool GetVerbose(void) const

Get verbose mode.

Simultaneously align multiple protein sequences.

vector< CSequence > m_AllQueryData

vector< vector< Uint4 > > m_ClusterGapPositions

CMultiAlignerOptions::EInClustAlnMethod m_ClustAlnMethod

void x_SetScoreMatrix(const char *matrix_name)

Set the score matrix the aligner will use.

SProgress m_ProgressMonitor

CRef< objects::CScope > m_Scope

void x_ComputeClusterTrees(vector< TPhyTreeNode * > &trees)

Compute independent phylogenetic trees each cluster.

void x_FindLocalInClusterHits(const vector< TPhyTreeNode * > &cluster_trees)

Run blast on sequences from each cluster subtree.

static void x_InitInsertColumn(vector< SColumn >::iterator &it, size_t len, int num, int cluster)

vector< int > m_Msa2Repr

Indices of sequence representatives in input alignment 2.

vector< CRef< objects::CSeq_loc > > m_tQueries

void x_MakeClusterResidueFrequencies()

Compute profile residue frequencies for clusters.

vector< CRef< objects::CSeq_loc > > m_AllQueries

TStatus Run(void)

Align the current set of input sequences (reset any existing alignment information).

struct CMultiAligner::SColumn SColumn

Column in an alignment used for combining result from multiple alignment and pair-wise in-cluster ali...

void x_ComputeTree()

Given the current list of domain and local hits, generate a phylogenetic tree that clusters the curre...

void x_FindLocalHits(const blast::TSeqLocVector &queries, const vector< int > &indices)

Run blast on selected input sequences and postprocess the results.

@ eOutOfMemory

Out of memory error.

@ eInternalError

Unexpected error occured.

@ eSuccess

Alignment successfully completed.

@ eInterrupt

Alignment interruped through callback function.

@ eOptionsError

Error related to options occured.

@ eDatabaseError

Error related to RPS database occured.

@ eQueriesError

Error related to query sequences occured.

void x_BuildFullTree(const vector< TPhyTreeNode * > &cluster_trees)

Combine alignment guide tree computed for clusters with guide trees computed for each cluster.

vector< CSequence > m_QueryData

bool x_ValidateInputMSAs(void) const

Validate input alignments.

bool x_ValidateQueries(void) const

Validate query sequences.

void x_CreatePatternQueries(vector< const CSequence * > &queries, vector< int > &indices)

Create query set for PROSITE pattern search along with indices in multiple alignment queries array.

void SetInputMSAs(const objects::CSeq_align &msa1, const objects::CSeq_align &msa2, const set< int > &representatives1, const set< int > &representatives2, CRef< objects::CScope > scope)

Set input alignments.

void x_AlignMSAs(void)

Align multiple sequence alignments.

void x_MultiAlignClusters()

Combine pair-wise in-cluster alignements with multiple alignments of cluster prototypes.

vector< CSequence > m_InMSA1

Input alignment.

vector< CSequence > m_Results

void x_FindConsistentHitSubset(void)

Find consistent subset of pair-wise hits that can be used as alignment constraints.

CConstRef< CMultiAlignerOptions > m_Options

void x_InitParams(void)

Initiate parameters using m_Options.

void x_AlignProfileProfile(vector< CTree::STreeLeaf > &node_list1, vector< CTree::STreeLeaf > &node_list2, vector< CSequence > &alignment, CNcbiMatrix< CHitList > &pair_info, int iteration)

Align two collections of sequences.

void SetQueries(const vector< CRef< objects::CSeq_loc > > &queries, CRef< objects::CScope > scope)

Set query sequences.

void Reset(void)

Clear out the state left by the previous alignment operation.

void x_AlignInClusters()

Pair-wise align each cluster sequence to cluster representative.

vector< string > m_Messages

static void x_InitColumn(vector< SColumn >::iterator &it, size_t len)

virtual void x_Run(void)

Align the current set of input sequences (reset any existing alignment information).

bool(* FInterruptFn)(SProgress *progress)

Prototype for function pointer to dertermine whether alignment should proceed of be interrupted.

void x_FindDomainHits(blast::TSeqLocVector &queries, const vector< int > &indices)

Run RPS blast on seletced input sequences and postprocess the results.

CMultiAligner(void)

Create mutli aligner with default options.

void x_BuildAlignment()

Given the current domain, local, pattern and user hits, along with the current tree,...

void x_Init(void)

Initiate class attributes that are not alignment parameters.

void x_FindPatternHits(const vector< const CSequence * > &queries, const vector< int > &indices)

Find PROSITE pattern hits on selected input sequences.

CRef< objects::CBioTreeContainer > GetTreeContainer(void) const

Get serializable tree used as guide in progressive alignment.

vector< int > m_Msa1Repr

Indices of sequence representatives in input alignment 1.

void x_AttachClusterTrees(const vector< TPhyTreeNode * > &cluster_trees, const vector< TPhyTreeNode * > &cluster_leaves)

Replace leaves in the alignment guide tree of clusters with cluster trees.

bool x_FindQueryClusters()

Find clusters of similar queries, select cluster representative sequences, and prepare input to multi...

void x_CreateBlastQueries(blast::TSeqLocVector &queries, vector< int > &indices)

Create query set for RPS Blast and Blastp searches along with indices in multiple alignment queries a...

bool x_ValidateUserHits(void)

Validate user constraints with queries.

void x_InitAligner(void)

Initiate PSSM aligner parameters.

static const int kClusterNodeId

FInterruptFn SetInterruptCallback(FInterruptFn fnptr, void *user_data=NULL)

Set a function callback to be invoked by multi aligner to allow interrupting alignment in progress.

vector< CSequence > m_InMSA2

Input alignment.

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

Class for representing protein sequences.

int GetLength() const

Get the length of the current sequence.

unsigned char GetLetter(int pos) const

Access the sequence letter at a specified position.

TFreqMatrix & GetFreqs()

Access the list of position frequencies associated with a sequence.

static void CompressSequences(vector< CSequence > &seq, vector< int > index_list)

Given a collection of sequences, remove all sequence positions where a subset of the sequences all co...

void PropagateGaps(const CNWAligner::TTranscript &transcript, CNWAligner::ETranscriptSymbol gap_choice)

Given an edit script, insert gaps into a sequence.

static const unsigned char kGapChar

The ncbistdaa code for a gap.

unsigned char * GetSequence()

Access the raw sequence data, in ncbistdaa format.

static void CreateMsa(const objects::CSeq_align &seq_align, objects::CScope &scope, vector< CSequence > &msa)

Create a vector of CSequence objects that represents the alignment in given Seq_align.

unsigned char GetPrintableLetter(int pos) const

Access the sequence letter at a specified position, and return an ASCII representation of that letter...

definition of a Culling tree

A wrapper for controlling access to the phylogenetic tree generated by CDistMethods.

void SetTree(TPhyTreeNode *tree)

Set tree.

static void PrintTree(const TPhyTreeNode *node, int level=0)

Debug routine to recursively print out a tree.

const TPhyTreeNode * GetTree() const

Access the current tree.

TPhyTreeNode * ReleaseTree()

Get the current tree and release ownership.

void ComputeTree(const CDistMethods::TMatrix &distances, bool use_fastme=false)

Compute a new tree.

static void ComputeDistMatrix(const vector< TKmerCounts > &counts, double(*fsim)(const TKmerCounts &, const TKmerCounts &), TDistMatrix &dmat)

Compute matrix of distances between given counts vectors.

static void ComputeCounts(const vector< CRef< objects::CSeq_loc > > &seqs, objects::CScope &scope, vector< TKmerCounts > &counts)

Create k-mer counts vectors for given sequences.

static void SetParams(unsigned kmer_len, unsigned alphabet_size)

Set default counts vector parameters.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

static TPhyTreeNode * s_MakeTwoLeafTree(const CClusterer::CSingleCluster &ids, double distance)

Create phylogenetic tree for two sequences.

static void s_ScaleTreeEdges(TPhyTreeNode *node, double scale)

Scale all tree edges by given factor (recursive).

static void s_SetLeafIds(TPhyTreeNode *node, const CClusterer::CSingleCluster &ids)

Change ids of leaf nodes in a given tree to desired values (recursive).

static double s_FindNodeDistance(const TPhyTreeNode *node, int id, double dist_from_root)

Find distance from root for selected node (recursive).

static void s_RescaleTree(TPhyTreeNode *tree, int id, double dist)

Rescale tree so that node with given id has desired distance from root.

static void s_FindLeafDistances(TPhyTreeNode *tree, double dist_from_root, vector< double > &leaf_dists, vector< TPhyTreeNode * > &leaf_nodes, bool last_edge_only=false)

Compute length of the edge or distance from root for each leaf (recursive).

Interface for CMultiAligner.

CRef< objects::CBioTreeContainer > MakeBioTreeContainer(const TPhyTreeNode *tree)

Conversion from TPhyTreeNode to CBioTreeContainer.

static const column_t columns[]

void SetStartWg(TScore value)

TTranscript GetTranscript(bool reversed=true) const

void SetEndWs(TScore value)

virtual CNWAligner::TScore Run(void)

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

SNCBIFullScoreMatrix & GetMatrix()

void SetEndWg(TScore value)

vector< ETranscriptSymbol > TTranscript

void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)

void SetEndSpaceFree(bool Left1, bool Right1, bool Left2, bool Right2)

void SetStartWs(TScore value)

#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.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

Convert int to string.

TNodeList::iterator TNodeList_I

TTreeType * DetachNode(TTreeType *subnode)

Remove the subtree from the tree without destroying it.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList::const_iterator TNodeList_CI

void AddNode(TTreeType *subnode)

Add new subnode.

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.

const TTreeType * GetParent(void) const

Get node's parent.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

constexpr bool empty(list< Ts... >) noexcept

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

CSequnceHelper< CObject > CSequence

int strcmp(const char *str1, const char *str2)

#define ASSERT

macro for assert.

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

CTreeNode< CPhyNodeData > TPhyTreeNode

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

const SNCBIPackedScoreMatrix NCBISM_Blosum80

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to hold the Karlin-Altschul parameters.

Structure for listing tree leaves.

static Uint4 letter(char c)

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