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

seqloc->

().SetFrom(from);

seqloc->

().SetTo(to);

loc_list.push_back(seqloc);

seg_list.push_back(

(query_index, from, to));

vector<SSegmentLoc>& filler_segs)

vector<CRangeCollection<TOffset> > sorted_segs(num_queries);

*subhit = *subitr;

(vector<int>, it, blastp_indices) {

itr->GetFrom() - 1, filler_segs,

);

seg_start = itr->GetToOpen();

seq_length - 1, filler_segs,

);

printf(

);

(

= 0;

< (

)filler_segs.size();

++) {

printf(

,

filler_segs[

].seq_index,

filler_segs[

].GetFrom(),

filler_segs[

].GetTo());

vector<int>& indices,

vector<SSegmentLoc>& filler_segs)

kBlastBatchSize = 10000;

num_full_queries = indices.size();

(filler_locs.empty())

blastp_opts->SetEvalueThreshold(

(blastp_evalue, 10.0));

blastp_opts->SetSegFiltering(

);

(batch_start < (

)filler_locs.size()) {

(

= batch_start;

< (

)filler_locs.size();

++) {

& curr_loc = *filler_locs[

];

fragment_size = curr_loc.

().

() -

(batch_size + fragment_size >= kBlastBatchSize && batch_size > 0)

batch_size += fragment_size;

blaster(curr_batch, queries, *blastp_opts);

);

(

= 0;

< (

)curr_batch.size();

++) {

list1_oid = filler_segs[batch_start +

].seq_index;

(

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

(list1_oid == indices[j])

v[

* num_full_queries + j]->

()) {

& curr_score = **score_itr;

(curr_score.

().

() ==

)

(evalue > blastp_evalue)

align_score, denseg));

& curr_score = **score_itr;

(evalue > blastp_evalue)

indices[j], align_score, dendiag));

batch_start += curr_batch.size();

vector<int>& indices)

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

vector<SSegmentLoc> filler_segs;

printf(

);

printf(

,

unique_ptr< vector<int> >

(

vector<int>());

left = -1, right = -1;

(

=0;

< left_inds->size();

++) {

(

j=0;j < right_inds->size();j++) {

(dist > dmat((*left_inds)[

], (*right_inds)[j]) || left < 0) {

left = (*left_inds)[

];

right = (*right_inds)[j];

dist = dmat(left, right);

blastp_opts->SetEvalueThreshold(

(blastp_evalue, 10.0));

blastp_opts->SetSegFiltering(

);

blaster(left_query, right_query, *blastp_opts);

& curr_score = **score_itr;

(curr_score.

().

() ==

)

(evalue > blastp_evalue)

& curr_score = **score_itr;

(evalue > blastp_evalue)

align_score, dendiag));

(vector<int>, it, *right_inds) {

left_inds->push_back(*it);

vector<TPhyTreeNode*>& cluster_trees)

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

printf(

);

printf(

,

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

int TOffset

Basic data type for offsets into a sequence.

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastProteinOptionsHandle class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

Runs the BLAST algorithm between 2 sequences.

Handle to the protein-protein options to the BLAST algorithm.

const TDistMatrix & GetDistMatrix(void) const

Get distance matrix.

void Append(CHitList &hitlist)

Append one hitlist to another.

int Size() const

Retrieve number of hits in list.

void PurgeAllHits()

Delete all hits unconditionally.

bool Empty()

Determine whether a list contains no hits.

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.

TSubHit & GetSubHit()

Retrieve a list of subhits.

int m_Score

Score of 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.

static const int kMinHitSize

Not always used, but useful to avoid extremely small hits.

TRange m_SeqRange2

The range of offsets on the second sequence.

bool HasSubHits()

Query if a CHit has a hierarchy of subhits available.

vector< CHit * > TSubHit

Hits can be grouped hierarchically.

double GetBlastpEvalue(void) const

Get e-value for accepting Blastp hits.

bool GetVerbose(void) const

Get verbose mode.

Simultaneously align multiple protein sequences.

SProgress m_ProgressMonitor

CRef< objects::CScope > m_Scope

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

Run blast on sequences from each cluster subtree.

vector< CRef< objects::CSeq_loc > > m_tQueries

CHitList m_LocalInClusterHits

void x_AlignFillerBlocks(const blast::TSeqLocVector &queries, const vector< int > &indices, vector< CRef< objects::CSeq_loc > > &filler_locs, vector< SSegmentLoc > &filler_segs)

Run blastp, aligning the collection of filler fragments against the entire input dataset.

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

Run blast on selected input sequences and postprocess the results.

@ eInterrupt

Alignment interruped through callback function.

vector< CSequence > m_QueryData

void x_AssignDefaultResFreqs()

CConstRef< CMultiAlignerOptions > m_Options

void x_AddNewSegment(vector< CRef< objects::CSeq_loc > > &loc_list, const CRef< objects::CSeq_loc > &query, TOffset from, TOffset to, vector< SSegmentLoc > &seg_list, int query_index)

Create a new query sequence that is a subset of a previous query sequence.

void x_MakeFillerBlocks(const vector< int > &indices, vector< CRef< objects::CSeq_loc > > &filler_locs, vector< SSegmentLoc > &filler_segs)

Turn all fragments of selected query sequence not already covered by a domain hit into a separate que...

unique_ptr< vector< int > > x_AlignClusterQueries(const TPhyTreeNode *node)

definition of a Culling tree

Interface for CMultiAligner.

CConstRef< objects::CSeq_align_set > GetSeqAlign() const

Accessor for the Seq-align results.

virtual TSeqAlignVector Run()

Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as fo...

CRef< CSearchResultSet > RunEx()

Performs the same functionality as Run(), but it returns a different data type.

CSearchResults & GetResults(size_type qi, size_type si)

Retrieve results for a query-subject pair contained by this object.

#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.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

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

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

#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.

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.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

const TScores & GetScores(void) const

Get the Scores member data.

E_Choice Which(void) const

Which variant is currently selected.

vector< CRef< CScore > > TScore

TInt GetInt(void) const

Get the variant data.

const TDendiag & GetDendiag(void) const

Get the variant data.

const TValue & GetValue(void) const

Get the Value member data.

vector< CRef< CScore > > TScores

list< CRef< CSeq_align > > Tdata

const TScore & GetScore(void) const

Get the Score member data.

TReal GetReal(void) const

Get the variant data.

list< CRef< CDense_diag > > TDendiag

const TId & GetId(void) const

Get the Id member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

TFrom GetFrom(void) const

Get the From member data.

TTo GetTo(void) const

Get the To member data.

const TInt & GetInt(void) const

Get the variant data.

unsigned int

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

const TYPE & Get(const CNamedParameterList *param)

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to represent a single sequence to be fed to BLAST.

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