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

= { {

,0}, {

,1}, {

,2}, {

,3},{

,4} };

= { {0,

}, {1,

}, {2,

}, {3,

},{4,

} };

bar_p = in_str.find(

);

colon_p = in_str.find(

);

(bar_p ==

&& colon_p ==

)

min_p =

(bar_p, colon_p);

in_str.substr(min_p+1,

);

new_str = in_str;

(!new_str.empty()) {

out_strs.push_back(new_str);

list<string> fasta_sub_strs;

(list<string>, sub_str_iter, fasta_sub_strs) {

sub_id->

(*sub_str_iter);

out_ids.push_back(sub_id);

vector<string> title_tokens;

(title_tokens.empty()){

id_token = title_tokens[0];

(obj_id.

())

id_token = obj_id.

();

obj_id->

(id_token);

retval->

(*sid_in);

list<CRef<CSeq_id> > out_list;

out_list.push_back(next_id);

vector<CConstRef<CSeq_id> > idl_copy;

idl_copy.push_back( cc);

list<CRef<objects::CSeq_id> > next_seqid_list;

out_list.push_back(next_id);

other_seq_id_str;

(title.find(

) !=

) {

pos = title.find(

);

title = title.substr(pos+1, title.length()-(pos+1));

list<CRef<CSeq_id> > id_list;

has_range=

;

range_start=0, range_stop=0;

id_list, has_range, range_start, range_stop, titles,

out_list.push_back(*ii);

(!titles.empty() && title.empty()) {

title = titles[0].m_sLineText;

out_list.push_back(next_id);

& db,

terminal_flexibility)

: m_SeqLoc(seq_loc),

(scope), m_DB(db),

m_TerminalFlexibility(terminal_flexibility), m_Vecscreen(0)

blaster(query_factory, opts, target_db);

& qid,

& qtitle,

& sid,

& stitle)

list<CRef<CSeq_id> > qidl, sidl;

kPrintAlignments =

(m_Outfmt == eShowAlignments);

kPrintBlastTab =

(m_Outfmt == eBlastTab);

kPrintJson =

(m_Outfmt == eJson);

kPrintAsnText =

(m_Outfmt == eAsnText || m_Outfmt == eAsnTextNoProcess);

custom_output = ( kPrintBlastTab ?

:

);

kBelieveQuery(

);

kShowGi(

);

kNumDescriptions(0);

kNumAlignments(50);

kIsTabular(

);

kBelieveQuery,

, kNumDescriptions,

kShowGi, m_HtmlOutput,

(!kPrintBlastTab && !kPrintJson && !kPrintAsnText ) {

list<SVecscreenSummary> match_list = m_Screener.GetList();

(kPrintBlastTab || kPrintJson || kPrintAsnText) {

(m_Outfmt == eAsnTextNoProcess) {

alignments = ((*result_set)[0]).SetSeqAlign().GetPointer();

(m_Outfmt != eAsnTextNoProcess) {

(list<SVecscreenSummary>, mi, match_list) {

(mi->range.IntersectionWith((*align_iter)->GetSeqRange(0))==mi->range ||

mi->range.IntersectionWith((*align_iter)->GetSeqRange(0))==(*align_iter)->GetSeqRange(0)) {

(mi->seqid->Equals( (*align_iter)->GetSeq_id(0))) {

(*align_iter)->SetNamedScore(

,

[mi->match_type]);

qid, qtitle, sid, stitle;

x_GetIdsAndTitlesForSeqAlign(**align_iter, qid, qtitle, sid, stitle);

fixed->

(**align_iter);

fixed->

().SetDenseg().SetIds()[0]->Set(qid);

fixed->

().SetDenseg().SetIds()[0]->Set(

+qid);

fixed->

().SetDenseg().SetIds()[1]->Set(sid);

fixed->

().SetDenseg().SetIds()[1]->Set(

+sid);

fixed_ids.

().push_back(fixed);

(*result_set)[0].SetSeqAlign()->Assign(fixed_ids);

m_Screener.m_Queries);

(kPrintBlastTab) {

(!match_list.empty()) {

<<

<< endl;

(list<SVecscreenSummary>, mi, match_list) {

qtitle=

, stitle=

;

qid=

, sid=

;

(!mi->aligns.empty()) {

x_GetIdsAndTitlesForSeqAlign(*mi->aligns.front(), qid, qtitle, sid, stitle);

qid = mi->seqid->GetSeqIdString(

);

qid=sid=qtitle=stitle=

;

x_GetIdsAndTitlesForSeqAlign(align, qid, qtitle, sid, stitle);

<< mi->drops.

() <<

}

(kPrintJson) {

qtitle=

, stitle=

;

qid=

, sid=

;

last_qid =

;

(list<SVecscreenSummary>, mi, match_list) {

qid=sid=qtitle=stitle=

;

x_GetIdsAndTitlesForSeqAlign(align, qid, qtitle, sid, stitle);

jobj.

(

, qid);

jobj.

(

, mi->drops.size());

jobj.

(

, sid);

jobj.

(

, stitle);

(align_count > 0) {

top_obj.

(

, last_qid);

(kPrintAlignments ==

) {

.GetBioseqHandle(*m_Screener.m_SeqLoc->GetId(),

message =

+m_Screener.m_SeqLoc->GetId()->AsFastaString();

CBlastFormatUtil::AcknowledgeBlastQuery(*bioseq,

m_HtmlOutput, kIsTabular);

m_Screener.m_Vecscreen->VecscreenPrint(

);

(match_list.empty() && !kPrintAlignments) {

<<

;

(match_list.empty() && !kPrintAlignments) {

<<

;

pair<string, string> TLabels;

vector<TLabels> match_labels;

match_labels.push_back(TLabels(

,

));

match_labels.push_back(TLabels(

,

));

match_labels.push_back(TLabels(

,

));

match_labels.push_back(TLabels(

,

));

list<SVecscreenSummary>::iterator boundary, itr;

boundary = stable_partition(match_list.begin(), match_list.end(),

(boundary != match_list.begin()) {

(itr = match_list.begin(); itr != boundary; ++itr) {

<< itr->range.GetFrom()+1 <<

<< itr->range.GetTo()+1 <<

;

match_list.erase(match_list.begin(), boundary);

(kPrintAlignments) {

m_Screener.m_Queries);

list<CVecscreenRun::SVecscreenSummary>

list<CVecscreenRun::SVecscreenSummary> retval;

list<CVecscreen::AlnInfo> aln_info;

(list<CVecscreen::AlnInfo*>, ai, *aln_info_ptr) {

aln_info.push_back(align_info);

(list<CVecscreen::AlnInfo>, ai, aln_info) {

summary.

= ai->range;

summary.

= ai->get_aligns();

summary.

= ai->align_drops;

retval.push_back(summary);

static CRef< CScope > m_Scope

Produce formatted blast output for command line applications.

Declares class to display one-line descriptions at the top of the BLAST report.

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

static string GetTitle(const objects::CBioseq_Handle &bh)

This class formats the BLAST results for command line applications.

void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)

Print all alignment information for a single query sequence along with any errors or warnings (errors...

void PrintEpilog(const blast::CBlastOptions &options)

Print the footer of the blast report.

@ kFormatLineLength

The line length of pairwise blast output.

void PrintProlog()

Print the header of the blast report.

Class for computing sequences' titles ("definitions").

vector< SLineTextAndLoc > TSeqTitles

EOutputFormat

Defines the output formats supported by our command line formatter.

@ ePairwise

Standard pairwise alignments.

@ eTabular

Tabular output.

@ eAsnText

ASN.1 text output.

CJson_Object push_back_object(void)

Add object type element to the end of the array.

bool Write(std::ostream &out, TJson_Write_Flags flags=fJson_Write_IndentWithSpace, unsigned int indent_char_count=4) const

Write JSON data into a stream.

CJson_Object SetObject(void)

Get JSON object contents of the node.

CJson_Array insert_array(const CJson_Node::TKeyType &name)

Insert array type element into the object.

void insert(const CJson_Node::TKeyType &name)

Insert null element into the object.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Search Results for One Query.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

static void GetBioseqHandleDeflineAndId(const objects::CBioseq_Handle &handle, list< TGi > &use_this_gi, string &seqid, string &defline, bool show_gi=true, TGi this_gi_first=INVALID_GI)

Returns sequence id and a BLAST defline as strings, given a Bioseq handle and a list of gis.

static void GetSeqIdList(const objects::CBioseq_Handle &bh, list< CRef< objects::CSeq_id > > &ids)

Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references,...

void x_GetIdsAndTitlesForSeqAlign(const objects::CSeq_align &align, string &qid, string &qtitle, string &sid, string &stitle)

CScope & m_Scope

from which we get the sequence data

void FormatResults(CNcbiOstream &out, CRef< blast::CBlastOptionsHandle > vs_opts)

Format the VecScreen results.

CRef< blast::CSearchResultSet > m_RawBlastResults

The raw BLAST results.

CRef< blast::CBlastQueryVector > m_Queries

The queries to run VecScreen on.

CRef< CSeq_loc > m_SeqLoc

Seq-loc to screen.

list< SVecscreenSummary > GetList() const

Fetches summary list.

CVecscreen * m_Vecscreen

vecscreen instance for search.

CRef< objects::CSeq_align_set > GetSeqalignSet() const

Fetches seqalign-set already processed by vecscreen.

CRef< blast::CSearchResultSet > GetSearchResultSet() const

CRef< CScope > m_Scope

Scope used to fetch query.

TSeqPos m_TerminalFlexibility

edge wiggle room

CRef< objects::CSeq_align_set > m_Seqalign_set

Processed Seq-align.

CVecscreenRun(CRef< CSeq_loc > seq_loc, CRef< CScope > scope, const string &db=string(kDefaultVectorDb), const TSeqPos terminal_flexibility=kDefaultTerminalFlexibility)

Constructor.

list< CRef< objects::CSeq_align > > TAlignList

string m_DB

Database to use (UniVec is default).

void x_RunBlast()

Runs the actual BLAST search.

static string GetStrengthString(MatchType match_type)

Returns a string concerning the strength of the match for a given enum value.

const list< AlnInfo * > * GetAlnInfoList() const

return alignment info list

CRef< objects::CSeq_align_set > ProcessSeqAlign(void)

Process alignment to show.

Class for the messages for an individual query sequence.

std::ofstream out("events_result.xml")

main entry point for tests

Operators to edit gaps in sequences.

CRef< CSearchResultSet > Run()

Executes the search.

size_type size() const

Identical to GetNumResults, provided to facilitate STL-style iteration.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

static CBlastOptionsHandle * CreateTask(string task, EAPILocality locality=CBlastOptions::eLocal)

Creates an options handle object configured with default options for the requested task,...

@ eBlastDbIsNucleotide

nucleotide

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

vector< ILineError::EProblem > TIgnoredProblems

static void ParseDefLine(const TStr &defLine, const SDefLineParseInfo &info, const TIgnoredProblems &ignoredErrors, list< CRef< CSeq_id >> &ids, bool &hasRange, TSeqPos &rangeStart, TSeqPos &rangeEnd, TSeqTitles &seqTitles, ILineErrorListener *pMessageListener)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

@ fLabel_Version

Show the version.

@ eContent

Untagged human-readable accession or the like.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

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

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

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

vector< CSeq_id_Handle > TId

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

const TId & GetId(void) const

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int to string.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

list< CRef< CSeq_id > > TSeqid

const Tdata & Get(void) const

Get the member data.

list< CRef< CBlast_def_line > > Tdata

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

TId GetId(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TLocal & SetLocal(void)

Select the variant.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

Main class to perform a BLAST search on the local machine.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Defines BLAST database access classes.

Definition of SSeqLoc structure.

const CSeq_id * seqid

Seq-id of query.

CRange< TSeqPos > range

range of match.

string match_type

Categorizes strength of match.

SVecscreenMatchFinder(const string &match_type)

bool operator()(const CVecscreenRun::SVecscreenSummary &rhs)

string s_PopIdPart(const string &in_str)

map< string, int > match_type_ints

void s_MakeFastaSubIds(const CSeq_id &in_id, list< CRef< CSeq_id > > &out_ids)

CRef< CSeq_id > s_ReplaceLocalId(const CBioseq_Handle &bh, CConstRef< CSeq_id > sid_in, bool parse_local)

map< int, string > match_type_strs

list< CRef< CSeq_id > > s_SetIdList(const CBioseq_Handle &bh, string &title)

void s_MakeFastaSubStrs(const string &in_str, list< string > &out_strs)

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