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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/remote__blast_8cpp_source.html below:

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

list< CRef<objects::CBlast4_error> > & errors = reply->GetErrors();

TErrorList::const_iterator

;

(

= errors.begin();

!= errors.end();

++) {

list< CRef<CBlast4_error> > & errors = reply->GetErrors();

TErrorList::const_iterator

;

(

= errors.begin();

!= errors.end();

++) {

((*i)->CanGetMessage() && (! (*i)->GetMessage().empty())) {

+= (*i)->GetMessage();

((*i)->GetCode()) {

.push_back(

(

) +

);

.push_back(

(

) +

);

.push_back(

(

) +

);

.push_back(

(

) +

);

.push_back(

(

) +

);

.push_back(

(

) +

cfg(

);

cfg +=

;

cfg +=

;

cfg +=

;

cfg +=

;

( !errors.empty() ) {

);

gsrr->SetRequest_id(

);

}

(!

&& errors.find(

) !=

) {

retval =

;

->GetBody().IsGet_search_results()) {

rv = & (

->SetBody().SetGet_search_results());

(gsrr && gsrr->CanGetAlignments()) {

rv = & (gsrr->SetAlignments());

query_index = 0;

temp.push_back(cur_set);

current_id = this_id;

cur_set->

().push_back(*it);

temp.push_back(cur_set);

TSeqAlignVector::size_type sap_index = 0;

query_index = 0;

(sap_index < temp.size())

list< CRef< CSeq_align > > sal = temp[sap_index]->Get();

(

== (*it)->Compare(sal.front()->GetSeq_id(query_index) ))

rv.push_back(temp[sap_index]);

rv.push_back(cur_set);

rv.push_back(cur_set);

(gsrr && gsrr->CanGetPhi_alignments()) {

rv = & (gsrr->SetPhi_alignments());

retval.resize(

()->GetNumQueries());

(network_masks.empty()) {

query_index = 0;

(TGSRR::TMasks, masks_for_frame, network_masks) {

(masks_for_frame->NotEmpty());

((*masks_for_frame)->GetLocations().front()->GetId());

(previous_seqid.

()) {

previous_seqid = current_seqid;

mqr = &retval[query_index];

mqr = &retval[++query_index];

previous_seqid = current_seqid;

((*masks_for_frame)->GetLocations().size() == (

) 1);

((*masks_for_frame)->GetLocations().front().NotEmpty());

(*masks_for_frame)->GetLocations().front();

(*mask)->GetFrom(), (*mask)->GetTo()));

(gsrr && gsrr->CanGetMasks()) {

rv = gsrr->SetMasks();

list< CRef<CBlast4_ka_block > > rv;

(gsrr && gsrr->CanGetKa_blocks()) {

rv = (gsrr->SetKa_blocks());

(gsrr && gsrr->CanGetSearch_stats()) {

rv = (gsrr->SetSearch_stats());

(gsrr && gsrr->CanGetPssm()) {

rv = & (gsrr->SetPssm());

}

(

.empty()) {

.push_back(

);

.push_back(

);

(reply->CanGetBody() &&

reply->GetBody().GetQueue_search().CanGetRequest_id()) {

= reply->GetBody().GetQueue_search().GetRequest_id();

try_again =

;

.push_back(

);

}

(

->CanGetBody() &&

->GetBody().IsGet_search_results()) {

.push_back(

);

cout <<

<< 0 << endl;

start_sec = 10.0;

increment = 1.30;

max_sleep = 300.0;

max_time = timeout;

cout <<

<< start_sec <<

<< increment <<

<< max_sleep <<

<< max_time <<

<< endl;

sleep_next = start_sec;

sleep_totl = 0.0;

cout <<

<< __LINE__ <<

<< sleep_next <<

<< sleep_totl << endl;

(

&& (sleep_totl < max_time)) {

cout <<

<< sleep_next << endl;

max_left = max_time - sleep_totl;

(sleep_next > max_left) {

sleep_next = max_left;

(sleep_next < 2.0)

sleep_totl += sleep_next;

cout <<

<< sleep_totl << endl;

(sleep_next < max_sleep) {

sleep_next *= increment;

(sleep_next > max_sleep) {

sleep_next = max_sleep;

cout <<

<< sleep_next << endl;

);

& program,

& service)

((! opts_handle) || program.empty() || service.empty()) {

);

(program.empty()) {

);

);

);

);

->SetOptions().GetBlast4AlgoOpts();

user_ipv6_address;

(

.Get(

) !=

)

user_ipv6_address =

.Get(

);

( !user_ipv6_address.empty() ){

algo_opts->

(

(

), user_ipv6_address );

->SetAlgorithm_options().Set() = *algo_opts;

p->SetName(field.GetName());

->SetProgram_options().Set().push_back(p);

p->SetName(field.GetName());

->SetProgram_options().Set().push_back(p);

p->SetName(field.GetName());

->SetProgram_options().Set().push_back(p);

list<Int8> * x)

p->SetName(field.GetName());

->SetProgram_options().Set().push_back(p);

v->

().assign((x && (*x)) ? (*x) :

);

p->SetName(field.GetName());

->SetProgram_options().Set().push_back(p);

(bioseqs.

()) {

);

(!

->IsSetQueries())

);

(seqlocs.empty()) {

);

->SetSeq_loc_list() = seqlocs;

(masking_locations.empty()) {

(

->GetQueries().GetNumQueries() != masking_locations.size()) {

oss <<

<<

->GetQueries().GetNumQueries()

<<

<< masking_locations.size() <<

;

(*masked_region)->GetFrom(),

(*masked_region)->GetTo()));

((*masked_region)->CanGetStrand() &&

retval->SetLocations().push_back(seqloc);

retval->SetFrame(frame);

vector<string>* warnings

)

(query_masks->empty()) {

current_frame = query_masks->front()->GetFrame();

(!packed_seqint.

())

retval.push_back(network_mask);

current_frame = (*mask_locs)->GetFrame();

packed_seqint->AddInterval((*mask_locs)->GetSeqId(),

(*mask_locs)->GetInterval().GetFrom(),

(*mask_locs)->GetInterval().GetTo());

(!packed_seqint.

())

retval.push_back(network_mask);

packed_seqint.

();

(pssm.

()) {

);

psi_program(

);

old_service(

);

new_service(

);

delta_service(

);

(

->GetProgram() != psi_program) {

);

(

->GetService().empty()) {

);

((

->GetService() != old_service) &&

(

->GetService() != new_service) &&

(

->GetService() != delta_service)) {

(

) +

->GetService() +

);

->SetQueries(*queries_p);

(

->GetService() != delta_service) {

->SetService(new_service);

rvalue =

[0];

(

= 1;

<

.size();

++) {

rvalue =

[0];

(

= 1;

<

.size();

++) {

(opts_handle, db);

(iter->NotEmpty()) {

(entry.

()) {

(queries.

()) {

);

(bss.

() && sll.empty()) {

);

has_local_ids =

;

( !sll.empty() ) {

(sll.front()->IsInt()) {

kRangeLength = kStop -

+ 1;

kFullLength =

bss->

().front()->GetSeq().GetInst().GetLength();

(kFullLength != kRangeLength) {

has_local_ids =

;

(has_local_ids) {

(pssm.

()) {

);

(opts_handle, db);

(opts_handle.

()) {

);

);

( !tmplist.empty() ) {

(tmplist.begin(), tmplist.end(), back_inserter(gilist));

( !tmplist.empty() ) {

(tmplist.begin(), tmplist.end(), back_inserter(gilist));

l_disk_cache_flag =

.Get(

);

(gi_list.empty()) {

);

list<int> int_gi_list;

( list<TGi>, it, gi_list ) {

int_gi_list.push_back(

(

, *it));

(gi_list.begin(), gi_list.end(), back_inserter(

));

*

= algo_key.c_str();

(gi_list.empty()) {

);

list<int> int_gi_list;

( list<TGi>, it, gi_list ) {

int_gi_list.push_back(

(

, *it));

->SetType(rtype);

);

->SetSubject(*subject_p);

(bss.

()) {

);

list< CRef<CBioseq> > seqs;

->SetSubject(*subject_p);

);

(3600*3.5);

list< CRef< CBlast4_error > > & msgs =

->GetMessages();

((*itr)->IsSetMessage()) {

= (*itr)->GetMessage();

((*itr)->IsSetCode()) {

((*itr)->GetCode()) {

(

.GetSubject()->IsDatabase())

);

(

.empty()) {

);

);

(reply->CanGetBody()) {

(reply->GetBody().IsGet_request_info()) {

(& reply->SetBody().SetGet_request_info());

(grir->GetDatabase().GetName() !=

) {

( grir->IsSetFormat_options() )

);

list< CRef<objects::CBioseq> >

(service ==

) {

(program ==

) {

}

(program ==

|| program ==

) {

(service ==

) {

(program ==

);

(frame == -1 || frame == 1);

(; itr; ++itr) {

(queries->

()) {

(seq_entry.

()) {

query_ids.push_back(

);

(vector<string>, itw,

) {

query_messages.push_back(sm);

(vector<string>, ite,

) {

query_messages.push_back(sm);

search_messages.insert(search_messages.end(),

alignments.empty() ? 1 : alignments.size(),

<<

<< search_messages.

() <<

<< endl;

(alignments.empty()) {

alignments.resize(1);

kTarget(

);

kLength_Adj(

);

effective_search_space = 0;

length_adjustment = 0;

effective_search_space =

kTmp(

);

->SetOptions().SetMatrixName((*itr).c_str());

found_gapped =

, found_ungapped =

;

pair<double, double> lambdas, Ks, Hs;

((*itr)->GetGapped()) {

lambdas.second = (*itr)->GetLambda();

Ks.second = (*itr)->GetK();

Hs.second = (*itr)->GetH();

found_gapped =

;

lambdas.first = (*itr)->GetLambda();

Ks.first = (*itr)->GetK();

Hs.first = (*itr)->GetH();

found_ungapped =

;

(found_gapped && found_ungapped) {

ancill_vector.insert(ancill_vector.end(), alignments.size(),

ancill_vector, &masks));

succeeded =

;

unique_ptr<CObjectIStream> is(

(is.get())->SetEnforcedStdXml(

);

*is >> *b4_ss_reply;

(b4_ss_reply.Empty());

retval.

(&b4_ss_reply->Set());

b4_ss_reply.

();

unique_ptr<CObjectIStream> is(

(is.get())->SetEnforcedStdXml(

);

);

& name,

&

)

info_request->SetRequest_id(rid);

info_request->SetInfo().Add(name,

);

& name,

&

)

(reply.

() || !reply->CanGetBody()) {

(reply->GetBody().IsGet_search_info()) {

reply_name =

( search_param.

() && search_param->GetValue().IsString()) {

retval = search_param->GetValue().GetString();

try_again =

;

.push_back(

);

( !

->CanGetBody() ) {

.push_back(

);

(

->CanGetBody() && !

->GetBody().IsGet_search_results()) {

.push_back(

);

.push_back(

);

(

->CanGetBody() && !

->GetBody().IsGet_search_results()) {

.push_back(

);

gsrr->SetRequest_id(

);

gsrr->ResetResult_types();

gsrr->SetResult_types( 16) ;

BLAST4_CONN_SERVICE_NAME =

;

(

.Get(

) !=

)

BLAST4_CONN_SERVICE_NAME =

.Get(

);

gsrr->SetRequest_id(

);

incoming_buffer[8192];

read_max = 8192;

l_total_bytes=0, n_read;

l_cached_ok =

;

l_total_bytes += n_read;

tmp_stream->write(incoming_buffer,n_read);

( tmp_stream->bad() || tmp_stream->fail() )

l_cached_ok =

;

(

<<

);

(

<<

<<err.what() );

l_cached_ok =

;

(

<<

);

tmp_stream->seekg(0);

unique_ptr<CObjectIStream>

(

<<

);

);

(reply->CanGetBody()) {

(reply->GetBody().IsGet_search_info()) {

( search_param.

() && search_param->GetValue().IsSeq_loc_list())

( search_param.

() && search_param->GetValue().IsBioseq_list())

);

iter_num = 0;

iter_num = param->GetValue().GetInteger();

(!

.empty())

retval=0;

( !num.empty() ) {

->GetRequest().GetBody().IsGet_request_info() &&

->GetRequest().GetBody().GetGet_request_info().IsSetRequest_id() &&

(

->GetRequest().GetBody().GetGet_request_info().GetRequest_id() ==

)) {

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

ESubjectMaskingType

Define the possible subject masking types.

const int kBlastMessageNoContext

Declared in blast_message.h as extern const.

Declares the CBlastOptionsBuilder class.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_QueryIsNucleotide(EBlastProgramType p)

Returns true if the query is nucleotide.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

Int2 BlastProgram2Number(const char *program, EBlastProgramType *number)

Set number for a given program type.

User-defined methods of the data storage class.

ncbi::TMaskedQueryRegions mask

const string & GetName() const

Get field name (key).

static CBlast4Field & Get(EBlastOptIdx opt)

CBlast4_get_search_info_reply –.

CBlast4_get_search_info_request –.

CBlast4_get_search_results_request –.

CBlast4_get_search_strategy_reply –.

CRef< CBlast4_parameter > GetParamByName(const string name) const

Returns Blast4_parameter with specified name.

CRef< CBlast4_parameter > Add(const string name, const int &value)

Append Blast4_parameter.

size_t GetNumQueries() const

Retrieve the number of queries in this object.

CBlast4_queue_search_request –.

CBlast4_request_body –.

Class used to return ancillary data from a blast search, i.e.

Defines BLAST error codes (user errors included)

Class to build CBlastOptionsHandle from blast4 ASN objects.

Handle to the options to the BLAST algorithm.

@ eRemote

To be used when running BLAST remotely.

virtual void GetRemoteProgramAndService_Blast3(string &p, string &s) const

Get the program and service name for remote blast.

This stream exchanges data with a named service, in a constraint that the service is implemented as o...

Class implements different ad-hoc unreliable file format identifications.

EFormat

The formats are checked in the same order as declared here.

@ eBinaryASN

Binary ASN.1.

Class to return parts of the CBlast4_request, or data associated with a CBlast4_request,...

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

NCBI C++ Object Manager dependant implementation of IQueryFactory.

CObjectIStreamAsnBinary –.

const CSeq_entry & GetQuery() const

Retrieve the query sequence.

Exception class for the CRemoteBlast class.

Error or Warning Message from search.

Search Results for All Queries.

structure for seqloc info

Root class for all serialization exceptions.

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

Collection of masked regions for a single query sequence.

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

iterator_bool insert(const value_type &val)

static const char si[8][64]

bool LoadFromArchive()

Loads next chunk of archive from file.

CRef< CBlastOptionsHandle > GetSearchOptions()

Get the search options used for this search.

string GetTitle(void)

Get the title assigned for this search.

void x_SearchErrors(CRef< objects::CBlast4_reply > reply)

Iterate over error list, splitting into errors and warnings.

string GetDatabaseName() const

Accessor for the database name.

void x_CheckResultsDC(void)

Try to get and process results using disk cache.

int GetFirstDbSeq()

Get the OID range start point.

CRef< objects::CPssmWithParameters > GetPSSM(void)

Get the PSSM produced by the search.

objects::CBlast4_get_search_results_reply TGSRR

An alias for the most commonly used part of the Blast4 search results.

ENeedConfig m_NeedConfig

Bitfield to track whether all necessary configuration is done.

static CRef< CBlast4_mask > s_CreateBlastMask(const CPacked_seqint &packed_int, EBlastProgramType program)

Creates a Blast4-mask which is supposed to contain all masked locations for a given query sequence an...

string x_GetStringFromSearchInfoReply(CRef< CBlast4_reply > reply, const string &name, const string &value)

CRef< objects::CBlast4_reply > x_GetSearchResults(void)

Try to get the search results.

list< CRef< objects::CBioseq > > m_SubjectSequences

Subject Sequences.

CRef< objects::CBlast4_queries > m_Queries

Queries associated with this search.

objects::EBlast4_frame_type FrameNumber2NetworkFrame(int frame, EBlastProgramType program)

Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field.

list< CRef< objects::CBlast4_ka_block > > TKarlinAltschulBlocks

Convenience typedef for a list of CRef<CBlast4_ka_block>

CRef< objects::CBlast4_reply > x_GetSearchResultsHTTP(void)

list< TGi > m_GiList

GI list.

bool HaveFirstDbSeq()

Check whether an OID range start point is specified.

string m_RID

Request ID of submitted or pre-existing search.

int GetDbFilteringAlgorithmId()

Get the database filtering algorithm ID.

string GetErrors(void)

This returns a string containing any errors that were produced by the search.

void SetDbFilteringAlgorithmKey(string algo_key, ESubjectMaskingType mask_type=eSoftSubjMasking)

Sets the filtering algorithm key to be applied to the BLAST database (not supported by server yet)

void x_CheckResults(void)

Try to get and process results.

TSeqLocInfoVector m_QueryMaskingLocations

Masking locations for queries.

TSeqAlignVector GetSeqAlignSets()

Get the seqalign vector from the results.

list< TGi > m_NegativeGiList

Negative GI list.

CFormatGuess::EFormat m_ObjectType

Type of object CBlast4_archive as determined by CFormatGuess.

bool x_IsUnknownRID(void)

Determine if this is an unknown RID.

bool HaveNegativeTaxidList()

Check whether a negative tax id list is specified.

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

const TGiList GetNegativeGiListLimitation() const

bool m_use_disk_cache

Use disk cache for retrieving results default: false.

ENeedConfig

This class attempts to verify whether all necessary configuration is complete before attempting to su...

CRef< objects::CBlast4_archive > m_Archive

Archive of BLAST search and results.

void x_InitQueries(CRef< IQueryFactory > queries)

Initialize queries based on a query factory.

static CRef< CBlast4_request_body > s_BuildSearchInfoRequest(const string &rid, const string &name, const string &value)

ESearchStatus CheckStatus()

Returns the status of a previously submitted search/RID.

void SetVerbose(EDebugMode verb=eDebug)

Adjust the debugging level.

void x_GetRequestInfoFromRID()

Fetch the requested info from splitd.

list< TGi > GetNegativeGiList()

Get the negative GI list.

string GetFilteringAlgorithmKey() const

Accessor for the filtering algorithm key.

CRef< objects::CBlast4_reply > x_GetSearchStatsOnly(void)

const string & GetRID(void)

Gets the request id (RID) associated with the search.

CRef< blast::CBlastOptionsHandle > m_CBOH

Options for new search.

void SetRID(const string &rid)

Sets the RID for these results.

ESearchStatus

Represents the status of previously submitted search/RID.

vector< CConstRef< objects::CSeq_id > > TQueryIdVector

List of query ids.

void SetDatabase(const string &x)

Set the name of the database to search against.

CRef< objects::CBlast4_parameters > m_FormatOpts

Options relevant to the format application.

void x_ExtractQueryIds(CSearchResultSet::TQueryIdVector &query_ids)

Extract the query IDs from the CBlast4_queries for a given search.

static objects::CBlast4_get_search_results_reply::TMasks ConvertToRemoteMasks(const TSeqLocInfoVector &masking_locations, EBlastProgramType program, vector< string > *warnings=NULL)

Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects.

TGSRR::TMasks x_GetMasks(void)

Get the query masks from the results.

vector< string > m_Warn

List of warnings encountered.

bool HaveGiList()

Check whether a GI list is specified.

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

EDebugMode

Debugging support can be turned on with eDebug or off with eSilent.

void SetSubjectSequences(CRef< IQueryFactory > subj)

Set a list of subject sequences to search against.

list< CRef< objects::CSeq_loc > > TSeqLocs

Type definition for CSeq_loc set used as queries in the BLAST remote search class.

CRef< objects::CBlast4_request_body > x_GetBlast4SearchRequestBody()

Retrieve the request body for a search submission.

static const string kNoRIDSpecified("Cannot fetch query info: No RID was specified.")

void SetGIList(const list< TGi > &gi_list)

This restricts the subject database to this list of GIs (this is not supported yet on the server end)...

CRef< objects::CBlast4_queries > GetQueries()

Get the queries used for this search.

list< TTaxId > GetTaxidList()

Get the Tax list.

void SetQueryMasks(const TSeqLocInfoVector &masking_locations)

Set the masking locations for queries.

int m_DbFilteringAlgorithmId

filtering algorithm to use in the database

EDebugMode m_Verbose

Verbosity mode: whether to produce debugging info on stdout.

EImmediacy

Indicates whether to use async mode.

ESubjectMaskingType GetSubjectMaskingType() const

set< TTaxId > m_NegativeTaxidList

vector< string > m_Errs

List of errors encountered.

void x_SetSubjectSequences(const list< CRef< objects::CBioseq > > &subj)

Set a list of subject sequences to search against (only m_SubjectSequences)

bool HaveEntrezQuery()

Check whether an Entrez query is specified.

list< TTaxId > GetNegativeTaxidList()

Get the negative tax id list.

void x_PollUntilDone(EImmediacy poll_immed, int seconds)

Poll until results are found, error occurs, or timeout expires.

~CRemoteBlast()

Destruct the search object.

void x_Init(CNcbiIstream &f)

Uses the file to populate results.

void x_ExtractUserSpecifiedMasks(CRef< IQueryFactory > query_factory, TSeqLocInfoVector &masks)

Extract the user specified masking locations from the query factory.

vector< TGi > TGiList

Define a list of gis.

void FlattenBioseqSet(const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)

void SetQueries(CRef< objects::CBioseq_set > bioseqs)

Set the query as a Bioseq_set.

void SetNegativeGIList(const list< TGi > &gi_list)

This excludes the provided GIs from the subject database (this is not supported yet on the server end...

unique_ptr< CObjectIStream > m_ObjectStream

Use to ready CBlast4_archive.

CRef< objects::CBlast4_request > ExtractBlast4Request(CNcbiIstream &in)

Extract a Blast4-request (a.k.a.

list< CRef< objects::CBlast4_error > > TErrorList

Error value type used by Blast4 ASN.1 objects.

void x_SetMaskingLocationsForQueries(const TSeqLocInfoVector &masking_locations)

Set the masking locations AFTER the queries have been set in the m_QSR field.

string m_Service

Service value used when submitting this search.

bool HasDbFilteringAlgorithmKey()

Check whether a database filtering algorithm key is specified.

static void s_ExtractQueryIdsFromBioseqSet(const CBioseq_set &bss, CSearchResultSet::TQueryIdVector &query_ids)

Extract the query IDs from a CBioseq_set.

CRef< objects::CSeq_align_set > GetAlignments(void)

Get the seqalign set from the results.

bool IsLocalId(const objects::CSeq_id *seqid)

Returns true if the CSeq_id is a local id.

void SetDbFilteringAlgorithmId(int algo_id, ESubjectMaskingType mask_type=eSoftSubjMasking)

Sets the filtering algorithm ID to be applied to the BLAST database (not supported by server yet)

string ToString() const

Converts messages to a string, which is returned.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

virtual CRef< objects::CBioseq_set > GetBioseqSet()=0

Accessor for the CBioseq_set.

void x_InitDiskCache(void)

Initialize disk caching.

bool Submit(void)

This submits the search (if necessary) and returns immediately.

bool m_ReadFile

true if a CBlast4_archive should be read in.

int GetFinalDbSeq()

Get the OID range end point.

CBlast4_subject::TSeq_loc_list m_SubjectSeqLocs

This field is populated when dealing with a remote bl2seq search (e.g.

TSeqLocInfoVector GetMasks(void)

Get the queries' masked locations.

string m_FinalDbSeq

Final database sequence.

CRef< objects::CBlast4_database > GetDatabases()

Get the database used by the search.

list< TGi > GetGiList()

Get the GI list.

CRef< objects::CBlast4_parameters > m_AlgoOpts

Options relevant to the search algorithm.

const vector< string > & GetErrorVector()

This returns any errors encountered as a vector of strings.

string m_FirstDbSeq

First database sequence.

EState

Various states the search can be in.

void x_SubmitSearch(void)

Submit the search and process results (of submit action).

CRef< objects::CBlast4_database > m_Dbs

Databases.

CRef< objects::CBlast4_request > GetSearchStrategy()

Fetch the search strategy for this object without submitting the search.

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

EBlastProgramType NetworkProgram2BlastProgramType(const string &program, const string &service)

Function to convert from program and service name into the CORE BLAST program type This is based on t...

string m_ClientId

Client ID submitting requests throw this interface.

TSeqLocInfoVector ExtractUserSpecifiedMasks()

Retrieve any user specified masking locations.

CRef< objects::CBlast4_parameters > m_ProgramOpts

Options relevant to the search application.

CRef< objects::CBlast4_reply > x_SendRequest(CRef< objects::CBlast4_request_body > body)

Send a Blast4 request and get a reply.

static void Pssm(const objects::CPssmWithParameters &pssm, bool require_scores=false)

Perform validation on the PSSM.

list< string > GetSearchStats(void)

Get the search statistics block as a list of strings.

const TGiList GetGiListLimitation() const

void x_GetRequestInfo()

Fetch the request info (wait for completion if necessary).

CRef< CSearchResultSet > GetResultSet()

Submit the search (if necessary) and return the results.

CRef< CBlastOptionsHandle > GetSearchOptions(const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, const objects::CBlast4_parameters *fopts, string *task_name=NULL)

Build and return options as a CBlastOptionsHandle.

void SetLengthAdjustment(int len_adj)

Set the length adjustment for boundary conditions.

CRef< objects::CBlast4_queue_search_request > m_QSR

Request object for new search.

set< TTaxId > m_TaxidList

int x_DefaultTimeout(void)

The default timeout is 3.5 hours.

void x_QueryMaskingLocationsToNetwork()

Converts the provided query masking locations (if any) to the network representation following the BL...

string GetService()

Get the service used for this search.

bool CheckDone(void)

Check whether the search has completed.

TKarlinAltschulBlocks GetKABlocks(void)

Get the Karlin/Altschul parameter blocks produced by the search.

string m_DbFilteringAlgorithmKey

filtering algorithm key to use in the database

CRef< objects::CBlast4_reply > m_Reply

Results of BLAST search.

CBlast4_subject::TSeq_loc_list GetSubjectSeqLocs()

list< CRef< objects::CSeq_loc > > TSeqLocList

Typedef for a list of Seq-locs.

string GetCreatedBy()

Get the created-by string associated with this search.

const vector< string > & GetWarningVector()

This returns any warnings encountered as a vector of strings.

string GetWarnings(void)

This returns any warnings encountered.

bool HaveNegativeGiList()

Check whether a negative GI list is specified.

string m_disk_cache_error_msg

disk cache error message

static const string kNoArchiveFile("Cannot fetch query info: No archive file.")

bool IsErrMsgArchive(void)

bool m_Pending

Pending state: indicates that search still needs to be queued.

string m_Task

Task used when the search was submitted (recovered via CBlastOptionsBuilder)

virtual TSeqLocs GetSeqLocs()=0

Accessor for the TSeqLocs.

bool m_disk_cache_error_flag

disk cache error flag

string GetEntrezQuery()

Get the Entrez query.

void x_SetAlgoOpts(void)

Configure new search from options handle passed to constructor.

ESubjectMaskingType m_SubjectMaskingType

string m_Program

Program value used when submitting this search.

void x_CheckConfig(void)

Verify that search object contains mandatory fields.

vector< CRef< CBlastAncillaryData > > TAncillaryVector

typedef for a vector of CRef<CBlastAncillaryData>

list< CRef< objects::CBioseq > > GetSubjectSequences()

Returns subject sequences if "bl2seq" mode used.

void x_GetRequestInfoFromFile()

Fetch the requested info from an archive file.

TGSRR * x_GetGSRR(void)

Poll until done, return the CBlast4_get_search_results_reply.

string m_EntrezQuery

Entrez Query, if any.

bool x_HasRetrievedSubjects() const

string GetDbFilteringAlgorithmKey()

Get the database filtering algorithm key.

TBlast4Opts * GetBlast4AlgoOpts()

CRemoteBlast(const string &RID)

Use the specified RID to get results for an existing search.

string m_CreatedBy

Created-by attribution for this search.

bool HasDbFilteringAlgorithmId()

Check whether a database filtering algorithm ID is specified.

void x_SetDatabase(const string &x)

Sets a subset (only m_Dbs) of what the public SetDatabase sets.

int m_ErrIgn

Count of server glitches (communication errors) to ignore.

bool IsDbSearch()

Return values states whether GetDatabases or GetSubjectSequences call should be used.

string GetEntrezQueryLimitation() const

Accessor for the entrez query.

string GetProgram()

Get the program used for this search.

bool HaveFinalDbSeq()

Check whether an OID range end point is specified.

void x_SetOneParam(objects::CBlast4Field &field, const int *value)

Set an integer parameter (not used yet).

CRef< objects::CBlast4_phi_alignments > GetPhiAlignments(void)

Get the results of a PHI-Align request, if PHI pattern was set.

void SetEntrezQuery(const char *x)

Restrict search to sequences matching this Entrez query.

EState x_GetState(void)

Determine what state the search is in.

unsigned int x_GetPsiIterationsFromServer(void)

unsigned int GetPsiNumberOfIterations(void)

static bool s_SearchPending(CRef< objects::CBlast4_reply > reply)

Determine whether the search is still running.

CSeqLocInfo::ETranslationFrame NetworkFrame2FrameNumber(objects::EBlast4_frame_type frame, EBlastProgramType program)

Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame.

bool SubmitSync(void)

This submits the search (if necessary) and polls for results.

@ eStatus_Failed

Completed but failed, call GetErrors/GetErrorVector()

@ eStatus_Pending

Not completed yet.

@ eStatus_Unknown

Never submitted or purged from the system.

@ eStatus_Done

Completed successfully.

#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 LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDiag_Trace

Trace message.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

void Critical(CExceptionArgs_Base &args)

void Error(CExceptionArgs_Base &args)

#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.

void Trace(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

void Fatal(CExceptionArgs_Base &args)

void Info(CExceptionArgs_Base &args)

static fstream * CreateTmpFile(const string &filename=kEmptyStr, ETextBinary text_binary=eBinary, EAllowRead allow_read=eAllowRead)

Create temporary file and return pointer to corresponding stream.

#define MSerial_AsnBinary

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnBinary

ASN.1 binary.

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

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

void SetPacked_int(TPacked_int &v)

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

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.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

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

int16_t Int2

2-byte (16-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static streamsize Readsome(CNcbiIstream &is, CT_CHAR_TYPE *buf, streamsize buf_size)

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

static bool MatchesMask(CTempString str, CTempString mask, ECase use_case=eCase)

Match "str" against the "mask".

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Convert string to unsigned int.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eNocase

Case insensitive compare.

double Restart(void)

Return time elapsed since first Start() or last Restart() call (in seconds).

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

@ eStart

Start timer immediately after creating.

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

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

strategy

Block allocation strategies.

void SetIdent(const TIdent &value)

Assign a value to Ident data member.

bool IsSeq_loc_list(void) const

Check if variant Seq_loc_list is selected.

const TInfo & GetInfo(void) const

Get the Info member data.

bool CanGetRequest_id(void) const

Check if it is safe to call GetRequest_id method.

TQuery_mask & SetQuery_mask(void)

Select the variant.

bool CanGetInfo(void) const

Check if it is safe to call GetInfo method.

TGet_search_results & SetGet_search_results(void)

Select the variant.

TInteger_list & SetInteger_list(void)

Select the variant.

bool IsPssm(void) const

Check if variant Pssm is selected.

void SetBody(TBody &value)

Assign a value to Body data member.

TSequences & SetSequences(void)

Select the variant.

list< CRef< CSeq_loc > > TSeq_loc_list

TGet_request_info & SetGet_request_info(void)

Select the variant.

const TBioseq_set & GetBioseq_set(void) const

Get the variant data.

bool IsBioseq_set(void) const

Check if variant Bioseq_set is selected.

const TSeq_loc_list & GetSeq_loc_list(void) const

Get the variant data.

TGet_search_info & SetGet_search_info(void)

Select the variant.

EBlast4_frame_type

Access to EBlast4_frame_type's attributes (values, names) as defined in spec.

const TRequest_id & GetRequest_id(void) const

Get the Request_id member data.

const TPssm & GetPssm(void) const

Get the variant data.

TQueue_search & SetQueue_search(void)

Select the variant.

TString & SetString(void)

Select the variant.

EBlast4_residue_type

Access to EBlast4_residue_type's attributes (values, names) as defined in spec.

TBig_integer_list & SetBig_integer_list(void)

Select the variant.

void SetRequest_id(const TRequest_id &value)

Assign a value to Request_id data member.

TInteger & SetInteger(void)

Select the variant.

list< CRef< CBlast4_mask > > TMasks

TPssm & SetPssm(void)

Select the variant.

list< CRef< CSeq_loc > > TSeq_loc_list

virtual void Ask(const TRequest &request, TReply &reply)

TDatabase & SetDatabase(void)

Select the variant.

@ eBlast4_error_code_bad_request_id

The RID requested is unknown or it has expired.

@ eBlast4_error_code_not_implemented

Request type is not implemented in the blast4 server.

@ eBlast4_error_code_search_pending

The search is pending.

@ eBlast4_error_code_conversion_warning

A conversion issue was found when converting to/from blast3 from/to blast4 protocol in the blast4 ser...

@ eBlast4_error_code_not_allowed

Request type is not allowed in the blast4 server.

@ eBlast4_error_code_bad_request

Malformed/invalid requests (e.g.: parsing errors or invalid data in request)

@ eBlast4_error_code_internal_error

Indicates internal errors in the blast4 server.

@ eBlast4_frame_type_minus2

@ eBlast4_frame_type_plus2

@ eBlast4_frame_type_plus3

@ eBlast4_frame_type_plus1

@ eBlast4_frame_type_minus3

@ eBlast4_frame_type_notset

@ eBlast4_frame_type_minus1

@ eBlast4_residue_type_nucleotide

@ eBlast4_residue_type_unknown

@ eBlast4_residue_type_protein

Tdata & Set(void)

Assign a value to data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

list< CRef< CSeq_interval > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

const TId & GetId(void) const

Get the Id member data.

unsigned int

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

Names used in blast4 network communications.

@ eBlastOpt_Web_StepNumber

@ eBlastOpt_DbFilteringAlgorithmKey

@ eBlastOpt_NegativeGiList

@ eBlastOpt_DbFilteringAlgorithmId

@ eBlastOpt_RequiredStart

@ eBlastOpt_SubjectMaskingType

string Blast4SearchInfo_BuildReplyName(const string &name, const string &value)

This function builds the reply name token in the get-search-info reply objects, provided a pair of st...

const char * kBlast4SearchInfoReqValue_Title

Used to retrieve the BLAST search title.

const char * kBlast4SearchInfoReqValue_Subjects

Used to retrieve the BLAST search subjects.

const char * kBlast4SearchInfoReqValue_PsiIterationNum

Used to retrieve the PSI-BLAST iteration number.

const char * kBlast4SearchInfoReqName_Search

Used to retrieve information about the BLAST search.

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

#define TRUE

bool replacment for C indicating true.

void SleepSec(unsigned long sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Sleep.

Defines: CTimeFormat - storage class for time format.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

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

Declarations of auxiliary functions/classes for PSI-BLAST.

Declares the CRemoteBlast class.

Declares the CImportStrategy and CExportStrategy.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static string kStart("Start")

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