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NCBI C++ ToolKit: src/objtools/blast/services/blast_services.cpp Source File

no_msg(

);

(reply->CanGetErrors() && (! reply->GetErrors().empty())) {

& message((*iter)->CanGetMessage()

? (*iter)->GetMessage()

(reply->CanGetBody() && reply->GetBody().IsGet_sequences()) {

list< CRef<CBioseq> > & bslist =

reply->SetBody().SetGet_sequences().Set();

bioseqs.reserve(bslist.size());

bioseqs.push_back(*iter);

errors =

;

errors =

;

(seqids.empty()) {

errors =

;

list< CRef< CSeq_id > > & seqid_list =

seqid_list.push_back(*iter);

(request.

()) {

);

errors =

;

(seqids.empty()) {

errors =

;

found_all =

;

vector< CRef<objects::CBlast4_database_info> >

=

(found_all && !

.empty())

((*dbinfo)->GetDatabase() == *blastdb) {

vector< CRef<objects::CBlast4_database_info> >

vector< CRef<objects::CBlast4_database_info> > retval;

((*dbinfo)->GetDatabase().GetName().find(

) !=

) {

retval.push_back(*dbinfo);

databases =

.AskGet_databases();

);

(blastdb.

()) {

);

vector< CRef<objects::CBlast4_database_info> >

vector<string> *missing_names)

vector<CRef<objects::CBlast4_database_info> > retval;

retval.push_back(

);

( missing_names ) missing_names->push_back( blastdb->

() );

vector< CRef<objects::CBlast4_database_info> >

vector<string> *missing_names)

vector<CRef<objects::CBlast4_database_info> > retval;

vector<string> all_db_names;

vector<string>::iterator it_db;

l_multiple_db =

;

(local_db_name,

, all_db_names);

l_multiple_db = ( all_db_names.size() > 1 );

db_ex_req->SetParams().Add(

,

(

));

db_ex_req->SetParams().Add(

,

);

db_ex_req->SetParams().Add(

,

(

));

db_ex_req->SetParams().Add(

,

(

));

);

( reply->GetBody().GetGet_databases_ex().Get().empty() ){

( !reply->CanGetBody() || !reply->GetBody().IsGet_databases_ex() ) {

(found_all ) *found_all =

;

);

list< CRef< CBlast4_database_info > >::const_iterator it;

it = reply->GetBody().GetGet_databases_ex().Get().begin();

( ; it != reply->GetBody().GetGet_databases_ex().

().end(); it++){

retval.push_back( *it );

( l_multiple_db ) {

current_dbname = (*(*it)).GetDatabase().GetName();

it_db = find(all_db_names.begin(),all_db_names.end(),current_dbname);

( it_db != all_db_names.end() ){

all_db_names.erase( it_db);

all_db_names.clear();

( all_db_names.empty() ) {

( missing_names ) missing_names->assign(all_db_names.begin(),all_db_names.end());

(reply->CanGetBody() && reply->GetBody().IsGet_sequence_parts()) {

reply->SetBody().SetGet_sequence_parts().Set();

ids.reserve(parts_rep.size());

seq_data.reserve(parts_rep.size());

(request.

()) {

);

objects::CBlast4_get_windowmasked_taxids_reply::Tdata

reply =

.AskGet_windowmasked_taxids();

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares the CBlastServices class.

User-defined methods of the data storage class.

CBlast4_get_databases_ex_request –.

CBlast4_get_seq_parts_request –.

CBlast4_request_body –.

static void s_ProcessErrorsFromReply(CRef< objects::CBlast4_reply > reply, string &errors, string &warnings)

Process error messages from a reply object.

static void GetSequenceParts(const TSeqIntervalVector &seqids, const string &database, char seqtype, TSeqIdVector &ids, TSeqDataVector &seq_data, string &errors, string &warnings, bool verbose=false)

This retrieves (partial) sequence data from the remote BLAST server.

static void GetSequencesInfo(TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false)

Get a set of Bioseqs without their sequence data given an input set of.

vector< CRef< objects::CBlast4_database_info > > GetDatabaseInfoLegacy(const string &dbname, bool is_protein, bool *found_all, vector< string > *missing_names=NULL)

Same as GetDatabaseInfo but retrieving whole list of database.

static void s_GetSeqsFromReply(CRef< objects::CBlast4_reply > reply, CBlastServices::TBioseqVector &bioseqs, string &errors, string &warnings)

Get bioseqs from a sequence fetching reply.

bool IsValidBlastDb(const string &dbname, bool is_protein)

Returns true if the BLAST database specified exists in the NCBI servers.

bool m_Verbose

Display verbose output to stdout?

static EBlast4_residue_type s_SeqTypeToResidue(char p, string &errors)

static void GetSequences(TSeqIdVector &seqids, const string &database, char seqtype, TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose=false, bool target_only=false)

Get a set of Bioseqs given an input set of Seq-ids.

vector< CRef< objects::CSeq_data > > TSeqDataVector

Defines a std::vector of CRef<CSeq_data>

static void s_GetPartsFromReply(CRef< objects::CBlast4_reply > reply, CBlastServices::TSeqIdVector &ids, CBlastServices::TSeqDataVector &seq_data, string &errors, string &warnings)

Extract information from the get-seq-parts reply object.

vector< CRef< objects::CBioseq > > TBioseqVector

Defines a std::vector of CRef<CBioseq>

CRef< objects::CBlast4_database_info > GetDatabaseInfo(CRef< objects::CBlast4_database > blastdb)

Retrieve detailed information for one BLAST database If information about multiple databases is neede...

objects::CBlast4_get_windowmasked_taxids_reply::Tdata m_WindowMaskedTaxIds

Taxonomy IDs for which there's windowmasker masking data at NCBI.

static CRef< objects::CBlast4_request > s_BuildGetSeqRequest(CBlastServices::TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, bool target_only, string &errors)

Build Sequence Fetching Request.

vector< CRef< objects::CSeq_interval > > TSeqIntervalVector

Defines a std::vector of CRef<CSeq_interval>

vector< CRef< objects::CSeq_id > > TSeqIdVector

Defines a std::vector of CRef<CSeq_id>

objects::CBlast4_get_databases_reply::Tdata m_AvailableDatabases

BLAST databases available to search.

static CRef< objects::CBlast4_request > s_BuildGetSeqPartsRequest(const CBlastServices::TSeqIntervalVector &seqids, const string &database, char seqtype, string &errors)

Build Sequence Parts Fetching Request.

static void s_GetSequences(CBlastServices::TSeqIdVector &seqids, const string &database, char seqtype, bool skip_seq_data, bool target_only, CBlastServices::TBioseqVector &bioseqs, string &errors, string &warnings, bool verbose)

Main function to issue a Blast4-get-sequences-request and collect its results from the remote BLAST s...

CRef< objects::CBlast4_database_info > x_FindDbInfoFromAvailableDatabases(CRef< objects::CBlast4_database > blastdb)

Look for a database matching this method's argument and returned detailed information about it.

objects::CBlast4_get_windowmasked_taxids_reply::Tdata GetTaxIdWithWindowMaskerSupport()

Retrieve a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support an a...

vector< CRef< objects::CBlast4_database_info > > GetOrganismSpecificRepeatsDatabases()

Retrieve organism specific repeats databases.

void x_GetAvailableDatabases()

Retrieve the BLAST databases available for searching.

#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 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 –.

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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

void SetDatabase(TDatabase &value)

Assign a value to Database data member.

TSeq_ids & SetSeq_ids(void)

Assign a value to Seq_ids data member.

void SetName(const TName &value)

Assign a value to Name data member.

TGet_sequence_parts & SetGet_sequence_parts(void)

Select the variant.

void SetTarget_only(TTarget_only value)

Assign a value to Target_only data member.

list< CRef< CBlast4_seq_part_data > > Tdata

const TName & GetName(void) const

Get the Name member data.

void SetBody(TBody &value)

Assign a value to Body data member.

TGet_sequences & SetGet_sequences(void)

Select the variant.

list< CRef< CBlast4_database_info > > Tdata

void SetType(TType value)

Assign a value to Type data member.

TGet_databases_ex & SetGet_databases_ex(void)

Select the variant.

EBlast4_residue_type

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

TSeq_locations & SetSeq_locations(void)

Assign a value to Seq_locations data member.

void SetDatabase(TDatabase &value)

Assign a value to Database data member.

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

void SetSkip_seq_data(TSkip_seq_data value)

Assign a value to Skip_seq_data data member.

@ eBlast4_error_flags_warning

@ eBlast4_residue_type_nucleotide

@ eBlast4_residue_type_unknown

@ eBlast4_residue_type_protein

char * dbname(DBPROCESS *dbproc)

Get name of current database.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

const TYPE & Get(const CNamedParameterList *param)

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

static CNamedPipeClient * client

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