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

);

( !kEntrezQuery.empty() ) {

( !kGiList.empty() ) {

list<TGi> temp(kGiList.begin(), kGiList.end());

((bss.

()) && (sll.empty())) {

);

(query_factory.

()) {

);

kSubjectIndex = 1;

current_subject = subj_id;

(current_hsp_list.

()) {

new_seq_align->

().push_back(current_hsp_list);

current_hsp_list->

(2);

current_hsp_list->

().SetDisc().Set().push_back(*hsp_itr);

current_hsp_list->

().SetDisc().Set().push_back(*hsp_itr);

(current_hsp_list.

()) {

new_seq_align->

().push_back(current_hsp_list);

*itr = new_seq_align;

msgs.push_back(

);

msgs.push_back(

);

(

= 0;

<aligns.size();

++) {

msg_vec.push_back(msgs);

);

( !kEntrezQuery.empty() ) {

( !kGiList.empty() ) {

list<TGi> temp(kGiList.begin(), kGiList.end());

(pssm.

()) {

);

User-defined methods of the data storage class.

Declares the CBlastProteinOptionsHandle class.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

@ eRemote

To be used when running BLAST remotely.

API for Remote Blast Requests.

Error or Warning Message from search.

Search Results for All Queries.

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...

CRemoteBlast & x_RemoteBlast()

Method to construct and run the remote blast search.

string GetDatabaseName() const

Accessor for the database name.

virtual void SetOptions(CRef< CBlastOptionsHandle > options)

Configure the search.

TSeqAlignVector GetSeqAlignSets()

Get the seqalign vector from the results.

virtual void SetQueryFactory(CRef< IQueryFactory > query_factory)

Set the factory which will return the queries to search for.

virtual CRef< IPssmSearch > GetPssmSearch()

Get an object to manage a remote PSSM search.

void SetDatabase(const string &x)

Set the name of the database to search against.

static CBlastOptionsHandle * Create(EProgram program, EAPILocality locality=CBlastOptions::eLocal)

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

list< CRef< objects::CSeq_loc > > TSeqLocs

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

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)...

static CRef< CSearchResultSet > s_BuildResultsRemote(CRemoteBlast &rb)

Build a result set from results in a remote blast search.

CConstRef< CSearchDatabase > m_Subject

Search subject.

CConstRef< CSearchDatabase > m_Subject

Search subject.

virtual CRef< ISeqSearch > GetSeqSearch()

Get an object to manage a remote sequence search.

vector< TGi > TGiList

Define a list of gis.

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

Set the query as a Bioseq_set.

virtual CRef< CBlastOptionsHandle > GetOptions(EProgram)

Get an options handle for a search of the specified type.

CRemoteBlast & x_RemoteBlast()

Method to construct and run the remote blast search.

virtual CRef< CSearchResultSet > Run()

Run the search.

virtual void SetOptions(CRef< CBlastOptionsHandle > options)

Configure the search.

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

Accessor for the CBioseq_set.

CRef< CBlastOptionsHandle > m_SearchOpts

Search configuration.

const vector< string > & GetErrorVector()

This returns any errors encountered as a vector of strings.

CRef< IRemoteQueryData > m_Queries

Search queries.

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

CRef< objects::CPssmWithParameters > m_Pssm

Search queries.

const TGiList GetGiListLimitation() const

CRef< CRemoteBlast > m_RemoteBlast

Remote search management object.

virtual CRef< CSearchResultSet > Run()

Run the search.

CRef< CBlastOptionsHandle > m_SearchOpts

Search configuration.

vector< string > m_Warnings

Warnings produced by the search.

const vector< string > & GetWarningVector()

This returns any warnings encountered as a vector of strings.

virtual void SetSubject(CConstRef< CSearchDatabase > subject)

Set the databases to search.

static TSeqAlignVector s_SplitAlignVectorBySubjects(TSeqAlignVector seqaligns)

CRemoteBlast does not separate each hit to the query in discontinuous Seq-aligns, so we do it here.

virtual TSeqLocs GetSeqLocs()=0

Accessor for the TSeqLocs.

virtual void SetQuery(CRef< objects::CPssmWithParameters > query)

Set the query to search with.

vector< string > m_Warnings

Warnings produced by the search.

string GetEntrezQueryLimitation() const

Accessor for the entrez query.

virtual void SetSubject(CConstRef< CSearchDatabase > subject)

Set the databases to search.

void SetEntrezQuery(const char *x)

Restrict search to sequences matching this Entrez query.

CRef< CRemoteBlast > m_RemoteBlast

Remote search management object.

bool SubmitSync(void)

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

#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.

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_NO

different SeqId types-can't compare

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.

#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.

Tdata & Set(void)

Assign a value to data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

list< CRef< CSeq_align > > Tdata

const Tdata & Get(void) const

Get the member data.

@ eType_disc

discontinuous alignment

@ e_Gi

GenInfo Integrated Database.

Remote implementation of the uniform BLAST search interface.

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

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