96 "No database name specified");
104 if ( !kEntrezQuery.empty() ) {
110 if ( !kGiList.empty() ) {
111 list<TGi> temp(kGiList.begin(), kGiList.end());
118 if ((bss.
Empty()) && (sll.empty())) {
120 "Empty queries object specified.");
171 if (query_factory.
Empty()) {
173 "CRemoteSeqSearch: empty query factory was specified.");
199 const int kSubjectIndex = 1;
205 current_subject = subj_id;
208 new_seq_align->
Set().push_back(current_hsp_list);
212 current_hsp_list->
SetDim(2);
213 current_hsp_list->
SetSegs().SetDisc().Set().push_back(*hsp_itr);
217 current_hsp_list->
SetSegs().SetDisc().Set().push_back(*hsp_itr);
221 new_seq_align->
Set().push_back(current_hsp_list);
224 *itr = new_seq_align;
278 for(
size_t i = 0;
i<aligns.size();
i++) {
279 msg_vec.push_back(msgs);
315 "No database name specified");
325 if ( !kEntrezQuery.empty() ) {
331 if ( !kGiList.empty() ) {
332 list<TGi> temp(kGiList.begin(), kGiList.end());
360 "CRemotePssmSearch: empty query object was specified.");
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.