blast_aux_priv.cpp

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/* ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Christiam Camacho
 *
 */
 
/// @file blast_aux_priv.cpp
/// Implements various auxiliary (private) functions for BLAST
 
#include <ncbi_pch.hpp>
#include "blast_aux_priv.hpp"
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_hspstream.h>
#include <algo/blast/api/blast_mtlock.hpp>
#include <algo/blast/api/seqinfosrc_seqdb.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include "psiblast_aux_priv.hpp"
#include "blast_memento_priv.hpp"
 
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/scoremat/PssmWithParameters.hpp>
 
/** @addtogroup AlgoBlast
 *
 * @{
 */
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(blast)
 
CConstRef<objects::CSeq_loc> 
CreateWholeSeqLocFromIds(const list< CRef<objects::CSeq_id> > seqids)
{
    _ASSERT(!seqids.empty());
    CRef<CSeq_loc> retval(new CSeq_loc);
    retval->SetWhole().Assign(**seqids.begin());
    return retval;
}
 
void
Blast_Message2TSearchMessages(const Blast_Message* blmsg,
                              const BlastQueryInfo* query_info,
                              TSearchMessages& messages)
{
    if ( !blmsg || !query_info ) {
        return;
    }
 
    if (messages.size() != (size_t) query_info->num_queries) {
        messages.resize(query_info->num_queries);
    }
 
    const BlastContextInfo* kCtxInfo = query_info->contexts;
 
    // First copy the errors...
    for (; blmsg; blmsg = blmsg->next)
    {
        const int kContext = blmsg->context;
        _ASSERT(blmsg->message);
        string msg(blmsg->message);
 
        if (kContext != kBlastMessageNoContext) {
            // applies only to a single query
            const int kQueryIndex = kCtxInfo[kContext].query_index;
            CRef<CSearchMessage> sm(new CSearchMessage(blmsg->severity,
                                                       kQueryIndex, msg));
            messages[kCtxInfo[kContext].query_index].push_back(sm);
        } else {
            // applies to all queries
            CRef<CSearchMessage> sm(new CSearchMessage(blmsg->severity,
                                                       kBlastMessageNoContext, 
                                                       msg));
            NON_CONST_ITERATE(TSearchMessages, query_messages, messages) {
                query_messages->push_back(sm);
            }
        }
 
 
    }
 
    // ... then remove duplicate error messages
    messages.RemoveDuplicates();
}
 
string
BlastErrorCode2String(Int2 error_code)
{
    Blast_Message* blast_msg = NULL;
    Blast_PerrorWithLocation(&blast_msg, error_code, kBlastMessageNoContext);
    string retval(blast_msg != NULL ? blast_msg->message : kEmptyStr);
    blast_msg = Blast_MessageFree(blast_msg);
    return retval;
}
 
CRef<SBlastSetupData>
BlastSetupPreliminarySearch(CRef<IQueryFactory> query_factory,
                            CRef<CBlastOptions> options,
                            size_t num_threads /* = 1 */)
{
    return BlastSetupPreliminarySearchEx(query_factory, options,
                                         CRef<CPssmWithParameters>(),
                                         NULL, num_threads);
}
 
CRef<SBlastSetupData>
BlastSetupPreliminarySearchEx(CRef<IQueryFactory> qf,
                              CRef<CBlastOptions> options,
                              CConstRef<CPssmWithParameters> pssm,
                              BlastSeqSrc* seqsrc,
                              size_t num_threads)
{
    CRef<SBlastSetupData> retval(new SBlastSetupData(qf, options));
    TSearchMessages m;
    options->Validate();
    bool is_multi_threaded = num_threads > 1;
 
    // 0. Initialize the megablast database index.
    if (options->GetUseIndex()) {
        CSetupFactory::InitializeMegablastDbIndex(options);
        ClearDbIndexCallbacks();
    }
 
    // 1. Initialize the query data (borrow it from the factory)
    CRef<ILocalQueryData> query_data(qf->MakeLocalQueryData(&*options));
    retval->m_InternalData->m_Queries = query_data->GetSequenceBlk();
    retval->m_InternalData->m_QueryInfo = query_data->GetQueryInfo();
    // get any warning messages from instantiating the queries
    query_data->GetMessages(m);
    retval->m_Messages.resize(query_data->GetNumQueries());
    retval->m_Messages.Combine(m);
 
    // 2. Take care of any rps information
    if (Blast_ProgramIsRpsBlast(options->GetProgramType())) {
        const char* name = BlastSeqSrcGetName(seqsrc);
        const string rps_dbname(name ? name : "");
        retval->m_InternalData->m_RpsData =
            CSetupFactory::CreateRpsStructures(rps_dbname, options);
    }
 
    // 3. Create the options memento
    unique_ptr<const CBlastOptionsMemento> opts_memento
        (options->CreateSnapshot());
 
    // 4. Create the BlastScoreBlk
    BlastSeqLoc* lookup_segments = NULL;
    BlastScoreBlk* sbp = NULL;
    try {
        sbp =
        CSetupFactory::CreateScoreBlock(opts_memento.get(), query_data, 
                                        &lookup_segments, retval->m_Messages, 
                                        &retval->m_Masks, 
                                        retval->m_InternalData->m_RpsData);
    } catch (CBlastException & e) {
        const string  kCatchThisError (kBlastErrMsg_CantCalculateUngappedKAParams);
        if(e.GetMsg() == kCatchThisError) {
            return retval;
        }
        else {
            NCBI_RETHROW(e, CBlastException, eCoreBlastError, e.GetMsg());
        }
    }
    CRef< CBlastSeqLocWrap > lookup_segments_wrap( 
            new CBlastSeqLocWrap( lookup_segments ) );
    retval->m_InternalData->m_ScoreBlk.Reset
        (new TBlastScoreBlk(sbp, BlastScoreBlkFree));
    if (pssm.NotEmpty()) {
        if (query_data->GetNumQueries() > 1) {
            NCBI_THROW(CBlastException, eNotSupported,
                       "Multiple queries cannot be specified with a PSSM");
        }
        PsiBlastSetupScoreBlock(sbp, pssm, retval->m_Messages, options);
    }
 
    // Initialize callbacks needed for indexed search.
    //
    if (options->GetUseIndex()) {
        SetUpDbIndexCallbacks();
    }
 
    // 5. Create the lookup table
    if ( !retval->m_QuerySplitter->IsQuerySplit() ) {
        LookupTableWrap* lut =
            CSetupFactory::CreateLookupTable(query_data, opts_memento.get(),
                                             sbp, lookup_segments_wrap,
                                             retval->m_InternalData->m_RpsData,
                                             seqsrc,
                                             num_threads);
        retval->m_InternalData->m_LookupTable.Reset
            (new TLookupTableWrap(lut, LookupTableWrapFree));
    }
 
    // 6. Create diagnostics
    BlastDiagnostics* diags = is_multi_threaded
        ? CSetupFactory::CreateDiagnosticsStructureMT()
        : CSetupFactory::CreateDiagnosticsStructure();
    retval->m_InternalData->m_Diagnostics.Reset
        (new TBlastDiagnostics(diags, Blast_DiagnosticsFree));
 
    // 7. Create the HSP stream
    BlastHSPStream* hsp_stream = 
        CSetupFactory::CreateHspStream(opts_memento.get(),
                                       query_data->GetNumQueries(),
        CSetupFactory::CreateHspWriter(opts_memento.get(),
                                       retval->m_InternalData->m_Queries,
                                       query_data->GetQueryInfo()));
    
    if (is_multi_threaded) 
        BlastHSPStreamRegisterMTLock(hsp_stream, Blast_CMT_LOCKInit());
 
    // 8. Register a traceback HSP Pipe(s)
    BlastHSPStreamRegisterPipe(hsp_stream, 
        CSetupFactory::CreateHspPipe(opts_memento.get(),
                                     query_data->GetQueryInfo()),
                                     eTracebackSearch);
 
    retval->m_InternalData->m_HspStream.Reset
        (new TBlastHSPStream(hsp_stream, BlastHSPStreamFree));
 
    // 8. Get errors/warnings
    query_data->GetMessages(m);
    retval->m_Messages.Combine(m);
 
    if (retval->m_QuerySplitter->IsQuerySplit()) {
        // We don't need the full sequence for the preliminary stage, so we
        // free it and NULL out references to it (this MUST be restored prior
        // to the traceback stage)
        query_data->FlushSequenceData();        
        retval->m_InternalData->m_Queries = NULL;
    }
 
    retval->m_InternalData->m_FnInterrupt = NULL;
    retval->m_InternalData->m_ProgressMonitor.Reset(new CSBlastProgress(NULL));
    return retval;
}
 
 
void
BuildBlastAncillaryData(EBlastProgramType program,
                        const vector< CConstRef<CSeq_id> >& query_ids,
                        const BlastScoreBlk* sbp,
                        const BlastQueryInfo* qinfo,
                        const TSeqAlignVector& alignments,
                        const EResultType result_type,
                        CSearchResultSet::TAncillaryVector& retval)
{
    retval.clear();
 
    if (Blast_ProgramIsPhiBlast(program)) {
        CRef<CBlastAncillaryData> s(new CBlastAncillaryData(program, 0, sbp,
                                                            qinfo));
        
        for(unsigned i = 0; i < alignments.size(); i++) {
            retval.push_back(s);
        }
    } else {
        if (result_type == ncbi::blast::eSequenceComparison) {
            const size_t num_subjects = alignments.size()/query_ids.size();
            for(size_t i = 0; i < alignments.size(); i += num_subjects) {
                CRef<CBlastAncillaryData> s
                    (new CBlastAncillaryData(program, i/num_subjects, sbp, 
                                             qinfo));
                for (size_t j = 0; j < num_subjects; j++) {
                    retval.push_back(s);
                }
            }
        } else {
            for(size_t i = 0; i < alignments.size(); i++) {
                CRef<CBlastAncillaryData> s(new CBlastAncillaryData(program, static_cast<int>(i),
                                                                    sbp,
                                                                    qinfo));
                retval.push_back(s);
            }
        }
    }
    
}
 
CRef<CSearchResultSet>
BlastBuildSearchResultSet(const vector< CConstRef<CSeq_id> >& query_ids,
                          const BlastScoreBlk* sbp,
                          const BlastQueryInfo* qinfo,
                          EBlastProgramType program,
                          const TSeqAlignVector& alignments,
                          TSearchMessages& messages,
                          const vector<TSeqLocInfoVector>& subj_masks,
                          const TSeqLocInfoVector* query_masks,
                          const EResultType result_type)
{
    const bool is_phi = !!Blast_ProgramIsPhiBlast(program);
 
    // Collect query Seq-locs
    
    vector< CConstRef<CSeq_id> > qlocs;
    
    if (is_phi) {
        qlocs.assign(alignments.size(), query_ids.front());
    } else {
        if (result_type == ncbi::blast::eSequenceComparison)
        {
            const size_t num_subjects = alignments.size()/query_ids.size();
            for (size_t i = 0; i < alignments.size(); i += num_subjects) {
                for (size_t j = 0; j < num_subjects; j++) {
                    qlocs.push_back(query_ids[i/num_subjects]);
                }
            }
        }
        else
            copy(query_ids.begin(), query_ids.end(), back_inserter(qlocs));
    }
    
    // Collect ancillary data
    
    CSearchResultSet::TAncillaryVector ancillary_data;
    BuildBlastAncillaryData(program, query_ids, sbp, qinfo, alignments,
                            result_type, ancillary_data);
    
    // The preliminary stage also produces errors and warnings; they
    // should be copied from that code to this class somehow, and
    // returned here if they have not been returned or reported yet.
    
    if (messages.size() < alignments.size()) {
        messages.resize(alignments.size());
    }
    
    // N.B.: the number of query masks for bl2seq will be adjusted in
    // CSearchResultSet::SetFilteredQueryRegions
    const SPHIQueryInfo* phi_query_info = is_phi ? qinfo->pattern_info : NULL;
    CRef<CSearchResultSet> retval(new CSearchResultSet(qlocs, alignments, 
                                                       messages, 
                                                       ancillary_data, 
                                                       query_masks, 
                                                       result_type,
                                                       phi_query_info));
    if (subj_masks.size() == retval->size()) {
        for (CSearchResultSet::size_type i = 0; i < retval->size(); i++) {
            (*retval)[i].SetSubjectMasks(subj_masks[i]);
        }
    }
    return retval;
}
 
TMaskedQueryRegions
PackedSeqLocToMaskedQueryRegions(CConstRef<objects::CSeq_loc> sloc_in,
                                 EBlastProgramType            prog,
                                 bool assume_both_strands)
{
    if (sloc_in.Empty() || 
        sloc_in->Which() == CSeq_loc::e_not_set ||
        sloc_in->IsEmpty() || 
        sloc_in->IsNull()) {
        return TMaskedQueryRegions();
    }
    
    CConstRef<CSeq_loc> sloc = sloc_in;
    
    if (sloc_in->IsInt()) {
        CRef<CSeq_interval>
            iv( const_cast<CSeq_interval *>(& sloc_in->GetInt()) );
        
        CRef<CSeq_loc> nsloc(new CSeq_loc);
        nsloc->SetPacked_int().Set().push_back(iv);
        
        sloc.Reset(&*nsloc);
    }
    
    if (! sloc->IsPacked_int()) {
        NCBI_THROW(CBlastException, eNotSupported, 
                   "Unsupported Seq-loc type used for mask");
    }
    
    const objects::CPacked_seqint & psi = sloc->GetPacked_int();
    
    TMaskedQueryRegions mqr;
    
    ITERATE(list< CRef< objects::CSeq_interval > >, iter, psi.Get()) {
        objects::CSeq_interval * iv =
            const_cast<objects::CSeq_interval*>(& (**iter));
        
        if (Blast_QueryIsProtein(prog)) {
            int fr = (int) CSeqLocInfo::eFrameNotSet;
            mqr.push_back(CRef<CSeqLocInfo>(new CSeqLocInfo(iv, fr)));
        } else {
            bool do_pos = false;
            bool do_neg = false;
        
            if (iv->CanGetStrand()) {
                switch(iv->GetStrand()) {
                case objects::eNa_strand_plus:
                    do_pos = true;
                    break;
                
                case objects::eNa_strand_minus:
                    do_neg = true;
                    break;
                
                case objects::eNa_strand_both:
                    do_pos = true;
                    do_neg = true;
                    break;
                
                default:
                    NCBI_THROW(CBlastException, eNotSupported, 
                               "Unsupported strand type used for query");
                }
            } else {
                // intervals with no strand assignment will use both.
                do_pos = do_neg = true;
            }
 
            // deliberately override the strand option above, if so requested
            if (assume_both_strands) {
                do_pos = do_neg = true;
            }
            
            if (do_pos) {
                int fr = (int) CSeqLocInfo::eFramePlus1;
                mqr.push_back(CRef<CSeqLocInfo>(new CSeqLocInfo(iv, fr)));
            }
            
            // No reversal is done here.  Tt seems that the code (in core)
            // that applies the mask reverses it.  Whether this is an
            // accidental or designed is not clear to me, but for now this
            // will remain as is.
            
            if (do_neg) {
                int fr = (int) CSeqLocInfo::eFrameMinus1;
                mqr.push_back(CRef<CSeqLocInfo>(new CSeqLocInfo(iv, fr)));
            }
        }
    }
    
    return mqr;
}
 
CRef<objects::CSeq_loc>
MaskedQueryRegionsToPackedSeqLoc( const TMaskedQueryRegions & sloc )
{
    if (sloc.empty()) {
        return CRef<objects::CSeq_loc>();
    }
 
    CRef<objects::CPacked_seqint> psi = sloc.ConvertToCPacked_seqint();
    CRef<objects::CSeq_loc> retval;
    if (psi.NotEmpty()) {
        retval.Reset(new objects::CSeq_loc);
        retval->SetPacked_int(*psi);
    }
    return retval;
}
 
END_SCOPE(blast)
END_NCBI_SCOPE
 
/* @} */