splign_tool.cpp

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/*  $Id: splign_tool.cpp 47464 2023-04-20 00:19:10Z evgeniev $
* ===========================================================================
*
*                            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.
*
* ===========================================================================
*
* Authors:  Roman Katargin
*
*/
 
#include <ncbi_pch.hpp>
 
#include <gui/packages/pkg_alignment/splign_tool.hpp>
#include <gui/packages/pkg_alignment/splign_panel.hpp>
 
 
#include <gui/widgets/wx/message_box.hpp>
 
#include <serial/typeinfo.hpp>
 
#include <objmgr/object_manager.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objects/seq/MolInfo.hpp>
 
#include <gui/objutils/user_type.hpp>
#include <gui/objutils/label.hpp>
 
#include <algo/align/splign/splign.hpp>
#include <algo/align/splign/splign_formatter.hpp>
#include <algo/blast/api/bl2seq.hpp>
 
#include <wx/msgdlg.h>
 
//#include <algo/align/splign/splign_simple.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
USING_SCOPE(blast);
 
 
///////////////////////////////////////////////////////////////////////////////
/// CSplignTool
CSplignTool::CSplignTool()
:   CAlgoToolManagerBase("SPLIGN (SPliced aLIGNment)",
                         "",
                         "SPLIGN (SPliced aLIGNment)",
                         "Compute cDNA-to-genomic spliced alignments",
                         "https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial2/",
                         "Alignment Creation"),
                         m_Panel()
{
}
 
string CSplignTool::GetExtensionIdentifier() const
{
    return "splign_tool";
}
 
 
string CSplignTool::GetExtensionLabel() const
{
    return "SPLIGN Tool";
}
 
void CSplignTool::InitUI()
{
    CAlgoToolManagerBase::InitUI();
 
    m_Panel = NULL;
}
 
void CSplignTool::CleanUI()
{
    m_Panel = NULL;
    CAlgoToolManagerBase::CleanUI();
}
 
bool CSplignTool::x_CreateParamsPanelIfNeeded()
{
    if (m_Panel == NULL) {
        x_SelectCompatibleInputObjects();
        if (m_GenomicObjects.empty() && m_NAObjects.empty()) {
            // canceled, or no input objects were found
            return false;
        }
 
        m_Panel = new CSplignPanel(m_ParentWindow, wxID_ANY,
            wxDefaultPosition, wxSize(0, 0), SYMBOL_CSPLIGNPANEL_STYLE, false);
        m_Panel->SetData(m_Params);
        m_Panel->SetObjects(&m_GenomicObjects, &m_NAObjects);
 
        m_Panel->SetRegistryPath(m_RegPath + ".ParamsPanel");
        m_Panel->LoadSettings();
    }
    return true;
}
 
bool CSplignTool::x_ValidateParams()
{
    return true;
}
 
void CSplignTool::x_SelectCompatibleInputObjects()
{
    m_GenomicObjects.clear();
    m_NAObjects.clear();
 
    TObjects results;
    x_ConvertInputObjects (CSeq_loc::GetTypeInfo(), results);
    if (results.empty()) {
        return;
    }
    NON_CONST_ITERATE(TObjects, it, results) {
        TConstScopedObjects genomic, na;
        NON_CONST_ITERATE(TConstScopedObjects, it2, it->second) {
            const CSeq_loc* loc = dynamic_cast<const CSeq_loc*>(it2->object.GetPointer());
            if( !loc ) continue;
 
            if( !loc->IsInt() && !loc->IsWhole() ) continue;
 
            CBioseq_Handle handle = it2->scope->GetBioseqHandle(*loc->GetId());
            
            const CMolInfo* molInfo = 0;
            CSeqdesc_CI desc_iter(handle, CSeqdesc::e_Molinfo);
            if (desc_iter) molInfo = &desc_iter->GetMolinfo();
            if (molInfo) {
                CMolInfo::TBiomol biomol = molInfo->GetBiomol();
                switch(biomol) {
                case CMolInfo::eBiomol_genomic :
                    genomic.push_back(*it2);
                    break;
                case CMolInfo::eBiomol_unknown :
                    genomic.push_back(*it2);
                    na.push_back(*it2);
                    break;
                case CMolInfo::eBiomol_peptide :
                    break;
                default :
                    na.push_back(*it2);
                    break;
                }
            }
            else {
                genomic.push_back(*it2);
                na.push_back(*it2);
            }
        }
 
        if (!genomic.empty()) {
            TConstScopedObjects& vec = m_GenomicObjects[it->first];
            copy(genomic.begin(), genomic.end(), back_inserter(vec));
        }
        if (!na.empty()) {
            TConstScopedObjects& vec = m_NAObjects[it->first];
            copy(na.begin(), na.end(), back_inserter(vec));
        }
    }
 
}
 
wxPanel* CSplignTool::GetMaxPanel()
{
    CSplignPanel* panel = new CSplignPanel();
    panel->Create(m_ParentWindow);
    return panel;
}
 
CAlgoToolManagerParamsPanel* CSplignTool::x_GetParamsPanel()
{
    return m_Panel;
}
 
IRegSettings* CSplignTool::x_GetParamsAsRegSetting()
{
    return &m_Params;
}
 
///////////////////////////////////////////////////////////////////////////////
/// CSplignJob
class  CSplignJob  : public CDataLoadingAppJob
{
public:
    CSplignJob (const CSplignParams& params,
                const TConstScopedObjects& genomic,
                const TConstScopedObjects& cdna);
    static bool s_SplignInterruptCallback(CNWAligner::SProgressInfo* prog);
    static Boolean s_BlastInterruptCallback(SBlastProgress* prog);
 
protected:
    virtual void    x_CreateProjectItems(); // overriding virtual function
 
protected:
    CSplignParams       m_Params;
    TConstScopedObjects m_Genomic;
    TConstScopedObjects m_cDNA;
};
 
bool CSplignJob::s_SplignInterruptCallback(CNWAligner::SProgressInfo* prog)
{
    if (prog  &&  prog->m_data) {
        CSplignJob* job =
            reinterpret_cast<CSplignJob*>(prog->m_data);
        if(job->IsCanceled())    {
            return true;
        }
    }
    return false;
}
 
Boolean CSplignJob::s_BlastInterruptCallback(SBlastProgress* prog)
{
    if (prog  &&  prog->user_data) {
        CSplignJob* job =
            reinterpret_cast<CSplignJob*>(prog->user_data);
        if(job->IsCanceled())    {
            return TRUE;
        }
    }
    return FALSE;
}
 
 
CDataLoadingAppJob* CSplignTool::x_CreateLoadingJob()
{
    TConstScopedObjects genomic, cdna;
 
    if (m_Panel) {
        m_Params = m_Panel->GetData();
        cdna = m_Panel->GetCDNASeqs();;
        genomic.push_back(m_Panel->GetGenomicSeq());
    }
    else {
        NON_CONST_ITERATE(TObjects, it, m_GenomicObjects) {
            TConstScopedObjects& vec = m_GenomicObjects[it->first];
            copy(vec.begin(), vec.end(), back_inserter(genomic));
        }
        NON_CONST_ITERATE(TObjects, it, m_NAObjects) {
            TConstScopedObjects& vec = m_NAObjects[it->first];
            copy(vec.begin(), vec.end(), back_inserter(cdna));
        }
    }
 
    #ifdef _DEBUG
    m_Params.DebugDumpText( cerr, "Splign Options", 0 );
    #endif
 
    CSplignJob* job = new CSplignJob(m_Params, genomic, cdna);
    return job;
}
 
IAppTask* CSplignTool::QuickLaunch()
{
    x_SelectCompatibleInputObjects();
 
    if (m_GenomicObjects.empty()) {
        wxMessageBox(wxT("No genomic objects sequences can be proccessed were selected."),
                     wxT("SPLIGN Tool Error"), wxOK | wxICON_ERROR);
        return 0;
    }
 
    if (m_NAObjects.empty()) {
        wxMessageBox(wxT("No cDNA/Transcript sequences that can be proccessed were selected."),
                     wxT("SPLIGN Tool Error"), wxOK | wxICON_ERROR);
        return 0;
    }
 
    CRef<CDataLoadingAppJob> job(x_CreateLoadingJob());
 
    vector<CProjectService::TProjectId> projects;
 
    CProjectService* prj_srv =
        m_SrvLocator->GetServiceByType<CProjectService>();
    {{
        TConstScopedObjects objects;
        NON_CONST_ITERATE(TObjects, it, m_GenomicObjects) {
            TConstScopedObjects& vec = m_GenomicObjects[it->first];
            copy(vec.begin(), vec.end(), back_inserter(objects));
        }
        NON_CONST_ITERATE(TObjects, it, m_NAObjects) {
            TConstScopedObjects& vec = m_NAObjects[it->first];
            copy(vec.begin(), vec.end(), back_inserter(objects));
        }
 
        prj_srv->GetObjProjects(objects, projects);
    }}
 
    CSelectProjectOptions options;
    if (projects.empty())
        options.Set_CreateNewProject();
    else
        options.Set_AddToExistingProject(projects.front());
 
    CRef<CDataLoadingAppTask> task(new CDataLoadingAppTask(prj_srv, options, *job));
    return task.Release();
}
 
///////////////////////////////////////////////////////////////////////////////
/// CSplignJob
CSplignJob::CSplignJob(const CSplignParams& params,
                       const TConstScopedObjects& genomic,
                       const TConstScopedObjects& cdna)
    : m_Params(params), m_Genomic(genomic), m_cDNA(cdna)
{
    m_Descr = "SPLIGN Job"; //TODO
}
 
void CSplignJob::x_CreateProjectItems()
{
    ITERATE(TConstScopedObjects, it, m_Genomic) {
        const CSeq_loc& seqloc_genomic =
            dynamic_cast<const CSeq_loc&>(it->object.GetObject());
 
        vector<string> not_found_labels;
 
        NON_CONST_ITERATE(TConstScopedObjects, iter, m_cDNA) {
            if (IsCanceled()) return;
 
            const CSeq_loc& seqloc_cdna = dynamic_cast<const CSeq_loc&>(iter->object.GetObject());
            CScope& scope = *iter->scope;
 
            CBl2Seq blast(
                SSeqLoc(seqloc_cdna, scope),
                SSeqLoc(seqloc_genomic, scope),
                eMegablast
            );
 
            CConstRef<objects::CSeq_id> transcript_id( &sequence::GetId( seqloc_cdna, &scope ) );
            CConstRef<objects::CSeq_id> genomic_id( &sequence::GetId( seqloc_genomic, &scope ) );
 
            //true for EST, false for mrna
            const bool query_low_quality = ( m_Params.GetDiscType() == 0 );
 
            CSplign splign;
            splign.SetAligner() = CSplign::s_CreateDefaultAligner( query_low_quality );
            splign.SetAligner()->SetSpaceLimit( numeric_limits<Uint4>::max() );
            splign.SetScope().Reset(&scope);
            splign.PreserveScope();
 
            splign.SetEndGapDetection( m_Params.GetEndGapDetect() );
            splign.SetPolyaDetection( m_Params.GetPolyADetect() );
            splign.SetStrand( m_Params.GetCDNAStrand() != 1 );
            splign.SetMaxGenomicExtent( m_Params.GetMaxGenomicExtent() );
            splign.SetCompartmentPenalty( m_Params.GetCompPenalty() );
            splign.SetMinExonIdentity( m_Params.GetMinExonIdentity() );
            splign.SetMaxIntron( m_Params.GetMaxIntron() );
 
            /// NB: these two values should be the same, if min signleton identity is not
            /// exposed for user modification
            splign.SetMinCompartmentIdentity( m_Params.GetMinCompIdentity() );
            splign.SetMinSingletonIdentity  ( m_Params.GetMinCompIdentity() );
 
            // set progress interrupt callbacks for Blast and NWAligner
            {
            splign.SetAligner()->SetProgressCallback( s_SplignInterruptCallback, this );
            blast.SetInterruptCallback(s_BlastInterruptCallback, this);
            }
 
            //splign_simple.Run();
 
            TSeqAlignVector blres( blast.Run() );
 
            CSplign::THitRefs hitrefs;
            ITERATE( TSeqAlignVector, ii, blres ){
                if( (*ii)->IsSet() ){
                    const CSeq_align_set::Tdata &sas0 = (*ii)->Get();
                    ITERATE( CSeq_align_set::Tdata, sa_iter, sas0 ){
                        CSplign::THitRef hitref( new CSplign::THit(**sa_iter) );
                        if( hitref->GetQueryStrand() == false ){
                            hitref->FlipStrands();
                        }
                        hitrefs.push_back( hitref );
                    }
                }
            }
 
            if( hitrefs.size() ){
                splign.Run( &hitrefs );
            }
 
            CSplignFormatter sf( splign );
            sf.SetSeqIds( transcript_id, genomic_id );
            CRef<CSeq_align_set> seqaln_set( 
                sf.AsSeqAlignSet( 0, CSplignFormatter::eAF_SplicedSegWithParts ) 
            );
 
            if( m_Params.GetCDNAStrand() == 2 ){
                splign.SetStrand( false );
 
                if( hitrefs.size() ){
                    splign.Run( &hitrefs );
                }
 
                CSplignFormatter sf( splign );
                sf.SetSeqIds( transcript_id, genomic_id );
                CRef<CSeq_align_set> seqaln_set_neg( 
                    sf.AsSeqAlignSet( 0, CSplignFormatter::eAF_SplicedSegWithParts ) 
                );
 
                if( !seqaln_set_neg->IsEmpty() ){
                    seqaln_set->Set().merge( seqaln_set_neg->Set() );
                }
            }
 
            typedef CSeq_annot::TData::TAlign TAlign;
 
            if( !seqaln_set->Get().empty() ){
                // pack the alignment in a Seq-annot and label it appropriately
                CRef<CSeq_annot> annot(new CSeq_annot());
                TAlign& seqannot_align = annot->SetData().SetAlign();
                ITERATE( CSeq_align_set::Tdata, align, seqaln_set->Get() ){
                    seqannot_align.push_back(*align);
                }
 
                // prepare a title
                string str;
                CLabel::GetLabel(seqloc_genomic, &str, CLabel::eDefault, &scope);
                str += " x ";
                CLabel::GetLabel(seqloc_cdna, &str, CLabel::eDefault, &scope);
                str += ": SPLIGN alignment";
                annot->SetNameDesc(str);
 
                annot->SetCreateDate(CurrentTime());
 
                /// now create a Project Item for the data
                CRef<CProjectItem> item(new CProjectItem());
                item->SetItem().SetAnnot(*annot);
 
                // TODO we need to generate title properly
                item->SetLabel(str);
                AddProjectItem(*item);
            }
            else {
                // no alignments - save cDNA label for info message
                string label;
                CLabel::GetLabel(seqloc_cdna, &label, CLabel::eDefault, &scope);
                not_found_labels.push_back(label);
            }
        }
    }
}
 
 
END_NCBI_SCOPE