test_helper.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: test_helper.cpp,v $
 * PRODUCTION Revision 1000.4  2004/06/01 19:25:11  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.58
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_helper.cpp,v 1000.4 2004/06/01 19:25:11 gouriano Exp $
* ===========================================================================
*
*                            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:  Eugene Vasilchenko, Aleksey Grichenko, Denis Vakatov
*
* File Description:
*   Bio sequence data generator to test Object Manager
*/

#include <ncbi_pch.hpp>
#include "test_helper.hpp"
#include <corelib/ncbithr.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <serial/object.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
#include <serial/objcopy.hpp>
#include <serial/objectinfo.hpp>
#include <serial/iterator.hpp>
#include <serial/objectiter.hpp>
#include <serial/serial.hpp>

#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/IUPACna.hpp>
#include <objects/seq/NCBIeaa.hpp>
#include <objects/seq/NCBI2na.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqalign/Dense_diag.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/seq_vector_ci.hpp>
#include <objmgr/seq_descr_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/general/Date.hpp>
// #include <objects/util/sequence.hpp>

#include <test/test_assert.h>  /* This header must go last */


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)

bool CDataGenerator::sm_DumpEntries = false;

/************************************************************************
    1.2.1.1. Bio sequences for testing
    Test entry = 1 top-level entry + 2 sub-entries (continuous sequence)
    TSE contains 1 description
    each sub-entry has
        two Seq_ids: local and GI, (local ids = 11+1000i, 12+1000i)
        one description,
        two annotations (Seq_feat)
            first - for an interval, local Seq_id:
                "plus" strand for one sub-entry,
                "minus" strand for another one
            second - for the whole seq, GI Seq_id
    one sub-entry has also an alignment annotation
************************************************************************/
CSeq_entry& CDataGenerator::CreateTestEntry1(int index)
{
    // create top level seq entry
    CRef<CSeq_entry> entry(new CSeq_entry);
    CBioseq_set& set = entry->SetSet();
    // class = nucleic acid and coded proteins
    set.SetClass(CBioseq_set::eClass_nuc_prot);
    // add description (name)
    list< CRef<CSeqdesc> >& descr = set.SetDescr().Set();
    CRef<CSeqdesc> desc(new CSeqdesc);
    desc->SetName("D1 from TSE1-"+NStr::IntToString(index));
    descr.push_back(desc);
    // list of sub-entries
    list< CRef<CSeq_entry> >& seq_set = set.SetSeq_set();

    // Sub-entry Seq 11
    {{
        CRef<CSeq_entry> sub_entry(new CSeq_entry);
        CBioseq& seq = sub_entry->SetSeq();
        CBioseq::TId& id_list = seq.SetId();

        // list of Ids (local + gi)
        CRef<CSeq_id> id(new CSeq_id);
        id->SetLocal().SetStr("seq"+NStr::IntToString(11+index*1000));
        id_list.push_back(id);
        id.Reset(new CSeq_id);
        id->SetGi(11+index*1000);
        id_list.push_back(id);

        // Description (name)
        list< CRef<CSeqdesc> >& descr1 = seq.SetDescr().Set();
        CRef<CSeqdesc> desc1(new CSeqdesc);
        desc1->SetName("D1 from BS11-"+NStr::IntToString(index));
        descr1.push_back(desc1);

        // Instance (sequence data)
        CSeq_inst& inst = seq.SetInst();
        // representation class = continuous sequence
        inst.SetRepr(CSeq_inst::eRepr_raw);
        // molecule class in living organism = dna
        inst.SetMol(CSeq_inst::eMol_dna);
        // length of sequence in residues
        inst.SetLength(40);
        // seq data in Iupacna
        inst.SetSeq_data().SetIupacna().Set(
            "CAGCAGCGGTACAGGAGGGTGAGACATCCCAGAGCGGTGC");
        // strandedness in living organism = double strand
        inst.SetStrand(CSeq_inst::eStrand_ds);

        // Annotations
        list< CRef<CSeq_annot> >& annot_list = seq.SetAnnot();
        CRef<CSeq_annot> annot(new CSeq_annot);
        // list of features
        list< CRef<CSeq_feat> >& ftable = annot->SetData().SetFtable();
        {{
            CRef<CSeq_feat> feat(new CSeq_feat);
            // feature Id
            feat->SetId().SetLocal().SetStr("F1: lcl|11");
            // the specific data
            CSeqFeatData& fdata = feat->SetData();
            CCdregion& cdreg = fdata.SetCdregion();
            cdreg.SetFrame(CCdregion::eFrame_one);
            // genetic code used
            list< CRef< CGenetic_code::C_E > >& gcode = cdreg.SetCode().Set();
            CRef< CGenetic_code::C_E > ce(new CGenetic_code::C_E);
            ce->SetId(111); // TSE=1; seq=1; feat=1
            gcode.push_back(ce);
            // feature location on the sequence: Seq_interval (local seq_Id)
            CSeq_interval& floc = feat->SetLocation().SetInt();
            floc.SetId().SetLocal().SetStr
                ("seq"+NStr::IntToString(11+index*1000));
            floc.SetFrom(20);
            floc.SetTo(30);
            ftable.push_back(feat);
        }}
        {{
            CRef<CSeq_feat> feat(new CSeq_feat);
            // feature Id
            feat->SetId().SetLocal().SetStr("F2: gi|11");
            // the specific data
            CSeqFeatData& fdata = feat->SetData();
            CCdregion& cdreg = fdata.SetCdregion();
            cdreg.SetFrame(CCdregion::eFrame_one);
            // genetic code used
            list< CRef< CGenetic_code::C_E > >& gcode = cdreg.SetCode().Set();
            CRef< CGenetic_code::C_E > ce(new CGenetic_code::C_E);
            ce->SetId(112); // TSE=1; seq=1; feat=2
            gcode.push_back(ce);
            // feature location on the sequence (seq_Id + "whole" sequence)
            feat->SetLocation().SetWhole().SetGi(11+index*1000);
            ftable.push_back(feat);
        }}
        annot_list.push_back(annot);

        // Add sub-entry
        seq_set.push_back(sub_entry);
    }}

    // Sub-entry Seq 12
    {{
        CRef<CSeq_entry> sub_entry(new CSeq_entry);
        CBioseq& seq = sub_entry->SetSeq();
        CBioseq::TId& id_list = seq.SetId();

        // list of Ids (local + gi)
        CRef<CSeq_id> id(new CSeq_id);
        id->SetLocal().SetStr("seq"+NStr::IntToString(12+index*1000));
        id_list.push_back(id);
        id.Reset(new CSeq_id);
        id->SetGi(12+index*1000);
        id_list.push_back(id);

        // Instance (sequence data)
        CSeq_inst& inst = seq.SetInst();
        // representation class = continuous sequence
        inst.SetRepr(CSeq_inst::eRepr_raw);
        // molecule class in living organism = dna
        inst.SetMol(CSeq_inst::eMol_dna);
        // length of sequence in residues
        inst.SetLength(40);
        // seq data in Iupacna
        inst.SetSeq_data().SetIupacna().Set(
            "CAATAACCTCAGCAGCAACAAGTGGCTTCCAGCGCCCTCC");
        // strandedness in living organism = double strand
        inst.SetStrand(CSeq_inst::eStrand_ds);

        // Annotations
        list< CRef<CSeq_annot> >& annot_list = seq.SetAnnot();
        {{
            CRef<CSeq_annot> annot(new CSeq_annot);
            // list of features
            list< CRef<CSeq_feat> >& ftable = annot->SetData().SetFtable();
            {{
                CRef<CSeq_feat> feat(new CSeq_feat);
                // feature Id
                feat->SetId().SetLocal().SetStr("F3: gi|12");
                // the specific data
                CSeqFeatData& fdata = feat->SetData();
                CCdregion& cdreg = fdata.SetCdregion();
                cdreg.SetFrame(CCdregion::eFrame_one);
                // genetic code used
                list< CRef< CGenetic_code::C_E > >& gcode =
                    cdreg.SetCode().Set();
                CRef< CGenetic_code::C_E > ce(new CGenetic_code::C_E);
                ce->SetId(123); // TSE=1; seq=2; feat=3
                gcode.push_back(ce);
                // feature location on the sequence: Seq_interval (gi seq_Id)
                CSeq_interval& floc = feat->SetLocation().SetInt();
                floc.SetId().SetGi(12+index*1000);
                floc.SetFrom(20);
                floc.SetTo(30);
                // minus strand
                floc.SetStrand(eNa_strand_minus);
                ftable.push_back(feat);
            }}
            {{
                CRef<CSeq_feat> feat(new CSeq_feat);
                // feature Id
                feat->SetId().SetLocal().SetStr("F4: lcl|12");
                // the specific data
                CSeqFeatData& fdata = feat->SetData();
                CCdregion& cdreg = fdata.SetCdregion();
                cdreg.SetFrame(CCdregion::eFrame_one);
                // genetic code used
                list< CRef< CGenetic_code::C_E > >& gcode =
                    cdreg.SetCode().Set();
                CRef< CGenetic_code::C_E > ce(new CGenetic_code::C_E);
                ce->SetId(124); // TSE=1; seq=2; feat=4
                gcode.push_back(ce);
                // feature location on the sequence (seq_Id + "whole" sequence)
                feat->SetLocation().SetWhole().SetLocal().SetStr
                    ("seq"+NStr::IntToString(12+index*1000));
                ftable.push_back(feat);
            }}
            annot_list.push_back(annot);
        }}
        {{
            CRef<CSeq_annot> annot(new CSeq_annot);
            // list of seq alignments
            list< CRef<CSeq_align> >& atable = annot->SetData().SetAlign();
            {{
                // CAGCAGC:
                // 11[0], 12[9]
                CRef<CSeq_align> align(new CSeq_align);
                align->SetType(CSeq_align::eType_not_set);
                // alignment data
                CSeq_align::C_Segs& segs = align->SetSegs();
                // for (multiway) diagonals
                CSeq_align::C_Segs::TDendiag& diag_list = segs.SetDendiag();
                CRef<CDense_diag> diag(new CDense_diag);
                // dimensionality = 2
                diag->SetDim(2);
                // list of Seq_ids (gi) (sequences in order)
                CDense_diag::TIds& id_list = diag->SetIds();
                CRef<CSeq_id> id(new CSeq_id);
                id->SetGi(11+index*1000);
                id_list.push_back(id);
                id.Reset(new CSeq_id);
                id->SetGi(12+index*1000);
                id_list.push_back(id);
                // start OFFSETS in ids order
                CDense_diag::TStarts& start_list = diag->SetStarts();
                start_list.push_back(0);
                start_list.push_back(9);
                diag->SetLen(7);
                diag_list.push_back(diag);
                atable.push_back(align);
            }}
            annot_list.push_back(annot);
        }}
        // Add sub-entry
        seq_set.push_back(sub_entry);
    }}

    if ( sm_DumpEntries ) {
        NcbiCout << "-------------------- "
            "TestEntry1 --------------------" << NcbiEndl;
        auto_ptr<CObjectOStream>
            out(CObjectOStream::Open(eSerial_AsnText, NcbiCout));
        *out << *entry;
    }
    return *entry.Release();
}


/************************************************************************
    1.2.1.2. Bio sequences for testing
    Test entry = 1 top-level entry + 2 sub-entries (continuous sequence)
    each sub-entry has
        two Seq_ids: local and GI, (local ids = 11+1000i, 12+1000i)
    No descriptions, No annotations
************************************************************************/
CSeq_entry& CDataGenerator::CreateTestEntry1a(int index)
{
    // create top level seq entry
    CRef<CSeq_entry> entry(new CSeq_entry);
    CBioseq_set& set = entry->SetSet();
    // class = nucleic acid and coded proteins
    set.SetClass(CBioseq_set::eClass_nuc_prot);
    list< CRef<CSeq_entry> >& seq_set = set.SetSeq_set();

    // Sub-entry Seq 11
    {{
        CRef<CSeq_entry> sub_entry(new CSeq_entry);
        CBioseq& seq = sub_entry->SetSeq();
        CBioseq::TId& id_list = seq.SetId();

        // list of Ids (local + gi)
        CRef<CSeq_id> id(new CSeq_id);
        id->SetLocal().SetStr("seq"+NStr::IntToString(11+index*1000));
        id_list.push_back(id);
        id.Reset(new CSeq_id);
        id->SetGi(11+index*1000);
        id_list.push_back(id);

        // Instance (sequence data)
        CSeq_inst& inst = seq.SetInst();
        // representation class = continuous sequence
        inst.SetRepr(CSeq_inst::eRepr_raw);
        // molecule class in living organism = dna
        inst.SetMol(CSeq_inst::eMol_dna);
        // length of sequence in residues
        inst.SetLength(40);
        // seq data in Iupacna
        inst.SetSeq_data().SetIupacna().Set(
            "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
        // strandedness in living organism = double strand
        inst.SetStrand(CSeq_inst::eStrand_ds);

        // Add sub-entry
        seq_set.push_back(sub_entry);
    }}

    // Sub-entry Seq 12
    {{
        CRef<CSeq_entry> sub_entry(new CSeq_entry);
        CBioseq& seq = sub_entry->SetSeq();
        CBioseq::TId& id_list = seq.SetId();

        // list of Ids (local + gi)
        CRef<CSeq_id> id(new CSeq_id);
        id->SetLocal().SetStr("seq"+NStr::IntToString(12+index*1000));
        id_list.push_back(id);
        id.Reset(new CSeq_id);
        id->SetGi(12+index*1000);
        id_list.push_back(id);

        // Instance (sequence data)
        CSeq_inst& inst = seq.SetInst();
        inst.SetRepr(CSeq_inst::eRepr_raw);
        inst.SetMol(CSeq_inst::eMol_dna);
        // length of sequence in residues
        inst.SetLength(40);
        // seq data in Iupacna
        inst.SetSeq_data().SetIupacna().Set(
            "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT");
        inst.SetStrand(CSeq_inst::eStrand_ds);

        // Add sub-entry
        seq_set.push_back(sub_entry);
    }}

    if ( sm_DumpEntries ) {
        NcbiCout << "-------------------- "