alnmrg.cpp

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            if (CType<CSeq_align>::Match(i)) {
                m_Mix->Add(*(CType<CSeq_align>::Get(i)), m_AddFlags);
            }
        }
    } else if (asn_type == "Seq-align-set") {
        CRef<CSeq_align_set> sas(new CSeq_align_set);
        in->Read(Begin(*sas), CObjectIStream::eNoFileHeader);
        *binout << *sas;
        for (i = Begin(*sas); i; ++i) {
            if (CType<CSeq_align>::Match(i)) {
                m_Mix->Add(*(CType<CSeq_align>::Get(i)), m_AddFlags);
            }
        }
    } else if (asn_type == "Seq-annot") {
        CRef<CSeq_annot> san(new CSeq_annot);
        in->Read(Begin(*san), CObjectIStream::eNoFileHeader);
        *binout << *san;
        for (i = Begin(*san); i; ++i) {
            if (CType<CSeq_align>::Match(i)) {
                m_Mix->Add(*(CType<CSeq_align>::Get(i)), m_AddFlags);
            }
        }
    } else if (asn_type == "Dense-seg") {
        CRef<CDense_seg> ds(new CDense_seg);
        in->Read(Begin(*ds), CObjectIStream::eNoFileHeader);
        *binout << *ds;
        m_Mix->Add(*ds, m_AddFlags);
    } else {
        cerr << "Cannot read: " << asn_type;
        return;
    }
}


void CAlnMrgApp::SetOptions(void)
{
    CArgs args = GetArgs();

    if ( args["log"] ) {
        SetDiagStream( &args["log"].AsOutputFile() );
    }

    m_MergeFlags = 0;
    m_AddFlags = 0;

    if (args["gapjoin"]  &&  args["gapjoin"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fGapJoin;
    }

    if (args["mingap"]  &&  args["mingap"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fMinGap;
    }

    if (args["gen2est"]  &&  args["gen2est"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fGen2EST | CAlnMix::fTruncateOverlaps;
    }

    if (args["minusstrand"]  &&  args["minusstrand"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fNegativeStrand;
    }

    if (args["queryseqmergeonly"]  &&  args["queryseqmergeonly"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fQuerySeqMergeOnly;
    }

    if (args["fillunaln"]  &&  args["fillunaln"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fFillUnalignedRegions;
    }

    if (args["truncateoverlaps"]  &&  args["truncateoverlaps"].AsBoolean()) {
        m_MergeFlags |= CAlnMix::fTruncateOverlaps;
    }

    if (args["forcetranslation"]  &&  args["forcetranslation"].AsBoolean()) {
        m_AddFlags |= CAlnMix::fForceTranslation;
    }

    if (args["calcscore"]  &&  args["calcscore"].AsBoolean()) {
        m_AddFlags |= CAlnMix::fCalcScore;
    }

    if (args["noobjmgr"]  &&  args["noobjmgr"].AsBoolean()) {
        m_AddFlags |= CAlnMix::fDontUseObjMgr;
    }
}

void CAlnMrgApp::PrintMergedAlignment(void)
{
    auto_ptr<CObjectOStream> asn_out 
        (CObjectOStream::Open(eSerial_AsnText, cout));

    *asn_out << m_Mix->GetDenseg();
}


void CAlnMrgApp::View4(int scrn_width)
{
    CAlnVec av(m_Mix->GetDenseg(), GetScope());
    CAlnMap::TNumrow row, nrows = av.GetNumRows();

    vector<string> buffer(nrows);
    vector<CAlnMap::TSeqPosList> insert_aln_starts(nrows);
    vector<CAlnMap::TSeqPosList> insert_starts(nrows);
    vector<CAlnMap::TSeqPosList> insert_lens(nrows);
    vector<CAlnMap::TSeqPosList> scrn_lefts(nrows);
    vector<CAlnMap::TSeqPosList> scrn_rights(nrows);
    
    // Fill in the vectors for each row
    for (row = 0; row < nrows; row++) {
        av.GetWholeAlnSeqString
            (row,
             buffer[row],
             &insert_aln_starts[row],
             &insert_starts[row],
             &insert_lens[row],
             scrn_width,
             &scrn_lefts[row],
             &scrn_rights[row]);
    }
        
    // Visualization
    TSeqPos pos = 0, aln_len = av.GetAlnStop() + 1;
    do {
        for (row = 0; row < nrows; row++) {
            cout << av.GetSeqId(row)
                 << "\t" 
                 << scrn_lefts[row].front()
                 << "\t"
                 << buffer[row].substr(pos, scrn_width)
                 << "\t"
                 << scrn_rights[row].front()
                 << endl;
            scrn_lefts[row].pop_front();
            scrn_rights[row].pop_front();
        }
        cout << endl;
        pos += scrn_width;
        if (pos + scrn_width > aln_len) {
            scrn_width = aln_len - pos;
        }
    } while (pos < aln_len);
}


int CAlnMrgApp::Run(void)
{
    SetOptions();

    m_Mix = new CAlnMix(GetScope());
    LoadInputAlignments();
    m_Mix->Merge(m_MergeFlags);
    PrintMergedAlignment();
    return 0;
}


/////////////////////////////////////////////////////////////////////////////
//  MAIN


int main(int argc, const char* argv[])
{
    // Execute main application function
    return CAlnMrgApp().AppMain(argc, argv, 0, eDS_Default, 0);
}


/*
* ===========================================================================
*
* $Log: alnmrg.cpp,v $
* Revision 1000.3  2004/06/01 19:40:52  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.20
*
* Revision 1.20  2004/05/21 21:42:51  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.19  2004/01/07 17:37:35  vasilche
* Fixed include path to genbank loader.
* Moved split_cache application.
*
* Revision 1.18  2003/12/22 20:28:11  ucko
* Added missing call to GetScope.
*
* Revision 1.17  2003/12/22 18:33:48  ucko
* Simplify format autodetection behavior by means of Read(..., eNoFileHeader);
* fixes problems observed with GCC 2.95.
*
* Revision 1.16  2003/12/20 03:39:12  ucko
* Reorder data members of CAlnMrgApp: m_Mix should follow m_ObjMgr so
* it's destroyed first by default, so that the scope will no longer be
* live by the time m_ObjMgr is destroyed.
*
* Revision 1.15  2003/12/19 19:38:34  todorov
* Demon creation of scope outside alnmix
*
* Revision 1.14  2003/12/08 21:28:04  todorov
* Forced Translation of Nucleotide Sequences
*
* Revision 1.13  2003/11/20 23:58:07  todorov
* Added CObjectIStream::Close before IStream::seekg
*
* Revision 1.12  2003/09/08 20:41:42  todorov
* binint fixed. binout added
*
* Revision 1.11  2003/09/08 19:33:12  todorov
* - unused var
*
* Revision 1.10  2003/09/08 17:05:57  todorov
* ability to read binary files
*
* Revision 1.9  2003/09/04 19:05:46  todorov
* Removed view. Should be optional
*
* Revision 1.8  2003/08/20 14:43:01  todorov
* Support for NA2AA Densegs
*
* Revision 1.7  2003/07/24 16:26:09  ucko
* Undouble CAlnMix:: prefix in one place.
*
* Revision 1.6  2003/07/23 16:14:18  todorov
* +trunacteoverlaps
*
* Revision 1.5  2003/06/26 22:00:25  todorov
* + fFillUnalignedRegions
*
* Revision 1.4  2003/06/24 19:23:37  todorov
* objmgr usage optional
*
* Revision 1.3  2003/06/02 16:06:41  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.2  2003/05/15 19:09:18  todorov
* Optional mixing of the query sequence only
*
* Revision 1.1  2003/04/03 21:17:48  todorov
* Adding demo projects
*
*
* ===========================================================================
*/