alnvwr.cpp

ncbi源码

        pos += screen_width;
        if (pos + screen_width > aln_len) {
            screen_width = aln_len - pos;
        }
    } while (pos < aln_len);
}


void CAlnMgrTestApp::View4(int scrn_width)
{
    CAlnMap::TNumrow row, nrows = m_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++) {
        m_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 = m_AV->GetAlnStop() + 1;
    do {
        for (row = 0; row < nrows; row++) {
            cout << row 
                 << "\t"
                 << m_AV->GetSeqId(row).AsFastaString()
                 << "\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);
}



// print segments

void CAlnMgrTestApp::View5()
{
    CAlnMap::TNumrow row;

    for (row=0; row<m_AV->GetNumRows(); row++) {
        cout << "Row: " << row << endl;
        for (int seg=0; seg<m_AV->GetNumSegs(); seg++) {
            
            // seg
            cout << "\t" << seg << ": ";

            // aln coords
            cout << m_AV->GetAlnStart(seg) << "-"
                 << m_AV->GetAlnStop(seg) << " ";


            // type
            CAlnMap::TSegTypeFlags type = m_AV->GetSegType(row, seg);
            if (type & CAlnMap::fSeq) {
                // seq coords
                cout << m_AV->GetStart(row, seg) << "-" 
                     << m_AV->GetStop(row, seg) << " (Seq)";
            } else {
                cout << "(Gap)";
            }

            if (type & CAlnMap::fNotAlignedToSeqOnAnchor) cout << "(NotAlignedToSeqOnAnchor)";
            if (CAlnMap::IsTypeInsert(type)) cout << "(Insert)";
            if (type & CAlnMap::fUnalignedOnRight) cout << "(UnalignedOnRight)";
            if (type & CAlnMap::fUnalignedOnLeft) cout << "(UnalignedOnLeft)";
            if (type & CAlnMap::fNoSeqOnRight) cout << "(NoSeqOnRight)";
            if (type & CAlnMap::fNoSeqOnLeft) cout << "(NoSeqOnLeft)";
            if (type & CAlnMap::fEndOnRight) cout << "(EndOnRight)";
            if (type & CAlnMap::fEndOnLeft) cout << "(EndOnLeft)";

            cout << NcbiEndl;
        }
    }
    cout << "---------" << endl;
}



// print chunks

void CAlnMgrTestApp::View6()
{
    CArgs args = GetArgs();
    CAlnMap::TNumrow row;

    CAlnMap::TSignedRange range(-1, m_AV->GetAlnStop()+1);

    for (row=0; row<m_AV->GetNumRows(); row++) {
        cout << "Row: " << row << endl;
        //CAlnMap::TSignedRange range(m_AV->GetSeqStart(row) -1,
        //m_AV->GetSeqStop(row) + 1);
        CRef<CAlnMap::CAlnChunkVec> chunk_vec = m_AV->GetAlnChunks(row, range, args["cf"].AsInteger());
    
        for (int i=0; i<chunk_vec->size(); i++) {
            CConstRef<CAlnMap::CAlnChunk> chunk = (*chunk_vec)[i];

            cout << "[row" << row << "|" << i << "]";
            cout << chunk->GetAlnRange().GetFrom() << "-"
                 << chunk->GetAlnRange().GetTo() << " ";

            if (!chunk->IsGap()) {
                cout << chunk->GetRange().GetFrom() << "-"
                    << chunk->GetRange().GetTo();
            } else {
                cout << "(Gap)";
            }

            if (chunk->GetType() & CAlnMap::fSeq) cout << "(Seq)";
            if (chunk->GetType() & CAlnMap::fNotAlignedToSeqOnAnchor) cout << "(NotAlignedToSeqOnAnchor)";
            if (CAlnMap::IsTypeInsert(chunk->GetType())) cout << "(Insert)";
            if (chunk->GetType() & CAlnMap::fUnalignedOnRight) cout << "(UnalignedOnRight)";
            if (chunk->GetType() & CAlnMap::fUnalignedOnLeft) cout << "(UnalignedOnLeft)";
            if (chunk->GetType() & CAlnMap::fNoSeqOnRight) cout << "(NoSeqOnRight)";
            if (chunk->GetType() & CAlnMap::fNoSeqOnLeft) cout << "(NoSeqOnLeft)";
            if (chunk->GetType() & CAlnMap::fEndOnRight) cout << "(EndOnRight)";
            if (chunk->GetType() & CAlnMap::fEndOnLeft) cout << "(EndOnLeft)";
            cout << NcbiEndl;
        }
    }
    cout << "---------" << endl;
}



// alternative ways to get the sequence

void CAlnMgrTestApp::View7()
{
    string buff;
    CAlnMap::TNumseg seg;
    CAlnMap::TNumrow row;

    m_AV->SetGapChar('-');
    m_AV->SetEndChar('.');
    for (seg=0; seg<m_AV->GetNumSegs(); seg++) {
        for (row=0; row<m_AV->GetNumRows(); row++) {
            cout << "row " << row << ", seg " << seg << " ";
            // if (m_AV->GetSegType(row, seg) & CAlnMap::fSeq) {
                cout << "["
                    << m_AV->GetStart(row, seg)
                    << "-"
                    << m_AV->GetStop(row, seg) 
                    << "]"
                    << NcbiEndl;
                for(int i=0; i<m_AV->GetLen(seg); i++) {
                    cout << m_AV->GetResidue(row, m_AV->GetAlnStart(seg)+i);
                }
                cout << NcbiEndl;
                cout << m_AV->GetSeqString(buff, row,
                                           m_AV->GetStart(row, seg),
                                           m_AV->GetStop(row, seg)) << NcbiEndl;
                cout << m_AV->GetSegSeqString(buff, row, seg) 
                    << NcbiEndl;
                //            } else {
                //                cout << "-" << NcbiEndl;
                //            }
            cout << NcbiEndl;
        }
    }
}


// Demonstrate obtaining column vector in two alternative ways.
// (Use numeric param n to choose alignment position)
void CAlnMgrTestApp::View8(int aln_pos)
{
    CAlnMap::TSignedRange rng;
    rng.Set(aln_pos, aln_pos); // range covers only a single position
    
    string buffer;
    
    // obtain all individual residues
    for (CAlnMap::TNumrow row=0; row<m_AV->GetNumRows(); row++) {
        cout << m_AV->GetAlnSeqString(buffer, row, rng);
    }
    cout << NcbiEndl;
    
    // get the column at once
    string column;
    column.resize(m_AV->GetNumRows());
    
    cout << m_AV->GetColumnVector(column, aln_pos) << NcbiEndl;
    
    // %ID
    cout << m_AV->CalculatePercentIdentity(aln_pos) << NcbiEndl;
}


void CAlnMgrTestApp::View9(int row0, int row1)
{
    vector<TSignedSeqPos> result;
    CAlnMap::TRange aln_rng(0, m_AV->GetAlnStop()), rng0, rng1;

    m_AV->GetResidueIndexMap(row0, row1, aln_rng, result, rng0, rng1);

    size_t size = result.size();
    cout << "(" << rng0.GetFrom() << "-" << rng0.GetTo() << ")" << endl;
    cout << "(" << rng1.GetFrom() << "-" << rng1.GetTo() << ")" << endl;
    for (size_t i = 0; i < size; i++) {
        cout << result[i] << " ";
    }
    cout << endl;
}


//////
// GetSeqPosFromAlnPos
void CAlnMgrTestApp::GetSeqPosFromAlnPosDemo()
{
    cout << "["
        << m_AV->GetSeqPosFromAlnPos(2, 1390, CAlnMap::eForward, false)
        << "-" 
        << m_AV->GetSeqPosFromAlnPos(2, 1390, (CAlnMap::ESearchDirection)7, false)
        << "]"
        << NcbiEndl;
}


int CAlnMgrTestApp::Run(void)
{
    CArgs args = GetArgs();

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

    LoadDenseg();

    cout << "-----" << endl;

    if (args["a"]) {
        m_AV->SetAnchor(args["a"].AsInteger());
    }

    int screen_width = args["w"].AsInteger();
    int number       = args["n"].AsInteger();
    int row0         = args["row0"].AsInteger();
    int row1         = args["row1"].AsInteger();
    m_AV->SetGapChar('-');
    m_AV->SetEndChar('.');
    if (args["v"]) {
        switch (args["v"].AsInteger()) {
        case 1: View1(); break;
        case 2: View2(screen_width); break;
        case 3: View3(screen_width); break;
        case 4: View4(screen_width); break;
        case 5: View5(); break;
        case 6: View6(); break;
        case 7: View7(); break;
        case 8: View8(number); break;
        case 9: View9(row0, row1); break;
        }
    }
    return 0;
}


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


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

/*
* ===========================================================================
*
* $Log: alnvwr.cpp,v $
* Revision 1000.2  2004/06/01 19:40:58  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.22
*
* Revision 1.22  2004/05/21 21:42:51  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.21  2004/03/03 19:41:59  todorov
* +GetResidueIndexMap
*
* Revision 1.20  2004/02/12 22:51:27  todorov
* +optinal seq-entry input file to read a local seq
*
* Revision 1.19  2004/02/03 19:52:25  todorov
* m_AV declared after m_OM so that its ref to scope is distroyed first
*
* Revision 1.18  2004/01/16 22:11:48  ucko
* Explicitly call DumpAsFasta() on Seq-ids intended to appear in FASTA format.
*
* Revision 1.17  2004/01/07 17:37:36  vasilche
* Fixed include path to genbank loader.
* Moved split_cache application.
*
* Revision 1.16  2003/12/19 19:37:26  todorov
* +comments
*
* Revision 1.15  2003/12/18 20:08:53  todorov
* Demo GetColumnVector & CalculatePercentIdentity
*
* Revision 1.14  2003/12/11 00:43:47  ucko
* Fix typo in previous revision: call Close on the CObjectIStream rather
* than the auto_ptr.
*
* Revision 1.13  2003/12/10 23:58:07  todorov
* Added CObjectIStream::Close before IStream::seekg
*
* Revision 1.12  2003/12/09 16:13:34  todorov
* code cleanup
*
* Revision 1.11  2003/12/08 21:28:04  todorov
* Forced Translation of Nucleotide Sequences
*
* Revision 1.10  2003/09/26 15:30:07  todorov
* +Print segments
*
* Revision 1.9  2003/07/23 21:01:08  ucko
* Revert use of (uncommitted) BLAST DB data loader.
*
* Revision 1.8  2003/07/23 20:52:07  todorov
* +width, +aln_starts for the inserts in GetWhole..
*
* Revision 1.7  2003/07/17 22:48:17  todorov
* View4 implemented in CAlnVec::GetWholeAlnSeqString
*
* Revision 1.6  2003/07/17 21:06:44  todorov
* -v is now required param
*
* Revision 1.5  2003/07/14 20:25:18  todorov
* Added another, even faster viewer
*
* Revision 1.4  2003/07/08 19:27:46  todorov
* Added an speed-optimized viewer
*
* Revision 1.3  2003/06/04 18:20:40  todorov
* read seq-submit
*
* Revision 1.2  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 1.1  2003/04/03 21:17:48  todorov
* Adding demo projects
*
*
* ===========================================================================
*/