cav_function.cpp

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                        ERR_POST(Error << "slave should be unaligned at alnLoc " << alnLoc
                            << " row " << (i+1));
                        return false;
                    }
                } else {    // aligned master
                    if (!IsAligned(slaveChar)) {
                        ERR_POST(Error << "slave should be aligned at alnLoc " << alnLoc
                            << " row " << (i+1));
                        return false;
                    }
                    if (currentSlaveLoc != alignment->masterToSlave[currentMasterLoc]) {
                        ERR_POST(Error << "wrong slave residue aligned to master at alnLoc " << alnLoc
                            << " row " << (i+1));
                        return false;
                    }
                }
            }
        }

        // check seequence lengths
        if (masterLoc != alignment->master->sequenceString.size() - 1 ||
            slaveLoc != alignment->slave->sequenceString.size() - 1) {
            ERR_POST(Error << "bad sequence lengths at row " << (i+1));
            return false;
        }
    }
    return true;
}

END_NCBI_SCOPE


// leave the main function outside the NCBI namespace, just in case that might
// cause any problems when linking it to C code...
USING_NCBI_SCOPE;

int CAV_DisplayMultiple(
    const void *asnDataBlock,
    unsigned int options,
    unsigned int paragraphWidth,
    double conservationThreshhold,
    const char *title,
    int nFeatures,
    const AlignmentFeature *features)
{
    return CAV_DisplayMultiple(asnDataBlock, options, paragraphWidth,
        conservationThreshhold, title, nFeatures, features, NULL, NULL);
}

int CAV_DisplayMultiple(
    const void *asnDataBlock,
    unsigned int options,
    unsigned int paragraphWidth,
    double conservationThreshhold,
    const char *title,
    int nFeatures,
    const AlignmentFeature *alnFeatures,
    CNcbiOstream *outputStream,
    CNcbiOstream *diagnosticStream)
{
    // make sure C++ output streams are sync'ed with C's stdio
    IOS_BASE::sync_with_stdio(true);

    // set up output streams (send all diagnostic messages to a different stream)
    CNcbiOstream *outStream;
    if (outputStream)
        outStream = outputStream;
    else
        outStream = &NcbiCout;
    if (diagnosticStream)
        SetDiagStream(diagnosticStream);
    else
        SetDiagStream(&NcbiCerr);
    if (options & CAV_DEBUG)
        SetDiagPostLevel(defaultDiagPostLevel = eDiag_Info);   // show all messages
    else
        SetDiagPostLevel(defaultDiagPostLevel = eDiag_Error);  // show only errors

    // check option consistency
    if (options & CAV_CONDENSED && !(options & CAV_TEXT || options & CAV_HTML)) {
        ERR_POST(Error << "Cannot do condensed display except with text/HTML output");
        return CAV_ERROR_BAD_PARAMS;
    }
    if (options & CAV_FASTA_LOWERCASE && !(options & CAV_FASTA)) {
        ERR_POST(Error << "Cannot do fasta_lc option except with FASTA output");
        return CAV_ERROR_BAD_PARAMS;
    }
    if (options & CAV_HTML_HEADER && !(options & CAV_HTML)) {
        ERR_POST(Error << "Cannot do HTML header without HTML output");
        return CAV_ERROR_BAD_PARAMS;
    }

    // load input data into an input stream
    if (!asnDataBlock) {
        ERR_POST(Critical << "NULL asnDataBlock parameter");
        return CAV_ERROR_BAD_ASN;
    }
    CNcbiIstrstream asnIstrstream(static_cast<const char*>(asnDataBlock), kMax_Int);

    // load asn data block
    const SeqEntryList *seqs;
    const SeqAnnotList *alns;
    int retval = LoadASNFromIstream(asnIstrstream, &seqs, &alns);
    if (retval != CAV_SUCCESS) {
        ERR_POST(Critical << "Couldn't get sequence and alignment ASN data");
        return retval;
    }
    auto_ptr<const SeqEntryList> sequencesASN(seqs);
    auto_ptr<const SeqAnnotList> alignmentsASN(alns);

    // process asn data, then free it
    auto_ptr<SequenceSet> sequenceSet(new SequenceSet(*(sequencesASN.get())));
    if (!sequenceSet.get() || sequenceSet->Status() != CAV_SUCCESS) {
        ERR_POST(Critical << "Error processing sequence data");
        return sequenceSet->Status();
    }
    auto_ptr<AlignmentSet> alignmentSet(new AlignmentSet(sequenceSet.get(), *(alignmentsASN.get())));
    if (!alignmentSet.get() || alignmentSet->Status() != CAV_SUCCESS) {
        ERR_POST(Critical << "Error processing alignment data");
        return alignmentSet->Status();
    }
    sequencesASN.reset();
    alignmentsASN.reset();

    // create the alignment display structure
    auto_ptr<AlignmentDisplay> display(new AlignmentDisplay(sequenceSet.get(), alignmentSet.get()));
    if (!display.get() || display->Status() != CAV_SUCCESS) {
        ERR_POST(Critical << "Error creating alignment display");
        return display->Status();
    }

    // do verification
    if (options & CAV_DEBUG) {
        if (!VerifyAlignmentData(alignmentSet.get(), display.get())) {
            ERR_POST(Critical << "AlignmentDisplay failed verification");
            return CAV_ERROR_DISPLAY;
        } else {
            ERR_POST(Info << "AlignmentDisplay passed verification");
        }
    }

    // display alignment with given parameters
    ERR_POST(Info << "writing output...");
    int
        from = (options & CAV_LEFTTAILS) ? 0 : display->GetFirstAlignedLoc(),
        to = (options & CAV_RIGHTTAILS) ? display->GetWidth()-1 : display->GetLastAlignedLoc();
    if (options & CAV_SHOW_IDENTITY) conservationThreshhold = AlignmentDisplay::SHOW_IDENTITY;
    if (options & CAV_TEXT || options & CAV_HTML) {
        if (options & CAV_CONDENSED)
            retval = display->DumpCondensed(*outStream, options,
                from, to, paragraphWidth, conservationThreshhold, title, nFeatures, alnFeatures);
        else
            retval = display->DumpText(*outStream, options,
                from, to, paragraphWidth, conservationThreshhold, title, nFeatures, alnFeatures);
    } else if (options & CAV_FASTA) {
        retval = display->DumpFASTA(from, to, paragraphWidth,
            ((options & CAV_FASTA_LOWERCASE) > 0), *outStream);
    }
//    if (outStream != &NcbiCout) delete outStream;
    if (retval != CAV_SUCCESS) {
        ERR_POST(Error << "Error dumping display to output");
        return retval;
    }

    return CAV_SUCCESS;
}

/*
* ---------------------------------------------------------------------------
* $Log: cav_function.cpp,v $
* Revision 1000.2  2004/06/01 19:41:19  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
*
* Revision 1.4  2004/05/21 21:42:51  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.3  2004/03/15 18:51:27  thiessen
* prefer prefix vs. postfix ++/-- operators
*
* 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  2003/03/19 19:04:12  thiessen
* move again
*
* Revision 1.2  2003/03/19 16:06:28  thiessen
* add <memory>
*
* Revision 1.1  2003/03/19 05:33:43  thiessen
* move to src/app/cddalignview
*
* Revision 1.11  2003/03/18 22:35:06  thiessen
* add C++ version of function that takes streams for output
*
* Revision 1.10  2003/02/03 17:52:03  thiessen
* move CVS Log to end of file
*
* Revision 1.9  2003/01/21 18:01:07  thiessen
* add condensed alignment display
*
* Revision 1.8  2002/11/08 19:38:11  thiessen
* add option for lowercase unaligned in FASTA
*
* Revision 1.7  2002/02/08 19:53:17  thiessen
* add annotation to text/HTML displays
*
* Revision 1.6  2001/05/17 15:01:41  lavr
* Typos corrected
*
* Revision 1.5  2001/03/02 01:19:24  thiessen
* add FASTA output
*
* Revision 1.4  2001/02/15 19:23:44  thiessen
* add identity coloring
*
* Revision 1.3  2001/02/14 16:06:10  thiessen
* add block and conservation coloring to HTML display
*
* Revision 1.2  2001/01/29 23:55:10  thiessen
* add AlignmentDisplay verification
*
* Revision 1.1  2001/01/29 18:13:34  thiessen
* split into C-callable library + main
*
*/