cobalt_app_util.cpp

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/*  $Id: cobalt_app_util.cpp 71954 2016-04-07 17:48:29Z boratyng $
* ===========================================================================
*
*                            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 offical 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
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/*****************************************************************************
 
File name: cobalt_app_util.cpp
 
Author: Jason Papadopoulos
 
Contents: Utility functions for COBALT command line applications
 
******************************************************************************/
 
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/blastdb/bdbloader.hpp>
#include <serial/iterator.hpp>
#include <objtools/readers/reader_exception.hpp>
 
#include "cobalt_app_util.hpp"
 
BEGIN_NCBI_SCOPE;
BEGIN_SCOPE(cobalt);
 
 
/// Modification of the CFastaReader class that allows for reading a single
/// sequence as a degenarate multiple sequence alignment
class CFastaReaderEx : public CFastaReader
{
public:
    /// Constructor
    CFastaReaderEx(ILineReader& reader, CFastaReader::TFlags flags=0)
        : CFastaReader(reader, flags) {}
 
    /// Read alignment
    /// Modified parent class function that allows reading one sequence as
    /// aligned set
    CRef<CSeq_entry> ReadAlignedSet(ILineErrorListener * pMessageListener = 0) {
        CFastaReader::TIds ids;
        CRef<CSeq_entry> entry = x_ReadSeqsToAlign(ids, pMessageListener);
        CRef<CSeq_annot> annot(new CSeq_annot);
 
        x_AddMultiwayAlignment(*annot, ids);
        entry->SetSet().SetAnnot().push_back(annot);
 
        return entry;
    }
};
 
void GetSeqLocFromStream(CNcbiIstream& instream,
                         vector< CRef<objects::CSeq_loc> >& seqs,
                         CRef<objects::CScope>& scope,
                         objects::CFastaReader::TFlags flags)
{
    seqs.clear();
 
    // read one query at a time, and use a separate seq_entry,
    // scope, and lowercase mask for each query. This lets different
    // query sequences have the same ID. Later code will distinguish
    // between queries by using different elements of retval[]
 
    CStreamLineReader line_reader(instream);
    CFastaReader fasta_reader(line_reader, flags);
 
    while (!line_reader.AtEOF()) {
 
        CRef<CSeq_entry> entry = fasta_reader.ReadOneSeq();
 
        if (entry == 0) {
            NCBI_THROW(CObjReaderException, eInvalid, 
                        "Could not retrieve seq entry");
        }
        scope->AddTopLevelSeqEntry(*entry);
        CTypeConstIterator<CBioseq> itr(ConstBegin(*entry));
        CRef<CSeq_loc> seqloc(new CSeq_loc());
        seqloc->SetWhole().Assign(*itr->GetId().front());
        seqs.push_back(seqloc);
    }
}
 
 
CRef<objects::CSeq_align> GetAlignmentFromStream(CNcbiIstream& instream,
                                     CRef<objects::CScope>& scope,
                                     objects::CFastaReader::TFlags flags,
                                     objects::CSeqIdGenerator& id_generator)
{
    // read all sequences as a multiple sequence alignment and put
    // the alignment in a single seq_entry
 
    CStreamLineReader line_reader(instream);
    CFastaReaderEx fasta_reader(line_reader, flags);
    fasta_reader.SetIDGenerator(id_generator);
 
    CRef<CSeq_entry> entry = fasta_reader.ReadAlignedSet();
 
    if (entry == 0) {
        NCBI_THROW(CObjReaderException, eInvalid, 
                   "Could not retrieve seq entry");
    }
    scope->AddTopLevelSeqEntry(*entry);
 
    // notify of a problem if the whole file was not read
    if (!line_reader.AtEOF()) {
        NCBI_THROW(CObjReaderException, eInvalid, "Problem reading MSA");
    }
 
    CRef<objects::CSeq_align> align
        = entry->GetAnnot().front()->GetData().GetAlign().front();
 
    return align;
}
 
 
END_SCOPE(cobalt);
END_NCBI_SCOPE;