feat_importer.cpp

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/*  $Id: feat_importer.cpp 86362 2019-05-02 15:04:11Z ludwigf $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author: Frank Ludwig
 *
 * File Description:  Iterate through file names matching a given glob pattern
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
 
#include <objtools/import/import_error.hpp>
#include <objtools/import/import_message_handler.hpp>
 
#include "feat_importer_impl.hpp"
#include "id_resolver_canonical.hpp"
#include "ftable/gtf_importer.hpp"
#include "ftable/gff3_importer.hpp"
#include "ftable/bed_importer.hpp"
#include "ftable/5col_importer.hpp"
#include "ftable/feat_line_reader.hpp"
#include "ftable/feat_import_data.hpp"
#include "ftable/feat_annot_assembler.hpp"
#include "annot_import_data.hpp"
 
#include <assert.h>
 
USING_NCBI_SCOPE;
USING_SCOPE(objects);
 
 
//  ============================================================================
CFeatImporter*
CFeatImporter::Get(
    const string& format,
    unsigned int flags,
    CImportMessageHandler& errorHandler
    )
//  ============================================================================
{
    if (format == "gtf") {
        return new CGtfImporter(flags, errorHandler);
    }
    if (format == "gff3") {
        return new CGff3Importer(flags, errorHandler);
    }
    if (format == "bed") {
        return new CBedImporter(flags, errorHandler);
    }
    if (format == "5col") {
        return new C5ColImporter(flags, errorHandler);
    }
    return nullptr;
};
 
 
//  ============================================================================
CFeatImporter_impl::CFeatImporter_impl(
    unsigned int flags,
    CImportMessageHandler& errorHandler):
//  ============================================================================
    mFlags(flags),
    mpReader(nullptr),
    mErrorHandler(errorHandler)
{
    bool allIdsAsLocal = (mFlags & CFeatImporter::fAllIdsAsLocal);
    bool numericIdsAsLocal = (mFlags & CFeatImporter::fNumericIdsAsLocal);
    SetIdResolver(new CIdResolverCanonical(allIdsAsLocal, numericIdsAsLocal));
};
 
 
//  ============================================================================
void
CFeatImporter_impl::SetIdResolver(
    CIdResolver* pIdResolver)
//  ============================================================================
{
    mpIdResolver.reset(pIdResolver);
}
 
//  =============================================================================
void
CFeatImporter::ReadSeqAnnot(
    CNcbiIstream& istr,
    CSeq_annot& annot)
//  =============================================================================
{
    CStreamLineReader lineReader(istr);
    ReadSeqAnnot(lineReader, annot);
}
 
//  =============================================================================
void
CFeatImporter_impl::ReadSeqAnnot(
    CStreamLineReader& lineReader,
    CSeq_annot& annot)
//  =============================================================================
{
    assert(mpReader  &&  mpImportData  &&  mpAssembler);
 
    //mpReader->SetInputStream(istr);
    if (mFlags & fReportProgress) {
        mpReader->SetProgressReportFrequency(5);
    }
 
    mpAssembler->InitializeAnnot(annot);
 
    bool terminateNow = false;
    while (!terminateNow) {
        try {
            if (!mpReader->GetNextRecord(lineReader, *mpImportData)) {
                break;
            }
            mpAssembler->ProcessRecord(*mpImportData, annot);
        }
        catch(CImportError& err) {
            if (err.LineNumber() == 0) {
                err.SetLineNumber(lineReader.GetLineNumber());
            }
            mErrorHandler.ReportError(err);
            switch(err.Severity()) {
            default:
                continue;
            case CImportError::CRITICAL:
                terminateNow = true;
                break;
            case CImportError::FATAL:
                throw;
            }
        }
    }
    const CAnnotImportData& annotMeta = mpReader->AnnotImportData();
    mpAssembler->FinalizeAnnot(annotMeta, annot);
}