gff_util.cpp

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/*  $Id: gff_util.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:  
 *
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include "gff_util.hpp"
 
#include <objtools/import/import_error.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
//  ============================================================================
bool
GffUtil::InitializeScore(
    const vector<string>& gffColumns,
    bool& scoreIsPresent,
    double& scoreValue)
//  ============================================================================
{
    auto score = gffColumns[5];
    if (score == ".") {
        scoreIsPresent = false;
        return true;
    }
 
    try {
        scoreValue = NStr::StringToDouble(score);
    }
    catch(std::exception&) {
        return false;
    }
    scoreIsPresent = true;
    return true;
}
    
//  ============================================================================
bool
GffUtil::InitializeFrame(
    const vector<string>& gffColumns,
    std::string& phase)
//  ============================================================================
{
    phase = gffColumns[7];
    vector<string> valid = {".", "0", "1", "2"};  
    auto validIt = find(valid.begin(), valid.end(), phase);
    return (validIt != valid.end());
}
 
//  ============================================================================
CCdregion::TFrame
GffUtil::PhaseToFrame(
    const std::string& phase)
//  ============================================================================
{
    vector<CCdregion::TFrame> frameValues = {
        CCdregion::eFrame_one, CCdregion::eFrame_two, CCdregion::eFrame_three};
 
    if (phase == ".") {
        return CCdregion::eFrame_not_set;
    }
    else {
        return frameValues[phase[0] - '0'];
    }
}
 
END_SCOPE(objects)
END_NCBI_SCOPE