cuSequenceTable.cpp

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/* $Id: cuSequenceTable.cpp 74244 2016-08-22 15:01:19Z lanczyck $
 * ===========================================================================
 *
 *                            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:  Charlie
 *
 * File Description:
 *
 *       Bioseq table indexed by seq-id
 *
 * ===========================================================================
 */
 
#include <ncbi_pch.hpp>
#include <algo/structure/cd_utils/cuSequenceTable.hpp>
#include <algo/structure/cd_utils/cuCdReadWriteASN.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(cd_utils)
 
SequenceTable::SequenceTable()
{
}
 
void SequenceTable::addSequences(vector< CRef< CBioseq > >& bioseqVec, bool grouped)
{
    if (!grouped)
    {
        for (unsigned int i = 0; i < bioseqVec.size(); i++)
        {
            addSequence(bioseqVec[i]);
        }
    }
    else
    {
        for (unsigned int i = 0; i < bioseqVec.size(); i++)
        {
            list< CRef< CSeq_id > >& seqIds = bioseqVec[i]->SetId();
            for (list< CRef< CSeq_id > >::iterator it= seqIds.begin(); it != seqIds.end(); it++)
            {
                for (unsigned int j = 0; j < bioseqVec.size(); j++)
                    m_table.insert(SeqidToBioseqMap::value_type(*it, bioseqVec[j]));
            }
        }
    }
}
 
void SequenceTable::addSequence(CRef< CBioseq > bioseq)
{
    list< CRef< CSeq_id > >& seqIds = bioseq->SetId();
    for (list< CRef< CSeq_id > >::iterator it= seqIds.begin(); it != seqIds.end(); it++)
    {
        m_table.insert(SeqidToBioseqMap::value_type(*it, bioseq));
    }
}
 
void SequenceTable::addSequences(CSeq_entry& seqEntry)
{
    if (seqEntry.IsSet())
    {
        list< CRef< CSeq_entry > >& seqSet = seqEntry.SetSet().SetSeq_set();
        list< CRef< CSeq_entry > >::iterator it = seqSet.begin();
        for (; it != seqSet.end(); it++)
            addSequences(*(*it));
    }
    else
    {
        CRef< CBioseq > bioseq(&(seqEntry.SetSeq()));
        addSequence(bioseq);
    }
}
 
void SequenceTable::addSequences(const SequenceTable& seqTable)
{
    m_table.insert(seqTable.m_table.begin(), seqTable.m_table.end());
}
 
unsigned SequenceTable::findSequencesInTheGroup(CRef< CSeq_id > seqId, vector< CRef< CBioseq > >& bioseqVec)const
{
    bioseqVec.clear();
    pair<SeqidToBioseqMap::const_iterator, SeqidToBioseqMap::const_iterator> range = m_table.equal_range(seqId);
    for (SeqidToBioseqMap::const_iterator it = range.first; it!= range.second; it++)
        bioseqVec.push_back(it->second);
    return bioseqVec.size();
}
 
bool SequenceTable::findSequence(CRef< CSeq_id > seqId, CRef< CBioseq >& bioseq)const
{
    vector< CRef< CBioseq > > bioseqVec;
    if (findSequencesInTheGroup(seqId, bioseqVec) == 0)
        return false;
    for (unsigned int i = 0; i < bioseqVec.size(); i++)
    {
        const CBioseq::TId& ids = bioseqVec[i]->GetId();
        CBioseq::TId::const_iterator it = ids.begin(), itend = ids.end();
        for (; it != itend; ++it) 
        {
            if ((*it)->Match(*seqId)) 
            {
                bioseq = bioseqVec[i];
                return true;
            }
        }
    }
    return false;
}
 
bool SequenceTable::findSequence(CRef< CSeq_id > seqId, CRef< CSeq_entry >& seqEntry)const
{
    CRef< CBioseq > bioseq;
    if (findSequence(seqId, bioseq))
    {
        seqEntry = new CSeq_entry;
        seqEntry->SetSeq(*bioseq);
        return true;
    }
    else
        return false;
}
 
void SequenceTable::dump(string filename)
{
    CNcbiOfstream outStream(filename.c_str(), IOS_BASE::out | IOS_BASE::binary);
    string err;
    if (!outStream) {
        err = "Cannot open file for writing";
    }
    SeqidToBioseqMap::iterator sit = m_table.begin();
    for (; sit != m_table.end(); sit++)
    {
        if (!WriteASNToStream(outStream, *(sit->first), false,&err))
            LOG_POST("Failed to write to "<<filename<<" because of "<<err);
        if (!WriteASNToStream(outStream, *(sit->second), false,&err))
            LOG_POST("Failed to write to "<<filename<< "because of "<<err);
    }
}
 
END_SCOPE(cd_utils)
END_NCBI_SCOPE