seq_annot_ci.cpp

来自「ncbi源码」· C++ 代码 · 共 276 行

/*
 * ===========================================================================
 * PRODUCTION $Log: seq_annot_ci.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:23:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: seq_annot_ci.cpp,v 1000.2 2004/06/01 19:23:46 gouriano Exp $
* ===========================================================================
*
*                            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: Aleksey Grichenko, Eugene Vasilchenko
*
* File Description:
*   Seq-annot iterator
*
*/

#include <ncbi_pch.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/impl/seq_entry_info.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CSeq_annot_CI::SEntryLevel_CI::SEntryLevel_CI(const CBioseq_set_Info& seqset,
                                              const TEntry_CI& iter)
    : m_Set(&seqset), m_Iter(iter)
{
}


CSeq_annot_CI::SEntryLevel_CI::SEntryLevel_CI(const SEntryLevel_CI& l)
    : m_Set(l.m_Set), m_Iter(l.m_Iter)
{
}


CSeq_annot_CI::SEntryLevel_CI&
CSeq_annot_CI::SEntryLevel_CI::operator=(const SEntryLevel_CI& l)
{
    m_Set = l.m_Set;
    m_Iter = l.m_Iter;
    return *this;
}


CSeq_annot_CI::SEntryLevel_CI::~SEntryLevel_CI(void)
{
}


CSeq_annot_CI::CSeq_annot_CI(void)
    : m_UpTree(false)
{
}


CSeq_annot_CI::~CSeq_annot_CI(void)
{
}


CSeq_annot_CI::CSeq_annot_CI(const CSeq_annot_CI& iter)
    : m_UpTree(false)
{
    *this = iter;
}


CSeq_annot_CI& CSeq_annot_CI::operator=(const CSeq_annot_CI& iter)
{
    if (this != &iter) {
        m_CurrentEntry = iter.m_CurrentEntry;
        m_AnnotIter = iter.m_AnnotIter;
        m_CurrentAnnot = iter.m_CurrentAnnot;
        m_EntryStack = iter.m_EntryStack;
        m_UpTree = iter.m_UpTree;
    }
    return *this;
}


CSeq_annot_CI::CSeq_annot_CI(CScope& scope, const CSeq_entry& entry,
                             EFlags flags)
    : m_Scope(scope),
      m_UpTree(false)
{
    x_Initialize(scope.GetSeq_entryHandle(entry), flags);
}


CSeq_annot_CI::CSeq_annot_CI(const CSeq_entry_Handle& entry, EFlags flags)
    : m_Scope(entry.GetScope()),
      m_UpTree(false)
{
    x_Initialize(entry, flags);
}


CSeq_annot_CI::CSeq_annot_CI(const CBioseq_Handle& bioseq)
    : m_Scope(bioseq.GetScope()),
      m_UpTree(true)
{
    x_Initialize(bioseq.GetParentEntry(), eSearch_entry);
}


CSeq_annot_CI::CSeq_annot_CI(const CBioseq_set_Handle& bioseq_set,
                             EFlags flags)
    : m_Scope(bioseq_set.GetScope()),
      m_UpTree(false)
{
    x_Initialize(bioseq_set.GetParentEntry(), flags);
}


inline
void CSeq_annot_CI::x_Push(void)
{
    if ( m_CurrentEntry->IsSet() ) {
        const CBioseq_set_Info& set = m_CurrentEntry->GetSet();
        m_EntryStack.push(SEntryLevel_CI(set, set.GetSeq_set().begin()));
    }
}


inline
void CSeq_annot_CI::x_SetEntry(const CSeq_entry_Info& entry)
{
    m_CurrentEntry.Reset(&entry);
    m_AnnotIter = entry.m_Contents->GetAnnot().begin();
    if ( !m_EntryStack.empty() ) {
        x_Push();
    }
}


void CSeq_annot_CI::x_Initialize(const CSeq_entry_Handle& entry, EFlags flags)
{
    if ( !entry ) {
        NCBI_THROW(CAnnotException, eFindFailed,
                   "Can not find seq-entry in the scope");
    }
    if ( entry.Which() == CSeq_entry::e_not_set ) {
        NCBI_THROW(CAnnotException, eFindFailed,
                   "seq-entry is empty");
    }

    x_SetEntry(entry.x_GetInfo());
    if ( flags == eSearch_recursive ) {
        x_Push();
    }
    
    x_Settle();
}


CSeq_annot_CI& CSeq_annot_CI::operator++(void)
{
    _ASSERT(*this);
    ++m_AnnotIter;
    x_Settle();
    return *this;
}


void CSeq_annot_CI::x_Settle(void)
{
    for ( ;; ) {
        if ( m_AnnotIter != m_CurrentEntry->m_Contents->GetAnnot().end() ) {
            m_CurrentAnnot = CSeq_annot_Handle(GetScope(), **m_AnnotIter);
            return;
        }

        if ( m_UpTree ) {
            // Iterating from a bioseq up to its TSE
            if ( m_CurrentEntry->HasParent_Info() ) {
                x_SetEntry(m_CurrentEntry->GetParentSeq_entry_Info());
                continue;
            }
            m_CurrentAnnot = CSeq_annot_Handle();
            return;
        }

        if ( m_EntryStack.empty() ) {
            m_CurrentAnnot = CSeq_annot_Handle();
            return;
        }
        
        if ( m_EntryStack.top().m_Iter !=
             m_EntryStack.top().m_Set->GetSeq_set().end() ) {
            x_SetEntry(**m_EntryStack.top().m_Iter++);
        }
        else {
            m_EntryStack.pop();
        }
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: seq_annot_ci.cpp,v $
* Revision 1000.2  2004/06/01 19:23:46  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.8
*
* Revision 1.8  2004/05/21 21:42:13  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.7  2004/04/26 14:13:46  grichenk
* Added constructors from bioseq-set handle and bioseq handle.
*
* Revision 1.6  2004/03/16 15:47:28  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.5  2003/10/08 14:14:27  vasilche
* Use CHeapScope instead of CRef<CScope> internally.
*
* Revision 1.4  2003/09/30 16:22:03  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.3  2003/09/05 17:29:40  grichenk
* Structurized Object Manager exceptions
*
* Revision 1.2  2003/07/25 21:41:30  grichenk
* Implemented non-recursive mode for CSeq_annot_CI,
* fixed friend declaration in CSeq_entry_Info.
*
* Revision 1.1  2003/07/25 15:23:42  grichenk
* Initial revision
*
*
* ===========================================================================
*/