seq_annot_ci.cpp
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- /*
- * ===========================================================================
- * 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
- *
- *
- * ===========================================================================
- */