annot_selector.cpp

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SAnnotSelector&
SAnnotSelector::ResetExcludedTSE(void)
{
    m_ExcludedTSE.clear();
    return *this;
}


bool SAnnotSelector::ExcludedTSE(const CSeq_entry_Handle& tse) const
{
    return find(m_ExcludedTSE.begin(), m_ExcludedTSE.end(), tse)
        != m_ExcludedTSE.end();
}


void SAnnotSelector::x_ClearAnnotTypesSet(void)
{
    m_AnnotTypesSet.clear();
}


void SAnnotSelector::x_InitializeAnnotTypesSet(bool default_value)
{
    if (m_AnnotTypesSet.size() > 0) {
        return;
    }
    m_AnnotTypesSet.resize(CAnnotType_Index::GetAnnotTypeRange(
        CSeq_annot::C_Data::e_Ftable).second, default_value);
    // Do not try to use flags from an uninitialized selector
    if (GetAnnotType() != CSeq_annot::C_Data::e_not_set) {
        // Copy current state to the set
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetIndexRange(*this);
        for (size_t i = range.first; i < range.second; ++i) {
            m_AnnotTypesSet[i] = true;
        }
    }
    // Do not call this->SetAnnotType() -- it will reset the types set.
    // Set type to Ftable -- only feature types/subtypes may be selected.
    SAnnotTypeSelector::SetAnnotType(CSeq_annot::C_Data::e_Ftable);
}


SAnnotSelector& SAnnotSelector::IncludeAnnotType(TAnnotType type)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set) {
        SAnnotTypeSelector::SetAnnotType(type);
    }
    else if (m_AnnotTypesSet.size() > 0  ||  !IncludedAnnotType(type)) {
        x_InitializeAnnotTypesSet(false);
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetAnnotTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            m_AnnotTypesSet[i] = true;
        }
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::ExcludeAnnotType(TAnnotType type)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set
        ||  m_AnnotTypesSet.size() > 0  ||  IncludedAnnotType(type)) {
        x_InitializeAnnotTypesSet(true);
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetAnnotTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            m_AnnotTypesSet[i] = false;
        }
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::IncludeFeatType(TFeatType type)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set) {
        SAnnotTypeSelector::SetFeatType(type);
    }
    else if (m_AnnotTypesSet.size() > 0  ||  !IncludedFeatType(type)) {
        x_InitializeAnnotTypesSet(false);
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetFeatTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            m_AnnotTypesSet[i] = true;
        }
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::ExcludeFeatType(TFeatType type)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set
        ||  m_AnnotTypesSet.size() > 0  ||  IncludedFeatType(type)) {
        x_InitializeAnnotTypesSet(true);
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetFeatTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            m_AnnotTypesSet[i] = false;
        }
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::IncludeFeatSubtype(TFeatSubtype subtype)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set) {
        SAnnotTypeSelector::SetFeatSubtype(subtype);
    }
    else if (m_AnnotTypesSet.size() > 0  ||  !IncludedFeatSubtype(subtype)) {
        x_InitializeAnnotTypesSet(false);
        m_AnnotTypesSet[CAnnotType_Index::GetSubtypeIndex(subtype)] = true;
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::ExcludeFeatSubtype(TFeatSubtype subtype)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set
        ||  m_AnnotTypesSet.size() > 0  ||  IncludedFeatSubtype(subtype)) {
        x_InitializeAnnotTypesSet(true);
        m_AnnotTypesSet[CAnnotType_Index::GetSubtypeIndex(subtype)] = false;
    }
    return *this;
}


SAnnotSelector& SAnnotSelector::CheckAnnotType(TAnnotType type)
{
    if (GetAnnotType() == CSeq_annot::C_Data::e_not_set) {
        SetAnnotType(type);
    }
    _ASSERT(GetAnnotType() == type);
    if (m_AnnotTypesSet.size() > 0) {
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetAnnotTypeRange(type);
        for (size_t i = 0; i < range.first; ++i) {
            m_AnnotTypesSet[i] = false;
        }
        for (size_t i = range.second; i < m_AnnotTypesSet.size(); ++i) {
            m_AnnotTypesSet[i] = false;
        }
    }
    return *this;
}


bool SAnnotSelector::IncludedAnnotType(TAnnotType type) const
{
    if (m_AnnotTypesSet.size() > 0) {
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetAnnotTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            if (m_AnnotTypesSet[i]) {
                return true;
            }
        }
        return false;
    }
    return GetAnnotType() == CSeq_annot::C_Data::e_not_set
        || GetAnnotType() == type;
}


bool SAnnotSelector::IncludedFeatType(TFeatType type) const
{
    if (m_AnnotTypesSet.size() > 0) {
        CAnnotType_Index::TIndexRange range =
            CAnnotType_Index::GetFeatTypeRange(type);
        for (size_t i = range.first; i < range.second; ++i) {
            if (m_AnnotTypesSet[i]) {
                return true;
            }
        }
        return false;
    }
    return GetFeatType() == CSeqFeatData::e_not_set
        || GetFeatType() == type;
}


bool SAnnotSelector::IncludedFeatSubtype(TFeatSubtype subtype) const
{
    if (m_AnnotTypesSet.size() > 0) {
        return m_AnnotTypesSet[CAnnotType_Index::GetSubtypeIndex(subtype)];
    }
    return GetFeatSubtype() == subtype
        ||  GetFeatSubtype() == CSeqFeatData::eSubtype_any;
}


bool SAnnotSelector::MatchType(const CAnnotObject_Info& annot_info) const
{
    if (annot_info.GetFeatSubtype() != CSeqFeatData::eSubtype_any) {
        return IncludedFeatSubtype(annot_info.GetFeatSubtype());
    }
    if (annot_info.GetFeatType() != CSeqFeatData::e_not_set) {
        return IncludedFeatType(annot_info.GetFeatType());
    }
    return IncludedAnnotType(annot_info.GetAnnotType());
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: annot_selector.cpp,v $
* Revision 1000.3  2004/06/01 19:22:41  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.12
*
* Revision 1.12  2004/05/21 21:42:12  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.11  2004/03/17 16:04:26  vasilche
* IRIX CC doesn't allow explicit call of implicit operator=()
*
* Revision 1.10  2004/03/16 15:47:27  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.9  2004/02/26 14:41:40  grichenk
* Fixed types excluding in SAnnotSelector and multiple types search
* in CAnnotTypes_CI.
*
* Revision 1.8  2004/02/11 22:19:24  grichenk
* Fixed annot type initialization in iterators
*
* Revision 1.7  2004/02/05 19:53:40  grichenk
* Fixed type matching in SAnnotSelector. Added IncludeAnnotType().
*
* Revision 1.6  2004/02/05 16:05:49  vasilche
* Fixed int <-> unsigned warning.
*
* Revision 1.5  2004/02/04 18:05:38  grichenk
* Added annotation filtering by set of types/subtypes.
* Renamed *Choice to *Type in SAnnotSelector.
*
* Revision 1.4  2004/01/23 16:14:47  grichenk
* Implemented alignment mapping
*
* Revision 1.3  2003/11/13 19:12:52  grichenk
* Added possibility to exclude TSEs from annotations request.
*
* Revision 1.2  2003/10/09 20:20:58  vasilche
* Added possibility to include and exclude Seq-annot names to annot iterator.
* Fixed adaptive search. It looked only on selected set of annot names before.
*
* Revision 1.1  2003/10/07 13:43:23  vasilche
* Added proper handling of named Seq-annots.
* Added feature search from named Seq-annots.
* Added configurable adaptive annotation search (default: gene, cds, mrna).
* Fixed selection of blobs for loading from GenBank.
* Added debug checks to CSeq_id_Mapper for easier finding lost CSeq_id_Handles.
* Fixed leaked split chunks annotation stubs.
* Moved some classes definitions in separate *.cpp files.
*
* Revision 1.27  2003/09/30 16:22:02  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 1.26  2003/08/27 21:24:51  vasilche
* Reordered member initializers.
*
* Revision 1.25  2003/08/27 14:29:52  vasilche
* Reduce object allocations in feature iterator.
*
* Revision 1.24  2003/08/26 21:28:47  grichenk
* Added seq-align verification
*
* Revision 1.23  2003/07/18 16:58:23  grichenk
* Fixed alignment coordinates
*
* Revision 1.22  2003/07/17 20:07:55  vasilche
* Reduced memory usage by feature indexes.
* SNP data is loaded separately through PUBSEQ_OS.
* String compression for SNP data.
*
* Revision 1.21  2003/06/02 16:06:37  dicuccio
* Rearranged src/objects/ subtree.  This includes the following shifts:
*     - src/objects/asn2asn --> arc/app/asn2asn
*     - src/objects/testmedline --> src/objects/ncbimime/test
*     - src/objects/objmgr --> src/objmgr
*     - src/objects/util --> src/objmgr/util
*     - src/objects/alnmgr --> src/objtools/alnmgr
*     - src/objects/flat --> src/objtools/flat
*     - src/objects/validator --> src/objtools/validator
*     - src/objects/cddalignview --> src/objtools/cddalignview
* In addition, libseq now includes six of the objects/seq... libs, and libmmdb
* replaces the three libmmdb? libs.
*
* Revision 1.20  2003/04/24 16:12:38  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.19  2003/03/11 15:51:06  kuznets
* iterate -> ITERATE
*
* Revision 1.18  2003/02/24 18:57:22  vasilche
* Make feature gathering in one linear pass using CSeqMap iterator.
* Do not use feture index by sub locations.
* Sort features at the end of gathering in one vector.
* Extracted some internal structures and classes in separate header.
* Delay creation of mapped features.
*
* Revision 1.17  2003/02/13 14:34:34  grichenk
* Renamed CAnnotObject -> CAnnotObject_Info
* + CSeq_annot_Info and CAnnotObject_Ref
* Moved some members of CAnnotObject to CSeq_annot_Info
* and CAnnotObject_Ref.
* Added feat/align/graph to CAnnotObject_Info map
* to CDataSource.
*
* Revision 1.16  2003/02/04 18:53:36  dicuccio
* Include file clean-up
*
* Revision 1.15  2003/01/22 20:11:54  vasilche
* Merged functionality of CSeqMapResolved_CI to CSeqMap_CI.
* CSeqMap_CI now supports resolution and iteration over sequence range.
* Added several caches to CScope.
* Optimized CSeqVector().
* Added serveral variants of CBioseqHandle::GetSeqVector().
* Tried to optimize annotations iterator (not much success).
* Rewritten CHandleRange and CHandleRangeMap classes to avoid sorting of list.
*
* Revision 1.14  2002/09/13 15:20:30  dicuccio
* Fix memory leak (static deleted before termination).
*
* Revision 1.13  2002/09/11 16:08:26  dicuccio
* Fixed memory leak in x_PrepareAlign().
*
* Revision 1.12  2002/09/03 17:45:45  ucko
* Avoid overrunning alignment data when the claimed dimensions are too high.
*
* Revision 1.11  2002/07/25 15:01:51  grichenk
* Replaced non-const GetXXX() with SetXXX()
*
* Revision 1.10  2002/07/08 20:51:00  grichenk
* Moved log to the end of file
* Replaced static mutex (in CScope, CDataSource) with the mutex
* pool. Redesigned CDataSource data locking.
*
* Revision 1.9  2002/07/01 15:31:57  grichenk
* Fixed 'enumeration value e_not_set...' warning
*
* Revision 1.8  2002/05/29 21:21:13  gouriano
* added debug dump
*
* Revision 1.7  2002/05/24 14:57:12  grichenk
* SerialAssign<>() -> CSerialObject::Assign()
*
* Revision 1.6  2002/05/03 21:28:08  ucko
* Introduce T(Signed)SeqPos.
*
* Revision 1.5  2002/04/05 21:26:19  grichenk
* Enabled iteration over annotations defined on segments of a
* delta-sequence.
*
* Revision 1.4  2002/02/21 19:27:04  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.3  2002/01/23 21:59:31  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.2  2002/01/16 16:25:56  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:06:16  gouriano
* restructured objmgr
*
*
* ===========================================================================
*/