objtools/edit/field_handler.cpp

/*  $Id: field_handler.cpp 632623 2021-06-03 17:38:11Z ivanov $
* ===========================================================================
*
*                            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: Colleen Bollin, NCBI
*
* File Description:
*   CFieldHandler parent class
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiobj.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/Object_id.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/seq_feat_handle.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/field_handler.hpp>
#include <objtools/edit/dblink_field.hpp>
#include <objtools/edit/gb_block_field.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
BEGIN_SCOPE(edit)

bool CFieldHandler::QualifierNamesAreEquivalent (string name1, string name2)
{
    // ignore protein at beginning
    const string protein("protein");
    if (NStr::StartsWith(name1, protein)) {
        name1 = name1.substr(protein.length());
    }
    if (NStr::StartsWith(name2, protein)) {
        name2 = name2.substr(protein.length());
    }

    // spaces, dashes, and underscores do not count
    NStr::ReplaceInPlace (name1, " ", "");
    NStr::ReplaceInPlace (name1, "_", "");
    NStr::ReplaceInPlace (name1, "-", "");
    NStr::ReplaceInPlace (name2, " ", "");
    NStr::ReplaceInPlace (name2, "_", "");
    NStr::ReplaceInPlace (name2, "-", "");

    return NStr::EqualNocase(name1, name2);
}


vector<CRef<CApplyObject> > CFieldHandler::GetRelatedApplyObjects(const CObject& object, CRef<CScope> scope)
{
    vector<CRef<CApplyObject> > related = GetApplyObjectsFromRelatedObjects(GetRelatedObjects(object, scope), scope);

    return related;
}


vector<CRef<CApplyObject> > CFieldHandler::GetApplyObjectsFromRelatedObjects(vector<CConstRef<CObject> > related, CRef<CScope> scope)
{
    vector<CRef<CApplyObject> > rval;

    ITERATE(vector<CConstRef<CObject> >, it, related) {
        const CSeqdesc * obj_desc = dynamic_cast<const CSeqdesc *>((*it).GetPointer());
        const CSeq_feat * obj_feat = dynamic_cast<const CSeq_feat *>((*it).GetPointer());
        if (obj_desc) {
            CSeq_entry_Handle seh = GetSeqEntryForSeqdesc(scope, *obj_desc);
            CRef<CSeqdesc> new_desc(new CSeqdesc());
            new_desc->Assign(*obj_desc);
            CRef<CObject> editable(new_desc.GetPointer());
            CRef<CApplyObject> apply(new CApplyObject(seh, *it, editable));
            rval.push_back(apply);
        } else {
            CBioseq_Handle bsh = scope->GetBioseqHandle(obj_feat->GetLocation());
            CRef<CApplyObject> apply(new CApplyObject(bsh, *obj_feat));
            rval.push_back(apply);
        }
    }

    return rval;
}


CRef<CFieldHandler>
CFieldHandlerFactory::Create(const string& field_name)
{
    CDBLinkField::EDBLinkFieldType dblink_field = CDBLinkField::GetTypeForLabel(field_name);
    if (dblink_field != CDBLinkField::eDBLinkFieldType_Unknown) {
        return CRef<CFieldHandler>(new CDBLinkField(dblink_field));
    }
#if 0
    if (s_IsSequenceIDField(field_name)) {
        return CRef<CFieldHandler>(new CSeqIdField());
    }
    CPubField::EPubFieldType pub_field = CPubField::GetTypeForLabel(field_name);
    if (pub_field != CPubField::ePubFieldType_Unknown) {
        return CRef<CFieldHandler>(new CPubField(pub_field));
    }
    CMolInfoField::EMolInfoFieldType molinfo_field = CMolInfoField::GetFieldType(field_name);
    if (molinfo_field != CMolInfoField::e_Unknown) {
        return CRef<CFieldHandler>(new CMolInfoField(molinfo_field));
    }

    if (NStr::EqualNocase(field_name, kGenomeProjectID)) {
        return CRef<CFieldHandler>(new CGenomeProjectField());
    }
#endif
    if (CFieldHandler::QualifierNamesAreEquivalent(field_name, kCommentDescriptorLabel)) {
        return CRef<CFieldHandler>(new CCommentDescField());
    }
    if (CFieldHandler::QualifierNamesAreEquivalent(field_name, kDefinitionLineLabel)) {
        return CRef<CFieldHandler>( new CDefinitionLineField());
    }
    CGBBlockField::EGBBlockFieldType gbblock_field = CGBBlockField::GetTypeForLabel(field_name);
    if (gbblock_field != CGBBlockField::eGBBlockFieldType_Unknown) {
        return CRef<CFieldHandler>(new CGBBlockField(gbblock_field));
    }

    // empty
    CRef<CFieldHandler> empty;
    return empty;
}


bool CFieldHandlerFactory::s_IsSequenceIDField(const string& field)
{
    return CFieldHandler::QualifierNamesAreEquivalent(field, kFieldTypeSeqId);
}


bool DoesObjectMatchFieldConstraint (const CObject& object, const string& field_name, CRef<CStringConstraint> string_constraint, CRef<CScope> scope)
{
    if (NStr::IsBlank(field_name) || !string_constraint) {
        return true;
    }

    CRef<CFieldHandler> fh = CFieldHandlerFactory::Create(field_name);
    if (!fh) {
        return false;
    }

    vector<string> val_list;
    vector<CConstRef<CObject> > objs = fh->GetRelatedObjects (object, scope);
    ITERATE(vector<CConstRef<CObject> >, it, objs) {
        vector<string> add = fh->GetVals(**it);
        val_list.insert(val_list.end(), add.begin(), add.end());
    }

    return string_constraint->DoesListMatch(val_list);
}


bool DoesApplyObjectMatchFieldConstraint (const CApplyObject& object, const string& field_name, CRef<CStringConstraint> string_constraint)
{
    if (NStr::IsBlank(field_name) || !string_constraint) {
        return true;
    }

    CRef<CFieldHandler> fh = CFieldHandlerFactory::Create(field_name);
    if (!fh) {
        return false;
    }

    vector<string> val_list;
    vector<CConstRef<CObject> > objs = fh->GetRelatedObjects (object);
    ITERATE(vector<CConstRef<CObject> >, it, objs) {
        vector<string> add = fh->GetVals(**it);
        val_list.insert(val_list.end(), add.begin(), add.end());
    }

    return string_constraint->DoesListMatch(val_list);
}

static vector<CConstRef<CSeq_feat> > s_GetProtFeatures(CBioseq_Handle p_bsh, CSeqFeatData::ESubtype constraint_type)
{
    vector<CConstRef<CSeq_feat> > feat_list;
    if (p_bsh) {
        CFeat_CI f(p_bsh, constraint_type);
        while (f) {
            CConstRef<CSeq_feat> object;
            object.Reset(f->GetOriginalSeq_feat());
            feat_list.push_back(object);
            ++f;
        }
    }
    return feat_list;
}


vector<CConstRef<CSeq_feat> > GetRelatedFeatures (const CSeq_feat& obj_feat, CSeqFeatData::ESubtype constraint_type, CRef<CScope> scope)
{
    vector<CConstRef<CSeq_feat> > feat_list;

    CSeqFeatData::ESubtype obj_type = obj_feat.GetData().GetSubtype();

    // is one feature type a protein and the other not?
    bool obj_is_prot = (CSeqFeatData::GetTypeFromSubtype(obj_type) == CSeqFeatData::e_Prot);
    bool constraint_is_prot = (CSeqFeatData::GetTypeFromSubtype(constraint_type) == CSeqFeatData::e_Prot);
    if (obj_is_prot && constraint_is_prot) {
        // find feature anywhere on protein sequence
        CBioseq_Handle p_bsh = scope->GetBioseqHandle(obj_feat.GetLocation());
        feat_list = s_GetProtFeatures(p_bsh, constraint_type);
    } else if (obj_is_prot && !constraint_is_prot) {
        // use coding region for starting point of overlap comparison
        CBioseq_Handle p_bsh = scope->GetBioseqHandle(obj_feat.GetLocation());
        const CSeq_feat* cds = sequence::GetCDSForProduct(p_bsh);
        if (cds) {
            if (CSeqFeatData::GetTypeFromSubtype(constraint_type) == CSeqFeatData::e_Cdregion) {
                feat_list.push_back(CConstRef<CSeq_feat>(cds));
            } else {
                feat_list = GetRelatedFeatures(*cds, constraint_type, scope);
            }
        }
    } else if (!obj_is_prot && constraint_is_prot) {
        // examine objects on protein sequence
        // need to find coding region for obj_feat
        if (obj_type == CSeqFeatData::eSubtype_cdregion) {
            if (obj_feat.IsSetProduct()) {
                CBioseq_Handle p_bsh = scope->GetBioseqHandle(obj_feat.GetProduct());
                feat_list = s_GetProtFeatures(p_bsh, constraint_type);
            }
        } else if (obj_type == CSeqFeatData::eSubtype_mRNA) {
            const CSeq_feat* cds = sequence::GetBestCdsForMrna(obj_feat, *scope);
            if (cds) {
                feat_list = GetRelatedFeatures(*cds, constraint_type, scope);
            }
        } else if (obj_type == CSeqFeatData::eSubtype_gene) {
            list<CMappedFeat> cds_feats;
            feature::GetCdssForGene(scope->GetSeq_featHandle(obj_feat), cds_feats);
            for (auto& cds_it : cds_feats) {
                vector<CConstRef<CSeq_feat> > this_list = GetRelatedFeatures(cds_it.GetOriginalFeature(), constraint_type, scope);
                feat_list.insert(feat_list.end(), this_list.begin(), this_list.end());
            }
        }
    } else {
        // neither is a protein
        if (constraint_type == CSeqFeatData::eSubtype_gene) {
            CConstRef<CSeq_feat> f = sequence::GetOverlappingGene(obj_feat.GetLocation(), *scope);
            if (f) {
                feat_list.push_back(f);
            }
        } else if (obj_type == CSeqFeatData::eSubtype_gene) {
            sequence::TFeatScores scores;
            sequence::GetOverlappingFeatures (obj_feat.GetLocation(),
                                              CSeqFeatData::GetTypeFromSubtype(constraint_type),
                                              constraint_type,
                                              sequence::eOverlap_Contains,
                                              scores, *scope);
            ITERATE (sequence::TFeatScores, it, scores) {
                feat_list.push_back(it->second);
            }
        } else if (obj_type == CSeqFeatData::eSubtype_cdregion
            && constraint_type == CSeqFeatData::eSubtype_mRNA) {
            CConstRef<CSeq_feat> f = sequence::GetBestMrnaForCds(obj_feat, *scope);
            if (f) {
                feat_list.push_back(f);
            }
        } else if (constraint_type == CSeqFeatData::eSubtype_any || constraint_type == obj_type) {
            CConstRef<CSeq_feat> f(&obj_feat);
            feat_list.push_back(f);
        }
    }
    return feat_list;
}

END_SCOPE(edit)
END_SCOPE(objects)
END_NCBI_SCOPE