feature.cpp

来自「ncbi源码」· C++ 代码 · 共 710 行 · 第 1/2 页

        } catch (CSeqportUtil::CBadIndex&) {
            // fall back to comment (if any)
            s_GetRnaRefLabelFromComment(feat, label, label_type, type_label);
        }
        
        break;
    }}       
}


// Appends a label to tlabel for a CImp_feat. A return value of true indicates 
// that the label was created for a CImp_feat key = "Site-ref" 
inline
static bool s_GetImpLabel
(const CSeq_feat&      feat, 
 string*               tlabel,
 ELabelType            label_type,
 const string*         type_label)
{
    // Return if tlablel does not exist or feature data is not Imp-feat
    if (!tlabel  ||  !feat.GetData().IsImp()) {
        return false;
    }
    
    const string& key = feat.GetData().GetImp().GetKey();
    bool empty = true;
    
    // If the key is Site-ref
    if (!NStr::CompareNocase(key, "Site-ref")) {
        if (feat.IsSetCit()) {
            // Create label based on Pub-set
            feat.GetCit().GetLabel(tlabel);
            return true;
        }
    // else if the key is not Site-ref
    } else if (label_type == eContent) {
        // If the key is CDS
        if (!NStr::CompareNocase(key, "CDS")) {
            *tlabel += "[CDS]";
        // else if the key is repeat_unit or repeat_region
        } else if (!NStr::CompareNocase(key, "repeat_unit")  ||
                   !NStr::CompareNocase(key, "repeat_region")) {
            if (feat.IsSetQual()) {
                // Loop thru the feature qualifiers
                ITERATE( CSeq_feat::TQual, it, feat.GetQual()) {
                    // If qualifier qual is rpt_family append qualifier val
                    if (!NStr::CompareNocase((*it)->GetQual(),"rpt_family")) { 
                        *tlabel += (*it)->GetVal();
                        empty = false;
                        break;
                    }
                }
            }
            
            // If nothing has been appended yet
            if (empty) {
                *tlabel += type_label ? *type_label : string("");
            }
        // else if the key is STS
        } else if (!NStr::CompareNocase(key, "STS")) {
            if (feat.IsSetQual()) {
                ITERATE( CSeq_feat::TQual, it, feat.GetQual()) {
                    if (!NStr::CompareNocase((*it)->GetQual(),"standard_name"))
                    { 
                           *tlabel = (*it)->GetVal();
                           empty = false;
                           break;
                    }
                }
            }
            
            // If nothing has been appended yet
            if (empty) {
                if (feat.IsSetComment()) {
                    size_t pos = feat.GetComment().find(";");
                    if (pos == string::npos) {
                        *tlabel += feat.GetComment();
                    } else {
                        *tlabel += feat.GetComment().substr(0, pos);
                    } 
                } else {
                    *tlabel += type_label ? *type_label : string("");
                }
            }
        // else if the key is misc_feature
        } else if (NStr::CompareNocase(key, "misc_feature")) {
            if (feat.IsSetQual()) {
                // Look for a single qualifier qual in order of preference 
                // "standard_name", "function", "number", any and
                // append to tlabel and return if found
                ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
                    if (!NStr::CompareNocase((*it)->GetQual(),"standard_name"))
                    {
                         *tlabel += (*it)->GetVal();
                         return false;
                    }
                }
                ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
                    if (!NStr::CompareNocase((*it)->GetQual(), "function")) {
                         *tlabel += (*it)->GetVal();
                         return false;
                    }
                }
                ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
                    if (!NStr::CompareNocase((*it)->GetQual(), "number")) {
                        *tlabel += (*it)->GetVal();
                        return false;
                    }
                }
                ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
                    *tlabel += (*it)->GetVal();
                    return false;
                }
                // Append type_label if there is one
                if (empty) {
                    *tlabel += type_label ? *type_label : string("");
                    return false;
                }
            }
        }
                
    } 
    return false;                
}

 
// Return a label based on the content of the feature
void s_GetContentLabel
(const CSeq_feat&      feat,
 string*               label,
 const string*         type_label,
 ELabelType            label_type, 
 CScope*               scope)
{
    string tlabel;
    
    // Get a content label dependent on the type of the feature data
    switch (feat.GetData().Which()) {
    case CSeqFeatData::e_Gene:
        feat.GetData().GetGene().GetLabel(&tlabel);
        break;
    case CSeqFeatData::e_Org:
        feat.GetData().GetOrg().GetLabel(&tlabel);
        break;
    case CSeqFeatData::e_Cdregion:
        s_GetCdregionLabel(feat, &tlabel, scope);
        break;
    case CSeqFeatData::e_Prot:
        feat.GetData().GetProt().GetLabel(&tlabel);
        break;
    case CSeqFeatData::e_Rna:
        s_GetRnaRefLabel(feat, &tlabel, label_type, type_label);
        break;  
    case CSeqFeatData::e_Pub:
        feat.GetData().GetPub().GetPub().GetLabel(&tlabel); 
        break;
    case CSeqFeatData::e_Seq:
        break;
    case CSeqFeatData::e_Imp:
        if (s_GetImpLabel(feat, &tlabel, label_type, type_label)) {
            *label += tlabel;
            return;
        }
        break;
    case CSeqFeatData::e_Region:
        if (feat.GetData().GetRegion().find("Domain") != string::npos  && 
                feat.IsSetComment()) {
            tlabel += feat.GetComment();
        } else {
            tlabel += feat.GetData().GetRegion();
        }
        break;
    case CSeqFeatData::e_Comment:
        tlabel += feat.IsSetComment() ? feat.GetComment() : string("");
        break;
    case CSeqFeatData::e_Bond:
        // Get the ASN string name for the enumerated EBond type
        tlabel += CSeqFeatData::GetTypeInfo_enum_EBond()
            ->FindName(feat.GetData().GetBond(), true);
        break;
    case CSeqFeatData::e_Site:
        // Get the ASN string name for the enumerated ESite type
        tlabel += CSeqFeatData::GetTypeInfo_enum_ESite()
            ->FindName(feat.GetData().GetSite(), true);
        break;
    case CSeqFeatData::e_Rsite:
        switch (feat.GetData().GetRsite().Which()) {
        case CRsite_ref::e_Str:
            tlabel += feat.GetData().GetRsite().GetStr();
            break;
        case CRsite_ref::e_Db:
            tlabel += feat.GetData().GetRsite().GetDb().GetTag().IsStr() ?
                feat.GetData().GetRsite().GetDb().GetTag().GetStr() : 
                string("?");
            break;
        default:
            break;
        }
        break;
    case CSeqFeatData::e_User:
        if (feat.GetData().GetUser().IsSetClass()) {
            tlabel += feat.GetData().GetUser().GetClass();
        } else if (feat.GetData().GetUser().GetType().IsStr()) {
            tlabel += feat.GetData().GetUser().GetType().GetStr();
        }
    case CSeqFeatData::e_Txinit:
        break;
    case CSeqFeatData::e_Num:
        break;
    case CSeqFeatData::e_Psec_str:
        tlabel += CSeqFeatData::GetTypeInfo_enum_EPsec_str()
            ->FindName(feat.GetData().GetPsec_str(), true);
        break;    
    case CSeqFeatData::e_Non_std_residue:
        tlabel += feat.GetData().GetNon_std_residue();
        break;
    case CSeqFeatData::e_Het:
        tlabel += feat.GetData().GetHet().Get();
        break;        
    case CSeqFeatData::e_Biosrc:
        feat.GetData().GetBiosrc().GetOrg().GetLabel(&tlabel);
        break;        
    default:
        break;
    }
    
    // Return if a label has been calculated above
    if (!tlabel.empty()) {
        *label += tlabel;
        return;
    }
    
    // Put Seq-feat qual into label
    if (feat.IsSetQual()) {
        string prefix("/");
        ITERATE(CSeq_feat::TQual, it, feat.GetQual()) {
            tlabel += prefix + (**it).GetQual();
            prefix = " ";
            if (!(**it).GetVal().empty()) {
                tlabel += "=" + (**it).GetVal();
            }
        }
    }
    
    // Put Seq-feat comment into label
    if (feat.IsSetComment()) {
        if (tlabel.empty()) {
            tlabel = feat.GetComment();
        } else {
            tlabel += "; " + feat.GetComment();
        }
    }
    
    *label += tlabel;
}


void GetLabel
(const CSeq_feat&    feat,
 string*             label,
 ELabelType          label_type,
 CScope*             scope)
{
 
    // Ensure that label exists
    if (!label) {
        return;
    }
    
    // Get the type label
    string type_label;
    s_GetTypeLabel(feat, &type_label);
    
    // Append the type label and return if content label not required
    if (label_type == eBoth) {
        *label += type_label + ": ";
    } else if (label_type == eType) {
        *label += type_label;
        return;
    }
    
    // Append the content label
    size_t label_len = label->size();
    s_GetContentLabel(feat, label, &type_label, label_type, scope);
    
    // If there is no content label, append the type label
    if (label->size() == label_len  &&  label_type == eContent) {
        *label += type_label;
    }
}


END_SCOPE(feature)
END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ===========================================================================
* $Log: feature.cpp,v $
* Revision 1000.1  2004/06/01 19:25:23  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
*
* Revision 1.13  2004/05/21 21:42:14  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.12  2003/08/21 12:09:08  dicuccio
* Added processing of CDS in case the CDS is just an open reading frame
*
* Revision 1.11  2003/08/08 18:12:19  dicuccio
* Fixed bug in s_GetRnaRefLabel(): inadverted '&' instead of '&&'
*
* Revision 1.10  2003/07/22 21:48:26  vasilche
* Use typedef for member access.
*
* Revision 1.9  2003/06/02 16:06:39  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 1.8  2003/03/11 16:00:58  kuznets
* iterate -> ITERATE
*
* Revision 1.7  2002/12/31 15:09:58  dicuccio
* Removed unneeded headers for Featdef classes
*
* Revision 1.6  2002/12/26 21:17:06  dicuccio
* Minor tweaks to avoid compiler warnings in MSVC (remove unused variables)
*
* Revision 1.5  2002/08/26 16:29:41  ucko
* Be even more careful with TRNA extensions.
*
* Revision 1.4  2002/08/21 15:30:30  ucko
* Handle empty tRNA extensions.
*
* Revision 1.3  2002/08/20 20:01:50  ucko
* s_GetRnaRefLabel: factor out code to look at comments, and fall back
* on it for bogus TRNA extensions.
*
* Revision 1.2  2002/06/07 16:11:21  ucko
* Move everything into the "feature" namespace.
*
* Revision 1.1  2002/06/06 18:45:03  clausen
* Initial version
*
* ===========================================================================
*/