taxon1.cpp

ncbi源码

	req.SetGetorgprop( *pProp );
	try {
	    if( SendRequest( req, resp ) ) {
		if( !resp.IsGetorgprop() ) { // error
		    ERR_POST( "Response type is not Getorgprop" );
		} else {
		    if( resp.GetGetorgprop().size() > 0 ) {
			CRef<CTaxon1_info> pInfo
			    ( resp.GetGetorgprop().front() );
			prop_val.assign( pInfo->GetSval() );
			return true;
		    }
		}
	    } else if( resp.IsError()
		       && resp.GetError().GetLevel() 
		       != CTaxon1_error::eLevel_none ) {
		string sErr;
		resp.GetError().GetErrorText( sErr );
		ERR_POST( sErr );
	    }
	} catch( exception& e ) {
	    ERR_POST( e.what() );
	    SetLastError( e.what() );
	}
    } else {
	SetLastError( "Empty property name is not accepted" );
	ERR_POST( GetLastError() );
    }
    return false;
}

bool
CTaxon1::GetNodeProperty( int tax_id, const string& prop_name,
			  bool& prop_val )
{
    SetLastError(NULL);
    CTaxon1_req req;
    CTaxon1_resp resp;
    CRef<CTaxon1_info> pProp( new CTaxon1_info() );

    CDiagAutoPrefix( "Taxon1::GetNodeProperty" );

    if( !prop_name.empty() ) {
	pProp->SetIval1( tax_id );
	pProp->SetIval2( -3 ); // Get bool property by name
	pProp->SetSval( prop_name );
	
	req.SetGetorgprop( *pProp );
	try {
	    if( SendRequest( req, resp ) ) {
		if( !resp.IsGetorgprop() ) { // error
		    ERR_POST( "Response type is not Getorgprop" );
		} else {
		    if( resp.GetGetorgprop().size() > 0 ) {
			CRef<CTaxon1_info> pInfo
			    = resp.GetGetorgprop().front();
			prop_val = pInfo->GetIval2() != 0;
			return true;
		    }
		}
	    } else if( resp.IsError()
		       && resp.GetError().GetLevel() 
		       != CTaxon1_error::eLevel_none ) {
		string sErr;
		resp.GetError().GetErrorText( sErr );
		ERR_POST( sErr );
	    }
	} catch( exception& e ) {
	    ERR_POST( e.what() );
	    SetLastError( e.what() );
	}
    } else {
	SetLastError( "Empty property name is not accepted" );
	ERR_POST( GetLastError() );
    }
    return false;
}

bool
CTaxon1::GetNodeProperty( int tax_id, const string& prop_name,
			  int& prop_val )
{
    SetLastError(NULL);
    CTaxon1_req req;
    CTaxon1_resp resp;
    CRef<CTaxon1_info> pProp( new CTaxon1_info() );

    CDiagAutoPrefix( "Taxon1::GetNodeProperty" );

    if( !prop_name.empty() ) {
	pProp->SetIval1( tax_id );
	pProp->SetIval2( -2 ); // Get int property by name
	pProp->SetSval( prop_name );
	
	req.SetGetorgprop( *pProp );
	try {
	    if( SendRequest( req, resp ) ) {
		if( !resp.IsGetorgprop() ) { // error
		    ERR_POST( "Response type is not Getorgprop" );
		} else {
		    if( resp.GetGetorgprop().size() > 0 ) {
			CRef<CTaxon1_info> pInfo
			    = resp.GetGetorgprop().front();
			prop_val = pInfo->GetIval2();
			return true;
		    }
		}
	    } else if( resp.IsError()
		       && resp.GetError().GetLevel() 
		       != CTaxon1_error::eLevel_none ) {
		string sErr;
		resp.GetError().GetErrorText( sErr );
		ERR_POST( sErr );
	    }
	} catch( exception& e ) {
	    ERR_POST( e.what() );
	    SetLastError( e.what() );
	}
    } else {
	SetLastError( "Empty property name is not accepted" );
	ERR_POST( GetLastError() );
    }
    return false;
}

//-----------------------------------
//  Iterator stuff
//
// 'Downward' traverse mode (nodes that closer to root processed first)
ITreeIterator::EAction 
ITreeIterator::TraverseDownward(I4Each& cb, unsigned levels)
{
    if( levels ) {
        switch( cb.Execute(GetNode()) ) {
        default:
        case eOk:
            if(!IsTerminal()) {
                switch( cb.LevelBegin(GetNode()) ) {
                case eStop: return eStop;
                default:
                case eOk:
                    if(GoChild()) {
                        do {
                            if(TraverseDownward(cb, levels-1)==eStop)
                                return eStop;
                        } while(GoSibling());
                    }
                case eSkip: // Means skip this level
                    break;
                }
                GoParent();
                if( cb.LevelEnd(GetNode()) == eStop )
                    return eStop;
            }
        case eSkip: break;
        case eStop: return eStop;
        }
    }
    return eOk;
}

// 'Upward' traverse mode (nodes that closer to leaves processed first)
ITreeIterator::EAction
ITreeIterator::TraverseUpward(I4Each& cb, unsigned levels)
{
    if( levels > 0 ) {
        if(!IsTerminal()) {
            switch( cb.LevelBegin(GetNode()) ) {
            case eStop: return eStop;
            default:
            case eOk:
                if(GoChild()) {
                    do {
                        if( TraverseUpward(cb, levels-1) == eStop )
                            return eStop;
                    } while(GoSibling());
                }
            case eSkip: // Means skip this level
                break;
            }
            GoParent();
            if( cb.LevelEnd(GetNode()) == eStop )
                return eStop;
        }
        return cb.Execute(GetNode());
    }
    return eOk;
}

// 'LevelByLevel' traverse (nodes that closer to root processed first)
ITreeIterator::EAction
ITreeIterator::TraverseLevelByLevel(I4Each& cb, unsigned levels)
{
    switch( cb.Execute( GetNode() ) ) {
    case eStop:
	return eStop;
    case eSkip:
	return eSkip;
    case eOk:
    default:
	break;
    }
    if(!IsTerminal()) {
	vector< const ITaxon1Node* > skippedNodes;
	return TraverseLevelByLevelInternal(cb, levels, skippedNodes);
    }
    return eOk;
}

ITreeIterator::EAction
ITreeIterator::TraverseLevelByLevelInternal(I4Each& cb, unsigned levels,
					    vector< const ITaxon1Node* >& skp)
{
    size_t skp_start = skp.size();
    if( levels > 1 ) {
	if(!IsTerminal()) {
	    switch( cb.LevelBegin(GetNode()) ) {
	    case eStop: return eStop;
	    default:
	    case eOk:
		if(GoChild()) {
		    // First pass - call Execute for all children
		    do {
			switch( cb.Execute(GetNode()) ) {
			default:
			case eOk:
			    break;
			case eSkip: // Means skip this node
			    skp.push_back( GetNode() );
			    break;
			case eStop: return eStop;
			}
		    } while( GoSibling() );
		    GoParent();
		    // Start second pass
		    size_t skp_cur = skp_start;
		    GoChild();
		    do {
			if( skp.size() == skp_start ||
			    skp[skp_cur] != GetNode() ) {
			    if(TraverseLevelByLevelInternal(cb, levels-1, skp)
			       == eStop ) {
				return eStop;
			    }
			} else {
			    ++skp_cur;
			}
		    } while(GoSibling());
		    GoParent();
		}
		if( cb.LevelEnd( GetNode() ) == eStop )
		    return eStop;
		break;
	    case eSkip:
		break;
	    }
	}
    }
    skp.resize( skp_start );
    return eOk;
}

// Scans all the ancestors starting from immediate parent up to the root
// (no levelBegin, levelEnd calls performed)
ITreeIterator::EAction
ITreeIterator::TraverseAncestors(I4Each& cb)
{
    const ITaxon1Node* pNode = GetNode();
    EAction stat = eOk;
    while( GoParent() ) {
	stat = cb.Execute(GetNode());
	switch( stat ) {
	case eStop: return eStop; // Stop scan, some error occurred
	default:
	case eOk:
	case eSkip: // Means skip further scan, no error generated
	    break;
	}
	if( stat == eSkip ) {
	    break;
	}
    }
    GoNode( pNode );
    return stat;
}

bool
CTaxon1::CheckOrgRef( const COrg_ref& orgRef, TOrgRefStatus& stat_out )
{
    CDiagAutoPrefix( "Taxon1::CheckOrgRef" );
    SetLastError(NULL);
    int tax_id;

    tax_id = GetTaxIdByOrgRef( orgRef );
    stat_out = eStatus_Ok;

    if( tax_id == 0 ) {
	SetLastError( "No organism found for specified org_ref" );
	ERR_POST( GetLastError() );
	return false;
    } else if( tax_id < 0 ) {
	SetLastError( "Multiple organisms found for specified org_ref" );
	ERR_POST( GetLastError() );
	return false;
    } else {
	CRef< CTaxon2_data > pData( GetById( tax_id ) );
	if( pData ) {
	    // Compare orgrefs
	    const COrg_ref& goodOr = pData->GetOrg();

	    if( !orgRef.IsSetOrgname() ) {
		stat_out |= eStatus_NoOrgname;
	    } else {
		const COrgName& goodOn = goodOr.GetOrgname();
		const COrgName& inpOn = orgRef.GetOrgname();

		if( !inpOn.IsSetGcode() || !goodOn.IsSetGcode() ||
		    inpOn.GetGcode() != goodOn.GetGcode() ) {
		    stat_out |= eStatus_WrongGC;
		}
		if( !inpOn.IsSetMgcode() ) { // mgc not set in input
		    if( goodOn.IsSetMgcode() &&
			goodOn.GetMgcode() != 0 ) {
			stat_out |= eStatus_WrongMGC;
		    }
		} else { // mgc set
		    if( !goodOn.IsSetMgcode() ) {
			if( inpOn.GetMgcode() != 0 ) { // not unassigned
			    stat_out |= eStatus_WrongMGC;
			}
		    } else if( inpOn.GetMgcode() != goodOn.GetMgcode() ) {
			stat_out |= eStatus_WrongMGC;
		    }
		}
		if( !inpOn.IsSetLineage() || !goodOn.IsSetLineage() ||
		    inpOn.GetLineage().compare( goodOn.GetLineage() ) != 0 ) {
		    stat_out |= eStatus_WrongLineage;
		}
		if( !inpOn.IsSetName() || !goodOn.IsSetName() ||
		    inpOn.GetName().Which() != goodOn.GetName().Which() ) {
		    stat_out |= eStatus_WrongOrgname;
		}
		if( !inpOn.IsSetDiv() ) {
		    if( goodOn.IsSetDiv() &&
			goodOn.GetDiv().compare( "UNA" ) != 0 ) {
			stat_out |= eStatus_WrongDivision;
		    }
		} else {
		    if( !goodOn.IsSetDiv() ) {
			if( inpOn.GetDiv().compare( "UNA" ) != 0 ) {
			    stat_out |= eStatus_WrongDivision;
			}
		    } else if( inpOn.GetDiv().compare( goodOn.GetDiv() )
			       != 0 ) {
			stat_out |= eStatus_WrongDivision;
		    }
		}
		if( goodOn.IsSetMod() ) {
		    if( inpOn.IsSetMod() ) {
			const COrgName::TMod& inpMods = inpOn.GetMod();
			const COrgName::TMod& goodMods = goodOn.GetMod();
			for( COrgName::TMod::const_iterator gi =
				 goodMods.begin();
			     gi != goodMods.end();
			     ++gi ) {
			    bool bFound = false;
			    for( COrgName::TMod::const_iterator ii = 
				     inpMods.begin();
				 ii != inpMods.end();
				 ++ii ) {
				if( (*gi)->GetSubtype() == (*ii)->GetSubtype()
				    && ((*gi)->GetSubname() ==
					(*ii)->GetSubname()) ) {
				    bFound = true;
				    break;
				}
			    }
			    if( !bFound ) {
				stat_out |= eStatus_WrongOrgmod;
				break;
			    }
			}
		    } else {
			stat_out |= eStatus_WrongOrgmod;
		    }
		}
	    }
	    // Check taxname
	    if( orgRef.IsSetTaxname() ) {
		if( !goodOr.IsSetTaxname() ||
		    orgRef.GetTaxname().compare( goodOr.GetTaxname() ) != 0 ) {
		    stat_out |= eStatus_WrongTaxname;
		}
	    } else if( goodOr.IsSetTaxname() ) {
		stat_out |= eStatus_WrongTaxname;
	    }
	    // Check common name
	    if( orgRef.IsSetCommon() ) {
		if( !goodOr.IsSetCommon() ||
		    orgRef.GetCommon().compare( goodOr.GetCommon() ) != 0 ) {
		    stat_out |= eStatus_WrongCommonName;
		}
	    } else if( goodOr.IsSetCommon() ) {
		stat_out |= eStatus_WrongCommonName;
	    }
	} else { // Internal error: Cannot find orgref by tax_id
	    SetLastError( "No organisms found for tax id" );
	    ERR_POST( GetLastError() );
	    return false;
	}
    }
    return true;
}

END_objects_SCOPE
END_NCBI_SCOPE



/*
 * $Log: taxon1.cpp,v $
 * Revision 1000.3  2004/06/01 19:35:15  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R6.25
 *
 * Revision 6.25  2004/05/19 17:27:10  gorelenk
 * Added include of PCH - ncbi_pch.hpp
 *
 * Revision 6.24  2004/04/01 14:14:02  lavr
 * Spell "occurred", "occurrence", and "occurring"
 *
 * Revision 6.23  2004/03/12 20:07:24  domrach
 * CheckOrgRef() function added for checking the user orgref against the orgref from Taxonomy db
 *
 * Revision 6.22  2004/02/04 16:14:44  domrach
 * New iterator types (modes of operation) are introduced. They include:
 * full tree, branches'n'leaves, best, and blast. Position inquiry f-ns
 * IsTerminal(), IsFirstChild(), and IsLastChild() has been moved from
 * ITreeNode to ITreeIterator. Node loading f-ns() now return the ITreeNode
 * for tax id.
 *
 * Revision 6.21  2003/11/20 15:42:19  ucko
 * Update for new (saner) treatment of ASN.1 NULLs.
 *
 * Revision 6.20  2003/11/18 17:50:51  dicuccio
 * Rearranged #include statements to avoid warning on MSVC
 *
 * Revision 6.19  2003/10/23 18:52:47  domrach
 * Unique name bug fixed
 *
 * Revision 6.18  2003/07/09 15:41:31  domrach
 * SearchTaxIdByName(), GetNameClass(), and GetNodeProperty() functions added
 *
 * Revision 6.17  2003/06/23 20:42:08  domrach
 * New treatment of subspecies names introduced
 *
 * Revision 6.16  2003/06/05 20:44:02  domrach
 * Adjusted to the new CanGetXxx verification methods
 *
 * Revision 6.15  2003/05/06 19:53:54  domrach
 * New functions and interfaces for traversing the cached partial taxonomy tree introduced. Convenience functions GetDivisionName() and GetRankName() were added
 *
 * Revision 6.14  2003/03/10 20:59:37  ucko
 * ThrowError1 -> ThrowError, per the recent change to <serial/objostr.hpp>.
 * Explicitly cast ints to COrgMod::TSubtype when setting OrgMod.subtype.
 *
 * Revision 6.13  2003/03/05 21:33:52  domrach
 * Enhanced orgref processing. Orgref cache capacity control added.
 *
 * Revision 6.12  2003/01/31 03:46:46  lavr
 * Heed int->bool performance warnings
 *
 * Revision 6.11  2003/01/21 19:38:59  domrach
 * GetPopsetJoin() member function optimized to copy partial tree from cached tree
 *
 * Revision 6.10  2003/01/10 19:58:46  domrach
 * Function GetPopsetJoin() added to CTaxon1 class
 *
 * Revision 6.9  2002/11/08 20:55:58  ucko
 * CConstRef<> now requires an explicit constructor.
 *
 * Revision 6.8  2002/11/08 14:39:52  domrach
 * Member function GetSuperkingdom() added
 *
 * Revision 6.7  2002/11/04 21:29:18  grichenk
 * Fixed usage of const CRef<> and CRef<> constructor
 *
 * Revision 6.6  2002/08/06 16:12:34  domrach
 * Merging of modifiers is now performed in LookupMerge
 *
 * Revision 6.5  2002/07/25 15:01:56  grichenk
 * Replaced non-const GetXXX() with SetXXX()
 *
 * Revision 6.4  2002/02/14 22:44:50  vakatov
 * Use STimeout instead of time_t.
 * Get rid of warnings and extraneous #include's, shuffled code a little.
 *
 * Revision 6.3  2002/01/31 00:31:26  vakatov
 * Follow the renaming of "CTreeCont.hpp" to "ctreecont.hpp".
 * Get rid of "std::" which is unnecessary and sometimes un-compilable.
 * Also done some source identation/beautification.
 *
 * Revision 6.2  2002/01/30 16:13:38  domrach
 * Changes made to pass through MSVC compiler. Some src files renamed
 *
 * Revision 6.1  2002/01/28 19:56:10  domrach
 * Initial checkin of the library implementation files
 *
 * ===========================================================================
 */