cuTaxTree.hpp

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/* $Id: cuTaxTree.hpp 101914 2024-03-01 17:18:17Z gouriano $
 * ===========================================================================
 *
 *                            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:  Charlie Liu
 *
 * File Description: Retrieve and create a Taxonomy tree for several CDs.
 *   part of CDTree app
 */
 
#ifndef CU_TAXTREE_HPP
#define CU_TAXTREE_HPP
#include <algo/structure/cd_utils/cuCppNCBI.hpp>
#include <algo/structure/cd_utils/tree_msvc7.hpp>
#include <algo/structure/cd_utils/cuTaxClient.hpp>
#include <algo/structure/cd_utils/cuAlignmentCollection.hpp>
#include <list>
#include <stack>
#include <algorithm>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(cd_utils)
 
class NCBI_CDUTILS_EXPORT TaxNode
{
public:
    //fields for internal tax nodes
    TTaxId taxId;
    std::string orgName;
    short rankId;
    //fields for external seq nodes
    int rowId;
    CCdCore* cd;
    std::string seqName;
    //total and selected leaf counts
    int numLeaves;
    int selectedLeaves; 
 
    //methods
    TaxNode();
    TaxNode(const TaxNode& rhs);
    bool operator==(const TaxNode& rhs) const {return taxId == rhs.taxId;};
    static bool isSeqLeaf(const TaxNode& node);
    static bool isSubSeqLeaf(const TaxNode& node);
    static TaxNode* makeTaxNode(TTaxId taxID, std::string taxName, short rankId=-1);
    static TaxNode* makeSeqLeaf(int rowID, std::string sequenceName);
    static TaxNode* makeSubSeqLeaf(int rowID, CCdCore* cd, int rowInCd);
 
private:
    void init();
};
 
typedef tree<TaxNode> TaxonomyTree;
typedef TaxonomyTree::iterator TaxTreeIterator;
//typedef list<CCd*> CDList;
 
/*  taxonomy ranking -- total 8 level
 Superkingdom: Eukaryota  
         Kingdom: Metazoa  
           Phylum: Chordata  
             Class: Mammalia  
               Order: Primata  
                 Family: Hominidae  
                   Genus: Homo  
                     Species: sapiens  
*/
 
// define a family hiearchy of CDs 
class NCBI_CDUTILS_EXPORT TaxTreeData : public TaxonomyTree
{
public:
    TaxTreeData(const AlignmentCollection& ac);
    
    const vector<int>& getFailedRows() { return m_failedRows;}
    void selectTaxNode(TaxTreeIterator& taxNode, bool select);
    void setSelections(const vector<int>& rowIDs, CCdCore* cd=0);
    int getSelections(vector<int>& rows);
    void clearSelection();
    void deselectAllTaxNodes();
    void fillLeafCount(const TaxTreeIterator& cursor);
    //bool isPreferredTaxNode(const TaxTreeIterator& taxNode);
    int getAllLeafNodes(const TaxTreeIterator& taxNode, vector<TaxTreeIterator>& nodes) const;
    short getRankId(string rankName);
    TaxTreeIterator getParentAtRank(int row, string rankName);
    bool isEmpty()const;
    //bool missLocalTaxFiles()const {return m_missLocalTaxFiles;}
    ~TaxTreeData();
 
    void addTaxToBioseq(CBioseq& bioseq, TTaxId taxid, string& taxName);
    bool writeToFile(string fname)const;
    bool writeToFileAsTable(string fname)const;
    bool write(std::ostream&os, const iterator& cursor)const;
    bool writeAsTable(std::ostream&os, const iterator& cursor, const iterator& branchingNode)const;
private:
    const AlignmentCollection& m_ac;
    typedef map<int, TaxonomyTree::iterator> RowToTaxNode;
    RowToTaxNode m_rowToTaxNode;
    typedef map<string, short> RankNameToId;
    RankNameToId m_rankNameToId;
     // wrapper of taxonomy server class
    TaxClient* m_taxDataSource;
    vector<int> m_failedRows;
 
    bool makeTaxonomyTree();
    void addRows(const AlignmentCollection& ac);
    // get integer taxid for a sequence
    TTaxId GetTaxIDForSequence(const AlignmentCollection& aligns, int rowID);
    // get info for taxid
    void selectTaxTreeLeaf(const TaxTreeIterator& cursor, bool select, CCdCore* cd=0);
    void addSeqTax(int rowID, string seqName, TTaxId taxid);
    void growAndInsertLineage(stack<TaxNode*>& lineage);
    void insertLineage(TaxTreeIterator& pos, stack<TaxNode*>& lineage);
    void cacheRank(short rank, string rankName);
    void writeOutRanks();
};
 
END_SCOPE(cd_utils)
END_NCBI_SCOPE
#endif