cuSeqtree.hpp

Go to the documentation of this file.

Go to the SVN repository for this file.

/* $Id: cuSeqtree.hpp 33815 2007-05-04 17:18:18Z kazimird $
 * ===========================================================================
 *
 *                            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:
 *   Define SeqTree and how to read and write it.
 */
 
#if !defined(CU_SEQTREE_HPP)
#define CU_SEQTREE_HPP
#include <algo/structure/cd_utils/cuAlignmentCollection.hpp>
#include <algo/structure/cd_utils/tree_msvc7.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>
 
#include <string>
#include <iostream>
#include <fstream>
#include <map>
#include <vector>
#include <queue>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(cd_utils)
 
typedef map<CCdCore*, bool> SelectionByCd;
 
class NCBI_CDUTILS_EXPORT SeqItem
{
    friend ostream &operator<<(ostream& os, const SeqItem&);
public:
    SeqItem();
    SeqItem(const SeqItem& rhs);
    SeqItem(int rowid, double dist=0.0);
    explicit SeqItem(const std::string nameDist);
    SeqItem(const std::string nameDist, int rowid, double dist=0.0);
    void select(bool on=true); //select all instances of this row
    void select(CCdCore* cd, bool on=true); //select the instance in this CD
    int getAllInstances();
    int getAllSelectedInstances();
    ~SeqItem(){};
 
    bool operator==(const SeqItem& rhs) const;
 
    std::string name;
    int id;
    double distance;
    double distanceToRoot;
    int x;
    int y;
    int rowID;
    SelectionByCd selections;
    bool selected;
    bool collapsed;
    bool interesting;
    long taxid;
    string membership; //child cd accession to color the tree
    CConstRef< CSeq_id > seqId;
private:
    void init();
};
 
typedef map<int, std::string> IntToStringMap;
typedef map<int, string> RowMembershipColor;
 
typedef tree<SeqItem> SeqTreeBase;
typedef SeqTreeBase::iterator SeqTreeIterator;
 
class NCBI_CDUTILS_EXPORT SeqTree: public SeqTreeBase
{
public:
    SeqTree();
    virtual ~SeqTree();
 
//  SeqTree(const SeqTree& rhs);
//  SeqTree& operator=(const SeqTree& rhs);
    
    //prepare deriative attributes for drawing
    void prepare();
    void forcePrepare();
    bool isPrepared();
    int getNumLeaf();
    double getMaxDistanceToRoot();
    std::string getLongestName();
    //get the order of aligntment rows in the tree.
    //master row (row=0) is not in the vector positions because it is not a real ealignment row.
    void getOrdersInTree(vector<int>& positions);
    void getDiversityRankToRow(int colRow, list<int>& rankList);
    SeqTreeIterator getLeafById(int id);
    //set child cd membership
    void setMembershipColor(const RowMembershipColor* rowColorMap);
    
    //node selection
    void getSelectedSequenceRowid(const iterator& node, vector<int>& selections);
    void getSequenceRowid(const iterator& node, vector<int>& selections);
    void clearInternalNodeSelection();
    void selectByRowID(const set<int>& receivedSelection, bool select=true, CCdCore* cd=0);
    void selectByTax(const vector<int>& rows, long taxid);
    void selectByGI(const AlignmentCollection& aligns,const vector< CRef <CSeq_id> >& gis);
    void selectNode(const iterator& node, bool select=true, CCdCore* cd=0);
    //void deselectNode(const iterator& node, bool all=false);
    void getDistantNodes(double dist, vector<SeqTreeIterator>& nodes);
    //void getPeerLeafNodes(const iterator& node, vector<SeqTreeIterator>& nodes);
    void uncollapseAll();
 
    //seq name
    enum SeqNameMode
    {
        eGI, 
        eSPECIES,
        eGI_SPECIES, 
        eGI_SEQLOC,
        eGI_SEQLOC_SPECIES
    };
    void fixRowName(AlignmentCollection& aligns, SeqNameMode mode);
    void fixRowNumber(AlignmentCollection& aligns);
    void addSelectionFields(AlignmentCollection& aligns);
    void updateSeqCounts(const AlignmentCollection& aligns);
    bool isSequenceCompositionSame(AlignmentCollection& aligns);
    bool compareSequenceCompositions(IntToStringMap& com1, IntToStringMap& com2);
    void getSequenceComposition(IntToStringMap& seqComposition);
    void getSequenceComposition(AlignmentCollection& aligns, 
                                IntToStringMap& seqComposition);
private:
    bool m_prepared;
    int m_numLeaf;
    double m_maxDist;
    std::string m_longestName;
    typedef map<int, iterator> RowLeafMap;
    RowLeafMap m_leafNodes;
    typedef queue<iterator> IteQueue;
    IteQueue m_collapsedNodes;  //used in prepare() only
    
    void prepare(int& numLeaf, double& maxDist, const iterator& cursor);
    void prepareCollapsedNodes(int& numLeaf);
    void clearTaxSelection();
    void getDistantNodes(const iterator& start, double dist, vector<SeqTreeIterator>& nodes);
    void getDiversityRankUnderNode(SeqTreeIterator node, list<int>& rankList);
    //void selectByInternalRowID(const vector<int>& selection);
};
 
END_SCOPE(cd_utils)
END_NCBI_SCOPE
#endif