cuRowSourceTable.hpp

Go to the documentation of this file.

Go to the SVN repository for this file.

#ifndef CU_ROW_SOURCE_TABLE_HPP
#define CU_ROW_SOURCE_TABLE_HPP
 
//#include <algo/structure/cd_utils/cuCppNCBI.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(cd_utils)
 
struct RowSource
{
    RowSource() : cd(0), normal(false), rowInSrc(-1), master(false){}
    RowSource(CCdCore* cd, int row, bool norm):cd(cd), normal(norm), rowInSrc(row)
        {master = (row==0) && normal;}
    RowSource(const RowSource& rhs):cd(rhs.cd), normal(rhs.normal), rowInSrc(rhs.rowInSrc), master(rhs.master){}
 
    bool isPending() const { return !normal;}
    bool wasMaster() const {return master;}
    CCdCore* cd;
    bool normal; //normal or pending
    int rowInSrc;  // row in the source cd
    bool master;
};
 
typedef map<CCdCore*, vector<int> >CDRowsMap;
class NCBI_CDUTILS_EXPORT RowSourceTable
{
public:
    RowSourceTable();
    
    void addEntry(int row, CCdCore* cd, int rowInCD, bool normal=true, bool scoped = true);
    void addEntry(int row, RowSource rs, bool scoped = true);
    int findEntries(int row, vector<RowSource>& src, bool scopedOnly=false)const;
    void removeEntriesForCD(vector<int>& colRows, CCdCore* cd);
    const RowSource& findEntry(int row)const ;
    RowSource& findEntry(int row);
    //int findEntriesBySourceCD(const CCdCore* cd, vector<int> rows)const;
    //int findRowBySource(const RowSource& rs)const;
    bool isPending(int row)const;
    void getMasterRows(vector<int>& masters);
    //get all CDs involved in this AlignmentCollection
    int getCDs(vector<CCdCore*>& cds);
    //get only CDs whose alignment rows are included
    int getCDsInScope(vector<CCdCore*>& cds);
    //get CDs which are only used to map row membership of duplicated SeqLoc
    int getCDsOutofScope(vector<CCdCore*>& cds);
    bool isCDInScope(CCdCore* cd)const;
    bool isEntryInScope(const RowSource& rs)const;
    void clear();
    void convertFromCDRows(CCdCore* cd, const vector<int>& cdRows, set<int>& colRows)const;
    int convertFromCDRow(CCdCore* cd, int cdRows)const;
    void convertToCDRows(const vector<int>& colRows, CDRowsMap& cdRows) const;
 
    //void getAllRowsForCD(CCdCore* cd, vector<int>& colRows)const;
    bool isRowInCD(int row, CCdCore* cd)const;
private:
    typedef multimap<int, RowSource> RowSourceMap;
    RowSourceMap m_table;
    set<int> m_masters;
    set<CCdCore*> m_cdsInScope;
    set<CCdCore*> m_cdsOutofScope;
    //pending row starts at CCdCore::PENDING_ROW_START
    string makeCDRowKey(CCdCore* cd, int row)const ;
    //necessary indice to speed lookup
    typedef map<string, int>CDRowIndexMap;
    CDRowIndexMap m_cdRowIndexMap;
 
    void transferCDs(const set<CCdCore*>& cdSet, vector<CCdCore*>& cdVec);
};
 
END_SCOPE(cd_utils)
END_NCBI_SCOPE
#endif