source: trunk/GDE/MUSCLE/src/diaglist.h

#ifndef diaglist_h
#define diaglist_h

const unsigned EMPTY = (unsigned) ~0;
const unsigned MAX_DIAGS = 1024;

struct Diag
        {
        unsigned m_uStartPosA;
        unsigned m_uStartPosB;
        unsigned m_uLength;
        };

struct Rect
        {
        unsigned m_uStartPosA;
        unsigned m_uStartPosB;
        unsigned m_uLengthA;
        unsigned m_uLengthB;
        };

class DiagList
        {
public:
        DiagList()
                {
                m_uCount = 0;
                }
        ~DiagList()
                {
                Free();
                }

public:
// Creation
        void Clear()
                {
                Free();
                }
        void FromPath(const PWPath &Path);
        void Add(const Diag &d);
        void Add(unsigned uStartPosA, unsigned uStartPosB, unsigned uLength);
        void DeleteIncompatible();

// Accessors
        unsigned GetCount() const
                {
                return m_uCount;
                }
        const Diag &Get(unsigned uIndex) const;

// Operations
        void Sort();
        void Copy(const DiagList &DL);

// Query
        // returns true iff given diagonal is included in the list
        // in whole or in part.
        bool NonZeroIntersection(const Diag &d) const;
        bool IsSorted() const;

// Diagnostics
        void LogMe() const;

private:
        void Free()
                {
                m_uCount = 0;
                }

private:
        unsigned m_uCount;
        Diag m_Diags[MAX_DIAGS];
        };

unsigned DiagOverlap(const Diag &d1, const Diag &d2);
unsigned DiagOverlapA(const Diag &d1, const Diag &d2);
unsigned DiagOverlapB(const Diag &d1, const Diag &d2);
unsigned DiagBreak(const Diag &d1, const Diag &d2);
bool DiagCompatible(const Diag &d1, const Diag &d2);
void CheckDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
  unsigned uLengthB, const MSA &msaA, const MSA &msaB, const PWPath &Path);
void FindDiags(const ProfPos *PX, unsigned uLengthX, const ProfPos *PY,
  unsigned uLengthY, DiagList &DL);
void FindDiagsNuc(const ProfPos *PX, unsigned uLengthX, const ProfPos *PY,
  unsigned uLengthY, DiagList &DL);
void MergeDiags(DiagList &DL);

#endif // diaglist_h