DynProg2D

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KEYWORD

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AUTHORS

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CHANGES LOG

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GOALS

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USAGE

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DynProg2D(int i_iN,int i_iM, float i_fOpenGapPenalty , float i_fGapPenalty );

relation matrix is initialized, O(n*m array allocation)

  DynProg2D(int i_iN,int i_iM, float i_fOpenGapPenalty=-11,  float i_fGapPenalty=-1); //default for BLOSUM62 (taken from Blastp)

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~DynProg2D() ;

  ~DynProg2D()                                                                                                                  
;

Function is currently defined inline.

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void setRelation(int i_iI,int i_iJ,float i_fRelation) ;

if relation value is negative (setRelation) symbols will not be aligned (gaps will be inserted)

  inline void setRelation(int i_iI,int i_iJ,float i_fRelation)                                                        
;

Function is currently defined inline.

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void setRelationGAPi(int i_iI,float i_fRelation) ;

  inline void setRelationGAPi(int i_iI,float i_fRelation)                                            
;

Function is currently defined inline.

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void setRelationGAPj(int i_iJ,float i_fRelation) ;

  inline void setRelationGAPj(int i_iJ,float i_fRelation)                                            
;

Function is currently defined inline.

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void getGlobalAlignmentGenGap(vector< pair< int,int> >& o_vPair, float& o_fMaxScore, bool bEndsFree );

O(n^2)

  void getGlobalAlignmentGenGap(vector< pair< int,int> >& o_vPair,
				float& o_fMaxScore, bool bEndsFree=false);

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const float NOT_MATCH;

  static const float NOT_MATCH;//=-numeric_limits<float>::max();//-3.40282347e+38F;//-MAXFLOAT

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const float m_fOpenGapPenalty;

  const float m_fOpenGapPenalty;

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const float m_fGapPenalty;

  const float m_fGapPenalty;

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enum DIRECTION ;

  enum DIRECTION {LEFT,TOP,DIAGONAL,NONE,TOP_GAP_OPEN,LEFT_GAP_OPEN};

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struct MElement

  struct MElement{
    float m_fV;
    DIRECTION m_Direction;
    bool m_E_gap_open;
    bool m_F_gap_open;

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float* m_fRelationMtrx;

  float* m_fRelationMtrx;

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MElement* m_fScoreMtrx;

  MElement* m_fScoreMtrx;

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int m_iN,m_iM;

  int m_iN,m_iM;

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float *m_fRelationGAPi;

  float *m_fRelationGAPi;

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float *m_fRelationGAPj;

  float *m_fRelationGAPj;

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All Members

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Ancestors

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Descendants

• DynProg2Dw

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