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Class Summary

class MSA
{

public:
static const int	GAP_INDEX=-1;
	MSA() ;
	MSA(const TSequence* mol);
	MSA(const vector< TColumn>& i_vCol, const vector< const TSequence*>& i_vSeq);
int	getSeqNum()const ;
vector< const TSequence*>	getSeqs()const ;
const TSequence*	getSeq(const int i)const ;
int	getLength()const ;
vector< TColumn>	getColumns()const ;
int	identityCount()const;
bool	ifIdentity(const int i_col)const;
void	reorder(const vector< const TSequence*>& vSeq);
template< class TTSequence> friend ostream&	operator<<(ostream& s, const MSA< TTSequence>& sp);
void	printClustalXformat(ostream& s)const;
void	printPIRformat(ostream& s)const;
protected:

}; // Log

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KEYWORD

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AUTHORS

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GOALS

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USAGE

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const int GAP_INDEX=-1;

  static const int GAP_INDEX=-1;//index for mol array

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MSA() ;

  MSA()  
;

Function is currently defined inline.

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MSA(const TSequence* mol);

  MSA(const TSequence* mol);

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MSA(const vector< TColumn>& i_vCol, const vector< const TSequence*>& i_vSeq);

  MSA(const vector< TColumn>& i_vCol,
      const vector< const TSequence*>& i_vSeq);

Function is currently defined inline.

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int getSeqNum()const ;

  int getSeqNum()const                       
;

Function is currently defined inline.

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vector< const TSequence*> getSeqs()const ;

  vector< const TSequence*> getSeqs()const                
;

Function is currently defined inline.

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const TSequence* getSeq(const int i)const ;

  const TSequence* getSeq(const int i)const                   
;

Function is currently defined inline.

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int getLength()const ;

  int getLength()const                       
;

Function is currently defined inline.

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vector< TColumn> getColumns()const ;

  vector< TColumn> getColumns()const                
;

Function is currently defined inline.

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int identityCount()const;

  int identityCount()const;

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bool ifIdentity(const int i_col)const;

  bool ifIdentity(const int i_col)const;

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void reorder(const vector< const TSequence*>& vSeq);

  void reorder(const vector< const TSequence*>& vSeq);

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template< class TTSequence> friend ostream& operator<<(ostream& s, const MSA< TTSequence>& sp);

printing class info

  template< class TTSequence>
////
  friend ostream& operator<<(ostream& s, const MSA< TTSequence>& sp);

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void printClustalXformat(ostream& s)const;

  void printClustalXformat(ostream& s)const;

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void printPIRformat(ostream& s)const;

  void printPIRformat(ostream& s)const;

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All Members

public:
static const int	GAP_INDEX=-1;
	MSA() ;
	MSA(const TSequence* mol);
	MSA(const vector< TColumn>& i_vCol, const vector< const TSequence*>& i_vSeq);
int	getSeqNum()const ;
vector< const TSequence*>	getSeqs()const ;
const TSequence*	getSeq(const int i)const ;
int	getLength()const ;
vector< TColumn>	getColumns()const ;
int	identityCount()const;
bool	ifIdentity(const int i_col)const;
void	reorder(const vector< const TSequence*>& vSeq);
template< class TTSequence> friend ostream&	operator<<(ostream& s, const MSA< TTSequence>& sp);
void	printClustalXformat(ostream& s)const;
void	printPIRformat(ostream& s)const;
protected:

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Ancestors

Class does not inherit from any other class.

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Descendants

Class is not inherited by any others.

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Generated from source by the Cocoon utilities on Tue Jan 5 18:47:30 2010 .

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