Alignment Class Reference

#include <ali.h>

Public Member Functions
int	get_count () const
bool	valid (int idx) const
int	get_len (int idx) const
const Seq &	get (int idx) const
SeqPtr	getSeqPtr (int idx)
int	get_max_len () const
void	add (SeqPtr sequence)
void	add (const char *name, const char *sequence, size_t seq_len)
void	add (const char *name, const char *sequence)
	Alignment (const char *name_, size_t len_)
const char *	get_name () const
size_t	get_len () const

Detailed Description

Definition at line 11 of file ali.h.

Constructor & Destructor Documentation

Alignment::Alignment ( const char *  name_, size_t  len_  )

inline

Definition at line 917 of file insdel.cxx.

Member Function Documentation

int Alignment::get_count ( ) const

inline

Definition at line 15 of file ali.h.

Referenced by get_max_len(), to_paup(), to_phylip(), to_printable(), and valid().

bool Alignment::valid ( int  idx ) const

inline

Definition at line 16 of file ali.h.

References get_count().

Referenced by get(), get_len(), and getSeqPtr().

int Alignment::get_len ( int  idx ) const

inline

Definition at line 18 of file ali.h.

References ca_assert, and valid().

Referenced by AliInsertCommand::check_applicable_to(), AliDeleteCommand::check_applicable_to(), FINAL_TYPE< SEQTYPE >::check_applicable_to(), AliAutoFormatCommand::check_applicable_to(), EditedTerminal::EditedTerminal(), and to_paup().

const Seq& Alignment::get ( int  idx ) const

inline

Definition at line 19 of file ali.h.

References ca_assert, and valid().

Referenced by to_paup(), to_phylip(), and to_printable().

SeqPtr Alignment::getSeqPtr ( int  idx )

inline

Definition at line 20 of file ali.h.

References ca_assert, and valid().

Referenced by to_paup().

int Alignment::get_max_len ( ) const

inline

Definition at line 22 of file ali.h.

References get_count(), get_len(), and max.

Referenced by to_paup(), to_phylip(), and to_printable().

void Alignment::add ( SeqPtr  sequence )

inline

Definition at line 28 of file ali.h.

Referenced by read_alignment().

void Alignment::add ( const char *  name, const char *  sequence, size_t  seq_len  )

inline

Definition at line 29 of file ali.h.

References add().

Referenced by add().

void Alignment::add ( const char *  name, const char *  sequence  )

inline

Definition at line 30 of file ali.h.

References add().

Referenced by add().

const char* Alignment::get_name ( ) const

inline

Definition at line 919 of file insdel.cxx.

Referenced by AliInsertCommand::check_applicable_to(), AliDeleteCommand::check_applicable_to(), and AliCompositeCommand::check_applicable_to().

size_t Alignment::get_len ( ) const

inline

Definition at line 920 of file insdel.cxx.

Referenced by get_max_len().

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The documentation for this class was generated from the following files:

• CONVERTALN/ali.h
• SL/INSDEL/insdel.cxx