BaseFrequencies Class Reference

#include <chartable.h>

Inheritance diagram for BaseFrequencies:

Collaboration diagram for BaseFrequencies:

Public Member Functions
bool	ok () const
bool	empty () const
	BaseFrequencies (int maxseqlength=0)
	~BaseFrequencies ()
void	ignore_me ()
int	is_ignored () const
void	init (int maxseqlength)
int	size () const
int	added_sequences () const
void	bases_and_gaps_at (int column, int *bases, int *gaps) const
double	max_frequency_at (int column, bool ignore_gaps) const
const PosRange *	changed_range (const BaseFrequencies &other) const
void	add (const BaseFrequencies &other)
void	sub (const BaseFrequencies &other)
void	sub_and_add (const BaseFrequencies &Sub, const BaseFrequencies &Add, PosRange range)
void	add (const char *string, int len)
void	sub (const char *string, int len)
void	sub_and_add (const char *old_string, const char *new_string, PosRange range)
void	build_consensus_string_to (char *consensus_string, ExplicitRange range, const ConsensusBuildParams &BK) const
char *	build_consensus_string (PosRange r, const ConsensusBuildParams &cbp) const
char *	build_consensus_string (const ConsensusBuildParams &cbp) const
void	change_table_length (int new_length)

Static Public Member Functions
static void	setup (const char *gap_chars, GB_alignment_type ali_type_)
static bool	isGap (char c)
static const PosRange *	changed_range (const char *string1, const char *string2, int min_len)

Detailed Description

Definition at line 162 of file chartable.h.

Constructor & Destructor Documentation

BaseFrequencies::BaseFrequencies

(

int

maxseqlength = 0

)

Definition at line 715 of file chartable.cxx.

References ct_assert.

BaseFrequencies::~BaseFrequencies

(

)

Definition at line 812 of file chartable.cxx.

Member Function Documentation

bool BaseFrequencies::ok

(

)

const

Definition at line 1148 of file chartable.cxx.

References added_sequences(), bases_and_gaps_at(), empty(), is_ignored(), NULp, and size().

Referenced by ED4_root::create_hierarchy().

bool BaseFrequencies::empty

(

)

const

Definition at line 1138 of file chartable.cxx.

Referenced by ED4_manager::create_consensus(), and ok().

void BaseFrequencies::setup ( const char *  gap_chars, GB_alignment_type  ali_type_  )

static

Definition at line 604 of file chartable.cxx.

References ct_assert, iupac::decode(), GB_AT_AA, GB_AT_DNA, GB_AT_RNA, getAAgroupDefinition(), chartable::Ambiguity::increment, chartable::Ambiguity::index, chartable::Ambiguity::indices, initialized, is_gap(), MAX_AMBIGUITY_CODES, MAX_INDEX_TABLES, MAX_TARGET_INDICES, MAX_USED_BASES_TABLES, MAXCHARTABLE, NULp, and safeCharIndex().

Referenced by CON_calc_max_freq(), CON_calculate(), and ED4_setup_gaps_and_alitype().

void BaseFrequencies::ignore_me ( )

inline

Definition at line 238 of file chartable.h.

Referenced by EDB_root_bact::fill_data().

int BaseFrequencies::is_ignored ( ) const

inline

Definition at line 239 of file chartable.h.

Referenced by ED4_manager::create_consensus(), and ok().

void BaseFrequencies::init

(

int

maxseqlength

)

Definition at line 729 of file chartable.cxx.

References chartable::SepBaseFreq::init().

Referenced by ED4_manager::create_consensus().

int BaseFrequencies::size ( ) const

inline

Definition at line 242 of file chartable.h.

References chartable::SepBaseFreq::size().

Referenced by add(), changed_range(), ED4_remap::compile(), ED4_consensus_sequence_terminal::get_length(), ok(), and sub().

int BaseFrequencies::added_sequences ( ) const

inline

Definition at line 243 of file chartable.h.

Referenced by add(), ED4_remap::compile(), CON_insertSequences(), and ok().

void BaseFrequencies::bases_and_gaps_at	(	int	column,
		int *	bases,
		int *	gaps
	)		const

Definition at line 738 of file chartable.cxx.

References column, ct_assert, and isGap().

Referenced by ED4_remap::compile(), and ok().

double BaseFrequencies::max_frequency_at	(	int	column,
		bool	ignore_gaps
	)		const

Definition at line 763 of file chartable.cxx.

References column, ct_assert, GB_AT_AA, isGap(), and max.

Referenced by CON_calc_max_freq().

static bool BaseFrequencies::isGap ( char  c )

inlinestatic

Definition at line 248 of file chartable.h.

References safeCharIndex().

Referenced by bases_and_gaps_at(), ED4_is_gap_character(), and max_frequency_at().

const PosRange * BaseFrequencies::changed_range

(

const BaseFrequencies &

other

)

const

Definition at line 821 of file chartable.cxx.

References ct_assert, chartable::SepBaseFreq::firstDifference(), chartable::SepBaseFreq::lastDifference(), NULp, size(), and start.

Referenced by ED4_manager::update_bases(), and ED4_manager::update_bases_and_rebuild_consensi().

const PosRange * BaseFrequencies::changed_range ( const char *  string1, const char *  string2, int  min_len  )

static

Definition at line 915 of file chartable.cxx.

References ct_assert, and NULp.

void BaseFrequencies::add

(

const BaseFrequencies &

other

)

Definition at line 853 of file chartable.cxx.

References added_sequences(), and size().

void BaseFrequencies::sub

(

const BaseFrequencies &

other

)

Definition at line 877 of file chartable.cxx.

References size().

void BaseFrequencies::sub_and_add	(	const BaseFrequencies &	Sub,
		const BaseFrequencies &	Add,
		PosRange	range
	)

Definition at line 899 of file chartable.cxx.

References ct_assert, PosRange::is_part(), and chartable::SepBaseFreq::sub_and_add().

void BaseFrequencies::add	(	const char *	string,
		int	len
	)

Definition at line 1020 of file chartable.cxx.

References chartable::SepBaseFreq::inc_long(), chartable::SepBaseFreq::inc_short(), SHORT_TABLE_ELEM_SIZE, and size().

void BaseFrequencies::sub	(	const char *	string,
		int	len
	)

Definition at line 1056 of file chartable.cxx.

References chartable::SepBaseFreq::dec_long(), chartable::SepBaseFreq::dec_short(), SHORT_TABLE_ELEM_SIZE, and size().

void BaseFrequencies::sub_and_add	(	const char *	old_string,
		const char *	new_string,
		PosRange	range
	)

Definition at line 1090 of file chartable.cxx.

References ct_assert, PosRange::end(), SHORT_TABLE_ELEM_SIZE, and PosRange::start().

void BaseFrequencies::build_consensus_string_to	(	char *	consensus_string,
		ExplicitRange	range,
		const ConsensusBuildParams &	BK
	)		const

Definition at line 386 of file chartable.cxx.

References iupac::AA_GROUP_COUNT, ConsensusBuildParams::considbound, ConsensusBuildParams::countgaps, ct_assert, DUMPINT, iupac::encode(), PosRange::end(), ConsensusBuildParams::gapbound, GB_AT_AA, GB_AT_DNA, GB_AT_RNA, iupac::get_amino_consensus_char(), iupac::get_amino_group_for(), ConsensusBuildParams::group, isGap(), ConsensusBuildParams::lower, MAX_BASES_TABLES, PERCENT, PosRange::start(), and ConsensusBuildParams::upper.

char * BaseFrequencies::build_consensus_string	(	PosRange	r,
		const ConsensusBuildParams &	cbp
	)		const

Definition at line 370 of file chartable.cxx.

References PosRange::size().

Referenced by CON_calculate().

char* BaseFrequencies::build_consensus_string ( const ConsensusBuildParams &  cbp ) const

inline

Definition at line 263 of file chartable.h.

References build_consensus_string(), and PosRange::whole().

Referenced by build_consensus_string().

void BaseFrequencies::change_table_length

(

int

new_length

)

Definition at line 1126 of file chartable.cxx.

References chartable::SepBaseFreq::change_table_length().

Referenced by change_char_table_length().

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

• SL/CONSENSUS/chartable.h
• SL/CONSENSUS/chartable.cxx