Public Member Functions | Static Public Member Functions | List of all members
BaseFrequencies Class Reference

#include <chartable.h>

Inheritance diagram for BaseFrequencies:
Inheritance graph
Collaboration diagram for BaseFrequencies:
Collaboration graph

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 PosRangechanged_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
charbuild_consensus_string (PosRange r, const ConsensusBuildParams &cbp) const
charbuild_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 PosRangechanged_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_ 
void BaseFrequencies::ignore_me ( )

Definition at line 238 of file chartable.h.

Referenced by EDB_root_bact::fill_data().

int BaseFrequencies::is_ignored ( ) const

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
int BaseFrequencies::added_sequences ( ) const

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)

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

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 
void BaseFrequencies::add ( const char string,
int  len 
void BaseFrequencies::sub ( const char string,
int  len 
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
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

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().

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