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Public Member Functions | List of all members
AP_filter Class Reference

#include <AP_filter.hxx>

Public Member Functions

 AP_filter (size_t size)
 
 AP_filter (const char *filter, const char *zerobases, size_t size)
 
 AP_filter (const AP_filter &other)
 
 AP_filter (AF_Not, const AP_filter &other)
 
 AP_filter (const AP_filter &f1, AF_Combine comb, const AP_filter &f2)
 
 ~AP_filter ()
 
 DECLARE_ASSIGNMENT_OPERATOR (AP_filter)
 
long get_timestamp () const
 
size_t get_filtered_length () const
 
size_t get_length () const
 
bool use_position (size_t pos) const
 
const size_t * get_filterpos_2_seqpos () const
 
void enable_simplify (AWT_FILTER_SIMPLIFY type)
 
const ucharget_simplify_table () const
 
void enable_bootstrap ()
 
bool does_bootstrap () const
 
size_t bootstrapped_seqpos (size_t bpos) const
 
charto_string () const
 
charblowup_string (const char *filtered_string, char insert) const
 
charfilter_string (const char *fulllen_string) const
 
GB_ERROR is_invalid () const
 
bool was_checked_for_validity () const
 

Detailed Description

Definition at line 38 of file AP_filter.hxx.

Constructor & Destructor Documentation

AP_filter::AP_filter ( size_t  size)

Definition at line 63 of file AP_filter.cxx.

AP_filter::AP_filter ( const char filter,
const char zerobases,
size_t  size 
)

Definition at line 93 of file AP_filter.cxx.

AP_filter::AP_filter ( const AP_filter other)

Definition at line 67 of file AP_filter.cxx.

AP_filter::AP_filter ( AF_Not  ,
const AP_filter other 
)

Definition at line 102 of file AP_filter.cxx.

References get_length().

AP_filter::AP_filter ( const AP_filter f1,
AF_Combine  comb,
const AP_filter f2 
)

Definition at line 112 of file AP_filter.cxx.

References af_assert, AND, get_length(), OR, and XOR.

AP_filter::~AP_filter ( )

Definition at line 140 of file AP_filter.cxx.

Member Function Documentation

AP_filter::DECLARE_ASSIGNMENT_OPERATOR ( AP_filter  )
long AP_filter::get_timestamp ( ) const
inline

Definition at line 81 of file AP_filter.hxx.

Referenced by AP_rates::init().

size_t AP_filter::get_filtered_length ( ) const
inline
size_t AP_filter::get_length ( ) const
inline
bool AP_filter::use_position ( size_t  pos) const
inline
const size_t* AP_filter::get_filterpos_2_seqpos ( ) const
inline
void AP_filter::enable_simplify ( AWT_FILTER_SIMPLIFY  type)
const uchar* AP_filter::get_simplify_table ( ) const
inline
void AP_filter::enable_bootstrap ( )

Definition at line 206 of file AP_filter.cxx.

References af_assert, and GB_random().

Referenced by di_calculate_matrix().

bool AP_filter::does_bootstrap ( ) const
inline

Definition at line 109 of file AP_filter.hxx.

size_t AP_filter::bootstrapped_seqpos ( size_t  bpos) const
inline

Definition at line 111 of file AP_filter.hxx.

References af_assert, and get_filterpos_2_seqpos().

char * AP_filter::to_string ( ) const

Definition at line 146 of file AP_filter.cxx.

References af_assert.

Referenced by InsertDatainGDE().

char * AP_filter::blowup_string ( const char filtered_string,
char  insert 
) const

blow up 'filtered_string' to unfiltered length by inserting 'fillChar' at filtered positions

Definition at line 222 of file AP_filter.cxx.

References af_assert, and use_position().

Referenced by st_ml_add_quality_string_to_species().

char * AP_filter::filter_string ( const char fulllen_string) const

filter given 'fulllen_string'

Definition at line 239 of file AP_filter.cxx.

References af_assert, and get_filterpos_2_seqpos().

GB_ERROR AP_filter::is_invalid ( ) const
inline

returns error

  • if filter is based on an empty alignment (i.e. no alignment is selected)
  • if all positions are filtered out (i.e. filtered sequences will be empty)

Definition at line 123 of file AP_filter.hxx.

References af_assert, get_filtered_length(), get_length(), and NULp.

Referenced by awt_invalid_filter(), ST_ML::calc_st_ml(), ColumnStat::calculate(), WeightedFilter::create_aliview(), di_autodetect_callback(), SEQIO::export_by_format(), and InsertDatainGDE().

bool AP_filter::was_checked_for_validity ( ) const
inline

Definition at line 140 of file AP_filter.hxx.


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