ARB
Public Member Functions | Public Attributes | Static Public Attributes | List of all members
MostLikelySeq Class Reference

#include <MostLikelySeq.hxx>

Inheritance diagram for MostLikelySeq:
Inheritance graph
[legend]
Collaboration diagram for MostLikelySeq:
Collaboration graph
[legend]

Public Member Functions

 MostLikelySeq (const AliView *aliview, ST_ML *st_ml_)
 
 ~MostLikelySeq () OVERRIDE
 
bool is_up_to_date () const
 
AP_sequencedup () const OVERRIDE
 
GB_ERROR bind_to_species (GBDATA *gb_species)
 
void unbind_from_species (bool remove_callbacks)
 
GBDATAget_bound_species_data () const
 
void sequence_change ()
 
void set_sequence ()
 
void calculate_ancestor (const MostLikelySeq *lefts, double leftl, const MostLikelySeq *rights, double rightl)
 
void forget_sequence ()
 
void calc_out (const MostLikelySeq *sequence_of_brother, double dist)
 
void print ()
 
- Public Member Functions inherited from AP_sequence
 AP_sequence (const AliView *aliview)
 
virtual ~AP_sequence ()
 
GB_ERROR bind_to_species (GBDATA *gb_species)
 
void unbind_from_species ()
 
bool is_bound_to_species () const
 
GBDATAget_bound_species_data () const
 
void lazy_load_sequence () const
 
void ensure_sequence_loaded () const
 
bool hasSequence () const
 
void forget_sequence ()
 
size_t get_sequence_length () const
 
const AP_filterget_filter () const
 
const AP_weightsget_weights () const
 
const AliViewget_aliview () const
 

Public Attributes

ST_ML_Colorcolor_out
 
intcolor_out_valid_till
 

Static Public Attributes

static ST_base_vectortmp_out = NULp
 

Additional Inherited Members

- Protected Member Functions inherited from AP_sequence
void mark_sequence_set (bool is_set)
 
void do_lazy_load () const
 
- Protected Attributes inherited from AP_sequence
AP_FLOAT cached_wbc
 

Detailed Description

Definition at line 39 of file MostLikelySeq.hxx.

Constructor & Destructor Documentation

MostLikelySeq::MostLikelySeq ( const AliView aliview,
ST_ML st_ml_ 
)

Definition at line 160 of file ST_ml.cxx.

Referenced by dup().

MostLikelySeq::~MostLikelySeq ( )

Definition at line 169 of file ST_ml.cxx.

References color_out, color_out_valid_till, and AP_sequence::unbind_from_species().

Member Function Documentation

bool MostLikelySeq::is_up_to_date ( ) const
inline

Definition at line 64 of file MostLikelySeq.hxx.

AP_sequence * MostLikelySeq::dup ( ) const
virtual

Implements AP_sequence.

Definition at line 213 of file ST_ml.cxx.

References AP_sequence::get_aliview(), and MostLikelySeq().

GB_ERROR MostLikelySeq::bind_to_species ( GBDATA gb_species)
void MostLikelySeq::unbind_from_species ( bool  remove_callbacks)
GBDATA* MostLikelySeq::get_bound_species_data ( ) const
inline
void MostLikelySeq::sequence_change ( )

Definition at line 209 of file ST_ml.cxx.

References ST_ML::clear_all().

Referenced by st_sequence_callback().

void MostLikelySeq::set_sequence ( )

Transform the sequence from character to vector for current range [ST_ML::first_pos .. ST_ML::last_pos]

Definition at line 224 of file ST_ml.cxx.

References GB_read_char_pntr(), GB_read_string_count(), get_bound_species_data(), ST_ML::get_first_pos(), ST_ML::get_inv_base_frequencies(), ST_ML::get_last_pos(), min, and st_assert.

void MostLikelySeq::calculate_ancestor ( const MostLikelySeq lefts,
double  leftl,
const MostLikelySeq rights,
double  rightl 
)
void MostLikelySeq::forget_sequence ( )
inline

Definition at line 76 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_ml_vectors().

void MostLikelySeq::calc_out ( const MostLikelySeq sequence_of_brother,
double  dist 
)
void MostLikelySeq::print ( )

Definition at line 305 of file ST_ml.cxx.

References GB_read_char_pntr(), get_bound_species_data(), and ST_MAX_SEQ_PART.

Member Data Documentation

ST_base_vector * MostLikelySeq::tmp_out = NULp
static

contains existing sequence or ancestor sequence as max. likelihood vectors

Definition at line 44 of file MostLikelySeq.hxx.

Referenced by calc_out(), ST_ML::cleanup(), ST_ML::get_color_string(), st_ml_add_sequence_part_to_stat(), and ST_ML::update_ml_likelihood().

ST_ML_Color* MostLikelySeq::color_out

Definition at line 52 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_color_string(), and ~MostLikelySeq().

int* MostLikelySeq::color_out_valid_till

Definition at line 53 of file MostLikelySeq.hxx.

Referenced by ST_ML::get_color_string(), and ~MostLikelySeq().


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