probe_input_data Class Reference

#include <probe.h>

Inheritance diagram for probe_input_data:

Collaboration diagram for probe_input_data:

Public Member Functions
	probe_input_data ()
	~probe_input_data ()
GB_ERROR	init (GBDATA *gb_species_)
SmartCharPtr	get_dataPtr () const
const char *	get_shortname () const
const char *	get_fullname () const
const char *	get_acc () const
int	get_start () const
int	get_stop () const
long	get_checksum () const
int	get_size () const
bool	valid_rel_pos (int rel_pos) const
bool	inside_group () const
bool	outside_group () const
void	set_group_state (bool isGroupMember)
long	get_geneabspos () const
void	preload_rel2abs () const
size_t	get_abspos (size_t rel_pos) const
size_t	calc_relpos (int abs_pos) const

Static Public Member Functions
static void	set_cache_sizes (size_t seq_cache_size, size_t abs_cache_size)

Detailed Description

Definition at line 127 of file probe.h.

Constructor & Destructor Documentation

probe_input_data::probe_input_data ( )

inline

Definition at line 148 of file probe.h.

probe_input_data::~probe_input_data ( )

inline

Definition at line 153 of file probe.h.

References cache::CacheHandle< SMARTPTR >::release().

Member Function Documentation

static void probe_input_data::set_cache_sizes ( size_t  seq_cache_size, size_t  abs_cache_size  )

inlinestatic

Definition at line 158 of file probe.h.

References cache::Cache< SMARTPTR >::resize().

Referenced by PT_init_cache_sizes().

GB_ERROR probe_input_data::init

(

GBDATA *

gb_species_

)

Definition at line 133 of file PT_io.cxx.

References error(), expect_entry(), GB_await_error(), GB_read_count(), and NULp.

Referenced by PT_init_input_data().

SmartCharPtr probe_input_data::get_dataPtr ( ) const

inline

Definition at line 165 of file probe.h.

References cache::CacheHandle< SMARTPTR >::access(), cache::CacheHandle< SMARTPTR >::assign(), and cache::CacheHandle< SMARTPTR >::is_cached().

Referenced by enter_stage_1_build_tree(), findLeftmostProbe(), DesignTargets::generate(), and get_match_overlay().

const char* probe_input_data::get_shortname ( ) const

inline

Definition at line 170 of file probe.h.

References GB_entry(), GB_read_char_pntr(), pt_assert, and ta.

Referenced by make_PT_family_list(), MP_all_species_string(), PT_dump_loc::operator()(), PT_build_species_hash(), virt_fullname(), and virt_name().

const char* probe_input_data::get_fullname ( ) const

inline

Definition at line 177 of file probe.h.

References GB_entry(), GB_read_char_pntr(), and ta.

Referenced by virt_fullname().

const char* probe_input_data::get_acc ( ) const

inline

Definition at line 184 of file probe.h.

References GB_entry(), GB_read_char_pntr(), NULp, pt_assert, and ta.

Referenced by get_match_acc().

int probe_input_data::get_start ( ) const

inline

Definition at line 191 of file probe.h.

References GB_entry(), GB_read_int(), and ta.

Referenced by get_match_start().

int probe_input_data::get_stop ( ) const

inline

Definition at line 197 of file probe.h.

References GB_entry(), GB_read_int(), and ta.

Referenced by get_match_stop().

long probe_input_data::get_checksum ( ) const

inline

Definition at line 204 of file probe.h.

References GB_entry(), GB_read_int(), pt_assert, and ta.

Referenced by ptpd_read_names().

int probe_input_data::get_size ( ) const

inline

Definition at line 211 of file probe.h.

Referenced by FamilyStat::calc_rel_matches(), calc_relpos(), count_mishits_for_matched(), enter_stage_1_build_tree(), findLeftmostProbe(), DesignTargets::generate(), get_match_overlay(), PT_build_species_hash(), and valid_rel_pos().

bool probe_input_data::valid_rel_pos ( int  rel_pos ) const

inline

Definition at line 213 of file probe.h.

References get_size().

Referenced by findLeftmostProbe(), and ReadableDataLoc::operator[]().

bool probe_input_data::inside_group ( ) const

inline

Definition at line 217 of file probe.h.

bool probe_input_data::outside_group ( ) const

inline

Definition at line 218 of file probe.h.

Referenced by count_mishits_for_all(), and ptnd_chain_count_mishits::operator()().

void probe_input_data::set_group_state ( bool  isGroupMember )

inline

Definition at line 220 of file probe.h.

Referenced by ptpd_read_names().

long probe_input_data::get_geneabspos ( ) const

inline

Definition at line 222 of file probe.h.

References GB_entry(), GB_read_int(), and pt_assert.

Referenced by gene_rel_2_abs().

void probe_input_data::preload_rel2abs ( ) const

inline

Definition at line 229 of file probe.h.

References abs, cache::CacheHandle< SMARTPTR >::assign(), GB_entry(), GB_read_ints_pntr(), cache::CacheHandle< SMARTPTR >::is_cached(), pt_assert, and ta.

Referenced by calc_relpos(), and enter_stage_1_build_tree().

size_t probe_input_data::get_abspos ( size_t  rel_pos ) const

inline

Definition at line 249 of file probe.h.

References cache::CacheHandle< SMARTPTR >::access(), cache::CacheHandle< SMARTPTR >::is_cached(), and pt_assert.

Referenced by enter_stage_1_build_tree().

size_t probe_input_data::calc_relpos ( int  abs_pos ) const

inline

Definition at line 254 of file probe.h.

References cache::CacheHandle< SMARTPTR >::access(), get_size(), and preload_rel2abs().

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

• PROBE/probe.h
• PROBE/PT_io.cxx