probe_tree.h File Reference

#include <bits/wordsize.h>
#include <static_assert.h>
#include "probe.h"

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Classes
struct	pt_global
struct	POS_TREE1
struct	POS_TREE2
struct	PT_short_chain_header
struct	PT_long_chain_header
class	AbsLoc
class	DataLoc
class	ReadableDataLoc
class	ChainIteratorStage1
struct	ChainIteratorStage1::_U::_S
struct	ChainIteratorStage1::_U::_L
class	ChainIteratorStage2

Macros
#define	PT_CHAIN_NTERM   250
#define	PT_SHORT_SIZE   0xffff
#define	PT_INIT_CHAIN_SIZE   20
#define	IS_SINGLE_BRANCH_NODE   0x40
#define	LONG_SONS   0x80
#define	PT1_BASE_SIZE   sizeof(POS_TREE1)
#define	PT1_EMPTY_LEAF_SIZE   (PT1_BASE_SIZE+6)
#define	PT1_LEAF_SIZE(leaf)   (PT1_BASE_SIZE+6+2*PT_GLOBAL.count_bits[3][(leaf)->flags])
#define	PT1_CHAIN_SHORT_HEAD_SIZE   (PT1_BASE_SIZE+2+sizeof(PT_PNTR))
#define	PT1_CHAIN_LONG_HEAD_SIZE   (PT1_CHAIN_SHORT_HEAD_SIZE+2)
#define	PT1_EMPTY_NODE_SIZE   PT1_BASE_SIZE
#define	PT1_MIN_CHAIN_ENTRY_SIZE   (sizeof(PT_PNTR)+3*sizeof(char))
#define	PT1_MAX_CHAIN_ENTRY_SIZE   (sizeof(PT_PNTR)+3*(sizeof(int)+1))
#define	PT1_NODE_WITHSONS_SIZE(sons)   (PT1_EMPTY_NODE_SIZE+sizeof(PT_PNTR)*(sons))
#define	PT_NODE_SON_COUNT(node)   (PT_GLOBAL.count_bits[PT_BASES][node->flags])
#define	PT1_NODE_SIZE(node)   PT1_NODE_WITHSONS_SIZE(PT_NODE_SON_COUNT(node))
#define	FLAG_TYPE_BITS   2
#define	FLAG_FREE_BITS   (8-FLAG_TYPE_BITS)
#define	FLAG_FREE_BITS_MASK   ((1<<FLAG_TYPE_BITS)-1)
#define	FLAG_TYPE_BITS_MASK   (0xFF^FLAG_FREE_BITS_MASK)
#define	SHORT_CHAIN_HEADER_ELEMS   3
#define	SHORT_CHAIN_HEADER_FLAG_BIT   (1<<4)
#define	SHORT_CHAIN_HEADER_SIZE_MASK   0x07

Typedefs
typedef PT1_TYPE	TYPE

Enumerations
enum	PT1_TYPE {   PT1_LEAF = 0, PT1_CHAIN = 1, PT1_NODE = 2, PT1_SAVED = 3,   PT1_UNDEF = 4 }
enum	PT2_TYPE { PT2_LEAF = PT1_LEAF, PT2_CHAIN = PT1_CHAIN, PT2_NODE = PT1_NODE }

Functions
struct POS_TREE1	__attribute__ ((packed))
static void	init_static ()
const char *	udata () const
POS_TREE1 *	get_father () const
void	set_father (POS_TREE1 *new_father)
void	clear_fathers ()
void	set_type (TYPE type)
TYPE	get_type () const
bool	is_node () const
bool	is_leaf () const
bool	is_chain () const
bool	is_saved () const
	STATIC_ASSERT (SHORT_CHAIN_HEADER_SIZE_MASK >=SHORT_CHAIN_HEADER_ELEMS)
	STATIC_ASSERT ((SHORT_CHAIN_HEADER_SIZE_MASK &SHORT_CHAIN_HEADER_FLAG_BIT)==0)
	STATIC_ASSERT (sizeof(PT_long_chain_header) >=sizeof(PT_short_chain_header))
	STATIC_ASSERT ((sizeof(PT_short_chain_header)/SHORT_CHAIN_HEADER_ELEMS *(SHORT_CHAIN_HEADER_ELEMS+1)) > sizeof(PT_long_chain_header))
size_t	PT_node_size (POS_TREE2 *node)
template<typename PT >
PT *	PT_read_son (PT *node, PT_base base)
template<>
POS_TREE2 *	PT_read_son< POS_TREE2 > (POS_TREE2 *node, PT_base base)
template<>
POS_TREE1 *	PT_read_son< POS_TREE1 > (POS_TREE1 *node, PT_base base)
size_t	PT_leaf_size (POS_TREE2 *node)
bool	operator== (const AbsLoc &loc1, const AbsLoc &loc2)
const char *	PT_READ_CHAIN_ENTRY_stage_2 (const char *ptr, int refabspos, AbsLoc &loc)
char *	PT_WRITE_CHAIN_ENTRY (char *ptr, int refabspos, int name, const int apos)
template<typename PT , typename T >
int	PT_forwhole_chain (PT *node, T &func)
template<typename T >
int	PT_forwhole_chain (POS_TREE1 *node, T &func)
template<typename T >
int	PT_forwhole_chain (POS_TREE2 *node, T &func)

Variables
pt_global	PT_GLOBAL
uchar	flags
POS_TREE1 *	father
static TYPE	flag_2_type [256]
struct PT_short_chain_header	__attribute__

Macro Definition Documentation

#define PT_CHAIN_NTERM   250

Definition at line 27 of file probe_tree.h.

#define PT_SHORT_SIZE   0xffff

Definition at line 28 of file probe_tree.h.

Referenced by PT_create_leaf().

#define PT_INIT_CHAIN_SIZE   20

Definition at line 29 of file probe_tree.h.

#define IS_SINGLE_BRANCH_NODE   0x40

Definition at line 150 of file probe_tree.h.

Referenced by PT_node_size(), and PT_read_son< POS_TREE2 >().

#define LONG_SONS   0x80

Definition at line 155 of file probe_tree.h.

Referenced by PT_node_size(), and PT_read_son< POS_TREE2 >().

#define PT1_BASE_SIZE   sizeof(POS_TREE1)

Definition at line 161 of file probe_tree.h.

Referenced by PTD_set_object_to_saved_status().

#define PT1_EMPTY_LEAF_SIZE   (PT1_BASE_SIZE+6)

Definition at line 163 of file probe_tree.h.

Referenced by PT_create_leaf().

#define PT1_LEAF_SIZE

(

leaf

)

(PT1_BASE_SIZE+6+2*PT_GLOBAL.count_bits[3][(leaf)->flags])

Definition at line 164 of file probe_tree.h.

Referenced by PT_change_leaf_to_node(), PT_leaf_to_chain(), and PTD_write_tip_to_disk().

#define PT1_CHAIN_SHORT_HEAD_SIZE   (PT1_BASE_SIZE+2+sizeof(PT_PNTR))

Definition at line 165 of file probe_tree.h.

#define PT1_CHAIN_LONG_HEAD_SIZE   (PT1_CHAIN_SHORT_HEAD_SIZE+2)

Definition at line 166 of file probe_tree.h.

#define PT1_EMPTY_NODE_SIZE   PT1_BASE_SIZE

Definition at line 167 of file probe_tree.h.

Referenced by PT_change_leaf_to_node(), and PTD_write_node_to_disk().

#define PT1_MIN_CHAIN_ENTRY_SIZE   (sizeof(PT_PNTR)+3*sizeof(char))

Definition at line 169 of file probe_tree.h.

#define PT1_MAX_CHAIN_ENTRY_SIZE   (sizeof(PT_PNTR)+3*(sizeof(int)+1))

Definition at line 170 of file probe_tree.h.

#define PT1_NODE_WITHSONS_SIZE

(

sons

)

(PT1_EMPTY_NODE_SIZE+sizeof(PT_PNTR)*(sons))

Definition at line 172 of file probe_tree.h.

#define PT_NODE_SON_COUNT

(

node

)

(PT_GLOBAL.count_bits[PT_BASES][node->flags])

Definition at line 174 of file probe_tree.h.

#define PT1_NODE_SIZE

(

node

)

PT1_NODE_WITHSONS_SIZE(PT_NODE_SON_COUNT(node))

Definition at line 175 of file probe_tree.h.

Referenced by PT_create_leaf().

#define FLAG_TYPE_BITS   2

Definition at line 180 of file probe_tree.h.

#define FLAG_FREE_BITS   (8-FLAG_TYPE_BITS)

Definition at line 181 of file probe_tree.h.

Referenced by PT_create_leaf(), POS_TREE1::set_type(), and POS_TREE2::set_type().

#define FLAG_FREE_BITS_MASK   ((1<<FLAG_TYPE_BITS)-1)

Definition at line 182 of file probe_tree.h.

#define FLAG_TYPE_BITS_MASK   (0xFF^FLAG_FREE_BITS_MASK)

Definition at line 183 of file probe_tree.h.

#define SHORT_CHAIN_HEADER_ELEMS   3

Definition at line 257 of file probe_tree.h.

Referenced by PT_add_to_chain(), and ChainIteratorStage1::_U::_S::set_loc().

#define SHORT_CHAIN_HEADER_FLAG_BIT   (1<<4)

Definition at line 260 of file probe_tree.h.

Referenced by ChainIteratorStage1::ChainIteratorStage1(), PT_add_to_chain(), PT_leaf_to_chain(), and PTD_write_chain_to_disk().

#define SHORT_CHAIN_HEADER_SIZE_MASK   0x07

Definition at line 261 of file probe_tree.h.

Referenced by ChainIteratorStage1::ChainIteratorStage1(), PT_add_to_chain(), and PT_leaf_to_chain().

Typedef Documentation

typedef PT2_TYPE TYPE

Definition at line 41 of file probe_tree.h.

Enumeration Type Documentation

enum PT1_TYPE

Enumerator
PT1_LEAF
PT1_CHAIN
PT1_NODE
PT1_SAVED
PT1_UNDEF

Definition at line 185 of file probe_tree.h.

enum PT2_TYPE

Enumerator
PT2_LEAF
PT2_CHAIN
PT2_NODE

Definition at line 193 of file probe_tree.h.

Function Documentation

struct POS_TREE1 __attribute__

(

(packed)

)

static void init_static ( )

static

char * udata

(

)

const

Definition at line 46 of file probe_tree.h.

POS_TREE1* __attribute__::get_father

(

)

const

Definition at line 49 of file probe_tree.h.

Referenced by TreeNode::ancestor_common_with(), TreeNode::find_parent_with_groupInfo(), TreeNode::get_brother(), AP_tree::is_folded_group(), TreeNode::is_inside(), AP_tree::is_inside_folded_group(), TreeNode::is_leftson(), TreeNode::is_rightson(), AP_tree::move_group_to(), AP_tree::moveNextTo(), FINAL_TYPE< SEQTYPE >::recalc_marked_from_sons_and_forward_upwards(), AP_tree::recompute_and_write_folding(), ARB_countedTree::relative_position_in(), AP_tree::REMOVE(), AP_tree::set_angle(), TreeNode::set_root(), TreeNode::swap_node_info(), and FINAL_TYPE< SEQTYPE >::tag_leaf().

void __attribute__::set_father

(

POS_TREE1 *

new_father

)

Definition at line 53 of file probe_tree.h.

void __attribute__::clear_fathers

(

)

void set_type

(

TYPE

type

)

Definition at line 59 of file probe_tree.h.

Referenced by ED4_block::autocorrect_type(), and ED4_block::toggle_type().

TYPE get_type

(

)

const

Definition at line 64 of file probe_tree.h.

Referenced by FINAL_TYPE< SEQTYPE >::firstListMember(), SaiOperator::get_description(), FINAL_TYPE< SEQTYPE >::get_enumeration(), FINAL_TYPE< SEQTYPE >::get_first_field(), FINAL_TYPE< SEQTYPE >::get_name(), ParentGroupNameQueryKey::get_name(), Parameter::get_TypeClass(), FINAL_TYPE< SEQTYPE >::is_itemlist_member(), FINAL_TYPE< SEQTYPE >::ItemQueryKey(), FINAL_TYPE< SEQTYPE >::iterate(), ParentGroupNameQueryKey::iterate(), FINAL_TYPE< SEQTYPE >::nextListMemberAfter(), SelectedDatabase::open_db_for_merge(), and FINAL_TYPE< SEQTYPE >::readable_type().

bool is_node

(

)

const

Definition at line 66 of file probe_tree.h.

bool is_leaf

(

)

const

Definition at line 67 of file probe_tree.h.

Referenced by AP_tree_edge::nni_rec(), FINAL_TYPE< SEQTYPE >::tag_leaf(), and NodeTextBuilder::work().

bool is_chain

(

)

const

Definition at line 68 of file probe_tree.h.

bool __attribute__::is_saved

(

)

const

Definition at line 69 of file probe_tree.h.

STATIC_ASSERT

(

SHORT_CHAIN_HEADER_SIZE_MASK >=

SHORT_CHAIN_HEADER_ELEMS

)

STATIC_ASSERT

(

(SHORT_CHAIN_HEADER_SIZE_MASK &SHORT_CHAIN_HEADER_FLAG_BIT)

= =0

)

STATIC_ASSERT

(

sizeof(PT_long_chain_header) >=sizeof(PT_short_chain_header)

)

STATIC_ASSERT	(	(sizeof(PT_short_chain_header)/SHORT_CHAIN_HEADER_ELEMS *(SHORT_CHAIN_HEADER_ELEMS+1))	,
		sizeof(PT_long_chain_header)
	)

size_t PT_node_size ( POS_TREE2 *  node )

inline

Definition at line 283 of file probe_tree.h.

References pt_global::count_bits, POS_TREE2::flags, IS_SINGLE_BRANCH_NODE, LONG_SONS, PT_BASES, and POS_TREE2::udata().

Referenced by PT_statistic::analyse().

template<typename PT >

PT* PT_read_son ( PT *  node, PT_base  base  )

inline

Referenced by MatchRequest::add_hits_for_children(), all_sons_saved(), PT_statistic::analyse(), build_pos_tree(), POS_TREE1::clear_fathers(), MatchRequest::collect_hits_for(), count_mishits_for_all(), count_mishits_for_matched(), findLeftmostProbe(), findNextProbe(), PT_Traversal::mark_matching(), PT_dump_POS_TREE(), PTD_write_leafs_to_disk(), PTD_write_node_to_disk(), and save_lower_subtree().

template<>

POS_TREE2* PT_read_son< POS_TREE2 > ( POS_TREE2 *  node, PT_base  base  )

inline

Definition at line 314 of file probe_tree.h.

References pt_global::count_bits, GBK_terminate(), IS_SINGLE_BRANCH_NODE, LONG_SONS, NULp, offset, pt_assert, pt_assert_stage, PT_read_char(), PT_read_int(), PT_read_short(), and STAGE2.

template<>

POS_TREE1* PT_read_son< POS_TREE1 > ( POS_TREE1 *  node, PT_base  base  )

inline

Definition at line 401 of file probe_tree.h.

References pt_global::count_bits, NULp, pt_assert_stage, and STAGE1.

size_t PT_leaf_size ( POS_TREE2 *  node )

inline

Definition at line 408 of file probe_tree.h.

References pt_global::count_bits, POS_TREE2::flags, and PT_BASES.

Referenced by PT_statistic::analyse().

bool operator== ( const AbsLoc &  loc1, const AbsLoc &  loc2  )

inline

Definition at line 489 of file probe_tree.h.

References AbsLoc::is_equal().

const char* PT_READ_CHAIN_ENTRY_stage_2 ( const char *  ptr, int  refabspos, AbsLoc &  loc  )

inline

Definition at line 529 of file probe_tree.h.

References AbsLoc::get_name(), pt_assert_stage, PT_read_compact_nat(), and STAGE2.

char* PT_WRITE_CHAIN_ENTRY ( char *  ptr, int  refabspos, int  name, const int  apos  )

inline

Definition at line 542 of file probe_tree.h.

References pt_assert_stage, PT_write_compact_nat(), and STAGE1.

template<typename PT , typename T >

int PT_forwhole_chain	(	PT *	node,
		T &	func
	)

Referenced by count_mishits_for_all(), count_mishits_for_matched(), PT_dump_POS_TREE(), and PT_dump_POS_TREE_recursive().

template<typename T >

int PT_forwhole_chain	(	POS_TREE1 *	node,
		T &	func
	)

Definition at line 693 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE1.

template<typename T >

int PT_forwhole_chain	(	POS_TREE2 *	node,
		T &	func
	)

Definition at line 702 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE2.

Variable Documentation

pt_global PT_GLOBAL

Definition at line 22 of file PT_prefixtree.cxx.

Referenced by probe_struct_global::enter_stage(), and PT_change_link_in_father().

uchar flags

Definition at line 38 of file probe_tree.h.

Referenced by AWT_graphic_tree::check_for_DB_update(), ED4_calc_terminal_extentions(), find_sub_by_quark(), find_sub_sub_by_quark(), GB_clear_user_flag(), gb_commit_transaction_local_rek(), gb_find_by_nr(), GB_number_of_marked_subentries(), GB_number_of_subentries(), GB_raise_user_flag(), GB_read_flag(), gb_search_marked(), gb_unfold(), gb_untouch_children(), gb_write_bin_sub_containers(), GB_write_flag(), gbcm_read_bin(), probe_match_event(), PTD_write_node_to_disk(), and write_GBDATA().

POS_TREE1* father

Definition at line 39 of file probe_tree.h.

Referenced by aisc_link(), aisc_talking_copy(), aisc_talking_create(), aisc_talking_find(), aisc_unlink(), aw_create_shell(), dump_internal(), gb_read_bin(), GB_resort_data_base(), gb_unlink_entry(), gbcmc_sendupdate_create(), gbcmc_sendupdate_update(), GBDATA::get_father(), get_upgroup(), insert_species_into_tree(), left_neighbour_leaf(), NodeState::move_info_to(), neighbourjoining(), nt_add_partial(), PT_change_leaf_to_node(), PT_create_leaf(), PT_leaf_to_chain(), and FINAL_TYPE< SEQTYPE >::recalc_marked_from_sons_and_forward_upwards().

static TYPE flag_2_type

static

Definition at line 43 of file probe_tree.h.

struct POS_TREE2 __attribute__