#include <list>#include <set>#include <arbdb.h>#include <PT_com.h>#include <PT_server.h>#include "PT_tools.h"#include <cache.h>
Go to the source code of this file.
Classes | |
| class | probe_input_data |
| struct | probe_statistic_struct |
| class | MostUsedPos |
| class | probe_struct_global |
| class | gene_struct |
| struct | ltByArbName |
| struct | ltByInternalName |
Macros | |
| #define | PT_SERVER_MAGIC 0x32108765 |
| #define | PT_SERVER_VERSION 3 |
| #define | CALCULATE_STATS_ON_QUERY |
| #define | pt_assert_stage(s) |
| #define | pt_assert_valid_chain_stage1(node) |
| #define | PT_MAX_PARTITION_DEPTH 4 |
| #define | PT_POS_TREE_HEIGHT 20 |
| #define | PT_MIN_TREE_HEIGHT PT_MAX_PARTITION_DEPTH |
| #define | MIN_PROBE_LENGTH 2 |
| #define | MATCHANSWER 50 |
| #define | CREATEANSWER 51 |
| #define | FINDANSWER 52 |
Typedefs | |
| typedef unsigned long | ULONG |
| typedef unsigned int | UINT |
| typedef unsigned char | uchar |
| typedef std::list< gene_struct > | gene_struct_list |
| typedef std::set< const gene_struct *, ltByInternalName > | gene_struct_index_internal |
| typedef std::set< const gene_struct *, ltByArbName > | gene_struct_index_arb |
Enumerations | |
| enum | PT_MATCH_TYPE { PT_MATCH_TYPE_INTEGER = 0, PT_MATCH_TYPE_WEIGHTED_PLUS_POS = 1, PT_MATCH_TYPE_WEIGHTED = -1 } |
| enum | type_types { t_int = 1, t_string = 0, t_float = 2 } |
| enum | PT_base { PT_QU = 0, PT_N = 1, PT_A, PT_C, PT_G, PT_T, PT_BASES, PT_B_UNDEF } |
| enum | Stage { STAGE1, STAGE2 } |
Functions | |
| CONSTEXPR_INLINE bool | is_std_base (char b) |
| CONSTEXPR_INLINE bool | is_std_base_or_N (char b) |
| CONSTEXPR_INLINE bool | is_ambig_base (char b) |
| CONSTEXPR_INLINE bool | is_valid_base (char b) |
| CONSTEXPR_INLINE char | base_2_readable (char base) |
| char * | probe_2_readable (char *id_string, int len) |
| void | reverse_probe (char *seq, int len) |
Variables | |
| int | gene_flag |
| probe_struct_global | psg |
| gene_struct_index_arb | gene_struct_arb2internal |
| gene_struct_index_internal | gene_struct_internal2arb |
Macro Definition Documentation
| #define PT_SERVER_MAGIC 0x32108765 |
Definition at line 27 of file probe.h.
Referenced by enter_stage_1_build_tree(), and PTD_read_leafs_from_disk().
| #define PT_SERVER_VERSION 3 |
Definition at line 28 of file probe.h.
Referenced by enter_stage_1_build_tree(), PTD_read_leafs_from_disk(), and start_pt_server().
| #define pt_assert_stage | ( | s | ) |
Definition at line 41 of file probe.h.
Referenced by ChainIteratorStage1::ChainIteratorStage1(), ChainIteratorStage2::ChainIteratorStage2(), PT_add_to_chain(), PT_change_leaf_to_node(), PT_change_link_in_father(), PT_create_leaf(), PT_forwhole_chain(), PT_leaf_to_chain(), PT_READ_CHAIN_ENTRY_stage_2(), PT_read_son< POS_TREE1 >(), PT_read_son< POS_TREE2 >(), PT_WRITE_CHAIN_ENTRY(), PTD_read_leafs_from_disk(), PTD_set_object_to_saved_status(), PTD_write_leafs_to_disk(), PTD_write_node_to_disk(), and write_subtree().
| #define pt_assert_valid_chain_stage1 | ( | node | ) |
Definition at line 47 of file probe.h.
Referenced by PTD_write_chain_to_disk().
| #define PT_MAX_PARTITION_DEPTH 4 |
Definition at line 54 of file probe.h.
Referenced by decide_passes_to_use().
| #define PT_POS_TREE_HEIGHT 20 |
Definition at line 56 of file probe.h.
Referenced by build_pos_tree().
| #define PT_MIN_TREE_HEIGHT PT_MAX_PARTITION_DEPTH |
Definition at line 57 of file probe.h.
Referenced by build_pos_tree(), and save_lower_subtree().
| #define MIN_PROBE_LENGTH 2 |
Definition at line 59 of file probe.h.
Referenced by probe_match().
Typedef Documentation
| typedef std::list<gene_struct> gene_struct_list |
| typedef std::set<const gene_struct *, ltByInternalName> gene_struct_index_internal |
| typedef std::set<const gene_struct *, ltByArbName> gene_struct_index_arb |
Enumeration Type Documentation
| enum PT_MATCH_TYPE |
| enum type_types |
| enum PT_base |
Function Documentation
| CONSTEXPR_INLINE bool is_std_base | ( | char | b | ) |
Definition at line 93 of file probe.h.
Referenced by Splits::check(), contains_ambiguities(), findNextProbe(), get_bond_val(), get_match_overlay(), MaxBond::get_max_bond(), and MaxBond::MaxBond().
| CONSTEXPR_INLINE bool is_std_base_or_N | ( | char | b | ) |
Definition at line 94 of file probe.h.
Referenced by MatchingOligo::bind_against().
| CONSTEXPR_INLINE bool is_ambig_base | ( | char | b | ) |
Definition at line 95 of file probe.h.
Referenced by Mismatches::count_weighted().
| CONSTEXPR_INLINE bool is_valid_base | ( | char | b | ) |
Definition at line 96 of file probe.h.
References PT_BASES, and PT_QU.
Referenced by MismatchWeights::get().
| CONSTEXPR_INLINE char base_2_readable | ( | char | base | ) |
Definition at line 98 of file probe.h.
References PT_BASES, and safeCharIndex().
Referenced by get_match_overlay(), probe_2_readable(), and PT_dump_POS_TREE_recursive().
translate a string containing PT_base into readable characters.
Definition at line 102 of file probe.h.
References base_2_readable().
Referenced by get_design_info(), and get_match_hinfo_formatted().
Definition at line 112 of file probe.h.
References swap().
Referenced by create_reversed_probe(), and find_family().
Variable Documentation
| int gene_flag |
Definition at line 39 of file PT_main.cxx.
Referenced by detect_format_props(), get_match_hinfo_formatted(), match_string(), probe_match_event(), PT_start_design(), ptpd_read_names(), virt_fullname(), and virt_name().
Definition at line 36 of file PT_main.cxx.
Referenced by MatchRequest::add_hit(), broadcast(), FamilyStat::calc_rel_matches(), OutgroupMatcher::calculate_outgroup_matches(), count_mishits_for_all(), Mismatches::count_weighted(), detect_format_props(), PT_statistic::dump(), enter_stage_1_build_tree(), enter_stage_2_load_tree(), find_family(), findLeftmostProbe(), gene_rel_2_abs(), DesignTargets::generate(), get_match_acc(), get_match_overlay(), get_match_start(), get_match_stop(), AbsLoc::get_pid(), AbsLoc::has_valid_name(), make_PT_family_list(), MP_all_species_string(), MP_count_all_species(), ptnd_chain_count_mishits::operator()(), probe_match(), probe_read_data_base(), PT_abs_2_ecoli_rel(), pt_build_pos_to_weight(), PT_build_species_hash(), PT_dump_POS_TREE_to_file(), PT_dump_tree_statistics(), PT_exit_psg(), PT_find_exProb(), PT_init_cache_sizes(), PT_init_input_data(), pt_init_main_struct(), PT_init_map(), PT_init_psg(), pt_sort_compare_match(), pt_sort_match_list(), PTD_read_leafs_from_disk(), PTD_write_node_to_disk(), ptpd_read_names(), remove_tprobes_with_too_many_mishits(), run_command(), server_shutdown(), start_pt_server(), virt_fullname(), and virt_name().
| gene_struct_index_arb gene_struct_arb2internal |
Definition at line 46 of file PT_main.cxx.
Referenced by get_gene_struct_by_arb_species_gene_name(), and PT_init_map().
| gene_struct_index_internal gene_struct_internal2arb |
Definition at line 47 of file PT_main.cxx.
Referenced by get_gene_struct_by_internal_gene_name(), and PT_init_map().
