#include <static_assert.h>#include <arb_assert.h>#include <byteswap.h>
Go to the source code of this file.
Classes | |
| struct | BitMask< B > |
| struct | BitsBelowBit< B > |
| struct | BitsBelowBit< 32 > |
| struct | BitsBelowBit< 31 > |
| struct | BitRange< HB, LB > |
Macros | |
| #define | pt_assert(bed) arb_assert(bed) |
Typedefs | |
| typedef void * | PT_PNTR |
| typedef unsigned char | uint_8 |
| typedef unsigned short | uint_16 |
| typedef unsigned int | uint_32 |
| typedef unsigned long | uint_64 |
| typedef uint_32 | uint_big |
Functions | |
| uint_8 | PT_read_char (const void *fromMem) |
| uint_16 | PT_read_short (const void *fromMem) |
| uint_32 | PT_read_int (const void *fromMem) |
| uint_big | PT_read_big (const void *fromMem) |
| void | PT_write_char (void *toMem, uint_8 i) |
| void | PT_write_short (void *toMem, uint_16 i) |
| void | PT_write_int (void *toMem, uint_32 i) |
| void | PT_write_big (void *toMem, uint_big i) |
| template<int R> | |
| void | write_nat_with_reserved_bits (char *&toMem, uint_32 nat, uint_8 reserved_bits) |
| template<int R> | |
| uint_32 | read_nat_with_reserved_bits (const char *&fromMem, uint_8 &reserved_bits) |
| template<int R> | |
| void | write_int_with_reserved_bits (char *&toMem, int32_t i, uint_8 reserved_bits) |
| template<int R> | |
| int32_t | read_int_with_reserved_bits (const char *&fromMem, uint_8 &reserved_bits) |
| uint_32 | PT_read_compact_nat (const char *&fromMem) |
| void | PT_write_compact_nat (char *&toMem, uint_32 nat) |
| STATIC_ASSERT (sizeof(void *)==sizeof(uint_big)) | |
| void * | PT_read_void_pointer (const void *fromMem) |
| void | PT_write_pointer (void *toMem, const void *thePtr) |
| template<typename POINTED > | |
| POINTED * | PT_read_pointer (const void *fromMem) |
| void | fflush_all () |
Macro Definition Documentation
| #define pt_assert | ( | bed | ) | arb_assert(bed) |
Definition at line 22 of file PT_tools.h.
Referenced by MatchRequest::accept_N_mismatches(), ChainEntryBuffer::add(), MatchRequest::add_hits_for_children(), all_sons_saved(), PT_statistic::analyse(), Oligo::at(), base_probability(), MatchingOligo::bind_against(), build_pos_tree(), MatchingOligo::calc_centigrade_pos(), OutgroupMatcher::calculate_outgroup_matches(), cat_internal(), ChainIteratorStage1::ChainIteratorStage1(), ChainIteratorStage2::ChainIteratorStage2(), Splits::check(), probe_struct_global::cleanup(), Memory::clear(), MatchRequest::collect_hits_for(), MemBlock::contains(), PrefixIterator::copy(), count_gaps_and_dots(), Mismatches::count_versus(), PT_compressed::createFrom(), MatchingOligo::dangling(), MatchingOligo::dangling_char(), DataLoc::DataLoc(), MatchingOligo::domainPossible(), PT_statistic::dump(), dump_POS_TREE_special(), probe_struct_global::enter_stage(), enter_stage_1_build_tree(), Partition::estimate_max_probes_for_any_pass(), Partition::estimate_probes_for_pass(), PrefixProbabilities::find_index_near_leftsum(), findLeftmostProbe(), findNextProbe(), gene_rel_2_abs(), MismatchWeights::get(), Memory::get(), probe_input_data::get_abspos(), probe_input_data::get_acc(), get_bond_val(), probe_input_data::get_checksum(), get_complement(), get_DB_state(), get_design_hinfo(), get_design_info(), POS_TREE1::get_father(), get_formatter(), probe_input_data::get_geneabspos(), get_list_part(), MaxBond::get_max_bond(), AbsLoc::get_pid(), probe_input_data::get_shortname(), hitgroup_idx2char(), FamilyStat::hits(), MarkedPrefixes::isMarked(), PrefixProbabilities::left_of(), MarkedPrefixes::mark(), PT_Traversal::mark_matching(), MaxBond::MaxBond(), PrefixProbabilities::of(), PrefixProbabilities::of_range(), ptnd_chain_count_mishits::operator()(), PrefixIterator::operator++(), Partition::Partition(), MarkedPrefixes::predecide(), PrefixProbabilities::PrefixProbabilities(), probe_input_data::preload_rel2abs(), probe_compress_sequence(), probe_match(), ProbeIterator::ProbeIterator(), PT_add_to_chain(), PT_chain_has_valid_entries(), PT_change_leaf_to_node(), PT_change_link_in_father(), PT_create_leaf(), PT_exit_psg(), PT_find_exProb(), PT_init_cache_sizes(), PT_init_psg(), PT_leaf_to_chain(), PT_prepare_data(), PT_read_son< POS_TREE2 >(), PT_start_design(), PTD_put_byte(), PTD_put_int(), PTD_put_short(), PTD_read_leafs_from_disk(), PTD_save_upper_tree(), PTD_set_object_to_saved_status(), PTD_write_chain_to_disk(), PTD_write_leafs_to_disk(), PTD_write_node_to_disk(), PTD_write_tip_to_disk(), ptpd_read_names(), Memory::put(), put_compact_nat(), run_command(), save_lower_subtree(), POS_TREE1::set_father(), ChainIteratorStage1::_U::_S::set_loc(), AbsLoc::set_name(), CentigradePos::set_pos_for(), DataLoc::set_position(), POS_TREE1::set_type(), PT_statistic::show_for_index(), CentigradePos::summarize_centigrade_hits(), TraversalHitLimit::TraversalHitLimit(), probe_struct_global::TREE_ROOT1(), probe_struct_global::TREE_ROOT2(), virt_name(), and write_nat_with_reserved_bits().
Typedef Documentation
| typedef void* PT_PNTR |
Definition at line 24 of file PT_tools.h.
Definition at line 26 of file PT_tools.h.
Definition at line 27 of file PT_tools.h.
Definition at line 28 of file PT_tools.h.
Definition at line 29 of file PT_tools.h.
Definition at line 34 of file PT_tools.h.
Function Documentation
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Definition at line 71 of file PT_tools.h.
Referenced by PT_read_son< POS_TREE2 >(), PTD_read_leafs_from_disk(), and read_nat_with_reserved_bits().
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Definition at line 72 of file PT_tools.h.
Referenced by ChainIteratorStage2::ChainIteratorStage2(), DataLoc::DataLoc(), PT_read_son< POS_TREE2 >(), PTD_read_leafs_from_disk(), and read_nat_with_reserved_bits().
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Definition at line 73 of file PT_tools.h.
Referenced by ChainIteratorStage2::ChainIteratorStage2(), DataLoc::DataLoc(), get_memsize_of_saved(), PT_read_big(), PT_read_son< POS_TREE2 >(), PTD_read_leafs_from_disk(), and read_nat_with_reserved_bits().
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Definition at line 78 of file PT_tools.h.
References PT_read_int().
Referenced by PT_read_void_pointer(), PTD_read_leafs_from_disk(), and PTD_write_leafs_to_disk().
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Definition at line 81 of file PT_tools.h.
Referenced by PTD_put_byte(), and write_nat_with_reserved_bits().
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Definition at line 82 of file PT_tools.h.
Referenced by PT_create_leaf(), PTD_put_short(), and write_nat_with_reserved_bits().
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Definition at line 83 of file PT_tools.h.
Referenced by PT_create_leaf(), PT_write_big(), PTD_put_int(), PTD_set_object_to_saved_status(), and write_nat_with_reserved_bits().
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Definition at line 88 of file PT_tools.h.
References PT_write_int().
Referenced by PT_write_pointer(), and PTD_set_object_to_saved_status().
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Definition at line 110 of file PT_tools.h.
References pt_assert, PT_write_char(), PT_write_int(), PT_write_short(), and BitMask< B >::value.
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Definition at line 147 of file PT_tools.h.
References PT_read_char(), PT_read_int(), PT_read_short(), and BitMask< B >::value.
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Definition at line 184 of file PT_tools.h.
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Definition at line 188 of file PT_tools.h.
Definition at line 196 of file PT_tools.h.
Referenced by PT_statistic::analyse(), ChainIteratorStage2::ChainIteratorStage2(), PT_READ_CHAIN_ENTRY_stage_2(), and ChainIteratorStage1::_U::_L::set_loc().
Definition at line 197 of file PT_tools.h.
Referenced by ChainEntryBuffer::add(), PT_WRITE_CHAIN_ENTRY(), and put_compact_nat().
| STATIC_ASSERT | ( | sizeof(void *) | = =sizeof(uint_big) | ) |
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Definition at line 205 of file PT_tools.h.
References PT_read_big().
Referenced by PT_read_pointer().
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Definition at line 206 of file PT_tools.h.
References PT_write_big().
Referenced by PT_change_link_in_father(), PT_create_leaf(), and Memory::put().
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Definition at line 209 of file PT_tools.h.
References PT_read_void_pointer().
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Definition at line 211 of file PT_tools.h.
References fflush().
Referenced by ARB_main(), decide_passes_to_use(), PT_statistic::dump(), enter_stage_1_build_tree(), PT_dump_POS_TREE(), PT_init_input_data(), PT_prepare_data(), server_shutdown(), and start_pt_server().
