| 1 | /* This file is generated by aisc_mkpt. |
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| 2 | * Any changes you make here will be overwritten later! |
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| 3 | */ |
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| 4 | |
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| 5 | #ifndef PT_PROTOTYPES_H |
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| 6 | #define PT_PROTOTYPES_H |
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| 7 | |
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| 8 | /* define ARB attributes: */ |
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| 9 | #ifndef ATTRIBUTES_H |
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| 10 | # include <attributes.h> |
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| 11 | #endif |
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| 12 | |
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| 13 | |
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| 14 | /* PT_buildtree.cxx */ |
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| 15 | |
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| 16 | class DataLoc; |
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| 17 | |
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| 18 | long PTD_save_lower_tree(FILE *out, POS_TREE1 *node, long pos, ARB_ERROR& error); |
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| 19 | long PTD_save_upper_tree(FILE *out, POS_TREE1*& node, long pos, long& node_pos, ARB_ERROR& error); |
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| 20 | ARB_ERROR enter_stage_1_build_tree(PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT; |
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| 21 | ARB_ERROR enter_stage_2_load_tree(PT_main *, const char *tname) __ATTR__USERESULT; |
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| 22 | |
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| 23 | /* PT_debug.cxx */ |
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| 24 | void PT_dump_tree_statistics(const char *indexfilename); |
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| 25 | template <typename PT >void PT_dump_POS_TREE_recursive(PT *pt, const char *prefix, FILE *out); |
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| 26 | void PT_dump_POS_TREE(POS_TREE1 *IF_DEBUG (node), FILE *IF_DEBUG (out)); |
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| 27 | int PT_index_dump(const PT_main *main); |
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| 28 | |
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| 29 | /* PT_etc.cxx */ |
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| 30 | void pt_export_error(PT_local *locs, const char *error); |
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| 31 | void pt_export_error_if(PT_local *locs, ARB_ERROR& error); |
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| 32 | const char *virt_name(const PT_probematch *ml); |
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| 33 | const char *virt_fullname(const PT_probematch *ml); |
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| 34 | char *ptpd_read_names(PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR& error); |
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| 35 | bytestring *PT_unknown_names(const PT_pdc *pdc); |
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| 36 | |
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| 37 | /* PT_family.cxx */ |
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| 38 | int find_family(PT_family *ffinder, bytestring *species); |
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| 39 | |
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| 40 | /* PT_findEx.cxx */ |
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| 41 | int PT_find_exProb(PT_exProb *pep, int dummy_1x); |
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| 42 | |
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| 43 | /* PT_io.cxx */ |
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| 44 | int compress_data(char *probestring); |
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| 45 | ARB_ERROR probe_read_data_base(const char *name, bool readOnly) __ATTR__USERESULT; |
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| 46 | size_t probe_compress_sequence(char *seq, size_t seqsize); |
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| 47 | char *readable_probe(const char *compressed_probe, size_t len, char T_or_U); |
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| 48 | GB_ERROR PT_prepare_data(GBDATA *gb_main); |
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| 49 | GB_ERROR PT_init_input_data(void); |
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| 50 | void PT_build_species_hash(void); |
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| 51 | long PT_abs_2_ecoli_rel(long pos); |
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| 52 | |
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| 53 | /* PT_main.cxx */ |
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| 54 | void PT_init_psg(void); |
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| 55 | void PT_exit_psg(void); |
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| 56 | int server_shutdown(PT_main *, aisc_string passwd); |
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| 57 | int broadcast(PT_main *main, int dummy_1x); |
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| 58 | int ARB_main(int argc, char *argv[]); |
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| 59 | |
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| 60 | /* PT_match.cxx */ |
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| 61 | char *create_reversed_probe(char *probe, int len); |
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| 62 | int probe_match(PT_local *locs, aisc_string probestring); |
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| 63 | const char *get_match_overlay(const PT_probematch *ml); |
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| 64 | const char *get_match_acc(const PT_probematch *ml); |
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| 65 | int get_match_start(const PT_probematch *ml); |
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| 66 | int get_match_stop(const PT_probematch *ml); |
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| 67 | bytestring *match_string(const PT_local *locs); |
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| 68 | bytestring *MP_match_string(const PT_local *locs); |
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| 69 | bytestring *MP_all_species_string(const PT_local *); |
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| 70 | int MP_count_all_species(const PT_local *); |
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| 71 | |
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| 72 | /* PT_new_design.cxx */ |
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| 73 | int pt_init_bond_matrix(PT_local *THIS); |
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| 74 | char *get_design_info(const PT_tprobes *tprobe); |
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| 75 | char *get_design_hinfo(const PT_pdc *pdc); |
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| 76 | int PT_start_design(PT_pdc *pdc, int dummy_1x); |
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| 77 | |
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| 78 | /* PT_prefixtree.cxx */ |
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| 79 | template <typename CHAINITER >bool PT_chain_has_valid_entries(const typename CHAINITER ::POS_TREE_TYPE *const node); |
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| 80 | void PT_init_cache_sizes(Stage stage); |
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| 81 | void PT_add_to_chain(POS_TREE1 *node, const DataLoc& loc); |
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| 82 | POS_TREE1 *PT_change_leaf_to_node(POS_TREE1 *node); |
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| 83 | POS_TREE1 *PT_leaf_to_chain(POS_TREE1 *node); |
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| 84 | POS_TREE1 *PT_create_leaf(POS_TREE1 **pfather, PT_base base, const DataLoc& loc); |
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| 85 | void PTD_put_longlong(FILE *out, ULONG i); |
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| 86 | void PTD_put_int(FILE *out, ULONG i); |
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| 87 | void PTD_put_short(FILE *out, ULONG i); |
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| 88 | void PTD_put_byte(FILE *out, ULONG i); |
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| 89 | int PTD_put_compact_nat(FILE *out, uint_32 nat); |
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| 90 | void PTD_debug_nodes(void); |
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| 91 | void PTD_delete_saved_node(POS_TREE1*& node); |
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| 92 | long PTD_write_leafs_to_disk(FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR& error); |
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| 93 | ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE2*& root_ptr) __ATTR__USERESULT; |
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| 94 | const char *get_blocksize_description(int blocksize); |
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| 95 | |
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| 96 | /* probe_tree.h */ |
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| 97 | template <typename T >int PT_forwhole_chain(POS_TREE1 *node, T& func); |
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| 98 | template <typename T >int PT_forwhole_chain(POS_TREE2 *node, T& func); |
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| 99 | |
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| 100 | #else |
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| 101 | #error pt_prototypes.h included twice |
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| 102 | #endif /* PT_PROTOTYPES_H */ |
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