1 | /* |
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2 | * This file is generated by aisc_mkpt. |
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3 | * Any changes you make here will be overwritten later! |
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4 | * |
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5 | */ |
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6 | |
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7 | #ifndef PT_PROTOTYPES_H |
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8 | #define PT_PROTOTYPES_H |
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9 | |
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10 | #ifndef P_ |
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11 | # if defined(__STDC__) || defined(__cplusplus) |
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12 | # define P_(s) s |
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13 | # else |
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14 | # define P_(s) () |
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15 | # endif |
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16 | #else |
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17 | # error P_ already defined elsewhere |
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18 | #endif |
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19 | |
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20 | |
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21 | /* PT_new_design.cxx */ |
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22 | int ptnd_check_pure P_((char *probe)); |
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23 | double ptnd_check_split P_((PT_pdc *pdc, char *probe, int pos, char ref)); |
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24 | extern "C" char *get_design_info P_((PT_tprobes *tprobe)); |
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25 | extern "C" char *get_design_hinfo P_((PT_tprobes *tprobe)); |
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26 | extern "C" int PT_start_design P_((PT_pdc *pdc, int dummy_1x)); |
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27 | void ptnd_new_match P_((PT_local *locs, char *probestring)); |
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28 | |
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29 | /* PT_family.cxx */ |
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30 | extern "C" int ff_find_family P_((PT_local *locs, bytestring *species)); |
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31 | |
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32 | /* PT_prefixtree.cxx */ |
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33 | void PT_init_count_bits P_((void)); |
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34 | char *PTM_get_mem P_((int size)); |
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35 | int PTM_destroy_mem P_((void)); |
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36 | void PTM_free_mem P_((char *data, int size)); |
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37 | void PTM_debug_mem P_((void)); |
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38 | PTM2 *PT_init P_((int base_count)); |
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39 | int PTD P_((POS_TREE *node)); |
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40 | void PT_change_father P_((POS_TREE *father, POS_TREE *source, POS_TREE *dest)); |
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41 | POS_TREE *PT_add_to_chain P_((PTM2 *ptmain, POS_TREE *node, int name, int apos, int rpos)); |
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42 | POS_TREE *PT_change_leaf_to_node P_((PTM2 *, POS_TREE *node)); |
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43 | POS_TREE *PT_leaf_to_chain P_((PTM2 *ptmain, POS_TREE *node)); |
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44 | POS_TREE *PT_create_leaf P_((PTM2 *ptmain, POS_TREE **pfather, PT_BASES base, int rpos, int apos, int name)); |
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45 | void PTD_clear_fathers P_((PTM2 *ptmain, POS_TREE *node)); |
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46 | void PTD_put_longlong P_((FILE *out, ULONG i)); |
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47 | void PTD_put_int P_((FILE *out, ULONG i)); |
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48 | void PTD_put_short P_((FILE *out, ULONG i)); |
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49 | void PTD_set_object_to_saved_status P_((POS_TREE *node, long pos, int size)); |
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50 | long PTD_write_tip_to_disk P_((FILE *out, PTM2 *, POS_TREE *node, long pos)); |
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51 | int ptd_count_chain_entries P_((char *entry)); |
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52 | void ptd_set_chain_references P_((char *entry, char **entry_tab)); |
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53 | void ptd_write_chain_entries P_((FILE *out, long *ppos, PTM2 *, char **entry_tab, int n_entries, int mainapos)); |
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54 | long PTD_write_chain_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long pos)); |
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55 | void PTD_debug_nodes P_((void)); |
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56 | long PTD_write_node_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long *r_poss, long pos)); |
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57 | long PTD_write_leafs_to_disk P_((FILE *out, PTM2 *ptmain, POS_TREE *node, long pos, long *pnodepos, int *pblock)); |
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58 | void PTD_read_leafs_from_disk P_((char *fname, PTM2 *ptmain, POS_TREE **pnode)); |
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59 | |
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60 | /* PT_main.cxx */ |
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61 | char *pt_init_main_struct P_((PT_main *main, char *filename)); |
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62 | extern "C" int server_shutdown P_((PT_main *pm, aisc_string passwd)); |
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63 | extern "C" int broadcast P_((PT_main *main, int dummy)); |
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64 | void PT_init_psg P_((void)); |
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65 | void PT_init_map P_((void)); |
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66 | |
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67 | /* PT_io.cxx */ |
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68 | int compress_data P_((char *probestring)); |
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69 | void PT_base_2_string P_((char *id_string, long len)); |
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70 | void probe_read_data_base P_((char *name)); |
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71 | int probe_compress_sequence P_((char *seq, int seqsize)); |
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72 | char *probe_read_alignment P_((int j, int *psize)); |
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73 | void probe_read_alignments P_((void)); |
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74 | void PT_build_species_hash P_((void)); |
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75 | long PT_abs_2_rel P_((long pos)); |
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76 | long PT_rel_2_abs P_((long pos)); |
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77 | |
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78 | /* PT_etc.cxx */ |
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79 | void set_table_for_PT_N_mis P_((void)); |
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80 | void pt_export_error P_((PT_local *locs, const char *error)); |
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81 | extern "C" const char *virt_name P_((PT_probematch *ml)); |
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82 | extern "C" const char *virt_fullname P_((PT_probematch *ml)); |
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83 | int *table_copy P_((int *mis_table, int length)); |
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84 | void table_add P_((int *mis_tabled, int *mis_tables, int length)); |
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85 | char *ptpd_read_names P_((PT_local *locs, const char *names_list, const char *checksums, const char *&error)); |
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86 | extern "C" bytestring *PT_unknown_names P_((struct_PT_pdc *pdc)); |
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87 | int get_clip_max_from_length P_((int length)); |
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88 | void PT_init_base_string_counter P_((char *str, char initval, int size)); |
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89 | void PT_inc_base_string_count P_((char *str, char initval, char maxval, int size)); |
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90 | |
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91 | /* PT_buildtree.cxx */ |
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92 | POS_TREE *build_pos_tree P_((POS_TREE *pt, int anfangs_pos, int apos, int RNS_nr, unsigned int end)); |
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93 | long PTD_save_partial_tree P_((FILE *out, PTM2 *ptmain, POS_TREE *node, char *partstring, int partsize, long pos, long *ppos)); |
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94 | void enter_stage_1_build_tree P_((PT_main *main, char *tname)); |
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95 | void enter_stage_3_load_tree P_((PT_main *main, char *tname)); |
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96 | void PT_analyse_tree P_((POS_TREE *pt, int height)); |
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97 | void PT_debug_tree P_((void)); |
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98 | |
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99 | /* PT_match.cxx */ |
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100 | int read_names_and_pos P_((PT_local *locs, POS_TREE *pt)); |
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101 | int get_info_about_probe P_((PT_local *locs, char *probe, POS_TREE *pt, int mismatches, double wmismatches, int N_mismatches, int height)); |
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102 | void pt_sort_match_list P_((PT_local *locs)); |
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103 | char *reverse_probe P_((char *probe, int probe_length)); |
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104 | int PT_complement P_((int base)); |
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105 | void complement_probe P_((char *probe, int probe_length)); |
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106 | void pt_build_pos_to_weight P_((PT_MATCH_TYPE type, const char *sequence)); |
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107 | extern "C" int probe_match P_((PT_local *locs, aisc_string probestring)); |
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108 | extern "C" bytestring *match_string P_((PT_local *locs)); |
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109 | extern "C" bytestring *MP_match_string P_((PT_local *locs)); |
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110 | extern "C" bytestring *MP_all_species_string P_((PT_local *)); |
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111 | extern "C" int MP_count_all_species P_((PT_local *)); |
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112 | |
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113 | /* PT_findEx.cxx */ |
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114 | extern "C" int PT_find_exProb P_((PT_exProb *pep)); |
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115 | |
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116 | /* probe_tree.hxx */ |
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117 | GB_INLINE const char *PT_READ_CHAIN_ENTRY P_((const char *ptr, int mainapos, int *name, int *apos, int *rpos)); |
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118 | GB_INLINE char *PT_WRITE_CHAIN_ENTRY P_((const char *const ptr, const int mainapos, int name, const int apos, const int rpos)); |
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119 | GB_INLINE POS_TREE *PT_read_son P_((PTM2 *ptmain, POS_TREE *node, PT_BASES base)); |
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120 | GB_INLINE POS_TREE *PT_read_son_stage_1 P_((PTM2 *ptmain, POS_TREE *node, PT_BASES base)); |
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121 | GB_INLINE PT_NODE_TYPE PT_read_type P_((POS_TREE *node)); |
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122 | GB_INLINE int PT_read_name P_((PTM2 *ptmain, POS_TREE *node)); |
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123 | GB_INLINE int PT_read_rpos P_((PTM2 *ptmain, POS_TREE *node)); |
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124 | GB_INLINE int PT_read_apos P_((PTM2 *ptmain, POS_TREE *node)); |
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125 | template <typename T >int PT_read_chain P_((PTM2 *ptmain, POS_TREE *node, T func)); |
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126 | |
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127 | #undef P_ |
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128 | |
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129 | #else |
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130 | #error pt_prototypes.h included twice |
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131 | #endif /* PT_PROTOTYPES_H */ |
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