source: tags/ms_r16q2/PROBE/pt_prototypes.h

Last change on this file was 14038, checked in by westram, 7 years ago
  • fix #618 (use ar for linking)
    • library order does matter now
      • PROBE_COM/server.a and PROBE/PROBE.a depend on each other → hack: unpack lib and directly link objects
    • do not export pt_init_bond_matrix "extern C"
    • sym2testcode.pl: ignore several additional lines from nm-output
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.9 KB
Line 
1/* This file is generated by aisc_mkpt.
2 * Any changes you make here will be overwritten later!
3 */
4
5#ifndef PT_PROTOTYPES_H
6#define PT_PROTOTYPES_H
7
8/* define ARB attributes: */
9#ifndef ATTRIBUTES_H
10# include <attributes.h>
11#endif
12
13
14/* PT_buildtree.cxx */
15
16 class DataLoc;
17
18long PTD_save_lower_tree(FILE *out, POS_TREE1 *node, long pos, ARB_ERROR& error);
19long PTD_save_upper_tree(FILE *out, POS_TREE1*& node, long pos, long& node_pos, ARB_ERROR& error);
20ARB_ERROR enter_stage_1_build_tree(PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT;
21ARB_ERROR enter_stage_2_load_tree(PT_main *, const char *tname) __ATTR__USERESULT;
22
23/* PT_debug.cxx */
24void PT_dump_tree_statistics(const char *indexfilename);
25template <typename PT >void PT_dump_POS_TREE_recursive(PT *pt, const char *prefix, FILE *out);
26void PT_dump_POS_TREE(POS_TREE1 *IF_DEBUG (node), FILE *IF_DEBUG (out));
27int PT_index_dump(const PT_main *main);
28
29/* PT_etc.cxx */
30void pt_export_error(PT_local *locs, const char *error);
31void pt_export_error_if(PT_local *locs, ARB_ERROR& error);
32const char *virt_name(const PT_probematch *ml);
33const char *virt_fullname(const PT_probematch *ml);
34char *ptpd_read_names(PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR& error);
35bytestring *PT_unknown_names(const PT_pdc *pdc);
36
37/* PT_family.cxx */
38int find_family(PT_family *ffinder, bytestring *species);
39
40/* PT_findEx.cxx */
41int PT_find_exProb(PT_exProb *pep, int dummy_1x);
42
43/* PT_io.cxx */
44int compress_data(char *probestring);
45ARB_ERROR probe_read_data_base(const char *name, bool readOnly) __ATTR__USERESULT;
46size_t probe_compress_sequence(char *seq, size_t seqsize);
47char *readable_probe(const char *compressed_probe, size_t len, char T_or_U);
48GB_ERROR PT_prepare_data(GBDATA *gb_main);
49GB_ERROR PT_init_input_data(void);
50void PT_build_species_hash(void);
51long PT_abs_2_ecoli_rel(long pos);
52
53/* PT_main.cxx */
54void PT_init_psg(void);
55void PT_exit_psg(void);
56int server_shutdown(PT_main *, aisc_string passwd);
57int broadcast(PT_main *main, int dummy_1x);
58int ARB_main(int argc, char *argv[]);
59
60/* PT_match.cxx */
61char *create_reversed_probe(char *probe, int len);
62int probe_match(PT_local *locs, aisc_string probestring);
63const char *get_match_overlay(const PT_probematch *ml);
64const char *get_match_acc(const PT_probematch *ml);
65int get_match_start(const PT_probematch *ml);
66int get_match_stop(const PT_probematch *ml);
67bytestring *match_string(const PT_local *locs);
68bytestring *MP_match_string(const PT_local *locs);
69bytestring *MP_all_species_string(const PT_local *);
70int MP_count_all_species(const PT_local *);
71
72/* PT_new_design.cxx */
73int pt_init_bond_matrix(PT_local *THIS);
74char *get_design_info(const PT_tprobes *tprobe);
75char *get_design_hinfo(const PT_pdc *pdc);
76int PT_start_design(PT_pdc *pdc, int dummy_1x);
77
78/* PT_prefixtree.cxx */
79template <typename CHAINITER >bool PT_chain_has_valid_entries(const typename CHAINITER ::POS_TREE_TYPE *const node);
80void PT_init_cache_sizes(Stage stage);
81void PT_add_to_chain(POS_TREE1 *node, const DataLoc& loc);
82POS_TREE1 *PT_change_leaf_to_node(POS_TREE1 *node);
83POS_TREE1 *PT_leaf_to_chain(POS_TREE1 *node);
84POS_TREE1 *PT_create_leaf(POS_TREE1 **pfather, PT_base base, const DataLoc& loc);
85void PTD_put_longlong(FILE *out, ULONG i);
86void PTD_put_int(FILE *out, ULONG i);
87void PTD_put_short(FILE *out, ULONG i);
88void PTD_put_byte(FILE *out, ULONG i);
89int PTD_put_compact_nat(FILE *out, uint_32 nat);
90void PTD_debug_nodes(void);
91void PTD_delete_saved_node(POS_TREE1*& node);
92long PTD_write_leafs_to_disk(FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR& error);
93ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE2*& root_ptr) __ATTR__USERESULT;
94const char *get_blocksize_description(int blocksize);
95
96/* probe_tree.h */
97template <typename T >int PT_forwhole_chain(POS_TREE1 *node, T& func);
98template <typename T >int PT_forwhole_chain(POS_TREE2 *node, T& func);
99
100#else
101#error pt_prototypes.h included twice
102#endif /* PT_PROTOTYPES_H */
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