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1 /* This file is generated by aisc_mkpt.
2  * Any changes you make here will be overwritten later!
3  */
8 /* define ARB attributes: */
9 #ifndef ATTRIBUTES_H
10 # include <attributes.h>
11 #endif
14 /* PT_buildtree.cxx */
16  class DataLoc;
18 long PTD_save_lower_tree(FILE *out, POS_TREE1 *node, long pos, ARB_ERROR& error);
19 long PTD_save_upper_tree(FILE *out, POS_TREE1*& node, long pos, long& node_pos, ARB_ERROR& error);
20 ARB_ERROR enter_stage_1_build_tree(PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT;
21 ARB_ERROR enter_stage_2_load_tree(PT_main *, const char *tname) __ATTR__USERESULT;
23 /* PT_debug.cxx */
24 void PT_dump_tree_statistics(const char *indexfilename);
25 template <typename PT >void PT_dump_POS_TREE_recursive(PT *pt, const char *prefix, FILE *out);
26 void PT_dump_POS_TREE(POS_TREE1 *IF_DEBUG (node), FILE *IF_DEBUG (out));
27 int PT_index_dump(const PT_main *main);
29 /* PT_etc.cxx */
30 void pt_export_error(PT_local *locs, const char *error);
31 void pt_export_error_if(PT_local *locs, ARB_ERROR& error);
32 const char *virt_name(const PT_probematch *ml);
33 const char *virt_fullname(const PT_probematch *ml);
34 char *ptpd_read_names(PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR& error);
35 bytestring *PT_unknown_names(const PT_pdc *pdc);
37 /* PT_family.cxx */
38 int find_family(PT_family *ffinder, bytestring *species);
40 /* PT_findEx.cxx */
41 int PT_find_exProb(PT_exProb *pep, int dummy_1x);
43 /* PT_io.cxx */
44 int compress_data(char *probestring);
45 ARB_ERROR probe_read_data_base(const char *name, bool readOnly) __ATTR__USERESULT;
46 size_t probe_compress_sequence(char *seq, size_t seqsize);
47 char *readable_probe(const char *compressed_probe, size_t len, char T_or_U);
50 void PT_build_species_hash(void);
51 long PT_abs_2_ecoli_rel(long pos);
53 /* PT_main.cxx */
54 void PT_init_psg(void);
55 void PT_exit_psg(void);
56 int server_shutdown(PT_main *, aisc_string passwd);
57 int broadcast(PT_main *main, int dummy_1x);
58 int ARB_main(int argc, char *argv[]);
60 /* PT_match.cxx */
61 char *create_reversed_probe(char *probe, int len);
62 int probe_match(PT_local *locs, aisc_string probestring);
63 const char *get_match_overlay(const PT_probematch *ml);
64 const char *get_match_acc(const PT_probematch *ml);
65 int get_match_start(const PT_probematch *ml);
66 int get_match_stop(const PT_probematch *ml);
67 bytestring *match_string(const PT_local *locs);
68 bytestring *MP_match_string(const PT_local *locs);
69 bytestring *MP_all_species_string(const PT_local *);
70 int MP_count_all_species(const PT_local *);
72 /* PT_new_design.cxx */
73 int pt_init_bond_matrix(PT_local *THIS);
74 char *get_design_info(const PT_tprobes *tprobe);
75 char *get_design_hinfo(const PT_pdc *pdc);
76 int PT_start_design(PT_pdc *pdc, int dummy_1x);
78 /* PT_prefixtree.cxx */
79 template <typename CHAINITER >bool PT_chain_has_valid_entries(const typename CHAINITER ::POS_TREE_TYPE *const node);
80 void PT_init_cache_sizes(Stage stage);
81 void PT_add_to_chain(POS_TREE1 *node, const DataLoc& loc);
84 POS_TREE1 *PT_create_leaf(POS_TREE1 **pfather, PT_base base, const DataLoc& loc);
85 void PTD_put_longlong(FILE *out, ULONG i);
86 void PTD_put_int(FILE *out, ULONG i);
87 void PTD_put_short(FILE *out, ULONG i);
88 void PTD_put_byte(FILE *out, ULONG i);
89 void PTD_debug_nodes(void);
91 long PTD_write_leafs_to_disk(FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR& error);
92 ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE2*& root_ptr) __ATTR__USERESULT;
93 const char *get_blocksize_description(int blocksize);
95 /* probe_tree.h */
96 template <typename T >int PT_forwhole_chain(POS_TREE1 *node, T& func);
97 template <typename T >int PT_forwhole_chain(POS_TREE2 *node, T& func);
99 #else
100 #error pt_prototypes.h included twice
101 #endif /* PT_PROTOTYPES_H */
const char * GB_ERROR
Definition: arb_core.h:25
ARB_ERROR enter_stage_2_load_tree(PT_main *, const char *tname) __ATTR__USERESULT
const char * get_match_acc(const PT_probematch *ml)
Definition: PT_match.cxx:605
void PTD_put_int(FILE *out, ULONG i)
void PT_dump_POS_TREE_recursive(PT *pt, const char *prefix, FILE *out)
Definition: PT_debug.cxx:369
POS_TREE1 * PT_change_leaf_to_node(POS_TREE1 *node)
int broadcast(PT_main *main, int dummy_1x)
Definition: PT_main.cxx:190
const char * get_match_overlay(const PT_probematch *ml)
Definition: PT_match.cxx:520
bytestring * match_string(const PT_local *locs)
Definition: PT_match.cxx:704
int PT_find_exProb(PT_exProb *pep, int dummy_1x)
Definition: PT_findEx.cxx:108
int main(int argc, char **argv)
Definition: aisc.c:359
long PTD_save_upper_tree(FILE *out, POS_TREE1 *&node, long pos, long &node_pos, ARB_ERROR &error)
GB_ERROR PT_prepare_data(GBDATA *gb_main)
Definition: PT_io.cxx:203
unsigned long ULONG
Definition: probe.h:50
void PTD_put_longlong(FILE *out, ULONG i)
void PT_dump_tree_statistics(const char *indexfilename)
Definition: PT_debug.cxx:326
GB_ERROR PT_init_input_data(void)
Definition: PT_io.cxx:263
int compress_data(char *probestring)
Definition: PT_io.cxx:21
int pt_init_bond_matrix(PT_local *THIS)
Definition: probe.h:122
void PTD_delete_saved_node(POS_TREE1 *&node)
int MP_count_all_species(const PT_local *)
Definition: PT_match.cxx:808
long PTD_save_lower_tree(FILE *out, POS_TREE1 *node, long pos, ARB_ERROR &error)
FILE * seq
Definition: rns.c:46
void pt_export_error(PT_local *locs, const char *error)
Definition: PT_etc.cxx:19
void PT_add_to_chain(POS_TREE1 *node, const DataLoc &loc)
bytestring * MP_all_species_string(const PT_local *)
Definition: PT_match.cxx:781
void PT_dump_POS_TREE(POS_TREE1 *IF_DEBUG(node), FILE *IF_DEBUG(out))
Definition: PT_debug.cxx:399
bytestring * MP_match_string(const PT_local *locs)
Definition: PT_match.cxx:746
void PT_build_species_hash(void)
Definition: PT_io.cxx:319
int PT_forwhole_chain(POS_TREE1 *node, T &func)
Definition: probe_tree.h:693
void PTD_put_short(FILE *out, ULONG i)
void pt_export_error_if(PT_local *locs, ARB_ERROR &error)
Definition: PT_etc.cxx:22
char * get_design_info(const PT_tprobes *tprobe)
char * create_reversed_probe(char *probe, int len)
Definition: PT_match.cxx:335
static void error(const char *msg)
Definition: mkptypes.cxx:96
int ARB_main(int argc, char *argv[])
Definition: mkptypes.cxx:1545
int get_match_stop(const PT_probematch *ml)
Definition: PT_match.cxx:611
int get_match_start(const PT_probematch *ml)
Definition: PT_match.cxx:608
size_t probe_compress_sequence(char *seq, size_t seqsize)
Definition: PT_io.cxx:78
int PT_start_design(PT_pdc *pdc, int dummy_1x)
const char * virt_name(const PT_probematch *ml)
Definition: PT_etc.cxx:57
POS_TREE1 * PT_leaf_to_chain(POS_TREE1 *node)
long PT_abs_2_ecoli_rel(long pos)
Definition: PT_io.cxx:341
void PTD_put_byte(FILE *out, ULONG i)
Definition: probe.h:82
const char * get_blocksize_description(int blocksize)
int server_shutdown(PT_main *, aisc_string passwd)
Definition: PT_main.cxx:171
T_PT_LOCS locs
void PT_init_psg(void)
Definition: PT_main.cxx:131
const char * virt_fullname(const PT_probematch *ml)
Definition: PT_etc.cxx:69
int probe_match(PT_local *locs, aisc_string probestring)
Definition: PT_match.cxx:364
Definition: attributes.h:58
long PTD_write_leafs_to_disk(FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR &error)
void PTD_debug_nodes(void)
int find_family(PT_family *ffinder, bytestring *species)
Definition: PT_family.cxx:389
void PT_init_cache_sizes(Stage stage)
ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE2 *&root_ptr) __ATTR__USERESULT
char * get_design_hinfo(const PT_pdc *pdc)
char * ptpd_read_names(PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR &error)
Definition: PT_etc.cxx:120
ARB_ERROR enter_stage_1_build_tree(PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT
Definition: trnsprob.h:20
bytestring * PT_unknown_names(const PT_pdc *pdc)
Definition: PT_etc.cxx:201
GBDATA * gb_main
Definition: adname.cxx:33
POS_TREE1 * PT_create_leaf(POS_TREE1 **pfather, PT_base base, const DataLoc &loc)
int PT_index_dump(const PT_main *main)
Definition: PT_debug.cxx:450
#define IF_DEBUG(x)
Definition: arb_assert.h:303
ARB_ERROR probe_read_data_base(const char *name, bool readOnly) __ATTR__USERESULT
Definition: PT_io.cxx:50
void PT_exit_psg(void)
Definition: PT_main.cxx:137
bool PT_chain_has_valid_entries(const typename CHAINITER::POS_TREE_TYPE *const node)
char * readable_probe(const char *compressed_probe, size_t len, char T_or_U)
Definition: PT_io.cxx:91