/* This file is generated by aisc_mkpt.
 * Any changes you make here will be overwritten later!
 */

#ifndef PT_PROTOTYPES_H
#define PT_PROTOTYPES_H

/* define ARB attributes: */
#ifndef ATTRIBUTES_H
# include <attributes.h>
#endif


/* PT_buildtree.cxx */

 class DataLoc;

long PTD_save_lower_tree(FILE *out, POS_TREE1 *node, long pos, ARB_ERROR& error);
long PTD_save_upper_tree(FILE *out, POS_TREE1*& node, long pos, long& node_pos, ARB_ERROR& error);
ARB_ERROR enter_stage_1_build_tree(PT_main *, const char *tname, ULONG ARM_size_kb) __ATTR__USERESULT;
ARB_ERROR enter_stage_2_load_tree(PT_main *, const char *tname) __ATTR__USERESULT;

/* PT_debug.cxx */
void PT_dump_tree_statistics(const char *indexfilename);
template <typename PT >void PT_dump_POS_TREE_recursive(PT *pt, const char *prefix, FILE *out);
void PT_dump_POS_TREE(POS_TREE1 *IF_DEBUG (node), FILE *IF_DEBUG (out));
int PT_index_dump(const PT_main *main);

/* PT_etc.cxx */
void pt_export_error(PT_local *locs, const char *error);
void pt_export_error_if(PT_local *locs, ARB_ERROR& error);
const char *virt_name(const PT_probematch *ml);
const char *virt_fullname(const PT_probematch *ml);
char *ptpd_read_names(PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR& error);
bytestring *PT_unknown_names(const PT_pdc *pdc);

/* PT_family.cxx */
int find_family(PT_family *ffinder, bytestring *species);

/* PT_findEx.cxx */
int PT_find_exProb(PT_exProb *pep, int dummy_1x);

/* PT_io.cxx */
int compress_data(char *probestring);
ARB_ERROR probe_read_data_base(const char *name, bool readOnly) __ATTR__USERESULT;
size_t probe_compress_sequence(char *seq, size_t seqsize);
char *readable_probe(const char *compressed_probe, size_t len, char T_or_U);
GB_ERROR PT_prepare_data(GBDATA *gb_main);
GB_ERROR PT_init_input_data(void);
void PT_build_species_hash(void);
long PT_abs_2_ecoli_rel(long pos);

/* PT_main.cxx */
void PT_init_psg(void);
void PT_exit_psg(void);
int server_shutdown(PT_main *, aisc_string passwd);
int broadcast(PT_main *main, int dummy_1x);
int ARB_main(int argc, char *argv[]);

/* PT_match.cxx */
char *create_reversed_probe(char *probe, int len);
int probe_match(PT_local *locs, aisc_string probestring);
const char *get_match_overlay(const PT_probematch *ml);
const char *get_match_acc(const PT_probematch *ml);
int get_match_start(const PT_probematch *ml);
int get_match_stop(const PT_probematch *ml);
bytestring *match_string(const PT_local *locs);
bytestring *MP_match_string(const PT_local *locs);
bytestring *MP_all_species_string(const PT_local *);
int MP_count_all_species(const PT_local *);

/* PT_new_design.cxx */
int pt_init_bond_matrix(PT_local *THIS);
char *get_design_info(const PT_tprobes *tprobe);
char *get_design_hinfo(const PT_pdc *pdc);
int PT_start_design(PT_pdc *pdc, int dummy_1x);

/* PT_prefixtree.cxx */
template <typename CHAINITER >bool PT_chain_has_valid_entries(const typename CHAINITER ::POS_TREE_TYPE *const node);
void PT_init_cache_sizes(Stage stage);
void PT_add_to_chain(POS_TREE1 *node, const DataLoc& loc);
POS_TREE1 *PT_change_leaf_to_node(POS_TREE1 *node);
POS_TREE1 *PT_leaf_to_chain(POS_TREE1 *node);
POS_TREE1 *PT_create_leaf(POS_TREE1 **pfather, PT_base base, const DataLoc& loc);
void PTD_put_longlong(FILE *out, ULONG i);
void PTD_put_int(FILE *out, ULONG i);
void PTD_put_short(FILE *out, ULONG i);
void PTD_put_byte(FILE *out, ULONG i);
void PTD_debug_nodes(void);
void PTD_delete_saved_node(POS_TREE1*& node);
long PTD_write_leafs_to_disk(FILE *out, POS_TREE1 *const node, long pos, long *node_pos, ARB_ERROR& error);
ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE2*& root_ptr) __ATTR__USERESULT;
const char *get_blocksize_description(int blocksize);

/* probe_tree.h */
template <typename T >int PT_forwhole_chain(POS_TREE1 *node, T& func);
template <typename T >int PT_forwhole_chain(POS_TREE2 *node, T& func);

#else
#error pt_prototypes.h included twice
#endif /* PT_PROTOTYPES_H */