ARB
Functions
pt_prototypes.h File Reference
#include <attributes.h>
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Functions

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
 
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)
 
void pt_export_error (PT_local *locs, const char *error)
 
void pt_export_error_if (PT_local *locs, ARB_ERROR &error)
 
const charvirt_name (const PT_probematch *ml)
 
const charvirt_fullname (const PT_probematch *ml)
 
charptpd_read_names (PT_local *locs, const char *names_list, const char *checksums, ARB_ERROR &error)
 
bytestringPT_unknown_names (const PT_pdc *pdc)
 
int find_family (PT_family *ffinder, bytestring *species)
 
int PT_find_exProb (PT_exProb *pep, int dummy_1x)
 
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)
 
charreadable_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)
 
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[])
 
charcreate_reversed_probe (char *probe, int len)
 
int probe_match (PT_local *locs, aisc_string probestring)
 
const charget_match_overlay (const PT_probematch *ml)
 
const charget_match_acc (const PT_probematch *ml)
 
int get_match_start (const PT_probematch *ml)
 
int get_match_stop (const PT_probematch *ml)
 
bytestringmatch_string (const PT_local *locs)
 
bytestringMP_match_string (const PT_local *locs)
 
bytestringMP_all_species_string (const PT_local *)
 
int MP_count_all_species (const PT_local *)
 
int pt_init_bond_matrix (PT_local *THIS)
 
charget_design_info (const PT_tprobes *tprobe)
 
charget_design_hinfo (const PT_pdc *pdc)
 
int PT_start_design (PT_pdc *pdc, int dummy_1x)
 
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_TREE1PT_change_leaf_to_node (POS_TREE1 *node)
 
POS_TREE1PT_leaf_to_chain (POS_TREE1 *node)
 
POS_TREE1PT_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 charget_blocksize_description (int blocksize)
 
template<typename T >
int PT_forwhole_chain (POS_TREE1 *node, T &func)
 
template<typename T >
int PT_forwhole_chain (POS_TREE2 *node, T &func)
 

Function Documentation

long PTD_save_lower_tree ( FILE *  out,
POS_TREE1 node,
long  pos,
ARB_ERROR error 
)

Definition at line 237 of file PT_buildtree.cxx.

References check_tree_was_saved(), and save_lower_subtree().

Referenced by enter_stage_1_build_tree().

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 
)
ARB_ERROR enter_stage_2_load_tree ( PT_main *  ,
const char tname 
)
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_DEBUGnode,
FILE *  IF_DEBUGout 
)
int PT_index_dump ( const PT_main *  main)

Definition at line 450 of file PT_debug.cxx.

References PT_dump_POS_TREE_to_file().

void pt_export_error ( PT_local *  locs,
const char error 
)

Definition at line 19 of file PT_etc.cxx.

Referenced by probe_match(), and pt_export_error_if().

void pt_export_error_if ( PT_local *  locs,
ARB_ERROR error 
)

Definition at line 22 of file PT_etc.cxx.

References ARB_ERROR::deliver(), ARB_ERROR::expect_no_error(), and pt_export_error().

Referenced by PT_start_design().

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)

Definition at line 201 of file PT_etc.cxx.

References locs, and NULp.

int find_family ( PT_family *  ffinder,
bytestring species 
)
int PT_find_exProb ( PT_exProb *  pep,
int  dummy_1x 
)
int compress_data ( char probestring)

change a sequence with normal bases the PT_? format and delete all other signs

Definition at line 21 of file PT_io.cxx.

References PT_A, PT_C, PT_G, PT_N, PT_QU, and PT_T.

Referenced by probe_match(), and PT_find_exProb().

ARB_ERROR probe_read_data_base ( const char name,
bool  readOnly 
)
size_t probe_compress_sequence ( char seq,
size_t  seqsize 
)
char* readable_probe ( const char compressed_probe,
size_t  len,
char  T_or_U 
)

Definition at line 91 of file PT_io.cxx.

References ARB_alloc(), NULp, PT_A, PT_B_UNDEF, PT_C, PT_G, PT_N, PT_QU, PT_T, result, safeCharIndex(), SmartMallocPtr, and tab().

Referenced by ProbeIterator::dump(), and PT_find_exProb().

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)
void PT_init_psg ( void  )

Definition at line 131 of file PT_main.cxx.

References psg, psg_initialized, pt_assert, and probe_struct_global::setup().

Referenced by ARB_main().

void PT_exit_psg ( void  )

Definition at line 137 of file PT_main.cxx.

References probe_struct_global::cleanup(), Memory::clear(), psg, psg_initialized, and pt_assert.

Referenced by PT_exit().

int server_shutdown ( PT_main *  ,
aisc_string  passwd 
)
int broadcast ( PT_main *  main,
int  dummy_1x 
)

Definition at line 190 of file PT_main.cxx.

References aisc_broadcast(), probe_struct_global::com_so, and psg.

int ARB_main ( int  argc,
char argv[] 
)

Definition at line 1545 of file mkptypes.cxx.

char* create_reversed_probe ( char probe,
int  len 
)

reverse order of bases in a probe

Definition at line 335 of file PT_match.cxx.

References ARB_strduplen(), and reverse_probe().

Referenced by get_design_info(), and probe_match().

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)

Definition at line 605 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_acc(), and psg.

int get_match_start ( const PT_probematch *  ml)

Definition at line 608 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_start(), and psg.

int get_match_stop ( const PT_probematch *  ml)

Definition at line 611 of file PT_match.cxx.

References probe_struct_global::data, probe_input_data::get_stop(), and psg.

bytestring* match_string ( const PT_local *  locs)

Create list of species where probe matches.

header^1name^1info^1name^1info....^0 (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MATCH_STRING'

Definition at line 704 of file PT_match.cxx.

References bytestring::data, detect_format_props(), format(), GBS_chrcat(), GBS_memoffset(), GBS_strcat(), GBS_strclose(), GBS_stropen(), gene_flag, gene_rel_2_abs(), get_match_hinfo_formatted(), get_match_info_formatted(), NULp, bytestring::size, and virt_name().

bytestring* MP_match_string ( const PT_local *  locs)

Create list of species where probe matches and append number of mismatches and weighted mismatches (used by multiprobe)

Format: "header^1name^1#mismatches^1#wmismatches^1name^1#mismatches^1#wmismatches....^0" (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MP_MATCH_STRING'

Definition at line 746 of file PT_match.cxx.

References buffer, bytestring::data, GBS_chrcat(), GBS_memoffset(), GBS_strcat(), GBS_strclose(), GBS_stropen(), NULp, bytestring::size, and virt_name().

bytestring* MP_all_species_string ( const PT_local *  )

Create list of all species known to PT server

Format: ^1name^1name....^0 (where ^0 and ^1 are ASCII 0 and 1)

Implements server function 'MP_ALL_SPECIES_STRING'

Definition at line 781 of file PT_match.cxx.

References bytestring::data, probe_struct_global::data, probe_struct_global::data_count, GBS_chrcat(), GBS_memoffset(), GBS_strcat(), GBS_strclose(), GBS_stropen(), probe_input_data::get_shortname(), NULp, psg, and bytestring::size.

int MP_count_all_species ( const PT_local *  )

Definition at line 808 of file PT_match.cxx.

References probe_struct_global::data_count, and psg.

int pt_init_bond_matrix ( PT_local *  THIS)

Definition at line 50 of file PT_new_design.cxx.

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 
)
template<typename CHAINITER >
bool PT_chain_has_valid_entries ( const typename CHAINITER::POS_TREE_TYPE *const  node)

Definition at line 51 of file PT_prefixtree.cxx.

References locs_in_chain_order(), and pt_assert.

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)

Definition at line 619 of file PT_prefixtree.cxx.

References get_memsize_of_saved(), MEM, NULp, and Memory::put().

Referenced by PTD_save_upper_tree().

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 
)
const char* get_blocksize_description ( int  blocksize)
template<typename T >
int PT_forwhole_chain ( POS_TREE1 node,
T func 
)

Definition at line 693 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE1.

template<typename T >
int PT_forwhole_chain ( POS_TREE2 node,
T func 
)

Definition at line 702 of file probe_tree.h.

References error(), pt_assert_stage, and STAGE2.