PT_io.cxx File Reference
#include "probe.h"
#include "pt_prototypes.h"
#include "PT_compress.h"
#include <arbdbt.h>
#include <BI_basepos.hxx>
#include <arb_progress.h>
#include <arb_file.h>
Include dependency graph for PT_io.cxx:

Go to the source code of this file.


int compress_data (char *probestring)
ARB_ERROR probe_read_data_base (const char *name, bool readOnly)
size_t probe_compress_sequence (char *seq, size_t seqsize)
charreadable_probe (const char *compressed_probe, size_t len, char T_or_U)
GBDATAexpect_entry (GBDATA *gb_species, const char *entry_name)
GB_ERROR PT_prepare_species_sequence (GBDATA *gb_species, const char *alignment_name, bool &data_missing, PT_compressed &compressed)
GB_ERROR PT_prepare_data (GBDATA *gb_main)
GB_ERROR PT_init_input_data ()
void PT_build_species_hash ()
long PT_abs_2_ecoli_rel (long pos)

Function Documentation

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().

GBDATA* expect_entry ( GBDATA gb_species,
const char entry_name 

Definition at line 121 of file PT_io.cxx.

References GB_entry(), GB_export_errorf(), and GBT_get_name_or_description().

Referenced by probe_input_data::init().

GB_ERROR PT_prepare_species_sequence ( GBDATA gb_species,
const char alignment_name,
bool &  data_missing,
PT_compressed compressed 
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)