chartable.cxx File Reference

#include "chartable.h"
#include <arb_msg.h>
#include <arb_mem.h>
#include <iupac.h>
#include <arb_defs.h>
#include <smartptr.h>
#include <cctype>
#include <consensus.h>

Include dependency graph for chartable.cxx:

Go to the source code of this file.

Macros
#define	CONSENSUS_AWAR_SOURCE   CAS_INTERNAL
#define	INVALID_TABLE_OPERATION()   GBK_terminatef("SepBaseFreq: invalid operation at %i", __LINE__)
#define	PERCENT(part, all)   ((100*(part))/(all))
#define	MAX_BASES_TABLES   41
#define	DUMPINT(var)
#define	INC_DEC(incdec)

Functions
static const char *	getAAgroupDefinition ()

Macro Definition Documentation

#define CONSENSUS_AWAR_SOURCE   CAS_INTERNAL

Definition at line 21 of file chartable.cxx.

#define INVALID_TABLE_OPERATION

(

)

GBK_terminatef("SepBaseFreq: invalid operation at %i", __LINE__)

Definition at line 78 of file chartable.cxx.

Referenced by chartable::SepBaseFreq::add(), chartable::SepBaseFreq::sub(), and chartable::SepBaseFreq::sub_and_add().

#define PERCENT	(		part,
			all
	)		((100*(part))/(all))

Referenced by BaseFrequencies::build_consensus_string_to().

#define MAX_BASES_TABLES   41

Referenced by BaseFrequencies::build_consensus_string_to().

#define DUMPINT

(

var

)

Referenced by BaseFrequencies::build_consensus_string_to(), and PART::distanceTo().

#define INC_DEC

(

incdec

)

Value:

do {                                                    \
        int idx = char_to_index_tab[c];                                         \
        if (idx<MAX_INDEX_TABLES) {                                             \
            table(c).incdec(offset, unitsPerSequence);                          \
        }                                                                       \
        else {                                                                  \
            Ambiguity& amb = ambiguity_table[idx-MAX_INDEX_TABLES];             \
            for (int i = 0; i<amb.indices; ++i) {                               \
                linear_table(amb.index[i]).incdec(offset, amb.increment);       \
            }                                                                   \
        }                                                                       \
    } while(0)

Definition at line 989 of file chartable.cxx.

Function Documentation

static const char* getAAgroupDefinition ( )

static

Definition at line 578 of file chartable.cxx.

References iupac::AA_GROUP_ILLEGAL, iupac::AA_GROUP_NONE, buffer, ct_assert, and iupac::get_amino_group_for().

Referenced by BaseFrequencies::setup().