seq_search.hxx File Reference

#include <aw_base.hxx>
#include <arbdb_base.h>
#include <aw_msg.hxx>
#include <arb_string.h>
#include <attributes.h>
#include <BI_basepos.hxx>
#include <arb_global_defs.h>

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Classes
class	Dots
class	CompactedSequence
class	CompactedSubSequence
class	SequencePosition
class	TripleOffset
class	AlignBuffer
class	FastAlignInsertion
class	FastAlignReport
class	FastSearchSequence
class	FastSearchOccurrence

Macros
#define	fa_assert(bed)   arb_assert(bed)
#define	SEQ_CHARS   26
#define	MAX_TRIPLES   (SEQ_CHARS*SEQ_CHARS*SEQ_CHARS+1)
#define	GAP_CHARS   ".-~?"

Functions
int	max (int i1, int i2)
bool	is_ali_gap (char c)
bool	is_gap (char c)

Macro Definition Documentation

#define fa_assert

(

bed

)

arb_assert(bed)

Definition at line 38 of file seq_search.hxx.

Referenced by AlignBuffer::copy(), CompactedSequence::expdPosition(), CompactedSubSequence::expdPosition(), FastSearchOccurrence::gotoNext(), AlignBuffer::quality(), AlignBuffer::reset(), AlignBuffer::set(), and AlignBuffer::text().

#define SEQ_CHARS   26

Definition at line 40 of file seq_search.hxx.

#define MAX_TRIPLES   (SEQ_CHARS*SEQ_CHARS*SEQ_CHARS+1)

Definition at line 41 of file seq_search.hxx.

Referenced by FastSearchSequence::FastSearchSequence(), and FastSearchSequence::~FastSearchSequence().

#define GAP_CHARS   ".-~?"

Definition at line 45 of file seq_search.hxx.

Referenced by calcSequenceChecksum(), and is_ali_gap().

Function Documentation

int max ( int  i1, int  i2  )

inline

Definition at line 43 of file seq_search.hxx.

bool is_ali_gap ( char  c )

inline

Definition at line 47 of file seq_search.hxx.

References GAP_CHARS.

Referenced by readCompactedSequence().

bool is_gap ( char  c )

inline

Definition at line 48 of file seq_search.hxx.

References GAP::is_std_gap().

Referenced by AlignBuffer::restoreDots(), ED4_reference::set_gap_handling(), AlignBuffer::setDotsAtEOSequence(), and BaseFrequencies::setup().