Initialization and freeing of structures containing traceback information. More...

#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/gapinfo.h>

Include dependency graph for gapinfo.c:

Functions
GapStateArrayStruct *	GapStateFree (GapStateArrayStruct *state_struct)
	Free the gap state structure. More...

GapEditScript *	GapEditScriptNew (Int4 size)
	Initialize the edit script structure. More...

GapEditScript *	GapEditScriptDelete (GapEditScript *old)
	Free edit script structure. More...

GapEditScript *	GapEditScriptDup (const GapEditScript *old)
	Duplicates the edit script structure. More...

Int2	GapEditScriptPartialCopy (GapEditScript new, int offset, const GapEditScript old, int start, int stop)
	Copies the portion of the GapEditScript specified by start and stop to a new one the new one should already exist. More...

static Int2	s_GapPrelimEditBlockRealloc (GapPrelimEditBlock *edit_block, Int4 total_ops)
	Ensures that a preliminary edit script has enough memory allocated to hold a given number of edit operations. More...

static Int2	s_GapPrelimEditBlockAddNew (GapPrelimEditBlock *edit_block, EGapAlignOpType op_type, Int4 num_ops)
	Add an edit operation to an edit script. More...

void	GapPrelimEditBlockAdd (GapPrelimEditBlock *edit_block, EGapAlignOpType op_type, Int4 num_ops)
	Add a new operation to a preliminary edit block, possibly combining it with the last operation if the two operations are identical. More...

GapPrelimEditBlock *	GapPrelimEditBlockNew (void)
	Allocates a preliminary edit block structure. More...

GapPrelimEditBlock *	GapPrelimEditBlockFree (GapPrelimEditBlock *edit_block)
	Frees a preliminary edit block structure. More...

void	GapPrelimEditBlockReset (GapPrelimEditBlock *edit_block)
	Reset a preliminary edit block without freeing it. More...

void	GapPrelimEditBlockAppend (GapPrelimEditBlock edit_block1, GapPrelimEditBlock edit_block2)
	Append one GapPrelimEditBlock to the end of the other. More...

Detailed Description

Initialization and freeing of structures containing traceback information.

Definition in file gapinfo.c.

Function Documentation

◆ GapEditScriptDelete()

GapEditScript* GapEditScriptDelete ( GapEditScript * esp )

Free edit script structure.

Parameters

esp	Pointer to the edit script [in]

Returns: NULL

Definition at line 75 of file gapinfo.c.

References GapEditScript::num, GapEditScript::op_type, and sfree.

Referenced by BLAST_GapAlignStructFree(), BLAST_GetGappedScore(), Blast_HSPFree(), Blast_TracebackFromHSPList(), BOOST_AUTO_TEST_CASE(), GapEditScriptCombine(), s_BlastOOFTracebackToGapEditScript(), s_CreateHSPForWordHit(), s_ExtendAlignmentCleanup(), s_FreeEditScript(), s_NewAlignmentUsingXdrop(), s_PHITracebackFromHSPList(), s_SetupHSPForGappedReevaluateTest(), and s_UpdateReevaluatedHSP().

◆ GapEditScriptDup()

GapEditScript* GapEditScriptDup ( const GapEditScript * old )

Duplicates the edit script structure.

Parameters

old	object to be duplicated [in]

Returns: Pointer to the new edit script

Definition at line 89 of file gapinfo.c.

References GapEditScriptNew(), NULL, GapEditScript::num, GapEditScript::op_type, and GapEditScript::size.

Referenced by Blast_HSPClone(), BOOST_AUTO_TEST_CASE(), and s_BlastHSPCopy().

◆ GapEditScriptNew()

GapEditScript* GapEditScriptNew ( Int4 size )

Initialize the edit script structure.

Parameters

size	number of elements to allocate.

Returns: Pointer to the new edit script

Definition at line 56 of file gapinfo.c.

References calloc(), NULL, and ncbi::grid::netcache::search::fields::size.

Referenced by Blast_PrelimEditBlockToGapEditScript(), BOOST_AUTO_TEST_CASE(), GapEditScriptDup(), JumperPrelimEditBlockToGapEditScript(), s_BlastOOFTracebackToGapEditScript(), s_CreateHSPForWordHit(), s_GetTraceback(), s_SetupHSPForGappedReevaluateTest(), and s_UpdateReevaluatedHSP().

◆ GapEditScriptPartialCopy()

Int2 GapEditScriptPartialCopy	(	GapEditScript *	new_esp,
		int	offset,
		const GapEditScript *	old_esp,
		int	start,
		int	stop
	)

Copies the portion of the GapEditScript specified by start and stop to a new one the new one should already exist.

Parameters

new_esp	edit script to copy to [in\|out]
offset	starting element in new one to copy to [in]
old_esp	edit script to copy from [in]
start	first element to copy from (zero-offset) [in]
stop	last element to copy [in]