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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gapinfo_8c_source.html below:

NCBI C++ ToolKit: src/algo/blast/core/gapinfo.c Source File

(state_struct) {

memcpy(new->num, old->

, (old->

)*

(

));

= 1+stop-start;

(old ==

||

==

|| stop-start+1 > new->size)

->num[new_index] = old->

[old_index];

->op_type[new_index] = old->

[old_index];

new_size = total_ops * 2;

new_ops = realloc(edit_block->

, new_size *

(new_ops ==

)

edit_block->

= op_type;

(edit_block->

== op_type)

(edit_block !=

) {

(edit_block ==

)

(index = 0, op = edit_block2->

; index < edit_block2->num_ops;

Definitions used throughout BLAST.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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...

GapPrelimEditBlock * GapPrelimEditBlockFree(GapPrelimEditBlock *edit_block)

Frees a preliminary edit block structure.

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 ope...

GapEditScript * GapEditScriptDup(const GapEditScript *old)

Duplicates the edit script structure.

GapStateArrayStruct * GapStateFree(GapStateArrayStruct *state_struct)

Free the gap state structure.

GapEditScript * GapEditScriptNew(Int4 size)

Initialize the edit script structure.

void GapPrelimEditBlockAppend(GapPrelimEditBlock *edit_block1, GapPrelimEditBlock *edit_block2)

Append one GapPrelimEditBlock to the end of the other.

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 a...

GapEditScript * GapEditScriptDelete(GapEditScript *old)

Free edit script structure.

GapPrelimEditBlock * GapPrelimEditBlockNew(void)

Allocates a preliminary edit block structure.

void GapPrelimEditBlockReset(GapPrelimEditBlock *edit_block)

Reset a preliminary edit block without freeing it.

static Int2 s_GapPrelimEditBlockAddNew(GapPrelimEditBlock *edit_block, EGapAlignOpType op_type, Int4 num_ops)

Add an edit operation to an edit script.

Definitions of structures used for saving traceback information.

EGapAlignOpType

Operation types within the edit script.

@ eGapAlignInvalid

Invalid operation.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

const struct ncbi::grid::netcache::search::fields::SIZE size

#define ASSERT

macro for assert.

Edit script: linked list of correspondencies between two sequences.

Int4 * num

Array of number of operations.

Int4 size

Size of above arrays.

EGapAlignOpType * op_type

Array of type of operation.

Preliminary version of GapEditBlock, used directly by the low- level dynamic programming routines.

Int4 num_ops_allocated

size of allocated array

GapPrelimEditScript * edit_ops

array of edit operations

EGapAlignOpType last_op

most recent operation added

Int4 num_ops

number of edit ops presently in use

A version of GapEditScript used to store initial results from the gapped alignment routines.

Int4 num

Number of operations.

EGapAlignOpType op_type

Type of operation.

Structure to keep memory for state structure.

struct GapStateArrayStruct * next

Next link in the list.

Uint1 * state_array

array to be used.

voidp calloc(uInt items, uInt size)

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