#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
struct GapPrelimEditScript GapPrelimEditScript
A version of GapEditScript used to store initial results from the gapped alignment routines.
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.
GapEditScript * GapEditScriptDup(const GapEditScript *old)
Duplicates the edit script structure.
struct GapPrelimEditBlock GapPrelimEditBlock
Preliminary version of GapEditBlock, used directly by the low- level dynamic programming routines.
GapStateArrayStruct * GapStateFree(GapStateArrayStruct *state_struct)
Free the gap state structure.
EGapAlignOpType
Operation types within the edit script.
@ eGapAlignDel2
Frame shift deletion of two nucleotides.
@ eGapAlignIns2
Frame shift insertion of two nucleotides.
@ eGapAlignInvalid
Invalid operation.
@ eGapAlignIns1
Frame shift insertion of one nucleotide.
@ eGapAlignIns
Insertion: a gap in subject.
@ eGapAlignDel1
Frame shift deletion of one nucleotide.
@ eGapAlignDecline
Non-aligned region.
@ eGapAlignSub
Substitution.
@ eGapAlignDel
Deletion: a gap in query.
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_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 a...
GapEditScript * GapEditScriptDelete(GapEditScript *esp)
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.
struct GapStateArrayStruct GapStateArrayStruct
Structure to keep memory for state structure.
struct GapEditScript GapEditScript
Edit script: linked list of correspondencies between two sequences.
uint8_t Uint1
1-byte (8-bit) unsigned integer
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
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
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.
Int4 used
how much of length is used.
Int4 length
length of the state_array.
Uint1 * state_array
array to be used.
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