min_diag_separation);
Structures and API used for saving BLAST hits.
Int4 BlastIntervalTreeNumRedundant(const BlastIntervalTree *tree, const BlastHSP *hsp, const BlastQueryInfo *query_info)
Determine the number of HSPs within an interval tree whose query range envelops the input HSP.
Boolean BlastIntervalTreeContainsHSP(const BlastIntervalTree *tree, const BlastHSP *hsp, const BlastQueryInfo *query_info, Int4 min_diag_separation)
Determine whether an interval tree contains an HSP that envelops an input HSP.
Int4 BlastIntervalTreeMasksHSP(const BlastIntervalTree *tree, const BlastHSP *hsp, const BlastQueryInfo *query_info, Int4 subtree_index, Int4 masklevel)
struct SIntervalNode SIntervalNode
Structure describing a node of an interval tree.
void Blast_IntervalTreeReset(BlastIntervalTree *tree)
Empty an interval tree structure but do not free it.
struct BlastIntervalTree BlastIntervalTree
Main structure describing an interval tree.
BlastIntervalTree * Blast_IntervalTreeInit(Int4 q_start, Int4 q_end, Int4 s_start, Int4 s_end)
Initialize an interval tree structure.
EITreeIndexMethod
How HSPs added to an interval tree are indexed.
@ eQueryOnlyStrandIndifferent
Index by query offset only.
@ eQueryOnly
Index by query offset only.
@ eQueryAndSubject
Index by query and then by subject offset.
Int2 BlastIntervalTreeAddHSP(BlastHSP *hsp, BlastIntervalTree *tree, const BlastQueryInfo *query_info, EITreeIndexMethod index_method)
Add an HSP to an existing interval tree.
BlastIntervalTree * Blast_IntervalTreeFree(BlastIntervalTree *tree)
Deallocate an interval tree structure.
Definitions and functions associated with the BlastQueryInfo structure.
int16_t Int2
2-byte (16-bit) signed integer
int32_t Int4
4-byte (32-bit) signed integer
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Uint1 Boolean
bool replacment for C
Structure holding all information about an HSP.
Main structure describing an interval tree.
SIntervalNode * nodes
Pool of tree nodes to allocate from.
Int4 s_max
maximum subject offset possible
Int4 num_used
Number of nodes actually in use.
Int4 num_alloc
Number of nodes allocated.
Int4 s_min
minimum subject offset possible
The query related information.
Structure describing a node of an interval tree.
Int4 leftend
The left endpoint of the region this node describes.
Int4 rightptr
Offset to the subtree describing the right half of the region.
Int4 rightend
The right endpoint of the region this node describes.
Int4 midptr
Used for linked list of segments that cross the center of the region.
BlastHSP * hsp
The HSP contained in this region (only non-NULL for leaf nodes)
Int4 leftptr
Offset to the subtree describing the left half of the region, OR the query start offset (leaf nodes o...
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