NCBI C++ ToolKit
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BlastMaskLoc Struct Reference

Search Toolkit Book for BlastMaskLoc

Structure for keeping the query masking information. More...

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

+ Collaboration diagram for BlastMaskLoc:

Public Attributes

Int4 total_size
 Total size of the BlastSeqLoc array below. More...
 
BlastSeqLoc ** seqloc_array
 Array of masked locations. More...
 

Detailed Description

Structure for keeping the query masking information.

Definition at line 210 of file blast_def.h.

Member Data Documentation

◆ seqloc_array

BlastSeqLoc** BlastMaskLoc::seqloc_array

Array of masked locations.

Every query is allocated the number of contexts associated with the program. In the case of nucleotide searches, the strand(s) to search dictatate which elements of the array for a given query are filled. For translated searches, this should also be the same (by design) but the C toolkit API does NOT implement this, it rather fills all elements for all queries with masked locations in protein coordinates (if any). The C++ API does follow the convention which populates each element, only if so dictated by the strand(s) to search for each query.

See also
BLAST_GetNumberOfContexts

Definition at line 231 of file blast_def.h.

Referenced by BLAST_ComplementMaskLocations(), BlastMaskLocDNAToProtein(), BlastMaskLocDup(), BlastMaskLocFree(), BlastMaskLocNew(), BlastMaskLocProteinToDNA(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), CBlastMaskLoc::DebugDump(), and s_GetFilteringLocationsForOneContext().

◆ total_size

Int4 BlastMaskLoc::total_size

Total size of the BlastSeqLoc array below.

This is always the number of queries times the number of contexts. Note that in the case of translated query searches, these locations must be provided in protein coordinates to BLAST_MainSetUp.

See also
BLAST_GetNumberOfContexts
BlastMaskLocDNAToProtein

Definition at line 218 of file blast_def.h.

Referenced by BlastMaskLocDNAToProtein(), BlastMaskLocDup(), BlastMaskLocFree(), BlastMaskLocNew(), BlastMaskLocProteinToDNA(), BlastSetUp_MaskQuery(), BOOST_AUTO_TEST_CASE(), and CBlastMaskLoc::DebugDump().


The documentation for this struct was generated from the following file:
Modified on Wed May 22 11:36:02 2024 by modify_doxy.py rev. 669887