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BlastGapAlignStruct Struct Reference

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Structure supporting the gapped alignment. More...

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

+ Collaboration diagram for BlastGapAlignStruct:

Public Attributes

Boolean positionBased
 Is this PSI-BLAST? More...
 
GapStateArrayStructstate_struct
 Structure to keep extension state information. More...
 
GapEditScriptedit_script
 The traceback (gap) information. More...
 
GapPrelimEditBlockfwd_prelim_tback
 traceback from right extensions More...
 
GapPrelimEditBlockrev_prelim_tback
 traceback from left extensions More...
 
SGreedyAlignMemgreedy_align_mem
 Preallocated memory for the greedy gapped extension. More...
 
BlastGapDPdp_mem
 scratch structures for dynamic programming More...
 
Int4 dp_mem_alloc
 current number of structures allocated More...
 
BlastScoreBlksbp
 Pointer to the scoring information block. More...
 
Int4 gap_x_dropoff
 X-dropoff parameter to use. More...
 
Int4 max_mismatches
 Max number of mismatches for jumper. More...
 
Int4 mismatch_window
 Window sie for mismatches for jumper. More...
 
Int4 query_start
 query start offset of current alignment More...
 
Int4 query_stop
 query end offseet of current alignment More...
 
Int4 subject_start
 subject start offset current alignment More...
 
Int4 subject_stop
 subject end offset of current alignment More...
 
Int4 greedy_query_seed_start
 for greedy alignments, the query offset of the gapped start point More...
 
Int4 greedy_subject_seed_start
 for greedy alignments, the subject offset of the gapped start point More...
 
Int4 score
 Return value: alignment score. More...
 
JumperGapAlignjumper
 data for jumper alignment More...
 

Detailed Description

Structure supporting the gapped alignment.

Definition at line 69 of file blast_gapalign.h.

Member Data Documentation

◆ dp_mem

BlastGapDP* BlastGapAlignStruct::dp_mem

◆ dp_mem_alloc

Int4 BlastGapAlignStruct::dp_mem_alloc

◆ edit_script

GapEditScript* BlastGapAlignStruct::edit_script

◆ fwd_prelim_tback

GapPrelimEditBlock* BlastGapAlignStruct::fwd_prelim_tback

◆ gap_x_dropoff

Int4 BlastGapAlignStruct::gap_x_dropoff

◆ greedy_align_mem

SGreedyAlignMem* BlastGapAlignStruct::greedy_align_mem

Preallocated memory for the greedy gapped extension.

Definition at line 76 of file blast_gapalign.h.

Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), and BLAST_GreedyGappedAlignment().

◆ greedy_query_seed_start

Int4 BlastGapAlignStruct::greedy_query_seed_start

for greedy alignments, the query offset of the gapped start point

Definition at line 88 of file blast_gapalign.h.

Referenced by BLAST_GetGappedScore(), and s_BlastGreedyGapAlignStructFill().

◆ greedy_subject_seed_start

Int4 BlastGapAlignStruct::greedy_subject_seed_start

for greedy alignments, the subject offset of the gapped start point

Definition at line 90 of file blast_gapalign.h.

Referenced by BLAST_GetGappedScore(), and s_BlastGreedyGapAlignStructFill().

◆ jumper

JumperGapAlign* BlastGapAlignStruct::jumper

◆ max_mismatches

Int4 BlastGapAlignStruct::max_mismatches

Max number of mismatches for jumper.

Definition at line 82 of file blast_gapalign.h.

Referenced by BLAST_GapAlignStructNew(), and JumperGappedAlignmentCompressedWithTraceback().

◆ mismatch_window

Int4 BlastGapAlignStruct::mismatch_window

Window sie for mismatches for jumper.

Definition at line 83 of file blast_gapalign.h.

Referenced by BLAST_GapAlignStructNew(), and JumperGappedAlignmentCompressedWithTraceback().

◆ positionBased

Boolean BlastGapAlignStruct::positionBased

◆ query_start

Int4 BlastGapAlignStruct::query_start

◆ query_stop

Int4 BlastGapAlignStruct::query_stop

◆ rev_prelim_tback

GapPrelimEditBlock* BlastGapAlignStruct::rev_prelim_tback

◆ sbp

BlastScoreBlk* BlastGapAlignStruct::sbp

◆ score

Int4 BlastGapAlignStruct::score

◆ state_struct

GapStateArrayStruct* BlastGapAlignStruct::state_struct

Structure to keep extension state information.

Definition at line 71 of file blast_gapalign.h.

Referenced by ALIGN_EX(), BLAST_GapAlignStructFree(), and s_OutOfFrameAlignWithTraceback().

◆ subject_start

Int4 BlastGapAlignStruct::subject_start

◆ subject_stop

Int4 BlastGapAlignStruct::subject_stop

The documentation for this struct was generated from the following file:
Modified on Wed Feb 21 09:55:27 2024 by modify_doxy.py rev. 669887