NCBI C++ ToolKit
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Search Toolkit Book for BlastGapAlignStruct
Structure supporting the gapped alignment. More...
#include <algo/blast/core/blast_gapalign.h>
Public Attributes | |
Boolean | positionBased |
Is this PSI-BLAST? More... | |
GapStateArrayStruct * | state_struct |
Structure to keep extension state information. More... | |
GapEditScript * | edit_script |
The traceback (gap) information. More... | |
GapPrelimEditBlock * | fwd_prelim_tback |
traceback from right extensions More... | |
GapPrelimEditBlock * | rev_prelim_tback |
traceback from left extensions More... | |
SGreedyAlignMem * | greedy_align_mem |
Preallocated memory for the greedy gapped extension. More... | |
BlastGapDP * | dp_mem |
scratch structures for dynamic programming More... | |
Int4 | dp_mem_alloc |
current number of structures allocated More... | |
BlastScoreBlk * | sbp |
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... | |
JumperGapAlign * | jumper |
data for jumper alignment More... | |
ChainingStruct * | chaining |
data for chaining More... | |
Structure supporting the gapped alignment.
Definition at line 70 of file blast_gapalign.h.
ChainingStruct* BlastGapAlignStruct::chaining |
data for chaining
Definition at line 96 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), and s_ChainingAlignment().
BlastGapDP* BlastGapAlignStruct::dp_mem |
scratch structures for dynamic programming
Definition at line 79 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), Blast_SemiGappedAlign(), s_BlastAlignPackedNucl(), s_NuclSmithWaterman(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RestrictedGappedAlign(), and s_SmithWatermanScoreOnly().
Int4 BlastGapAlignStruct::dp_mem_alloc |
current number of structures allocated
Definition at line 80 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructNew(), Blast_SemiGappedAlign(), s_BlastAlignPackedNucl(), s_NuclSmithWaterman(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RestrictedGappedAlign(), and s_SmithWatermanScoreOnly().
GapEditScript* BlastGapAlignStruct::edit_script |
The traceback (gap) information.
Definition at line 74 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), Blast_TracebackFromHSPList(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastGreedyGapAlignStructFill(), s_CreateHSP(), s_PHITracebackFromHSPList(), s_RedoOneAlignment(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().
GapPrelimEditBlock* BlastGapAlignStruct::fwd_prelim_tback |
traceback from right extensions
Definition at line 75 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), BLAST_GappedAlignmentWithTraceback(), BLAST_GreedyGappedAlignment(), PHIGappedAlignmentWithTraceback(), s_GetTraceback(), s_NewAlignmentUsingXdrop(), and s_SWFindFinalEndsUsingXdrop().
Int4 BlastGapAlignStruct::gap_x_dropoff |
X-dropoff parameter to use.
Definition at line 82 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructNew(), BLAST_GreedyGappedAlignment(), Blast_SemiGappedAlign(), JumperGappedAlignmentCompressedWithTraceback(), s_BlastDynProgNtGappedAlignment(), s_NewAlignmentUsingXdrop(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RedoOneAlignment(), s_RestrictedGappedAlign(), and s_SWFindFinalEndsUsingXdrop().
SGreedyAlignMem* BlastGapAlignStruct::greedy_align_mem |
Preallocated memory for the greedy gapped extension.
Definition at line 77 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), and BLAST_GreedyGappedAlignment().
Int4 BlastGapAlignStruct::greedy_query_seed_start |
for greedy alignments, the query offset of the gapped start point
Definition at line 89 of file blast_gapalign.h.
Referenced by BLAST_GetGappedScore(), and s_BlastGreedyGapAlignStructFill().
Int4 BlastGapAlignStruct::greedy_subject_seed_start |
for greedy alignments, the subject offset of the gapped start point
Definition at line 91 of file blast_gapalign.h.
Referenced by BLAST_GetGappedScore(), and s_BlastGreedyGapAlignStructFill().
JumperGapAlign* BlastGapAlignStruct::jumper |
data for jumper alignment
Definition at line 95 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), BlastNaExtendJumper(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), s_CreateHSP(), s_ExtendAlignment(), s_ShiftGaps(), and ShortRead_IndexedWordFinder().
Int4 BlastGapAlignStruct::max_mismatches |
Max number of mismatches for jumper.
Definition at line 83 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructNew(), and JumperGappedAlignmentCompressedWithTraceback().
Int4 BlastGapAlignStruct::mismatch_window |
Window sie for mismatches for jumper.
Definition at line 84 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructNew(), and JumperGappedAlignmentCompressedWithTraceback().
Boolean BlastGapAlignStruct::positionBased |
Is this PSI-BLAST?
Definition at line 71 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructNew(), Blast_SemiGappedAlign(), s_BlastSearchEngineOneContext(), s_GetTraceback(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RestrictedGappedAlign(), s_RPSComputeTraceback(), s_RPSGapAlignDataPrepare(), s_RPSPreliminarySearchEngine(), s_SmithWatermanScoreOnly(), and SmithWatermanScoreWithTraceback().
Int4 BlastGapAlignStruct::query_start |
query start offset of current alignment
Definition at line 85 of file blast_gapalign.h.
Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), Blast_TracebackFromHSPList(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperGoodAlign(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastDynProgNtGappedAlignment(), s_BlastGreedyGapAlignStructFill(), s_BlastProtGappedAlignment(), s_CreateHSP(), s_ExtendAlignment(), s_NewAlignmentFromGapAlign(), s_PHIGappedAlignment(), s_ShiftGaps(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().
Int4 BlastGapAlignStruct::query_stop |
query end offseet of current alignment
Definition at line 86 of file blast_gapalign.h.
Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperGoodAlign(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastDynProgNtGappedAlignment(), s_BlastGreedyGapAlignStructFill(), s_BlastProtGappedAlignment(), s_CreateHSP(), s_ExtendAlignment(), s_NewAlignmentFromGapAlign(), s_PHIGappedAlignment(), s_ShiftGaps(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().
GapPrelimEditBlock* BlastGapAlignStruct::rev_prelim_tback |
traceback from left extensions
Definition at line 76 of file blast_gapalign.h.
Referenced by BLAST_GapAlignStructFree(), BLAST_GapAlignStructNew(), BLAST_GappedAlignmentWithTraceback(), BLAST_GreedyGappedAlignment(), PHIGappedAlignmentWithTraceback(), s_NewAlignmentUsingXdrop(), and s_SWFindFinalEndsUsingXdrop().
BlastScoreBlk* BlastGapAlignStruct::sbp |
Pointer to the scoring information block.
Definition at line 81 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_ComputeTraceback(), BLAST_ComputeTraceback_MT(), BLAST_GapAlignStructNew(), BLAST_GetGappedScore(), BLAST_PreliminarySearchEngine(), Blast_RedoAlignmentCore_MT(), Blast_RunPreliminarySearchWithInterrupt(), Blast_SemiGappedAlign(), BLAST_SmithWatermanGetGappedScore(), PHIGappedAlignmentWithTraceback(), s_BlastAlignPackedNucl(), s_BlastRunFullSearchCleanUp(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_GetTraceback(), s_NuclSmithWaterman(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_RestrictedGappedAlign(), s_RPSComputeTraceback(), s_RPSGapAlignDataPrepare(), s_RPSPreliminarySearchEngine(), s_SmithWatermanScoreOnly(), SmithWatermanScoreWithTraceback(), and SThreadLocalDataFree().
Int4 BlastGapAlignStruct::score |
Return value: alignment score.
Definition at line 93 of file blast_gapalign.h.
Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), Blast_TracebackFromHSPList(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), DoAnchoredScan(), JumperGappedAlignmentCompressedWithTraceback(), JumperGoodAlign(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastDynProgNtGappedAlignment(), s_BlastGreedyGapAlignStructFill(), s_BlastProtGappedAlignment(), s_CreateHSP(), s_NewAlignmentFromGapAlign(), s_PHIGappedAlignment(), s_PHITracebackFromHSPList(), s_ShiftGaps(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().
GapStateArrayStruct* BlastGapAlignStruct::state_struct |
Structure to keep extension state information.
Definition at line 72 of file blast_gapalign.h.
Referenced by ALIGN_EX(), BLAST_GapAlignStructFree(), and s_OutOfFrameAlignWithTraceback().
Int4 BlastGapAlignStruct::subject_start |
subject start offset current alignment
Definition at line 87 of file blast_gapalign.h.
Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), Blast_TracebackFromHSPList(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperGoodAlign(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastDynProgNtGappedAlignment(), s_BlastGreedyGapAlignStructFill(), s_BlastProtGappedAlignment(), s_CreateHSP(), s_ExtendAlignment(), s_NewAlignmentFromGapAlign(), s_PHIGappedAlignment(), s_ShiftGaps(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().
Int4 BlastGapAlignStruct::subject_stop |
subject end offset of current alignment
Definition at line 88 of file blast_gapalign.h.
Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_HSPUpdateWithTraceback(), BlastNaExtendJumper(), BOOST_AUTO_TEST_CASE(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperGoodAlign(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), s_BlastDynProgNtGappedAlignment(), s_BlastGreedyGapAlignStructFill(), s_BlastProtGappedAlignment(), s_CreateHSP(), s_ExtendAlignment(), s_NewAlignmentFromGapAlign(), s_PHIGappedAlignment(), s_ShiftGaps(), ShortRead_IndexedWordFinder(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().