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NCBI C++ ToolKit: GapEditScript Struct Reference

Search Toolkit Book for GapEditScript

Edit script: linked list of correspondencies between two sequences. More...

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

Edit script: linked list of correspondencies between two sequences.

Definition at line 57 of file gapinfo.h.

Array of number of operations.

Definition at line 59 of file gapinfo.h.

Referenced by BLAST_GappedAlignmentWithTraceback(), Blast_HSPCalcLengthAndGaps(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_PrelimEditBlockToGapEditScript(), Blast_TracebackFromHSPList(), BOOST_AUTO_TEST_CASE(), CEditScript::CEditScript(), checkReevaluateResultsGapped(), GapEditScriptCombine(), GapEditScriptDelete(), GapEditScriptDup(), GapEditScriptPartialCopy(), JumperPrelimEditBlockToGapEditScript(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastGapAlignStruct_Copy(), s_BlastOOFTracebackToGapEditScript(), s_CollectSeqAlignData(), s_CorrectUASequence(), s_CreateHSPForWordHit(), s_CutOffGapEditScript(), s_FindSpliceJunctionsForOverlaps(), s_GetTraceback(), s_MergeHSPs(), s_OOFBlastHSP2SeqAlign(), s_RebuildEditScript(), s_ReduceGaps(), s_SetupHSPForGappedReevaluateTest(), s_TestHSPRanges(), s_TrimHSP(), s_UpdateEditScript(), s_UpdateReevaluatedHSP(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().

Array of type of operation.

Definition at line 58 of file gapinfo.h.

Referenced by BLAST_GappedAlignmentWithTraceback(), Blast_HSPCalcLengthAndGaps(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_PrelimEditBlockToGapEditScript(), Blast_TracebackFromHSPList(), BOOST_AUTO_TEST_CASE(), CEditScript::CEditScript(), checkReevaluateResultsGapped(), GapEditScriptCombine(), GapEditScriptDelete(), GapEditScriptDup(), GapEditScriptPartialCopy(), JumperPrelimEditBlockToGapEditScript(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastGapAlignStruct_Copy(), s_BlastHSP2SeqAlign(), s_BlastHSPRPSUpdate(), s_BlastOOFTracebackToGapEditScript(), s_CollectSeqAlignData(), s_CorrectUASequence(), s_CreateHSPForWordHit(), s_CutOffGapEditScript(), s_GetTraceback(), s_MergeHSPs(), s_OOFBlastHSP2SeqAlign(), s_RebuildEditScript(), s_ReduceGaps(), s_SetupHSPForGappedReevaluateTest(), s_TestHSPRanges(), s_TrimHSP(), and s_UpdateEditScript().

Size of above arrays.

Definition at line 60 of file gapinfo.h.

Referenced by BLAST_GappedAlignmentWithTraceback(), Blast_HSPCalcLengthAndGaps(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_TracebackFromHSPList(), BOOST_AUTO_TEST_CASE(), CEditScript::CEditScript(), GapEditScriptCombine(), GapEditScriptDup(), MakeSplicedSeg(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastGapAlignStruct_Copy(), s_BlastHSP2SeqAlign(), s_BlastHSPRPSUpdate(), s_BlastOOFTracebackToGapEditScript(), s_CollectSeqAlignData(), s_CorrectUASequence(), s_CutOffGapEditScript(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_MergeHSPs(), s_OOFBlastHSP2SeqAlign(), s_RebuildEditScript(), s_ReduceGaps(), s_TestChains(), s_TestHSPRanges(), s_TrimHSP(), s_UpdateEditScript(), s_UpdateReevaluatedHSP(), and CPhiblastTestFixture::x_CheckGappedAlignmentResults().

The documentation for this struct was generated from the following file:

• include/algo/blast/core/gapinfo.h

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