Search Toolkit Book for _dp_demo_8cpp
#include <ncbi_pch.hpp>#include <corelib/ncbistd.hpp>#include <corelib/ncbi_limits.h>#include <util/tables/raw_scoremat.h>#include <map>#include <string>#include <algo/structure/struct_dp/struct_dp.h>#include "struct_dp_demo.hpp"
Include dependency graph for struct_dp_demo.cpp:
Go to the source code of this file.
Macros | |
| #define | ERROR_MESSAGE(s) ERR_POST(Error << "struct_dp_demo: " << s << '!') |
| #define | INFO_MESSAGE(s) ERR_POST(Info << "struct_dp_demo: " << s) |
Functions | |
| static unsigned int | ScreenResidueCharacter (char original) |
| static int | GetBLOSUM62Score (char a, char b) |
| int | ScoreByBlosum62 (unsigned int block, unsigned int queryPos) |
| USING_SCOPE (struct_dp) | |
| int | main (int argc, const char *argv[]) |
Variables | |
| USING_NCBI_SCOPE | |
| static DP_BlockInfo * | blocks = NULL |
| static string | subject |
| static string | query |
Macro Definition Documentation
◆ ERROR_MESSAGE
Definition at line 51 of file struct_dp_demo.cpp.
◆ INFO_MESSAGE
Definition at line 52 of file struct_dp_demo.cpp.
Function Documentation
◆ GetBLOSUM62Score()
Definition at line 74 of file struct_dp_demo.cpp.
References a, b, NCBISM_Blosum62, NCBISM_Unpack(), SNCBIFullScoreMatrix::s, and ScreenResidueCharacter().
Referenced by Threader::CreateSeqMtf(), PSSMWrapper::GetPSSMScore(), AlignmentManager::MergeUpdates(), SequenceDisplay::ProximitySort(), and ScoreByBlosum62().
◆ main()
Definition at line 192 of file struct_dp_demo.cpp.
References eDiag_Info, eDS_Default, NcbiCerr, NULL, SetDiagPostLevel(), and SetDiagStream().
◆ ScoreByBlosum62()
Definition at line 91 of file struct_dp_demo.cpp.
References DP_BlockInfo::blockPositions, blocks, DP_BlockInfo::blockSizes, DP_NEGATIVE_INFINITY, ERROR_MESSAGE, GetBLOSUM62Score(), i, DP_BlockInfo::nBlocks, query, and subject.
Referenced by DPApp::Run().
◆ ScreenResidueCharacter()
Definition at line 58 of file struct_dp_demo.cpp.
References toupper().
Referenced by GetBLOSUM62Score().
◆ USING_SCOPE()
| USING_SCOPE | ( | struct_dp | ) |
Variable Documentation
◆ blocks
|
static |
Definition at line 87 of file struct_dp_demo.cpp.
Referenced by BlockIntersector::addOneAlignment(), CalculateGlobalMatrix(), CalculateGlobalMatrixGeneric(), CalculateLocalMatrix(), CalculateLocalMatrixGeneric(), Block::concatenate(), AlignmentSet::CreateFromMultiple(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), CreatePairwiseSeqAlignFromMultipleRow(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), DP_CreateBlockInfo(), DP_DestroyBlockInfo(), DP_GlobalBlockAlign(), DP_GlobalBlockAlignGeneric(), DP_LocalBlockAlign(), DP_LocalBlockAlignGeneric(), DP_MultipleLocalBlockAlign(), DP_MultipleLocalBlockAlignGeneric(), FillInAlignmentData(), CDDAnnotateDialog::GetCurrentHighlightedIntervals(), BlockIntersector::getIntersectedAlignment(), BlockExtender::getScoringTerm(), IsFirstResidueOfABlock(), AlignmentManager::MergeUpdates(), StructureWindow::OnAlignStructures(), SequenceViewerWindow::OnHighlight(), bm::print_stat(), ProjectExon_newlogic(), SequenceDisplay::ProximitySort(), PSSMWrapper::PSSMWrapper(), AlignmentManager::RealignAllDependentStructures(), StructureObject::RealignStructure(), BlockIntersector::removeOneAlignment(), CMultiApplication::Run(), DPApp::Run(), s_Dump(), s_DumpSparse(), s_ReleaseToFreePages(), s_SetAmbiguitiesBlocks(), UpdateViewer::SaveAlignments(), SBlocks::SBlocks(), ScoreByBlosum62(), AlignmentUtility::ScoreRowByPSSM(), CBedImportData::Serialize(), CBedFeatureRecord::SetBlocks(), TracebackGlobalAlignment(), TracebackLocalAlignment(), TracebackMultipleLocalAlignments(), UnpackDPResult(), CClickableSortUniqueCount::UpdateTree(), ValidateFrozenBlockPositions(), CTar::x_Skip(), CBedReader::xSetFeatureLocationBlock(), and CBedReader::xSetFeatureLocationRna().
◆ query
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static |
Definition at line 88 of file struct_dp_demo.cpp.
Referenced by _IMPALAScaleMatrix(), _PSICalculateInformationContentFromScoreMatrix(), _PSIComputeScoreProbabilities(), _PSIConvertFreqRatiosToPSSM(), _PSICreateAndScalePssmFromFrequencyRatios(), _PSIScaleMatrix(), _PSIUpdateLambdaK(), _SQLNativeSql(), CAlignFilter::AddQSRangeRestriction(), CSequenceInputStats::AddQueryBatch(), BDB_ParseQuery(), BDB_PrintQueryTree(), CdBlaster::blast(), BLAST_ComputeTraceback(), BLAST_ComputeTraceback_MT(), Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), Blast_FindWindowMaskerLoc_Fwd(), BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), Blast_GetOneQueryStructs(), BLAST_GreedyGappedAlignment(), Blast_HSPGetNumIdentities(), Blast_HSPGetNumIdentitiesAndPositives(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListsMerge(), Blast_HSPListSubjectBestHit(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_HSPTestIdentityAndLength(), BLAST_PreliminarySearchEngine(), Blast_RedoOneMatch(), Blast_RedoOneMatchSmithWaterman(), Blast_RunFullSearch(), Blast_RunPreliminarySearch(), Blast_RunPreliminarySearchWithInterrupt(), Blast_RunTracebackSearch(), Blast_RunTracebackSearchWithInterrupt(), Blast_ScoreBlkKbpUngappedCalc(), Blast_SetPHIPatternInfo(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastAaLookupIndexQuery(), BlastAaWordFinder(), BlastCompressedAaLookupTableNew(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignment(), BlastGetStartForGappedAlignmentNucl(), BlastHashLookupIndexQueryExactMatches(), BlastHSPWriterNew(), BlastKmerGetKmerSet(), BlastKmerGetKmerSet2(), BlastKmerGetKmerSetStats(), BlastLookupIndexQueryExactMatches(), BlastMBLookupTableNew(), BlastNaExtendJumper(), BlastNaHashLookupTableNew(), BlastNaLookupTableNew(), BlastNaWordFinder(), BlastRPSWordFinder(), BlastSmallNaLookupTableNew(), BLbasicSmithWatermanScoreOnly(), BLSmithWatermanFindStart(), BLspecialSmithWatermanFindStart(), BLspecialSmithWatermanScoreOnly(), BOOST_AUTO_TEST_CASE(), CAlignCompare::SAlignment::BreakOnBoundaries(), CAlignFilter::CAlignFilter(), CCassBlobWaiter::CanRestart(), CBl2Seq::CBl2Seq(), CBlastKmer::CBlastKmer(), CBlobRetriever::CBlobRetriever(), CCddInputData::CCddInputData(), CExportStrategy::CExportStrategy(), change_database(), change_txn(), CheckForEmptySequences(), CODBC_CursorCmdBase::CODBC_CursorCmdBase(), CMultiAlignerTest::CompareDomainHits(), CAlignCompare::SAlignment::CompareGroup(), CScoreBuilderBase::ComputeScore(), continue_logging_in(), CPepXML::ConvertScanID(), CPsiBl2Seq::CPsiBl2Seq(), CPsiBlastInputClustalW::CPsiBlastInputClustalW(), CPsiBlastInputData::CPsiBlastInputData(), CSetupFactory::CreateHspWriter(), CTL_CursorCmd::CTL_CursorCmd(), CTL_CursorCmdExpl::CTL_CursorCmdExpl(), CUrlArgs::CUrlArgs(), SPSG_ArgsBase::CUrlArgs(), I_Connection::Cursor(), CDB_Connection::Cursor(), CTL_Connection::Cursor(), CODBC_Connection::Cursor(), DBAPI_MakeTrans(), dbuse(), CSdbapiSimpleApp::DemoDynamicSql(), CSdbapiSimpleApp::DemoParamerizedSql(), CSdbapiSimpleApp::DemoStaticSql(), CSdbapiSimpleApp::DemoStoredProc(), CCigar::DetailedCigarString(), CCigar::Distance(), CAdvancedAlignCleanup::DivideByQuerySubjectPairs(), DoAnchoredSearch(), CSimpleB2SWrapper::DoBlast2Seqs(), DoCompartments(), pub_report::DoHydraSearch(), CHydraSearch::DoHydraSearch(), CPsiBlastApp::DoIterations(), CEJournalSearch::DoOneESearch(), CEJournalSearch::DoOneESummary(), CDeltaBlastApp::DoPsiBlastIterations(), CEUtilsUpdater::DoPubSearch(), DoTest(), CBDB_FileScanner::Evaluate(), exec_query(), CNSTDatabase::ExecSP_AddAttribute(), CNSTDatabase::ExecSP_CreateClient(), CNSTDatabase::ExecSP_CreateObjectWithClientID(), CNSTDatabase::ExecSP_CreateUser(), CNSTDatabase::ExecSP_DelAttribute(), CNSTDatabase::ExecSP_DoesObjectExist(), CNSTDatabase::ExecSP_GetAttribute(), CNSTDatabase::ExecSP_GetAttributeNames(), CNSTDatabase::ExecSP_GetClientObjects(), CNSTDatabase::ExecSP_GetClients(), CNSTDatabase::ExecSP_GetGeneralDBInfo(), CNSTDatabase::ExecSP_GetObjectExpiration(), CNSTDatabase::ExecSP_GetObjectFixedAttributes(), CNSTDatabase::ExecSP_GetObjectSize(), CNSTDatabase::ExecSP_GetObjectSizeAndLocator(), CNSTDatabase::ExecSP_GetStatDBInfo(), CNSTDatabase::ExecSP_GetUserObjects(), CNSTDatabase::ExecSP_GetUsers(), CNSTDatabase::ExecSP_RemoveObject(), CNSTDatabase::ExecSP_SetExpiration(), CNSTDatabase::ExecSP_UpdateObjectOnRead(), CNSTDatabase::ExecSP_UpdateObjectOnRelocate(), CNSTDatabase::ExecSP_UpdateObjectOnWrite(), CNSTDatabase::ExecSP_UpdateObjectSizeIfNULL(), CNSTDatabase::ExecSP_UpdateUserIDForObject(), CNSTDatabase::ExecSP_UpdateUserKeyObjectOnWrite(), CCassandraFullscanRunner::Execute(), CTDQueryDataSource::ExecuteStringQuery(), CPhyloTreeDataSource::ExecuteStringQuery(), FetchBioseqInfo(), FetchCanonicalSeqId(), CDbapiTestSpeedApp::FetchFile(), CPubseqGatewayHugeIpgReportHelper::FetchHugeIpgConfigResult(), CDbapiTestSpeedApp::FetchResults(), CPhyloTreeDataSource::FindNodes(), NAdapterSearch::CSimpleUngappedAligner::FindSingleBest(), CCassOneExecConsumer::Finish(), impl::g_SubstituteParam(), CFlatSeqLoc::CGuardedToAccessionMap::Get(), CNetStorageGCDatabase::GetAppLock(), CdBlaster::getCompositeIndex(), CCassConnection::GetDatacenterName(), CNetStorageGCDatabase::GetDBStructureVersion(), CNetStorageGCDatabase::GetGCCandidates(), CCigar::GetInDels(), GetInteractionDataFromIbis(), CCassConnection::GetLocalPeersAddressList(), CCassandraFullscanPlan::GetNextQuery(), CCassandraFullscanPlan::GetPartitionCountEstimate(), CScoreBuilderBase::GetPercentCoverage(), IAlnGraphicDataSource::GetQuery(), CUrlArgs::GetQueryString(), CCassConnection::GetSizeEstimates(), CAdvancedAlignCleanup::GetSplignCompartments(), CCassConnection::GetTokenRanges(), GetUnalignedRegionLength(), CBlastFormatUtil::GetWholeAlnSeqStrings(), CCassBlobTaskLoadBlob::InitBlobChunkDataQuery(), InitializeBlastScoreBlk(), CDatabase::IsConnected(), CAssemblyInfo::IsSameAssembly(), JumperExtendLeft(), JumperExtendLeftCompressed(), JumperExtendLeftCompressedWithTraceback(), JumperExtendLeftCompressedWithTracebackOptimal(), JumperExtendRight(), JumperExtendRightCompressed(), JumperExtendRightCompressedWithTraceback(), JumperExtendRightCompressedWithTracebackOptimal(), JumperExtendRightWithTraceback(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperNaWordFinder(), Kappa_compactSearchItemsNew(), LookupTableWrapInit(), LookupTableWrapInit_MT(), main(), CTblastnNode::Main(), CIgBlastnApp::CIgWorker::Main(), CIgBlastnApp::CIgFormatter::Main(), PssmMaker::make(), CValidator::MakeTaxUpdateFunction(), MapperWordHitsNew(), CAlignFilter::Match(), CCigar::Matches(), MB_IndexedWordFinder(), minhash_query(), minhash_query2(), PssmMaker::modifyQuery(), RpsTestFixture::NuclSearch(), odbc_check_no_row(), CQueryParsePanel::OnRecentQuery(), CBLAST_DB_Dialog::OnSearchTextUpdated(), CItemSelectionPanel::OnSearchUpdated(), CTaxTreeTestDlg::OnSubmitClick(), CQueryParsePanel::OnToggleHideUnselected(), CCassandraFullscanWorker::operator()(), PhiBlastResults2SeqAlign_OMF(), PHIBlastWordFinder(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), PHIGetPatternOccurrences(), CAlignCompare::SAlignment::PopulateBoundariesMap(), PopulateEntry(), IBISAnnotateDialog::PopulateInteractionData(), CCassConnection::Prepare(), CPubseqGatewayHugeIpgReportHelper::PrepareHugeIpgConfigQuery(), CBlastFormatUtil::PrintAsciiPssm(), PrintCompartments(), ProduceCassandraQueryErrorMessage(), CCassBlobWaiter::ProduceQuery(), PsiBlastComputePssmFromAlignment(), PsiBlastComputePssmScores(), PSICreatePssmFromFrequencyRatios(), CSearchToolBase::PullSearch(), CEntrez2Client::Query(), SequenceViewerWindow::QueryShowAllRows(), CSplitQueryTestFixture::QuerySplitter_BlastnSingleQueryMultiChunk(), CSplitQueryTestFixture::QuerySplitter_BlastxSingleQueryMultiChunk(), ReadCassandraMessages(), ReadCassandraSatInfo(), ReadSecureSatUsers(), CNetStorageGCDatabase::ReleaseAppLock(), RemapToQueryLoc(), CNetStorageGCDatabase::RemoveObject(), CBDB_FileScanner::ResolveFields(), CLocalPssmSearch::Run(), CPsiBlastApp::Run(), CIgBlastpApp::Run(), CSdbapiTest::Run(), CVectorScreen::Run(), DPApp::Run(), CVDBTblastnApp::Run(), CId1FetchApp::Run(), CIdfetchApplication::Run(), CEntrez2ClientApp::Run(), CBlastSampleApplication::Run(), run_query(), CHydraServer::RunHydraSearch(), CLangQueryApp::RunSample(), s_AddNeighboringWords(), s_AddWordHits(), s_AdjustHspOffsetsAndGetQueryData(), CUpdateSeq_Input::s_Align2IdenticalSeq(), CIgBlast::s_AppendResults(), s_AreSequencesEqual(), CMixedStrands::s_Blast2NASeq(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastAaExtendLeft(), s_BlastAaExtendOneHit(), s_BlastAaExtendRight(), s_BlastAaExtendTwoHit(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastDynProgNtGappedAlignment(), s_BlastHSPListRPSUpdate(), s_BlastHSPMapperPairedNew(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), s_BlastProtGappedAlignment(), s_BlastResults2SeqAlignDatabaseSearch_OMF(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_BlastSeqLoc2CSeqloc(), s_BlastSeqLoc2MaskedRegions(), s_BlastSetUpAuxStructures(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_BlastSmallNaLookupFinalize(), s_CodonVariation(), s_CompressedAddNeighboringWords(), s_CompressedAddWordHits(), s_ComputeNumIdentities(), s_ComputeTraceback(), s_CreateAlign(), s_CreateHSPForWordHit(), s_ExtendAlignment(), s_FillContigMBTable(), s_FillDiscMBTable(), s_FillMaskLocFromBlastResults(), s_FillPV(), s_FindAdapterInSequence(), s_FindAdapters(), s_FindPolyATails(), s_FindSpliceJunctions(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_GetBioseqValues(), s_GetCSIValues(), CAdapterSearchApplication::s_GetIdentity(), s_GetPercentCoverage(), s_GetPosBasedStartFreqRatios(), s_GetQueryAndSubjectStrings(), s_GetQueryBioseq(), s_IntronToGap(), s_MakeQueryFactory(), s_MergeHSPs(), s_MinhashSequences(), s_MinhashSequences2(), s_NaHashLookupFillPV(), s_NewAlignmentUsingXdrop(), s_NuclUngappedExtend(), s_NuclUngappedExtendExact(), CCassQueryCbRef::s_OnFutureCb(), s_OutOfFrameSemiGappedAlignWrap(), s_PHIGappedAlignment(), s_PHITracebackFromHSPList(), CAsnSubCacheCreateApplication::SBlobVersion::s_PopulateSatelliteMap(), s_ReadAndTestQueryFromString(), s_RPSComputeTraceback(), s_RPSPreliminarySearchEngine(), s_RunBlast2AASeq(), s_RunBlast2NASeq(), s_ScalePosMatrix(), s_SequenceGetRange(), s_SetAdapter(), s_SetAirrAlignmentInfo(), s_ShiftGaps(), s_ShiftGapsRight(), s_SWFindFinalEndsUsingXdrop(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), s_TrimOverlap(), s_TSeqLocVectorToBioseqSet(), s_TSeqLocVectorToTSeqLocs(), CBDB_FileScanner::Scan(), CCigar::Score(), ScoreByBlosum62(), CDbIndex::Search(), CCachedTaxon3_impl::SendOrgRefList(), variation::SeqsMatch(), CCassConnection::SetKeyspace(), CBl2Seq::SetQuery(), SetQueryString(), CUrlArgs_Parser::SetQueryString(), CCassBlobWaiter::SetupQueryCB3(), ShortRead_IndexedWordFinder(), CDbapiSampleApp::ShowResults(), CCassOneExecConsumer::Start(), CSearchToolBase::StartSearch(), CBDB_FileScanner::StaticEvaluate(), tds5_fix_dot_query(), tds71_submit_prepexec(), tds7_build_param_def_from_params(), tds7_put_query_params(), tds7_write_param_def_from_params(), tds_alloc_cursor(), tds_bcp_start_insert_stmt(), tds_count_placeholders(), tds_count_placeholders_ucs2le(), tds_multiple_query(), tds_send_emulated_execute(), tds_start_query_head(), tds_submit_execdirect(), tds_submit_prepare(), tds_submit_query(), tds_submit_query_params(), tds_submit_queryf(), Test(), test(), CCigar::ToAlign(), CBLASTSearchOptionsPanel::TransferDataToWindow(), CEUtilsGeneric::TryQuery(), UnpackDPResult(), CRCache::update(), CNSTDatabase::UpdateExpirationIfExists(), CCassAccVerHistoryTaskFetch::Wait1(), CCassBioseqInfoTaskFetch::Wait1(), CCassBlobTaskFetchSplitHistory::Wait1(), CCassNAnnotTaskFetch::Wait1(), CCassSI2CSITaskFetch::Wait1(), CCassStatusHistoryTaskFetch::Wait1(), CCassStatusHistoryTaskGetPublicComment::Wait1(), CPubseqGatewayFetchIpgReport::Wait1(), CMultiAligner::x_AddNewSegment(), CMultiAligner::x_AlignProfileProfile(), CMultiAligner::x_AlignProfileProfileUsingHit(), CIgBlast::x_AnnotateDomain(), CCassNAnnotTaskFetch::x_AnnotNamesBind(), CMultiAligner::x_AssignDefaultResFreqs(), CMultiAligner::x_AssignRPSResFreqs(), CBlastQuerySourceOM::x_AutoDetectGeneticCodes(), CPhyTreeCalc::x_CalcAlnSegInfo(), CNSTDatabase::x_CheckStatus(), CPsiBlastTestFixture::x_ComputePssmForNextIteration(), CNetBLAST_DMSearchTool::x_CreateJob(), CSNPSearchTool::x_CreateJob(), CComponentSearchTool::x_CreateJob(), CCpgSearchTool::x_CreateJob(), CEntrezSearchTool::x_CreateJob(), CFeatureSearchTool::x_CreateJob(), COrfSearchTool::x_CreateJob(), CSequenceSearchTool::x_CreateJob(), CVcfSearchTool::x_CreateJob(), CFindOverlapJob::x_CreateProjectItems(), CPssmEngine::x_CreatePssmFromCDD(), CPssmEngine::x_CreatePssmFromFreqRatios(), CPssmEngine::x_CreatePssmFromMsa(), CCompartApp::x_DoWithExternalHits(), CEntrez2ClientApp::x_EvalBoolean(), CQueryParsePanel::x_ExecuteQuery(), CDataMiningPanel::x_ExecuteSearch(), CBlastFormatterApp::x_ExtractQueries(), CBlastFormatterVdbApp::x_ExtractQueries(), CItemSelectionPanel::x_FilterItems(), CBLAST_DB_Dialog::x_FilterItems(), CUpdateMultiSeq_Dlg::x_GenerateAlignments(), CEntrez2ClientApp::x_GetCount(), CEntrez2ClientApp::x_GetDocsums(), CTL_LangCmd::x_GetDynamicID(), CEntrez2ClientApp::x_GetLinkCounts(), CSplignApp::x_GetNextPair(), CEntrez2ClientApp::x_GetParsedQuery(), CSearchToolBase::x_GetSessionIndexByQuery(), CEntrez2ClientApp::x_GetUids(), CPssmEngine::x_GuardProteinQuery(), CPssmCreateTestFixture::x_GuardProteinQuery(), CPssmEngine::x_InitializeScoreBlock(), CTL_Connection::x_IsLegacyBlobColumnType(), CQueryParsePanel::x_IsValidQuery(), CUpdateMultiSeq_Dlg::x_LaunchJobs(), CSplignApp::x_LogCompartmentStatus(), CFastCgiThreadedRequest::x_ParseEnv(), CCassBioseqInfoTaskFetch::x_PopulateRecord(), CExportStrategy::x_Process_Query(), CSplignApp::x_ProcessPair(), CCassandraFullscanWorker::x_ProcessQueryResult(), CCassBioseqInfoTaskFetch::x_ReadingLoop(), CMultiAligner::x_RealignBlocks(), CMakeProfileDBApp::x_RPSUpdateStatistics(), CPsiBlastApp::x_RunLocalPsiBlastIterations(), CDBLBClientApp::x_RunLookup(), CTblastnApp::x_RunMTBySplitDB(), CUrlArgs_Parser::x_SetIndexString(), CProSplignJob::x_SetupAndRuntBlastn(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), CCassBioseqInfoTaskFetch::x_StartQuery(), CQueryParsePanel::x_StartQueryJob(), CTracebackSearchTestFixture::x_Traceback(), CDataMiningPanel::x_UpdateWidgetAndTool(), x_ValidateResultsForShortProteinSearch(), and CRemoteUpdater::xSetFromConfig().
◆ subject
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static |
Definition at line 88 of file struct_dp_demo.cpp.
Referenced by CSeedRoots::Add(), CSeedRoots::Add2(), ctll::empty_actions::apply(), CdBlaster::blast(), BLAST_GappedAlignmentWithTraceback(), BLAST_GetGappedScore(), BLAST_GetUngappedHSPList(), BLAST_GreedyGappedAlignment(), Blast_HSPGetNumIdentities(), Blast_HSPGetNumIdentitiesAndPositives(), Blast_HSPGetPartialSubjectTranslation(), Blast_HSPReevaluateWithAmbiguitiesGapped(), Blast_HSPReevaluateWithAmbiguitiesUngapped(), Blast_HSPTestIdentityAndLength(), Blast_RedoOneMatch(), Blast_RedoOneMatchSmithWaterman(), BLAST_SmithWatermanGetGappedScore(), Blast_TracebackFromHSPList(), BlastAaWordFinder(), BlastGetOffsetsForGappedAlignment(), BlastGetStartForGappedAlignment(), BlastGetStartForGappedAlignmentNucl(), BlastNaExtendJumper(), BlastNaWordFinder(), BlastRPSWordFinder(), BOOST_AUTO_TEST_CASE(), CAlignCompare::SAlignment::BreakOnBoundaries(), CBl2Seq::CBl2Seq(), CExportStrategy::CExportStrategy(), CMultiAlignerTest::CompareDomainHits(), CAlignCompare::SAlignment::CompareGroup(), CORE_SendMail(), CORE_SendMailEx(), CPsiBl2Seq::CPsiBl2Seq(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::decide(), CCigar::DetailedCigarString(), CCigar::Distance(), CAdvancedAlignCleanup::DivideByQuerySubjectPairs(), DoAnchoredScan(), DoAnchoredSearch(), CSimpleB2SWrapper::DoBlast2Seqs(), estimate_jaccard(), estimate_jaccard2(), CdBlaster::getCompositeIndex(), CCigar::GetInDels(), CAdvancedAlignCleanup::GetProsplignCompartments(), CAdvancedAlignCleanup::GetSplignCompartments(), CPssmCddInputTest::GetSubjectMsaIndex(), CSeedRoots::GetSubjInfo(), CSeedRoots::GetSubjRoots(), CBlastFormatUtil::GetWholeAlnSeqStrings(), JumperExtendLeft(), JumperExtendLeftCompressed(), JumperExtendLeftCompressedWithTraceback(), JumperExtendLeftCompressedWithTracebackOptimal(), JumperExtendRight(), JumperExtendRightCompressed(), JumperExtendRightCompressedWithTraceback(), JumperExtendRightCompressedWithTracebackOptimal(), JumperExtendRightWithTraceback(), JumperFindEdits(), JumperFindSpliceSignals(), JumperGappedAlignmentCompressedWithTraceback(), JumperNaWordFinder(), main(), impl::CDriverContext::MakePooledConnection(), CSubjectMap::MapSubject(), CAlignFilter::Match(), CCigar::Matches(), MB_IndexedWordFinder(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::move(), pcre_copy_named_substring(), pcre_copy_substring(), pcre_dfa_exec(), pcre_exec(), pcre_get_named_substring(), pcre_get_substring(), pcre_get_substring_list(), PHIBlastScanSubject(), PHIBlastWordFinder(), PHIGappedAlignmentWithTraceback(), PHIGetGappedScore(), CAlignCompare::SAlignment::PopulateBoundariesMap(), CdBlaster::psiBlast(), CSeedTop::Run(), DPApp::Run(), CBlastSampleApplication::Run(), RunMultipleProteinSearch(), CUpdateSeq_Input::s_Align2IdenticalSeq(), s_AllocateSeqRange(), s_BackupSubject(), CMixedStrands::s_Blast2NASeq(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BlastAaExtendLeft(), s_BlastAaExtendOneHit(), s_BlastAaExtendRight(), s_BlastAaExtendTwoHit(), s_BlastAaScanSubject(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastCompressedAaScanSubject(), s_BlastDynProgNtGappedAlignment(), s_BlastNaExtend(), s_BlastNaExtendAligned(), s_BlastNaExtendDirect(), s_BlastNaHashScanSubject_Any(), s_BlastNaScanSubject_8_4(), s_BlastNaScanSubject_Any(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), s_BlastProtGappedAlignment(), s_BlastPSSMExtendLeft(), s_BlastPSSMExtendRight(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastSearchEngineCore(), s_BlastSearchEngineOneContext(), s_BlastSmallAaScanSubject(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_BlastSmallNaScanSubject_4_1(), s_BlastSmallNaScanSubject_5_1(), s_BlastSmallNaScanSubject_6_1(), s_BlastSmallNaScanSubject_6_2(), s_BlastSmallNaScanSubject_7_1(), s_BlastSmallNaScanSubject_7_2(), s_BlastSmallNaScanSubject_7_3(), s_BlastSmallNaScanSubject_8_1Mod4(), s_BlastSmallNaScanSubject_8_2Mod4(), s_BlastSmallNaScanSubject_8_3Mod4(), s_BlastSmallNaScanSubject_8_4(), s_BlastSmallNaScanSubject_Any(), s_CodonVariation(), s_ComputeNumIdentities(), s_ComputeTraceback(), s_CreateAlign(), s_CreateHSP(), s_CreateHSPForWordHit(), s_DetermineScanningOffsets(), s_ExtendAlignment(), s_ExtendAlignmentCleanup(), s_FindSpliceJunctionsForOverlaps(), s_GetNextSubjectChunk(), s_GetQueryAndSubjectStrings(), s_IsSeedMasked(), s_MB_DiscWordScanSubject_1(), s_MB_DiscWordScanSubject_11_18_1(), s_MB_DiscWordScanSubject_11_21_1(), s_MB_DiscWordScanSubject_TwoTemplates_1(), s_MBScanSubject_10_1(), s_MBScanSubject_10_2(), s_MBScanSubject_10_3(), s_MBScanSubject_11_1Mod4(), s_MBScanSubject_11_2Mod4(), s_MBScanSubject_11_3Mod4(), s_MBScanSubject_9_1(), s_MBScanSubject_9_2(), s_MBScanSubject_Any(), s_NewAlignmentUsingXdrop(), s_NuclUngappedExtend(), s_NuclUngappedExtendExact(), s_OutOfFrameSemiGappedAlignWrap(), s_PHIGappedAlignment(), s_PHITracebackFromHSPList(), s_RestoreSubject(), s_RunBlast2AASeq(), s_RunBlast2NASeq(), s_SaveSubjectOverhangs(), s_SetAirrAlignmentInfo(), s_ShiftGaps(), s_ShiftGapsRight(), s_SWFindFinalEndsUsingXdrop(), s_TrimChainEndToSubjPos(), s_TrimChainStartToSubjPos(), s_TrimHSP(), s_TypeOfWord(), CCigar::Score(), ScoreByBlosum62(), CLocalSeqSearch::SetSubject(), CLocalPssmSearch::SetSubject(), CRemoteSeqSearch::SetSubject(), CRemotePssmSearch::SetSubject(), CBl2Seq::SetSubject(), ShortRead_IndexedWordFinder(), SubjectIndexNew(), CCigar::ToAlign(), CIgBlast::x_AnnotateDomain(), CNGAlignJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CSequenceUpdater::x_FormNewAlignment(), CUpdateMultiSeq_Dlg::x_GenerateAlignments(), CwxChooseSeqDlg::x_GetSelectedId(), CPsiBl2Seq::x_InitSubject(), CwxChooseSeqDlg::x_InitTable(), CUpdateMultiSeq_Dlg::x_LaunchJobs(), CExportStrategy::x_Process_Subject(), CProSplignJob::x_SetupAndRuntBlastn(), and x_ValidateResultsForShortProteinSearch().
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 46 of file struct_dp_demo.cpp.
