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NCBI C++ ToolKit: src/algo/blast/format/blastxml_format.cpp File Reference

Formatting of BLAST results in XML form, using the BLAST XML specification. More...

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Formatting of BLAST results in XML form, using the BLAST XML specification.

Definition in file blastxml_format.cpp.

Fills all fields in the data structure for a BLAST XML report.

Parameters

bxmlout BLAST XML report data structure to fill [in] [out] data Data structure, from which all necessary information can be retrieved [in] out_stream Output stream for incremental output, ignore if NULL [out]

Definition at line 679 of file blastxml_format.cpp.

References CSeq_id::AsFastaString(), CBlastFormatUtil::BlastGetVersion(), bool, data, ERR_POST, Error(), eUnknown, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), GetId(), GetLength(), GetSeqIdString(), CReference::GetString(), NStr::IntToString(), SBlastXMLIncremental::m_IterationNum, SBlastXMLIncremental::m_SerialXmlEnd, NCBI_THROW, NcbiEmptyString, NStr::NumericToString(), s_BlastXMLAddIteration(), s_BlastXMLGetStatistics(), s_GetBlastPublication(), s_SerializeAndSplitBy(), s_SetBlastXMLParameters(), CBlastOutput_Base::SetDb(), CBlastOutput_Base::SetProgram(), CBlastOutput_Base::SetQuery_def(), CBlastOutput_Base::SetQuery_ID(), CBlastOutput_Base::SetQuery_len(), CBlastOutput_Base::SetReference(), CBlastOutput_Base::SetVersion(), string, and CException::what().

Add an "iteration" to the BLAST XML report, corresponding to all alignments for a single query.

Parameters

bxmlout BLAST XML output object [in] alnset Set of aligments for a given query. [in] seqloc This query's Seq-loc. [in] scope Scope for retrieving sequences. [in] matrix ASCII-alphabet matrix for calculation of positives. [in] mask_info List of masking locations. [in] index This query's index [in] stat Search statistics for this query, already filled. [in] is_ungapped Is this an ungapped search? [in] out_stream Stream for incremental output, ignore if NULL [out]

Definition at line 532 of file blastxml_format.cpp.

References CSeq_id::AsFastaString(), bool, CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), GetId(), GetLength(), GetSeqIdString(), NcbiEmptyString, s_SeqAlignSetToXMLHits(), s_SerializeAndSplitBy(), and CBlastOutput_Base::SetIterations().

Referenced by BlastXML_FormatReport().

Given BLAST task, returns enumerated value for the publication to be referenced.

Parameters

Returns

What publication to reference?

Definition at line 653 of file blastxml_format.cpp.

References CReference::eCompBasedStats, eDeltaBlast, CReference::eDeltaBlast, CReference::eGappedBlast, eMapper, CReference::eMaxPublications, eMegablast, CReference::eMegaBlast, CReference::ePhiBlast, ePHIBlastn, ePHIBlastp, and ePSIBlast.

Referenced by BlastXML_FormatReport().

Returns translation frame given the strand, alignment endpoints and total sequence length.

Parameters

plus_strand Is this position on a forward strand? [in] start Starting position, in 1-offset coordinates. [in] end Ending position in 1-offset coordinates [in] seq_length Total length of sequence [in]

Returns

Frame number.

Definition at line 86 of file blastxml_format.cpp.

Referenced by s_SeqAlignSetToXMLHsps().

Fills the list of CHit objects, given a list of Seq-aligns.

Parameters

hits List of CHit objects to fill [in] [out] alnset Seq-align-set object containing a list of sequence alignments. [in] scope Scope for retrieving sequences. [in] matrix ASCII-alphabet matrix for calculation of positives. [in] mask_info List of masking locations. [in] ungapped Is this an ungapped search? [in]

Definition at line 453 of file blastxml_format.cpp.

References bool, eEncoding_Ascii, eNoOwnership, CSeq_align_set_Base::Get(), CSeq_id::Match(), s_GetSubjectId(), s_SeqAlignToXMLHit(), CSeq_align_set_Base::Set(), CSeq_align_Base::SetSegs(), and string.

Referenced by s_BlastXMLAddIteration().

Creates a list of CHsp structures for the XML output, given a list of Seq-aligns.

Parameters

xhsp_list List of CHsp's to populate [in] [out] alnset Set of alignments to get data from [in] scope Scope for retrieving sequences [in] matrix 256x256 matrix for calculating positives for a protein search. NULL is passed for a nucleotide search. mask_info Masking locations [in]

Definition at line 108 of file blastxml_format.cpp.

References CDense_seg::Assign(), CreateDensegFromDendiag(), CSeq_align::CreateDensegFromStdseg(), CSeq_align::CreateTranslatedDensegFromNADenseg(), CDisplaySeqalign::eN, eNa_strand_minus, CDisplaySeqalign::eX, CSeq_align_set_Base::Get(), CSeq_align::GetAlignLength(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStop(), CSeq_align::GetSeqStrand(), CDense_seg_Base::GetStrands(), CSeq_align::GetTotalGapCount(), CBlastFormatUtil::GetWholeAlnSeqStrings(), i, CSeq_align_Base::C_Segs::IsDendiag(), CBioseq_Handle::IsNa(), CDense_seg_Base::IsSetStrands(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, min(), NcbiEmptyString, CRef< C, Locker >::Reset(), CDense_seg::Reverse(), s_GetTranslationFrame(), and tmp.

Referenced by s_SeqAlignToXMLHit().

Fill the CHit object in BLAST XML output, given an alignment and other information.

Parameters

hit CHit object to fill [in] [out] align_in Sequence alignment [in] scope Scope for retrieving sequences [in] matrix ASCII-alphabet matrix for calculation of positives [in] mask_info List of masking locations [in] ungapped Is this an ungapped search? [in]

Definition at line 357 of file blastxml_format.cpp.

References _ASSERT, CSeq_id::AsFastaString(), eGetId_Best, CSeq_align_set_Base::Get(), CScope::GetBioseqHandle(), CShowBlastDefline::GetBioseqHandleDeflineAndId(), CSeq_align_Base::C_Segs::GetDisc(), GetId(), CAlignFormatUtil::GetLabel(), GetLength(), CSeq_align_Base::GetSegs(), CSeq_id_Handle::GetSeqId(), CSeq_align_Base::C_Segs::IsDisc(), NcbiEmptyString, CDisplaySeqalign::PrepareBlastUngappedSeqalign(), CRef< C, Locker >::Reset(), and s_SeqAlignSetToXMLHsps().

Referenced by s_SeqAlignSetToXMLHits().

Fills the parameters part of the BLAST XML output.

Parameters

bxmlout BLAST XML output object [in] [out] data Data structure, from which all necessary information can be retrieved [in]

Definition at line 599 of file blastxml_format.cpp.

References data, NcbiEmptyString, CParameters_Base::SetExpect(), CParameters_Base::SetFilter(), CParameters_Base::SetGap_extend(), CParameters_Base::SetGap_open(), CParameters_Base::SetMatrix(), CBlastOutput_Base::SetParam(), CParameters_Base::SetPattern(), CParameters_Base::SetSc_match(), CParameters_Base::SetSc_mismatch(), str(), and val.

Referenced by BlastXML_FormatReport().

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.

Definition at line 59 of file blastxml_format.cpp.

Referenced by _mm_addsub_pd(), _mm_addsub_ps(), _mm_blend_ps(), _mm_blendv_epi8(), _mm_blendv_pd(), _mm_blendv_ps(), _mm_cvtps_pi8(), _mm_maskmove_si64(), _mm_maskmoveu_si128(), _mm_test_all_zeros(), _mm_test_mix_ones_zeros(), _PHIBlastFindHitsShort(), _PHIGetRightOneBits(), CMask::Add(), CWGSMasterDescrSetter::AddChunksToWait(), CWGSMasterDescrSetter::AddChunkToWait(), CMask::AddExclusion(), CWriteDB_GiMask::AddGiMask(), AddMasterDescr(), CRequestContext::AddPassThroughProperty(), CArgDescriptions::AddStdArguments(), CCommandArgDescriptions::AddStdArguments(), CWGSMasterSupport::AddWGSMaster(), bm::bvector< Alloc >::and_bit_no_check(), CAgpErr::AppliesTo(), CSeqDB_BitSet::AssignBitRange(), bm::avx2_andnot_arr_2_mask(), bm::avx2_bit_block_gather_scatter(), bm::avx2_bit_block_xor(), bm::avx2_bit_find_first(), bm::avx2_bit_find_first_diff(), bm::avx2_bit_to_gap(), bm::avx2_cmpge_u16(), bm::avx2_cmpge_u32(), bm::avx2_gap_bfind(), bm::avx2_lower_bound_scan_u32(), bm::avx2_set_block_bits(), bm::avx2_set_block_bits3(), bm::avx2_xor_arr_2_mask(), bm::avx512_andnot_arr_2_mask(), bm::avx512_xor_arr_2_mask(), bm::bit_block_and(), bm::bit_block_and_2way(), bm::bit_block_and_3way(), bm::bit_block_and_5way(), bm::bit_block_and_or_2way(), bm::bit_block_any_range(), bm::bit_block_is_all_one_range(), bm::bit_block_sub(), bm::bit_block_sub_2way(), bm::bit_block_sub_3way(), bm::bit_block_sub_5way(), bm::bit_block_xor(), bit_convert_to_gap(), CSeqMaskerUtil::BitCount(), Blast_FindRepeatFilterLoc(), Blast_FindWindowMaskerLoc(), Blast_GetSeqLocInfoVector(), BLAST_MainSetUp(), BlastHashLookupIndexQueryExactMatches(), BlastResCompStr(), BlastSeqLoc_RestrictToInterval(), bm::block_init_digest0(), BOOST_AUTO_TEST_CASE(), brc(), brcl(), BVImportTest(), bm::calc_block_digest0(), CalcBeginMask(), CalcEndMask(), CGlAttrGuard::CGlAttrGuard(), bm::check_zero_digest(), CDirEntry::CheckAccess(), bm::bvector_mini< A >::clear_bit(), CWriteDB_LMDB::SKeyValuePair::cmp_key(), compute_imm(), CSeqDBAliasNode::ComputeMasks(), ComputeTableIndexIncremental(), TMaskedQueryRegions::ConvertToCPacked_seqint(), DeBruijn::CReadHolder::CopyBits(), CountNs(), CountNucleotides(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::ct_set(), compile_time_bits::const_bitset< int(ParseFlags::MaxValue), ParseFlags >::ct_set(), CWGSMasterDescrSetter::CWGSMasterDescrSetter(), dbnextrow(), dbreadtext(), bm::digest_mask(), DoAnchoredScan(), CSeqMasker::DoMask(), emit_op_mem(), xml::impl::epimpl::epimpl(), xml::event_parser::event_parser(), CPipe::ExecWait(), CTar::Extract(), bm::sparse_vector< Val, BV >::extract(), bm::sparse_vector< Val, BV >::extract_planes(), CBlastDBExtractor::ExtractFasta(), CBlastDBExtractor::ExtractSeqData(), FF_FUN(), CNCBlobStorage::FindBlob(), CSampleLibraryObject::FindInPath(), CAtomicBitSet::flip(), flip_bit(), FNV_hash(), bm::for_each_bit_blk(), bm::bit_out< TEncoder >::gamma(), bitvec< unsigned int >::get(), bm::bit_in< TDecoder >::get_bit(), bm::bvector_mini< A >::get_next(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_slice_mask(), CNCBlobStorage::GetBList(), CGBDataLoader_Native::GetBlobs(), GetDefaultLogLocation(), CCgiApplication::GetDefaultLogPath(), CDir::GetEntries(), CDir::GetEntriesPtr(), CAgpErr::GetErrorMessage(), CBlastQuerySourceOM::GetMaskedRegions(), CSeqDBAliasNode::GetMaskList(), CSeqVecSeqInfoSrc::GetMasks(), CRemoteBlast::GetMasks(), CSparseGraph::GetMissingRegions(), CGBDataLoader_Native::GetOrphanAnnotRecordsNA(), CSnpBitfield1_2::GetWeight(), CSnpBitfield2::GetWeight(), TMaskedQueryRegions::HasNegativeStrandMasks(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::import_char_slice(), bm::bvector< Alloc >::inc(), inflate_table(), CInputStreamSource::InitArgs(), CSeqportUtil_implementation::InitMasks(), bm::sparse_vector< Val, BV >::insert_value_no_null(), bm::bvector_mini< A >::is_bit_true(), bm::is_digest_one_range(), CGridCommandLineInterfaceApp::IsOptionAccepted(), CComponentIDToolApp::IsOptionAccepted(), CGridCommandLineInterfaceApp::IsOptionExplicitlySet(), CComponentIDToolApp::IsOptionExplicitlySet(), CGridCommandLineInterfaceApp::IsOptionSet(), CComponentIDToolApp::IsOptionSet(), LBSM_LookupService(), LBSM_LookupServiceEx(), CAgpRow::LinkageEvidenceFlagsToString(), CReadDispatcher::LoadBlobs(), CId2ReaderBase::LoadBlobs(), CReader::LoadBlobs(), CWGSMasterDescrSetter::Loaded(), logical_imm(), LZCNTTest(), mark_fd(), MarkUsed(), CPathHook::Match(), CBlob_Info::Matches(), CDirEntry::MatchesMask(), NStr::MatchesMask(), mbedtls_ct_memcpy_if(), CGlState::MergeStates(), mgf_mask(), NcbiGetHostIfConfEx(), NcbiIPv6Subnet(), NcbiIPv6Suffix(), NcbiIsInIPv6Network(), CSubjectMap_Factory_Base::NewSequenceInit(), DeBruijn::LargeInt< precision >::oahash(), odbc_set_string_flag(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::cast_from_other::operator()(), CPipeHandle::Poll(), CPipe::Poll(), CGlRender::PolygonStipple(), CGlRenderDebug::PolygonStipple(), CGlState::PolygonStipple(), CRenderVector::PolygonStipple(), CSparseKmerCounts::PreCount(), bm::sparse_vector_scanner< SV, S_FACTOR >::prepare_and_sub_aggregator(), CMaskWriterBlastDbMaskInfo::Print(), CMaskWriterFasta::Print(), CMaskWriterInt::Print(), CMaskWriterSeqLoc::Print(), CMaskWriterTabular::Print(), CMaskWriterInt::PrintMasks(), CNCActiveSyncControl::PrintState(), bm::aggregator< BV >::process_bit_blocks_and(), bm::aggregator< BV >::process_bit_blocks_sub(), bm::random_subset< BV >::process_word(), CTbl2AsnApp::ProcessOneDirectory(), CTAbleValApp::ProcessOneDirectory(), CGlRender::PushAttrib(), CGlRenderDebug::PushAttrib(), CRenderVector::PushAttrib(), bm::bit_out< TEncoder >::put_bits(), CObjectIStreamAsn::ReadBitString(), CObjectIStreamAsnBinary::ReadBitString(), CObjectIStreamXml::ReadBitString(), CObjectIStreamJson::ReadCustomBytes(), CMask::Remove(), CFileObsolete::Remove(), CMask::RemoveExclusion(), CSparseKmerCounts::Reset(), compile_time_bits::const_bitset< int(ParseFlags::MaxValue), ParseFlags >::reset(), CAtomicBitSet::reset(), CPluginManager_DllResolver::ResolveFile(), TMaskedQueryRegions::RestrictToSeqInt(), subfuse::CSubfuseApp::Run(), CTLSApp::Run(), s_AddMask(), s_AddWordHit(), s_BlastNaHashScanSubject_Any(), s_BlastNaScanSubject_Any(), s_BlastSmallNaScanSubject_Any(), s_ConvertBlastnMasks(), s_ConvertToBlastQueries(), s_CreateWordArray(), s_FillMaskLocFromBlastResults(), s_FindHitProbability(), s_FindHitsLong(), s_FindNumIdentical(), s_FindPrefixAndSuffixPos(), s_GetBlastnMask(), s_GetMaskSeqLoc(), s_GuessProgram(), s_HexDumpText(), s_IncludeDefline_MaskFilter(), s_IsGoodDescr(), s_LenOf(), s_LenOfL(), CBinaryRangeCacheWithLock< Position, Value >::s_MakeRange(), s_MaskingTest(), s_MatchesMask(), s_MatchExcludeMask(), s_MBCountWordsInSubject_16_1(), s_MBScanSubject_Any(), s_ModeToTar(), s_NaHashLookupCountWordsInSubject_16_1(), s_PHIGetLongPattern(), s_PHIGetShortPattern(), s_TestMaskingLimits(), NAdapterSearch::s_Translate(), SERV_PrintFirewallPorts(), bm::miniset< A, N >::set(), bm::bvmini< N >::set(), compile_time_bits::const_bitset< int(ParseFlags::MaxValue), ParseFlags >::set(), CAtomicBitSet::set(), bitvec< unsigned int >::set(), bm::bvector_mini< A >::set_bit(), bm::bvector< Alloc >::set_bit_conditional_impl(), bm::bvector< Alloc >::set_bit_no_check(), bm::sparse_vector< Val, BV >::set_value_no_null(), CRemoteBlast::SetDbFilteringAlgorithmId(), CRemoteBlast::SetDbFilteringAlgorithmKey(), CGridJobBatchSubmitter::SetJobMask(), CGridClient::SetJobMask(), CPdfObject::SetLineDashStyle(), CBlastInputSourceConfig::SetLowercaseMask(), CTar::SetMask(), CArchive::SetMask(), CJob::SetMask(), CBDB_BufferManager::SetNullBit(), CAlnRowState::SetRowState(), SetSeqAnnotChoiceMask(), SetSeqIdChoiceMask(), SetupQueries_OMF(), sljit_emit_atomic_store(), sljit_emit_jump(), sljit_emit_op_flags(), sljit_emit_select(), sljit_emit_shift_into(), bm::sse2_andnot_arr_2_mask(), bm::sse2_bit_block_xor(), bm::sse2_bit_find_first(), bm::sse2_bit_find_first_diff(), bm::sse2_lower_bound_scan_u32(), bm::sse2_xor_arr_2_mask(), bm::sse42_bit_block_xor(), bm::sse42_bit_find_first(), bm::sse42_bit_find_first_diff(), bm::sse42_cmpge_u32(), SSeqLoc::SSeqLoc(), StringToCode(), TestBlockToGAP(), CBDB_BufferManager::TestNullBit(), TestSignedSparseVectorSerial(), TestSparseVector_XOR_Scanner(), TestSparseVectorSerial(), Uint8ToBytes(), bm::update_block_digest0(), update_mem_addr(), UTIL_MatchesMask(), UTIL_MatchesMaskEx(), CAsnvalApp::ValidateOneDirectory(), bm::widx_to_digest_mask(), CRegexp::WildcardToRegexp(), CBlastDB_SeqFormatter::Write(), CObjectOStreamAsn::WriteBitString(), CObjectOStreamAsnBinary::WriteBitString(), CObjectOStreamJson::WriteBitString(), CObjectOStreamXml::WriteBitString(), CNCBlobStorage::WriteBlobList(), CObjectOStreamJson::WriteCustomBytes(), CNCBlobStorage::WriteDbInfo(), CWriteDB_GiMaskData::WriteMask(), CSeqdesc_CI::x_AddChoice(), CNcbiApplicationAPI::x_AddDefaultArgs(), CTar::x_Append(), CSQLITE_Connection::x_CheckFlagsValidity(), CElementaryMatching::x_CleanVolumes(), CSeqDBOIDList::x_ComputeFilters(), seqmasks_io_fixture::x_ConvertMasks(), CWriteDB_OidList::x_CreateBitMap(), CNCMessageHandler::x_DoCmd_GetConfig(), CString_constraint::x_DoesSingleStringMatchConstraint(), CWGSMasterDescrSetter::x_GetActualExistingDescrMask(), CBioseq_Base_Info::x_GetExistingDescrMask(), CGBDataLoader_Native::x_GetRecords(), CEnvironmentRegistry::x_HasSection(), CRequestContext::x_LoadEnvContextProperties(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CGBDataLoader_Native::x_MakeContentMask(), x_MatchesMask(), CGlState::x_MergeFlag(), x_NameMatch(), CPipeHandle::x_Poll(), CId2ReaderBase::x_ProcessGetBlobId(), CAsn2FastaApp::x_ProcessISubdirectory(), CCleanupApp::x_ProcessOneDirectory(), CTar::x_ReadAndProcess(), CSeqdesc_CI::x_RemoveChoice(), CBioseq_Base_Info::x_SearchFirstDesc(), CSNPDbFeatIterator::x_SetFilter(), CRemoteBlast::x_SetOneParam(), CMenuItem::x_SetState(), CIgBlast::x_SetupCRegionSearch(), CIgBlast::x_SetupDbSearch(), CIgBlast::x_SetupDJSearch(), CIgBlast::x_SetupNoOverlapDSearch(), NFast::x_sse_ConvertBuffer(), x_TestGetFilteredQueryRegions(), x_TestGetSeqLocInfoVector(), CBlastFilterTest::x_TestLowerCaseMaskWith(), CBDB_Cache::x_TruncateDB(), CSeqDBDemo_Thread::x_UseOID(), and bm::xor_bit_block().

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