Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__entry__edit_8hpp.html below:

NCBI C++ ToolKit: include/objtools/edit/seq_entry_edit.hpp File Reference

Go to the source code of this file.

Go to the SVN repository for this file.

Any internal cut listed in TCuts will be converted to a terminal cut using one of these options.

The default is eTrimToClosestEnd.

Definition at line 225 of file seq_entry_edit.hpp.

Add a Bioseq to a Bioseq-set.

This function will add the Bioseq to the set if: 1. The set is of class 'parts' and the Bioseq has the same molecular type as the other parts. 2.

Parameters

bsst Bioseq to change seq Bioseq to add

See also

AddSeqEntryToSeqEntry()

Definition at line 469 of file seq_entry_edit.cpp.

References CBioseq_set_Base::eClass_conset, CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_equiv, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_gi, CBioseq_set_Base::eClass_gibb, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Base::eClass_other, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_pdb_entry, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pir, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_pub_set, CBioseq_set_Base::eClass_segset, CBioseq_set_Base::eClass_swissprot, CBioseq_set_Base::eClass_wgs_set, CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetEditHandle(), CBioseq_EditHandle::MoveTo(), s_AddBioseqToNucProtSet(), s_AddBioseqToPartsSet(), and s_AddBioseqToSegset().

Referenced by AddSeqEntryToSeqEntry().

Creates a User-object descriptor on every sequence that has a local ID Contains the original local ID.

Definition at line 1583 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CUser_object_Base::IsSetData(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), ITERATE, MakeOriginalIdField(), NON_CONST_ITERATE, CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetUser().

Referenced by BOOST_AUTO_TEST_CASE(), HandleCollidingIds(), and TestCollidingAccessionFixes().

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then adjust cdregion frame.

Definition at line 3214 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::CanGetLocation(), eExtreme_Biological, eNa_strand_minus, eNa_strand_unknown, CSeqFeatData::eSubtype_cdregion, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CRange_Base::GetFrom(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CSeqFeatData_Base::IsCdregion(), CSeq_loc::IsPartialStart(), and CSeq_feat_Base::SetData().

Moves descriptors down to children of the given bioseq-set.

Each child gets a copy of all the descriptors. It does NOT check for duplicate Seqdescs.

Parameters

bioseq_set_h This is the bioseq_set whose descriptors we're moving. choices_to_delete If non-empty, it indicates the types of CSeqdescs to delete instead of propagating.

Definition at line 1447 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::AddDescr(), CSeqdesc_Base::e_not_set, CSeq_entry_CI::eNonRecursive, CBioseq_set_Handle::GetEditHandle(), CSeq_entry_Handle::GetEditHandle(), CBioseq_set_Handle::GetParentEntry(), CBioseq_set_EditHandle::ResetDescr(), SerialClone(), CSeq_descr_Base::Set(), and CSeqdesc_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and s_PromoteSingletonSetsInSet().

Moves descriptors up from children of the given bioseq-set if each child has an identical copy of the descriptor.

It does NOT check for duplicate Seqdescs. Will not move molinfo, title, or source descriptors.

Parameters

bioseq_set_h This is the bioseq_set whose descriptors we're moving.

Definition at line 1368 of file seq_entry_edit.cpp.

References CBioseq_set_EditHandle::AddSeqdesc(), CSerialObject::Assign(), first(), CSeq_descr_Base::Get(), CBioseq_set_Base::GetSeq_set(), CSeq_descr_Base::IsSet(), ITERATE, CBioseq_EditHandle::RemoveSeqdesc(), CBioseq_set_EditHandle::RemoveSeqdesc(), CSeq_descr_Base::Reset(), CSeq_descr_Base::Set(), CBioseq_EditHandle::SetDescr(), and CBioseq_set_EditHandle::SetDescr().

Referenced by BOOST_AUTO_TEST_CASE().

Definition at line 1944 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), ConvertRawToDeltaByNs(), f, FeatureAdjustForInsert(), FeatureAdjustForTrim(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), NormalizeUnknownLengthGaps(), CSeq_feat_EditHandle::Remove(), CSeq_feat_EditHandle::Replace(), and CBioseq_EditHandle::SetInst().

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to determine the gap location.

The size of the run of Ns determines whether a gap should be created and whether the gap should be of type known or unknown. Note that if the ranges overlap, unknown gaps will be preferred (allowing the user to create known length gaps for 20-forever, but unknown length gaps for 100, for example). Use a negative number for a maximum to indicate that there is no upper limit.

Parameters

inst The Seq-inst to adjust min_unknown The minimum number of Ns to be converted to a gap of unknown length max_unknown The maximum number of Ns to be converted to a gap of unknown length min_known The minimum number of Ns to be converted to a gap of known length max_known The maximum number of Ns to be converted to a gap of known length

Returns

none

Definition at line 1804 of file seq_entry_edit.cpp.

References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi8na, CSeqUtil::e_Ncbi8na, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, CAliasBase< TPrim >::Get(), CSeq_data_Base::GetIupacna(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbi2na(), CSeq_data_Base::GetNcbi4na(), CSeq_data_Base::GetNcbi8na(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::GetSeq_data(), CSeq_inst_Base::IsSetRepr(), CSeq_inst_Base::IsSetSeq_data(), ITERATE, CSeq_inst_Base::ResetSeq_data(), s_AddGap(), s_AddLiteral(), CSeq_inst_Base::SetRepr(), and CSeq_data_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

Secondary function needed after trimming Seq-feat.

If the trim completely covers the feature (boolean reference bFeatureDeleted from TrimSeqFeat() returns true), then delete protein sequence and re-normalize nuc-prot set.

Definition at line 3171 of file seq_entry_edit.cpp.

References CSeq_entry_EditHandle::ConvertSetToSeq(), CSeqFeatData_Base::e_Cdregion, CBioseq_set_Base::eClass_nuc_prot, CBioseq_set_Handle::GetBioseq_setCore(), CScope::GetBioseqHandle(), CBioseq_set_Handle::GetClass(), CSeq_feat_Handle::GetData(), CSeq_entry_Handle::GetEditHandle(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CMappedFeat::GetProduct(), CSeq_feat_Handle::GetScope(), CBioseq_set_Base::GetSeq_set(), CBioseq_set_Handle::IsEmptySeq_set(), CBioseq_Handle::IsProtein(), CBioseq_Handle::IsRemoved(), CBioseq_set_Handle::IsSetClass(), CSeq_feat_Handle::IsSetData(), CSeq_feat_Handle::IsSetProduct(), CBioseq_EditHandle::Remove(), CSeq_feat_EditHandle::Remove(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

Call this if the alignments directly under these seq-entries are all jumbled up between each other.

It will move each Seq-align into the proper location. In particular, it looks at all the seq-ids in each seq-align. If none of them belong to any member of vecOfSeqEntryHandles, then that Seq-align is copied to all members of vecOfSeqEntryHandles. If it belongs to only one member of vecOfSeqEntryHandles, then it goes there. If the align belongs to more than one, it's destroyed.

Parameters

vecOfSeqEntryHandles The Seq-entries we're considering for alignments.

Definition at line 1304 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_entry_EditHandle::AttachAnnot(), CSeq_entry_CI::eRecursive, CSeq_annot_CI::eSearch_entry, CSeq_entry_Handle::GetEditHandle(), ITERATE, and s_DivvyUpAlignments_ProcessAnnot().

Referenced by SegregateSetsByBioseqList().

Definition at line 3558 of file seq_entry_edit.cpp.

References CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Imp, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, NStr::EqualNocase(), CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mobile_element, NStr::Find(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CSeqFeatData_Base::GetProt(), CSeq_feat_Base::GetQual(), CSeqFeatData_Base::GetRna(), CSeqFeatData::GetSubtype(), GetTargetedLocusName(), CSeq_feat_Base::IsSetComment(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetQual(), NStr::TruncateSpacesInPlace(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID User-object descriptor.

Definition at line 1683 of file seq_entry_edit.cpp.

References CUser_object::eObjectType_OriginalId, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), HasRepairedIDs(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_Base::IsSetId(), CBioseq_set_Base::IsSetSeq_set(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE(), s_CollidedIds(), and TestCollidingAccessionFixes().

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific length (100 by default).

Parameters

inst The Seq-inst to adjust

Returns

A vector of the adjustments to the sequence, which can be used to fix the locations of features on the sequence.

Definition at line 1907 of file seq_entry_edit.cpp.

References CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetRepr(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetRepr(), NON_CONST_ITERATE, CSeq_inst_Base::SetExt(), and CSeq_inst_Base::SetLength().

Referenced by CRawSeqToDeltaSeqByLoc::apply_impl(), BOOST_AUTO_TEST_CASE(), ConvertRawToDeltaByNs(), ConvertRawToDeltaByNsCommand_impl(), and ConvertRawToDeltaByNsHugeFileCmd_impl().

Removes User-object descriptors of a certain type from the seq-entry.

Definition at line 1711 of file seq_entry_edit.cpp.

References EDIT_EACH_SEQDESC_ON_BIOSEQ, EDIT_EACH_SEQDESC_ON_SEQSET, ERASE_SEQDESC_ON_BIOSEQ, ERASE_SEQDESC_ON_SEQSET, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), CBioseq_Base::ResetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by BOOST_AUTO_TEST_CASE(), and HandleCollidingIds().

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then retranslate cdregion.

Definition at line 3304 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CSeq_feat_Base::CanGetLocation(), CSeq_interval_Base::CanGetTo(), CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, eExtreme_Biological, eNa_strand_unknown, CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_loc_Base::GetInt(), CBioseq::GetLength(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_feat_Base::GetProduct(), CBioseq_Handle::GetScope(), CSeq_loc::GetStrand(), CSeq_loc_Base::IsInt(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsProtein(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_EditHandle::Replace(), CMolInfo_Base::SetBiomol(), CMolInfo_Base::SetCompleteness(), CBioseq_EditHandle::SetDescr(), CBioseq_EditHandle::SetInst(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), SetNewProteinSequence(), SetPartial(), and CSeqFeatData_Base::Which().

Referenced by TrimSequenceAndAnnotation().

Create a Seq-entry from a Seq-submit.

Parameters

submit Seq-submit to create Seq-entry from

Definition at line 591 of file seq_entry_edit.cpp.

References AddSeqdescToBioseq(), AddSeqdescToSeqEntryRecursively(), CSerialObject::Assign(), CBioseq_set_Base::eClass_genbank, CSubmit_block_Base::GetCit(), CSeq_submit_Base::GetData(), CSeq_submit_Base::C_Data::GetEntrys(), CSeq_submit_Base::GetSub(), CSeq_submit::IsEntrys(), CSeq_entry_Base::IsSeq(), CSubmit_block_Base::IsSetCit(), CSeq_submit_Base::IsSetSub(), ITERATE, CBioseq_set_Base::SetClass(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CPub_Base::SetSub().

Referenced by BOOST_AUTO_TEST_CASE(), CLocalFileRestorer::x_AttachNewObject(), CUpdateSeq_Input::x_ReadUpdateSeq_ASN(), and CUpdateMultipleSeq_Input::x_ReadUpdateSeqs_ASN().

Secondary function needed after trimming Seq-feat.

If TrimSeqFeat()'s bFeatureTrimmed returns true, then make new protein sequence.

Definition at line 3274 of file seq_entry_edit.cpp.

References CAliasBase< TPrim >::Get(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacaa(), CSeq_inst_Base::GetLength(), CSeq_data_Base::GetNcbieaa(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsIupacaa(), CSeq_data_Base::IsNcbieaa(), CSeq_inst_Base::IsSetSeq_data(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetSeq_data(), and CSeqTranslator::TranslateToProtein().

Referenced by RetranslateCdregion().

Definition at line 3653 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CUser_object::eObjectType_AutodefOptions, CBioseq_Handle::GetCompleteBioseq(), CAutoDefOptions::InitFromUserObject(), CBioseq_Base::IsSetDescr(), CAutoDefOptions::MakeUserObject(), NON_CONST_ITERATE, CBioseq_EditHandle::SetDescr(), CAutoDefOptions::SetTargetedLocusName(), and CSeqdesc_Base::SetUser().

Referenced by CTLSContigHandler::ProcessBioseq(), and CTLSMasterHandler::ProcessBioseq().

Trim Seq-align annotation.

Definition at line 3032 of file seq_entry_edit.cpp.

References CDense_seg_Base::CanGetDim(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CBioseq_Handle::GetSeqId(), CDense_seg_Base::GetStarts(), CRange_Base::GetTo(), row, s_CutDensegSegment(), and CSeq_align_Base::SetSegs().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

Trim sequence data.

Definition at line 2498 of file seq_entry_edit.cpp.

References CScope::AddBioseq(), CSerialObject::Assign(), eNa_strand_plus, CSeq_inst_Base::eRepr_raw, CSeqMap::eSeqData, CSeqMap::fFindAny, CSeqMap::fIgnoreUnresolved, CBioseq_Handle::GetCompleteBioseq(), CSeq_inst_Base::GetLength(), CBioseq_Handle::GetScope(), CSeq_entry_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetTopLevelEntry(), CSeqMap_CI::GetType(), CBioseq_Handle::IsNucleotide(), CScope::RemoveBioseq(), CSeq_inst_Base::ResetExt(), CSeq_inst_Base::ResetSeq_data(), CSeqMap::ResolvedRangeIterator(), CAutoInitRef< T >::Set(), CSeq_inst_Base::SetExt(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), and UpdateSeqLength().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

Trim Seq-feat annotation.

Definition at line 3114 of file seq_entry_edit.cpp.

References CSeq_feat_Base::CanGetLocation(), CSeq_feat_Base::CanGetProduct(), eExtreme_Positional, eNa_strand_unknown, CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), GetStart(), GetStop(), CSeq_loc::GetStrand(), s_SeqLocDelete(), CSeq_feat_Base::SetLocation(), SetPartial(), and CSeq_feat_Base::SetProduct().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

Trim Seq-graph annotation.

Definition at line 2815 of file seq_entry_edit.cpp.

References eExtreme_Positional, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetLoc(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CByte_graph_Base::GetValues(), CSeq_graph_Base::C_Graph::IsByte(), s_GetTrimCoordinates(), s_UpdateSeqGraphLoc(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetNumval(), and CByte_graph_Base::SetValues().

Referenced by BOOST_AUTO_TEST_CASE(), and TrimSequenceAndAnnotation().

Trim sequence data and all associated annotation.

Trim sequence data and all associated annotation.

Definition at line 2147 of file seq_entry_edit.cpp.

References CSerialObject::Assign(), CDense_seg_Base::CanGetDim(), CDense_seg_Base::CanGetIds(), CSeq_inst_Base::CanGetLength(), CDense_seg_Base::CanGetLens(), CDense_seg_Base::CanGetNumseg(), CSeq_align_Base::CanGetSegs(), CDense_seg_Base::CanGetStarts(), NStr::CompareNocase(), DeleteProteinAndRenormalizeNucProtSet(), CSeq_annot_Base::C_Data::e_Align, CSeqFeatData_Base::e_Cdregion, CSeq_align_Base::C_Segs::e_Denseg, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CCdregion_Base::eFrame_not_set, CSeq_feat_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CBioseq_Handle::GetEditHandle(), CBioseq_Handle::GetInst(), CSeq_inst_Base::GetLength(), CMappedFeat::GetOriginalFeature(), CMappedGraph::GetOriginalGraph(), CAlign_CI::GetOriginalSeq_align(), CSeq_align_Base::GetSegs(), CAlign_CI::GetSeq_align_Handle(), CMappedGraph::GetSeq_graph_Handle(), GetSortedCuts(), CMappedGraph::GetTitle(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetProduct(), CMappedGraph::IsSetTitle(), CSeq_align_Handle::Replace(), CSeq_feat_EditHandle::Replace(), CSeq_graph_Handle::Replace(), RetranslateCdregion(), s_BasicValidation(), s_GetRetainedRange(), CSeq_feat_Base::SetData(), CBioseq_EditHandle::SetInst(), TrimSeqAlign(), TrimSeqData(), TrimSeqFeat(), TrimSeqGraph(), CSeq_align_Base::C_Segs::Which(), and CSeqFeatData_Base::Which().

Referenced by BOOST_AUTO_TEST_CASE().

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4