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

vector<CSeqdesc::E_Choice> &choices_to_delete =

vector<CSeqdesc::E_Choice>() );

min_unknown,

max_unknown,

min_known,

max_known,

is_assembly_gap =

,

gap_type =

,

linkage = -1,

linkage_evidence = -1 );

min_unknown,

max_unknown,

min_known,

max_known,

is_assembly_gap =

,

gap_type =

,

linkage = -1,

linkage_evidence = -1 );

& sorted_cuts);

& sorted_cuts);

& sorted_cuts);

& sorted_cuts,

& bFeatureDeleted,

& bFeatureTrimmed,

& partial_start,

& partial_stop);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@Seq_descr.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

vector< CBioseq_Handle > TBioseqHandles

#define NCBI_STD_DEPRECATED(message)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJEDIT_EXPORT

void TrimSeqAlign(CBioseq_Handle bsh, CRef< CSeq_align > align, const TCuts &sorted_cuts)

Trim Seq-align annotation.

void SetLinkageType(CSeq_ext &ext, CSeq_gap::TType linkage_type)

SetLinkageType A function to set the linkage_type for gaps in a delta sequence.

void DivvyUpAlignments(const TVecOfSeqEntryHandles &vecOfSeqEntryHandles)

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

void AddBioseqToBioseq(const CBioseq_Handle &to, const CBioseq_Handle &add)

Attach one Bioseq to another.

void TrimSequenceAndAnnotation(CBioseq_Handle bsh, const TCuts &cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)

Trim sequence data and all associated annotation.

void AddSeqEntryToSeqEntry(const CSeq_entry_Handle &to, const CSeq_entry_Handle &add)

Attach one Seq-entry to another.

void TrimSeqData(CBioseq_Handle bsh, CRef< CSeq_inst > inst, const TCuts &sorted_cuts)

Trim sequence data.

TLocAdjustmentVector NormalizeUnknownLengthGaps(CSeq_inst &inst, TSeqPos unknown_length=100)

NormalizeUnknownLengthGaps A function to adjust the length of unknown-length gaps to a specific lengt...

void AddBioseqToBioseqSet(const CBioseq_set_Handle &bsst, const CBioseq_Handle &seq)

Add a Bioseq to a Bioseq-set.

CRef< CSeqdesc > FindUnverified(const CBioseq &seq)

void RetranslateCdregion(CBioseq_Handle nuc_bsh, bool partial_start, bool partial_stop, CRef< CSeq_inst > trimmed_nuc_inst, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)

Secondary function needed after trimming Seq-feat.

void SortSeqDescr(CSeq_entry &entry)

void TrimSeqGraph(CBioseq_Handle bsh, CRef< CSeq_graph > graph, const TCuts &sorted_cuts)

Trim Seq-graph annotation.

void SetTargetedLocusName(CBioseq_Handle seq, const string &tls)

bool IsUnverifiedMisassembled(const CBioseq &seq)

string GetTargetedLocusName(const CSeq_feat &feat)

vector< TLocAdjustment > TLocAdjustmentVector

void AddLocalIdUserObjects(CSeq_entry &entry)

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

CRef< CSeq_entry > SeqEntryFromSeqSubmit(const CSeq_submit &submit)

Create a Seq-entry from a Seq-submit.

void BioseqSetDescriptorPropagateDown(const CBioseq_set_Handle &bioseq_set_h, const vector< CSeqdesc::E_Choice > &choices_to_delete=vector< CSeqdesc::E_Choice >())

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

NCBI_XOBJEDIT_EXPORT void AdjustCdregionFrame(TSeqPos original_nuc_len, CRef< CSeq_feat > cds, const TCuts &sorted_cuts)

Secondary function needed after trimming Seq-feat.

bool HasRepairedIDs(const CSeq_entry &entry)

Detects whether colliding IDs were fixed by comparing sequence IDs to the contents of the OriginalID ...

void RemoveUserObjectType(CSeq_entry &entry, CUser_object::EObjectType type)

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

bool IsUnverifiedOrganism(const CBioseq &seq)

vector< CSeq_entry_Handle > TVecOfSeqEntryHandles

CRef< CBioseq > SetNewProteinSequence(CScope &new_scope, CRef< CSeq_feat > cds, CRef< CSeq_inst > new_inst)

Secondary function needed after trimming Seq-feat.

void SetLinkageTypeScaffold(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

SetLinkageTypeScaffold A special case of SetLinkageType.

void SetLinkageTypeLinkedRepeat(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

void DeleteProteinAndRenormalizeNucProtSet(const CSeq_feat_Handle &feat_h)

Secondary function needed after trimming Seq-feat.

void ConvertRawToDeltaByNs(CSeq_inst &inst, size_t min_unknown, int max_unknown, size_t min_known, int max_known, bool is_assembly_gap=false, int gap_type=CSeq_gap::eType_unknown, int linkage=-1, int linkage_evidence=-1)

ConvertRawToDeltaByNs A function to convert a raw sequence to a delta sequence, using runs of Ns to d...

string GetTargetedLocusNameConsensus(const string &tls1, const string &tls2)

void TrimSeqFeat(CRef< CSeq_feat > feat, const TCuts &sorted_cuts, bool &bFeatureDeleted, bool &bFeatureTrimmed, bool &partial_start, bool &partial_stop)

Trim Seq-feat annotation.

void GetSortedCuts(CBioseq_Handle bsh, const TCuts &cuts, TCuts &sorted_cuts, EInternalTrimType internal_cut_conversion=eTrimToClosestEnd)

1) Merge abutting and overlapping cuts.

void ResetLinkageEvidence(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

bool IsUnverifiedContaminant(const CBioseq &seq)

bool IsUnverifiedFeature(const CBioseq &seq)

EInternalTrimType

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

void AddLinkageEvidence(CSeq_ext &ext, CLinkage_evidence::TType evidence_type)

AddLinkageEvidence A function to add linkage evidence for gaps in a delta sequence.

CRange< TSeqPos > TRange

A list of trim coordinates.

string GenerateTargetedLocusName(CBioseq_Handle seq)

NCBI_XOBJEDIT_EXPORT void SegregateSetsByBioseqList(const CSeq_entry_Handle &target, const CScope::TBioseqHandles &bioseq_handles)

Split a Seq-entry, where the second part holds the given bioseqs.

void BioseqSetDescriptorPropagateUp(CBioseq_set_Handle set)

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

pair< TSeqPos, int > TLocAdjustment

void HandleCollidingIds(CSeq_entry &entry)

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