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NCBI C++ ToolKit: include/objmgr/util/sequence.hpp Source File

CSeq_entry_handle;

* scope = 0,

* frame = 0);

unique_ptr<CFeat_CI> &feat_ci,

&shouldContinueToNextIteration,

&revert_locations_this_iteration,

search_both_strands =

);

search_both_strands =

);

fAssembleParts = 1 << 0,

fInstantiateGaps = 1 << 1,

fSuppressRange = 1 << 2,

fReverseStrand = 1 << 3,

fKeepGTSigns = 1 << 4,

fMapMasksUp = 1 << 5,

fMapMasksDown = 1 << 6,

fNoExpensiveOps = 1 << 7,

fShowModifiers = 1 << 8,

fNoDupCheck = 1 << 9,

fShowGapModifiers = 1 << 10,

fKeepUnknGapNomLen = 1 << 11,

fShowGapsOfSizeZero = 1 << 12,

fHideGenBankPrefix = 1 << 14,

fHTMLEncode = 1 << 15,

fIgnoreOriginalID = 1 << 16,

eAssembleParts = fAssembleParts,

eInstantiateGaps = fInstantiateGaps,

fUseAutoDef = 1 << 17,

fBaseFirstUnused = 1 << 18,

fDoNotUseAutoDef = 1 << 19,

fShowGnlAndAcc = 1 << 20,

& custom_title =

);

& custom_title =

);

no_scope =

);

no_scope =

,

& custom_title =

);

no_scope=

,

& custom_title=

);

SetWidth (

width);

unique_ptr<sequence::CDeflineGenerator>

;

x_WriteSeqIds (

& bioseq,

x_WriteAsFasta (

& bioseq );

& custom_title);

sequence::CDeflineGenerator::TUserFlags x_GetTitleFlags(

)

;

x_GetMaskingStates(

& masking_states,

& masking_state);

TranslateCdregion (

&

,

include_stop =

,

remove_trailing_X =

,

* alt_start = 0,

ETranslationLengthProblemOptions options = eThrowException);

TranslateCdregion(

&

,

include_stop =

,

remove_trailing_X =

,

* alt_start = 0,

ETranslationLengthProblemOptions options = eThrowException);

fRemoveTrailingX = (1<<1),

fIs5PrimePartial = (1<<2),

fIs3PrimePartial = (1<<3)

include_stop =

,

remove_trailing_X =

,

* alt_start =

,

is_5prime_complete =

,

is_3prime_complete =

);

(

& seq,

* alt_start =

);

include_stop =

,

remove_trailing_X =

,

* alt_start =

,

is_5prime_complete =

,

is_3prime_complete =

);

* alt_start =

);

include_stop =

,

remove_trailing_X =

,

* alt_start = 0);

include_stop =

,

remove_trailing_X =

,

* alt_start = 0);

include_stop =

,

remove_trailing_X =

,

* alt_start = 0);

ChangeDeltaProteinToRawProtein(

protein);

: m_ParentLoc(&parent), m_Ranges(ranges) { }

TFlags

= 0)

;

& sequence,

m_Name(name), m_Sequence(sequence), m_CutSite(cut_site),

&

(

)

{

m_Name; }

AddNucleotidePattern(

& name,

& sequence,

Search(

current_state,

ch,

position,

length =

);

x_AddNucleotidePattern(

& name,

& pattern,

x_ExpandPattern(

& sequence,

&

,

pos,

TPatternInfo& pat_info, TSearchFlags

);

x_AddPattern(TPatternInfo& pat_info,

& sequence, TSearchFlags

);

x_StorePattern(TPatternInfo& pat_info,

& sequence);

((m_Flags |

) & fJustTopStrand) != 0;

((m_Flags |

) & fExpandPattern) != 0;

((m_Flags |

) & fAllowMismatch) != 0;

fFlags_DoNotTrimBeginning = (1 << 0),

fFlags_DoNotTrimEnd = (1 << 1),

fFlags_DoNotTrimSeqGap = (1 << 2),

& GetDefaultTrimRules(

);

& vecTrimRules = GetDefaultTrimRules(),

eResult_NoTrimNeeded

( ( m_fFlags & fFlag ) != 0 );

x_NormalizeVecTrimRules( TTrimRuleVec & vecTrimRules );

EResult x_TrimToNothing(

&bioseq_handle );

x_EdgeSeqMapGapAdjust(

(iTrimDirection > 0)

x_CountAmbigInRange(

x_SegmentGetEndInclusive( segment, -iTrimDirection );

TAmbigLookupTable[26];

num_gaps_seen_so_far_on_this_seq(0) { }

x_GetCurrent();

&x_GetCurrent();

x_Next(

);

x_NextBioseq(

);

EFindNext x_FindNextGapOnBioseq(

pos_to_start_looking,

& out_len_of_gap )

;

User-defined methods of the data storage class.

ncbi::TMaskedQueryRegions mask

This iterates over the runs of Ns of each sequence.

Public interface for coding region translation function Uses CTrans_table in <objects/seqfeat/Genetic...

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

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

Holds information associated with a pattern, such as the name of the restriction enzyme,...

Client interface: ================== A class that uses the SeqSearch facility should implement the Cl...

============================================================================// Sequence Search // ===...

namespace ncbi::objects::

This trims ambiguous bases from the start and/or end of sequences, using customizable rules.

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

API (CDeflineGenerator) for computing sequences' titles ("definitions").

std::ofstream out("events_result.xml")

main entry point for tests

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

SStrictId_Tax::TId TTaxId

Taxon id type.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#define EXCEPTION_VIRTUAL_BASE

Do not use virtual base classes in exception declaration at all, because in this case derived class s...

void Write(CObjectOStream &out, TConstObjectPtr object, const CTypeRef &type)

EOpFlags

CSeq_loc operations.

TSignedSeqPos pos_after_last_gap

Inclusive.

CRef< CSeq_loc > ProductToSource(const CSeq_feat &feat, const CSeq_loc &prod_loc, TP2SFlags flags=0, CScope *scope=0)

virtual void processSAnnotSelector(SAnnotSelector &sel)=0

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

const IClient * GetClient() const

Get / Set client.

CTextFsm< TPatternInfo > m_Fsa

CConstRef< CSeq_feat > GetOverlappingSource(const CSeq_loc &loc, CScope &scope)

virtual void setUpFeatureIterator(CBioseq_Handle &bioseq_handle, unique_ptr< CFeat_CI > &feat_ci, TSeqPos circular_length, CRange< TSeqPos > &range, const CSeq_loc &loc, SAnnotSelector &sel, CScope &scope, ENa_strand &strand)=0

CConstRef< CSeq_feat > GetOverlappingmRNA(const CSeq_loc &loc, CScope &scope)

NCBI_EXCEPTION_DEFAULT(CSeqIdFromHandleException, CException)

virtual bool SkipBioseq(const CBioseq_Handle &handle)

Delegates to the non-handle version by default for compatibility with older code; newer code should o...

EGetIdFlags

Retrieve a particular seq-id from a given bioseq handle.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag=CScope::eGetBioseq_Loaded)

Retrieve the Bioseq Handle from a location.

TSeqPos length

the length of the current gap

virtual void processLoc(CBioseq_Handle &bioseq_handle, CRef< CSeq_loc > &loc, TSeqPos circular_length)=0

EMeaningOfAmbig m_eMeaningOfAmbig

This holds the current interpretation for "ambiguous".

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

Int2 m_CutSite

nucleotide sequence

EGetTitleFlags

This function is here rather than in CBioseq because it may need to inspect other sequences.

SRelLoc(const CSeq_loc &parent, const TRanges &ranges)

For manual work. As noted above, ranges need not contain any IDs.

TSignedSeqPos m_uMinSeqLen

When the bioseq gets trimmed down to less than this size, we halt the trimming.

CConstRef< CSeq_loc > m_HardMask

vector< CRef< TRange > > TRanges

string GetProteinName(const CBioseq_Handle &seq)

Return protein name from corresponding Prot-ref feature.

virtual bool SkipBioseq(const CBioseq &)

Used only by Write(CSeq_entry[_Handle], ...); permissive by default.

CConstRef< CSeq_feat > GetBestCdsForMrna(const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

void GetOrg_refForProduct(const CBioseq_Handle &bsh, const COrg_ref *)

size_t num_seqs_seen_so_far

This indicates how many sequences we've seen so far, including the one we're currently on.

CBioseq_CI m_bioseq_CI

This points to the bioseq we're currently on.

TSignedSeqPos max_bases_allowed_to_be_ambig

SAmbigCount(const TSignedSeqPos iTrimDirection)

long TFlags

binary OR of EFlags

const string & GetSequence(void) const

TGi GetGiForAccession(const string &acc, CScope &scope, EGetIdType flags=0)

Given an accession string retrieve the GI id.

const string & GetName(void) const

map< TSeqPos, int > TMSMap

SCurrentGapInfo m_infoOnCurrentGap

This indicates information about the gap we're currently on.

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession string for a Seq-id.

ETranslationLengthProblemOptions

TSeqPos max_num_seqs

We only return gaps on up to this many sequences.

CConstRef< CSeq_feat > GetSourceFeatForProduct(const CBioseq_Handle &bsh)

vector< string > gap_linkage_evidences

A vector representing the linkage-evidences of the gap.

EFindNext

This indicates what happened when we tried to run x_FindNextGapOnBioseq.

TFlags GetAllFlags(void) const

CSeqSearch::TPatternInfo TPatternInfo

CConstRef< CSeq_loc > m_ParentLoc

virtual bool OnPatternFound(const TPatternInfo &pat_info, TSeqPos pos)=0

CRef< CSeq_loc > Resolve(CScope *scope=0, TFlags flags=0) const

CConstRef< CSeq_feat > GetOverlappingCDS(const CSeq_loc &loc, CScope &scope)

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

ETransSplicing

Convenience functions for popular overlapping types.

pair< Int8, CConstRef< CSeq_feat > > TFeatScore

Storage for features and scores.

CPatternInfo TPatternInfo

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

TSeq_id_HandleSet m_PreviousWholeIds

unique_ptr< sequence::CDeflineGenerator > m_Gen

CConstRef< CSeq_feat > GetBestGeneForMrna(const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

CBioseq_CI::EBioseqLevelFlag level_filter

Works like the level filter in CBioseq_CI.

CConstRef< CSeq_feat > GetBestMrnaForCds(const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

CSeq_inst::EMol mol_filter

CSeq_inst::eMol_na to only look at gaps on nucleotide sequences.

TFlags m_fFlags

This holds the flags that affect the behavior of this class.

Int2 GetCutSite(void) const

Params m_Params

This holds the params the caller gave when this object was initially created.

string m_Sequence

user defined name

bool x_IsAllowMismatch(TSearchFlags flags) const

CSeq_id_Handle GetId(const CBioseq_Handle &handle, EGetIdType type=eGetId_Default)

Return a selected ID type for a given bioseq handle.

TTaxId GetTaxIdForProduct(const CBioseq_Handle &bsh)

CConstRef< CSeq_feat > GetBestOverlapForSNP(const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CScope &scope, bool search_both_strands=true)

Get the best overlapping feature for a SNP (variation) feature.

EMeaningOfAmbig

This enum is used to set what is meant by "ambiguous".

CConstRef< CSeq_loc > m_SoftMask

EMaskType

Which residues to mask out in subsequent output.

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)

Given a Seq-id retrieve the corresponding GI.

TSeqPos max_num_gaps_per_seq

We only return up to this many gaps for each sequence.

virtual void postProcessDiffAmount(Int8 &cur_diff, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, CScope &scope, SAnnotSelector &sel, TSeqPos circular_length)=0

CConstRef< CSeq_feat > GetOverlappingPub(const CSeq_loc &loc, CScope &scope)

virtual ~CGetOverlappingFeaturesPlugin()

void SetClient(IClient *client)

CConstRef< CSeq_feat > GetOverlappingOperon(const CSeq_loc &loc, CScope &scope)

CBioseq_Handle GetParentForPart(const CBioseq_Handle &part)

Get the parent bioseq for a part of a segmented bioseq.

const SCurrentGapInfo & operator*(void) const

Get information about the gap we're currently on.

CConstRef< CSeq_id > FindLatestSequence(const CSeq_id &id, CScope &scope)

Given a seq-id check its replace history and try to find the latest revision.

string GetAccessionForGi(TGi gi, CScope &scope, EAccessionVersion use_version=eWithAccessionVersion, EGetIdType flags=0)

Retrieve the accession for a given GI.

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

ENa_strand GetStrand(void) const

TAmbigLookupTable m_arrNucAmbigLookupTable

TSeqPos start_pos

the 0-based position at which the current gap starts on the current sequence.

void GetMrnasForGene(const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

CRef< CSeq_loc > SourceToProduct(const CSeq_feat &feat, const CSeq_loc &source_loc, TS2PFlags flags=0, CScope *scope=0, int *frame=0)

const CSeq_feat * GetPROTForProduct(const CBioseq &product, CScope *scope)

Get the mature peptide feature of a protein.

EResult

This indicates what happened with the trim.

AutoPtr< char, ArrayDeleter< char > > TCharBuf

TSignedSeqPos bases_to_check

CConstRef< CSeq_feat > GetBestGeneForCds(const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

const COrg_ref * GetOrg_refOrNull(const CBioseq_Handle &handle)

Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associa...

vector< STrimRule > TTrimRuleVec

Multiple STrimRules are allowed, which are applied from smallest bases_to_check to largest bases_to_c...

void SetFlag(EFlags flag)

EGapMode GetGapMode(void) const

virtual ~CSequenceAmbigTrimmer()

Do-nothing destructor just to allow inheritance.

CPatternInfo(const string &name, const string &sequence, Int2 cut_site)

constructor

TAmbigLookupTable m_arrProtAmbigLookupTable

string gap_type

String representing the gap type.

virtual void processMainLoop(bool &shouldContinueToNextIteration, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, EOverlapType &overlap_type_this_iteration, bool &revert_locations_this_iteration, CBioseq_Handle &bioseq_handle, const CMappedFeat &feat, TSeqPos circular_length, SAnnotSelector::EOverlapType annot_overlap_type)=0

CMappedFeat GetMappedCDSForProduct(const CBioseq_Handle &product)

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

CSeq_interval TRange

For relative ranges (ONLY), id is irrelevant and normally unset.

const CBioSource * GetBioSourceForBioseq(const CBioseq_Handle &bsh)

Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the prod...

SCurrentGapInfo(void)

Constructor initializes to state that it should be when the iterator first starts.

vector< TFeatScore > TFeatScores

virtual void x_WriteBuffer(const char *buf, unsigned int count)

const CSeq_feat * GetmRNAForProduct(const CBioseq &product, CScope *scope)

Get the encoding mRNA feature of a given mRNA (cDNA) bioseq.

void SetAllFlags(TFlags flags)

EGapMode

How to represent gaps with fInstantiateGaps enabled, as it is by default.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

bool x_IsExpandPattern(TSearchFlags flags) const

CConstRef< CSeq_feat > GetBestOverlappingFeat(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

See the note above on 'overlap_type' meaning.

void GetCdssForGene(const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts=fBestFeat_Defaults, CGetOverlappingFeaturesPlugin *plugin=NULL)

void ReverseComplement(CSeq_inst &seq, CScope *scope)

Reverse complement a Bioseq in place.

TSignedSeqPos x_SegmentGetBeginningInclusive(const CSeqMap_CI &segment, const TSignedSeqPos iTrimDirection)

This returns the (inclusive) position at the beginning of the segment.

CMappedFeat GetMappedmRNAForProduct(const CBioseq_Handle &product)

unsigned int TSearchFlags

binary OR of ESearchFlag

Params(void)

Default ctor gives params which are usually reasonable.

const CBioseq * GetNucleotideParent(const CBioseq &product, CScope *scope)

Get the encoding nucleotide sequnce of a protein.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

bool x_IsJustTopStrand(TSearchFlags flags) const

CSeq_id_Handle seq_id

The seq-id that this gap is on.

size_t num_gaps_seen_so_far_on_this_seq

how many gaps we've seen so far on this sequence.

void ResetFlag(EFlags flag)

TSeqPos GetWidth(void) const

Other parameters...

void GetOverlappingFeatures(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, CSeqFeatData::ESubtype feat_subtype, EOverlapType overlap_type, TFeatScores &feats, CScope &scope, const TBestFeatOpts opts=0, CGetOverlappingFeaturesPlugin *plugin=NULL)

Find all features overlapping the location.

const COrg_ref * GetOrg_refForBioseq(const CBioseq_Handle &bsh)

Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the produc...

int TFlags

binary OR of EFlags

TSeqPos max_gap_len_to_ignore

We completely ignore any gaps we find that have this number of bases or fewer.

TSignedSeqPos num_ambig_bases

the number of ambiguous bases found in the range supplied to x_CountAmbigInRange

TTrimRuleVec m_vecTrimRules

This holds the trimming rules that will be applied.

DECLARE_OPERATOR_BOOL(m_bioseq_CI)

void SetGapMode(EGapMode mode)

bool x_TestFlag(TFlags fFlag)

Test if a given flag is set.

@ eWithAccessionVersion

accession.version (when possible)

@ eWithoutAccessionVersion

accession only, even if version is available

@ fS2P_NoMerge

don't merge adjacent intervals on the product

@ fS2P_AllowTer

map the termination codon as a legal location

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_Seq_id_FastaNARank

use CSeq_id::FastaNARank() as the scoring function

@ eGetId_Seq_id_WorstRank

use CSeq_id::WorstRank() as the scoring function

@ eGetId_ThrowOnError

Throw exception on errors. If not set, an empty value is returned.

@ eGetId_ForceAcc

return only an accession based seq-id

@ eGetId_ForceGi

return only a gi-based seq-id

@ eGetId_Seq_id_Score

use CSeq_id::Score() as the scoring function

@ eGetId_Seq_id_FastaAARank

use CSeq_id::FastaAARank() as the scoring function

@ eGetId_Seq_id_BestRank

use CSeq_id::BestRank() as the scoring function

@ eGetId_VerifyId

Check if the seq-id is present in the scope.

@ eGetId_HandleDefault

returns the ID associated with a bioseq-handle

@ eGetId_TypeMask

Mask for requested id type.

@ fGetTitle_Organism

append [organism]

@ fGetTitle_Reconstruct

ignore existing title Seqdesc.

@ fGetTitle_NoExpensive

skip potential expensive operations

@ fGetTitle_AllProteins

normally just names the first

@ eFindNext_NotFound

No more relevant gaps were found on this bioseq.

@ eTransSplicing_Auto

Ignore overlap strand if the source location has mixed/both strand.

@ eMeaningOfAmbig_AnyAmbig

Here, anything that's not certain is considered ambiguous.

@ eMeaningOfAmbig_OnlyCompletelyUnknown

Here, only N for nucleotides and X for amino acids is considered ambiguous.

@ eResult_SuccessfullyTrimmed

Bioseq is now trimmed.

@ fP2S_Extend

if hitting ends, extend to include partial codons

@ eGM_letters

Multiple inline Ns or Xs as appropriate (default).

@ eGM_dashes

Multiple inline dashes.

@ eGM_one_dash

A single dash, followed by a line break.

@ fBestFeat_NoExpensive

don't perform any expensive tests, such as ones that require fetching additional sequences

@ fBestFeat_FavorLonger

favor longer features over shorter features

@ fBestFeat_Defaults

default options: do everything

@ fBestFeat_StrictMatch

requires explicit association, rather than analysis based on overlaps

@ fBestFeat_IgnoreStrand

Pay no attention to strands when finding the best feat.

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

EBioseqLevelFlag

Class of bioseqs to iterate.

EOverlapType

Flag to indicate location overlapping method.

int16_t Int2

2-byte (16-bit) signed integer

#define numeric_limits

Pre-declaration of the "numeric_limits<>" template Forcibly overrides (using preprocessor) the origin...

int64_t Int8

8-byte (64-bit) signed integer

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_XOBJUTIL_EXPORT

E_Choice

Choice variants.

ENa_strand

strand of nucleic acid

list< CRef< CSeq_id > > TId

EMol

molecule class in living organism

@ Resolve

Try to resolve provided seq-ids.

static CNamedPipeClient * client

The params that control the behavior of CBioseqGaps_CI.

This indicates the state of the iterator right now.

This indicates the text of the modifiers of a gap.

This holds the output of x_CountAmbigInRange.

For example, if bases_to_check is 10 and max_bases_allowed_to_be_ambig is 5, then on each iteration w...

Location relative to a base Seq-loc: one (usually) or more ranges of offsets.

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