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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/loc__edit_8hpp_source.html below:

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

ePartialPolicy_eNoChange = 0,

ePartialPolicy_eClearForGoodEnd };

eMergePolicy_NoChange = 0,

eMergePolicy_SingleInterval };

extend_5 =

,

extend_3 =

,

: m_PartialPolicy5(partial5),

m_PartialPolicy3(partial3),

Interpret5Policy(

& orig_feat,

& scope,

& do_set_5_partial,

& do_clear_5_partial)

;

Interpret3Policy(

& orig_feat,

& scope,

& do_set_3_partial,

& do_clear_3_partial)

;

HasNulls(

& orig_loc);

Is5AtEndOfSeq(

& loc,

& scope,

& confident);

Is3AtEndOfSeq(

& loc,

& scope,

& confident);

adjust_gene,

retranslate_cds);

start,

stop,

EPartialPolicy GetPartial5Policy()

void SetPartial3Policy(EPartialPolicy policy)

EPartialPolicy m_PartialPolicy3

EPartialPolicy GetPartial3Policy()

void SetPartial5Policy(EPartialPolicy policy)

CLocationEditPolicy(EPartialPolicy partial5=ePartialPolicy_eNoChange, EPartialPolicy partial3=ePartialPolicy_eNoChange, bool extend_5=true, bool extend_3=true, EMergePolicy merge=eMergePolicy_NoChange)

EPartialPolicy m_PartialPolicy5

@ ePartialPolicy_eSetForFrame

@ ePartialPolicy_eSetAtEnd

@ ePartialPolicy_eSetForBadEnd

@ ePartialPolicy_eClearNotAtEnd

EMergePolicy m_MergePolicy

void SetExtend3(bool policy)

void SetMergePolicy(EMergePolicy policy)

EMergePolicy GetMergePolicy()

void SetExtend5(bool policy)

namespace ncbi::objects::

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#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

bool CorrectIntervalOrder(CSeq_loc &loc)

Correct the order of consecutive intervals with the same Seq-id on the same strand.

@ eSplitLocOption_split_in_intron

@ eSplitLocOption_make_partial

@ eSplitLocOption_split_in_exon

void FeatureAdjustForInsert(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

bool ExtendPartialFeatureEnds(CBioseq_Handle bsh)

void ReverseComplementFeature(CSeq_feat &feat, CScope &scope)

string PrintSeqIntUseBestID(const CSeq_interval &seq_int, CScope &scope, bool range_only)

string PrintBestSeqId(const CSeq_id &sid, CScope &scope)

bool ApplyPolicyToFeature(const CLocationEditPolicy &policy, const CSeq_feat &orig_feat, CScope &scope, bool adjust_gene, bool retranslate_cds)

void FeatureAdjustForTrim(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bAdjusted)

bool IsExtendable(const CSeq_feat &cds, CScope &scope)

string PrintPntAndPntsUseBestID(const CSeq_loc &seq_loc, CScope &scope, bool range_only=false)

void SeqLocAdjustForInsert(CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

string SeqLocPrintUseBestID(const CSeq_loc &seq_loc, CScope &scope, bool range_only=false)

void SplitLocationForGap(CSeq_loc &loc1, CSeq_loc &loc2, size_t start, size_t stop, const CSeq_id *seqid, unsigned int options=eSplitLocOption_make_partial|eSplitLocOption_split_in_exon)

void SeqLocAdjustForTrim(CSeq_loc &loc, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted)

void ReverseComplementLocation(CSeq_loc &loc, CScope &scope)

CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, size_t pos, CScope *scope)

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