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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/trim__n_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/trim_n.cpp Source File

&scope = tse.GetScope();

eTrimResult = trimmer.

( edited_bsh, from, to );

(

exception&) {}

<<

<<

<< from <<

;

orig_inst->Assign(bsh.

());

trimmer.

(bsh, length, from, to, composite, scope, product_to_cds);

(!

.IsEmpty())

report->SetTitle(

(

));

report->Show(

);

void AddCommand(IEditCommand &command)

void SetText(const wxString &text)

void SetWorkDir(const wxString &workDir)

virtual EResult Trim(objects::CBioseq_Handle &bioseq_handle, TSignedSeqPos &left, TSignedSeqPos &right)

void TrimAlignments(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to)

void AdjustAndTranslate(objects::CBioseq_Handle bsh, int length, int from, int to, CRef< CCmdComposite > command, objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

void TrimSeqGraphs(CRef< CCmdComposite > command, objects::CBioseq_Handle bsh, const objects::CBioseq::TId &seqids, TSeqPos from, TSeqPos to, int length)

bool apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, string title, wxWindow *parent, const wxString &workDir, const CSequenceAmbigTrimmer::TTrimRuleVec &trim_rules=CSequenceAmbigTrimmer::GetDefaultTrimRules())

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

int TSignedSeqPos

Type for signed sequence position.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

EResult

This indicates what happened with the trim.

vector< STrimRule > TTrimRuleVec

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

@ eMeaningOfAmbig_OnlyCompletelyUnknown

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

@ eResult_NoTrimNeeded

Bioseq is left unchanged because it did not need to be trimmed at all.

@ eResult_SuccessfullyTrimmed

Bioseq is now trimmed.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

void SetInst(TInst &v) const

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Length GetInst_Length(void) const

const TInst & GetInst(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static const char label[]

const TId & GetId(void) const

Get the Id member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetId(void) const

equivalent identifiers Check if a value has been assigned to Id data member.

@ eMol_na

just a nucleic acid

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void GetProductToCDSMap(objects::CScope &scope, map< objects::CBioseq_Handle, set< objects::CSeq_feat_Handle > > &product_to_cds)

CRef< CCmdComposite > GetDeleteSequenceCommand(objects::CBioseq_Handle bsh)

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