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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/update__seq__input_8cpp_source.html below:

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

: m_OldSeq(old_bsh), m_UpdSeq(upd_bsh), m_Align(0)

.GetTopLevelEntry().GetEditHandle().Remove();

dense_seg->

().push_back(query_id);

dense_seg->

().push_back(subject_id);

dense_seg->

().push_back(

.GetBioseqLength() - 1);

align->

().SetDenseg(*dense_seg);

annot->

().SetAlign().push_back(align);

desc->

(

);

annot->

().Set().push_back(desc);

sel_srv->GetActiveObjects(

);

accept_atleast_one =

;

accept_atleast_one =

;

(align_vector.size() > 1) {

(

<<

);

(align_vector.empty()) {

(

<<

);

best_align = 0;

(

= 0;

< align_vector.size(); ++

) {

(

j =

+ 1; j < align_vector.size(); ++j) {

(best_align < align_vector.size());

(set_seqs && no_mismatch);

has_feat =

;

(

feat_it(*bseq_it); feat_it && !has_feat; ++feat_it) {

feat = feat_it->GetOriginalSeq_feat();

(feat->IsSetData() && feat->GetData().IsProt() && !feat->GetData().GetProt().IsSetProcessed())

wxFileDialog openDlg(

,

(

), wxEmptyString, wxEmptyString, ext, wxFD_OPEN | wxFD_FILE_MUST_EXIST);

(openDlg.ShowModal() != wxID_OK)

wxString path = openDlg.GetPath();

+ e.

());

oi = objIstrm->ReadObject();

(oi.

() ==

) {

(oi.

() ==

) {

seq_entry =

(entry);

(oi.

() ==

) {

(msg_listener && msg_listener->

() > 0) {

= 0;

(!

.IsGap()){

(!it->IsLiteral()) {

(!

)

;

bseq.

().SetRepr(objects::CSeq_inst::eRepr_raw);

bseq.

().SetSeq_data().SetIupacna().Set(seqdata);

seq_ids.push_back(*upd_id);

old_ids.push_back(*upd_id);

(seq_dlg.ShowModal() == wxID_OK) {

acc_id = seq_dlg.

();

=

+ acc_id +

;

=

+ acc_id +

;

((*id_iter)->Which() == feat_id_type){

new_inst->

(objects::CSeq_inst::eRepr_raw);

new_inst->

().SetIupacna().Set(seqdata);

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

TSeqPos GetLength(void) const

Base class for reading FASTA sequences.

static wxString GetDialogFilter(EFileType fileType)

CFormatHints & AddPreferredFormat(TFormat fmt)

Mark the format as preferred.

CFormatHints & DisableAllNonpreferred(void)

Disable all formats not marked as preferred.

Class implements different ad-hoc unreliable file format identifications.

CFormatHints & GetFormatHints(void)

Get format hints.

EFormat

The formats are checked in the same order as declared here.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

EFormat GuessFormat(EMode)

Sequence update exception class.

void ReassignConflictingIds(void)

static TSeqPos Pack(CSeq_data *in_seq, TSeqPos uLength=ncbi::numeric_limits< TSeqPos >::max())

static CSimpleClipboard & Instance()

bool IsReadyForUpdate(void) const

bool x_ReadUpdateSeq_ASN(CNcbiIstream &istr)

bool SetOldBioseqAndScope(IWorkbench *workbench, const objects::CSeq_entry_Handle &tse)

bool SetUpdateBioseq(const objects::CBioseq_Handle &bsh)

unsigned int CountBioseqs()

void CalculateAlignmentForUnitTest(void)

Calculates the alignment between the old and the update sequence, sets m_Align member.

objects::CBioseq_Handle m_UpdSeq

bool OldSeqHasProteinFeats() const

static void s_FixCollidingIDs_Entry(objects::CSeq_entry &entry, const objects::CBioseq::TId &seq_ids)

When the old and the update sequences have the same ID, the ID of the update sequence is modified.

static void s_ConvertDeltaToRawEntry(objects::CSeq_entry &entry)

Converts delta literals to raw sequence, applies only to NA sequences.

bool x_ReadAccession(const string &acc_id)

bool ReadSingleAccession(void)

Reads single update sequence identified by an accession.

bool ReadSingleUpdateSequence(objects::ILineErrorListener *msg_listener)

Reads (ASN.1 or FASTA) single update sequence from a file.

bool x_ReadUpdateSeq_Fasta(CNcbiIstream &istr, objects::ILineErrorListener *msg_listener)

bool UpdateSeqHasFeatures(void) const

static bool s_IsDeltaWithFarPointers(const objects::CBioseq &bseq)

void x_FixCollidingIDs_Entry(objects::CSeq_entry &entry)

CRef< objects::CScope > m_Scope

objects::CBioseq_Handle m_OldSeq

void x_AddNewEntryToScope(CRef< objects::CSeq_entry > entry)

Function fixes colliding IDs, add the update entry to the scope and sets m_UpdSeq member.

bool HaveIdenticalResidues(void) const

static CRef< objects::CSeq_annot > s_Align2IdenticalSeq(const objects::CBioseq_Handle &subject, const objects::CBioseq_Handle &query)

static void s_ConvertDeltaToRawBioseq(objects::CBioseq &bseq)

void x_FixCollidingIDs_Bioseq(objects::CBioseq &bioseq)

bool ReadUpdateSequenceFromClipboard(objects::ILineErrorListener *msg_listener)

Reads single update sequence from the clipboard. It supports FASTA and text ASN formats.

CConstRef< objects::CSeq_align > m_Align

void ResetUpdateSequence()

bool OldSeqHasFeatures(void) const

static bool s_IsGoodLiteral(const objects::CSeq_literal &lit)

static bool s_IsDeltaWithNoGaps(const objects::CBioseq &bseq)

bool x_ReadFromStream(CNcbiIstream &istr, objects::ILineErrorListener *msg_listener)

virtual size_t Count() const =0

virtual const ILineError & GetError(size_t) const =0

0-based error retrieval.

virtual const string & ErrorMessage() const

IWorkbench is the central interface in the application framework.

static bool CompareAlignments(const objects::CSeq_align &align_first, const objects::CSeq_align &align_sec)

Returns true if the first alignment is 'better' than the second one Compares the Blast scores and in ...

static vector< CConstRef< objects::CSeq_align > > RunBlast2Seq(const objects::CBioseq_Handle &subject, const objects::CBioseq_Handle &query, bool accept_atleast_one, ICanceled *canceled=nullptr)

static bool HaveIdenticalResidues(const objects::CBioseq_Handle &bsh1, const objects::CBioseq_Handle &bsh2)

static void FixCollidingIDs_Bioseq(objects::CBioseq &bseq, const objects::CBioseq::TId &seq_ids)

Operators to edit gaps in sequences.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

@ eNoOwnership

No ownership is assumed.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

CIRef< T > GetServiceByType()

retrieves a typed reference to a service, the name of C++ type is used as the name of the service.

EDialogReturnValue NcbiMessageBox(const string &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const string &title="Error", EDialogTextMode text_mode=eRaw)

vector< SConstScopedObject > TConstScopedObjects

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

Set object to copy of another one.

static const TObjectType * SafeCast(TTypeInfo type)

@ eSerial_AsnText

ASN.1 text.

CRef< CSeq_entry > ReadSet(int max_seqs=kMax_Int, ILineErrorListener *pMessageListener=nullptr)

Read multiple sequences (by default, as many as are available.)

long TFlags

binary OR of EFlags

@ fDLOptional

Don't require a leading defline.

@ fHyphensIgnoreAndWarn

When a hyphen is encountered in seq data, ignore it but warn.

@ fNoSplit

Don't split out ambiguous sequence regions.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

CSeq_id::E_Choice Which(void) const

TObjectPtr GetObjectPtr(void) const

Get pointer to object.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

const string & GetName(void) const

Get type name.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void SetInst(TInst &v) const

CScope & GetScope(void) const

Get scope this handle belongs to.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

CSeq_id_Handle GetLocationId(void) const

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void SetCoding(TCoding coding)

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

TObjectType * GetNCPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

TLens & SetLens(void)

Assign a value to Lens data member.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetType(TType value)

Assign a value to Type data member.

TStarts & SetStarts(void)

Assign a value to Starts data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

TIds & SetIds(void)

Assign a value to Ids data member.

@ eType_partial

mapping pieces together

E_Choice

Choice variants.

@ e_not_set

No variant selected.

const TSeq & GetSeq(void) const

Get the variant data.

TSet & SetSet(void)

Select the variant.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetSeq_set(void) const

Check if a value has been assigned to Seq_set data member.

bool IsSet(void) const

Check if variant Set is selected.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

bool IsSetLinkage(void) const

Check if a value has been assigned to Linkage data member.

TRepr GetRepr(void) const

Get the Repr member data.

void SetData(TData &value)

Assign a value to Data data member.

const TInst & GetInst(void) const

Get the Inst member data.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

bool IsSetRepr(void) const

Check if a value has been assigned to Repr data member.

TType GetType(void) const

Get the Type member data.

const TId & GetId(void) const

Get the Id member data.

TName & SetName(void)

Select the variant.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool IsSetType(void) const

Check if a value has been assigned to Type data member.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

void SetRepr(TRepr value)

Assign a value to Repr data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void ResetExt(void)

Reset Ext data member.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

@ eRepr_delta

sequence made by changes (delta) to others

@ e_Iupacna

IUPAC 1 letter nuc acid code.

@ eMol_na

just a nucleic acid

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

void GetViewObjects(IWorkbench *workbench, TConstScopedObjects &objects)

bool FocusedOnAll(TConstScopedObjects &objects, const objects::CSeq_entry_Handle &tse)

CRef< CSeq_entry > SeqEntryFromSeqSubmit(const CSeq_submit &submit)

Create a Seq-entry from a Seq-submit.

Utility macros and typedefs for exploring NCBI objects from seq.asn.

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

static const char * kNASeqCouldNotRead

static void s_CollectCollidingIDs_Entry(CSeq_entry &entry, CBioseq::TId &seq_ids, CScope &scope)

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