Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/update__multi__seq__input_8cpp_source.html below:

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

: m_NumUpdated(0), m_NumSkipped(0), m_UpdEntry(0),

(0)

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.

() ==

) {

(

= 0;

< msg_listener->

(); ++

) {

only_proteins =

;

only_proteins =

;

(matches.

(idh) == matches.

())

(

& m : matches) {

(update_pairs.

()) {

(

&& it : update_pairs) {

(!old_bsh || !upd_bsh) {

toAppendIdent.emplace(old_idh, upd_idh);

toAppendNonIdent.emplace(old_idh, upd_idh);

(toAppendNonIdent.

() && toAppendIdent.

()) {

(

<<

);

nonidenticalsOk && identicalsOk;

(updatepairs.

()) {

(

&& it : updatepairs) {

inputmap.

(make_pair(it.first, updInput));

nonidenticalsOk && identicalsOk;

(updatepairs.

()) {

(

&& it : updatepairs) {

(exception &) {

(

);

.append(it.first.AsString());

.append(

);

.append(it.second.AsString());

.append(

);

inputmap.

(make_pair(it.first, updInput));

nonident_it->second;

ident_it->second;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

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.

static CSimpleClipboard & Instance()

Template class for iteration on objects of class C (non-medifiable version)

TSeqIDHVector m_UnmatchedUpdates

objects::CSeq_inst::EMol m_MolType

TOldToUpdateMap m_NonIdentPairs

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

objects::CSeq_entry_Handle m_OldSeh

vector< objects::CSeq_id_Handle > TSeqIDHVector

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

TOldToUpdateMap m_IdenticalPairs

bool HaveIdenticalResidues(const objects::CSeq_id_Handle &idh1, const objects::CSeq_id_Handle &idh2)

CRef< CUpdateSeq_Input > GetUpdateInput(const objects::CSeq_id_Handle &idh) const

bool ReadUpdSeqs_FromClipboard(objects::ILineErrorListener *msg_listener)

~CUpdateMultipleSeq_Input()

CRef< objects::CSeq_entry > m_UpdEntry

bool PrepareMultipleSequenceInputsForUnitTest()

bool SetOldEntryAndScope(const objects::CSeq_entry_Handle &tse)

bool x_ReadUpdateSeqs_ASN(CNcbiIstream &istr)

void PrepareMultipleSequenceInputs()

bool x_CreateUpdateSeqInputForUnitTest(const TOldToUpdateMap &updatepairs, TIDToUpdInputMap &inputmap)

bool ReadUpdSeqs_FromFile(objects::ILineErrorListener *msg_listener)

CRef< objects::CScope > m_Scope

bool AppendOld_UpdateSeqPairs(const TOldToUpdateMap &update_pairs)

TIDToUpdInputMap m_IdenticalUpdates

bool SetUpdateEntry(CRef< objects::CSeq_entry > update)

TIDToUpdInputMap m_NonIdentUpdates

TSeqIDHVector m_WithoutUpdates

CUpdateMultipleSeq_Input(void)

bool x_MatchIdsAndAddUpdateToScope()

bool x_CreateUpdateSeqInput(const TOldToUpdateMap &updatepairs, TIDToUpdInputMap &inputmap)

Sets up the old and the update sequences, and generates the alignment between them.

void CalculateAlignmentForUnitTest(void)

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

virtual size_t Count() const =0

virtual const ILineError & GetError(size_t) const =0

0-based error retrieval.

@ eProblem_InvalidResidue

@ eProblem_IgnoredResidue

@ eProblem_GeneralParsingError

virtual EProblem Problem(void) const =0

virtual const string & ErrorMessage() const

virtual EDiagSev GetSeverity(void) const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

static void FindMatches(objects::CSeq_inst::EMol type, objects::CSeq_entry_Handle &oldSeq, objects::CSeq_entry &updEntry, TSeqIdHMap &matches, TSeqIdHVector &unmatched)

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

static objects::CSeq_id_Handle GetGoodSeqIdHandle(const objects::CBioseq_Handle &bsh)

Operators to edit gaps in sequences.

@ eNoOwnership

No ownership is assumed.

EDiagSev

Severity level for the posted diagnostics.

#define LOG_POST(message)

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

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

@ eDiag_Critical

Critical error message.

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)

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

@ fHyphensIgnoreAndWarn

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

@ fUniqueIDs

Forbid duplicate IDs.

@ fAddMods

Parse defline mods and add to SeqEntry.

@ fNoSplit

Don't split out ambiguous sequence regions.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

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.

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.

bool IsNull(void) const THROWS_NONE

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

#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.

@ 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

CRef< CSeq_entry > SeqEntryFromSeqSubmit(const CSeq_submit &submit)

Create a Seq-entry from a Seq-submit.

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

static const char * kNASeqCouldNotRead

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4