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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/multireader_2multireader_8cpp_source.html below:

NCBI C++ ToolKit: src/app/multireader/multireader.cpp Source File

<<

.GetID() <<

<<

(

.GetCategory()) <<

<<

.GetLineNum() <<

<<

.GetMsg() <<

);

pReaderMessage->

(cerr);

ostream & ostr,

& line_error_p);

()

;

()

;

bytesDone,

(

<< bytesDone <<

));

bytesDone,

(

<<

<< bytesDone <<

));

arg_desc->SetUsageContext(

,

);

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

arg_desc->AddAlias(

,

);

arg_desc->AddDefaultKey(

arg_desc->AddAlias(

,

);

arg_desc->AddDefaultKey(

arg_desc->AddAlias(

,

);

arg_desc->AddDefaultKey(

arg_desc->AddAlias(

,

);

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

,

,

,

,

,

,

,

,

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->SetConstraint(

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetCurrentGroup(

);

,

,

,

,

,

,

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

,

,

) );

arg_desc->AddFlag(

,

);

arg_desc->SetCurrentGroup(

);

,

,

,

,

,

,

,

,

,

,

,

arg_desc->AddDefaultKey(

,

arg_desc->AddOptionalKey(

,

arg_desc->SetCurrentGroup(

);

,

,

,

,

,

arg_desc->SetCurrentGroup(

);

,

,

arg_desc->SetCurrentGroup(

);

,

arg_desc->SetCurrentGroup(

);

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->AddDefaultKey(

,

arg_desc->SetConstraint(

arg_desc->AddDefaultKey(

,

,

,

,

arg_desc->SetCurrentGroup(

);

);

);

arg_desc->AddDefaultKey(

,

arg_desc->SetCurrentGroup(

);

argInFile = args[

].AsString();

argOutFile = args[

].AsString();

argInDir = args[

].AsString();

argOutDir = args[

].AsString();

((argInFile !=

) && !argInDir.empty()) {

cerr <<

((argOutFile !=

) && !argOutDir.empty()) {

cerr <<

(argInDir.empty() && !argOutDir.empty()) {

cerr <<

(argOutDir.empty() && !argInDir.empty()) {

cerr <<

(args[

].AsBoolean() && args[

].AsBoolean()) {

cerr <<

(!args[

].AsString().

() && args[

].AsBoolean()) {

cerr <<

(argInFile ==

&& args[

].AsString() ==

) {

cerr <<

(!argInDir.empty()) {

inFile, outFile;

retIn = fileSource.

(inFile);

(!fileDestination.

(inFile, outFile)) {

cerr <<

<< outFile <<

<< endl;

retIn = fileSource.

(inFile);

retCode =

;

(args, args[

].AsString());

message.

(cerr);

,

);

(osEx.tellp() > 0) {

os <<

<< osEx.str() <<

;

+ os.str());

(

std::exception & std_ex) {

<< std_ex.what()));

list<CRef<CSeq_annot> > ANNOTS;

unique_ptr<CReaderBase> pReader(

pReader->SetProgressReportInterval(10);

pReader->ReadSeqAnnots(annots, istr,

.get());

list<CRef<CSeq_annot> > ANNOTS;

(args[

]) {

(!reader.

(args[

].AsString())) {

(args[

].AsString() ==

) {

(args[

].AsString() ==

) {

&

= it->GetData();

(

.IsFtable()) {

& features = it->GetData().GetFtable();

(features.empty()) {

(args[

].AsString() ==

) {

(args[

].AsString() ==

) {

(!istr.eof()) {

iErrCode = reader.

(istr);

( iErrCode != 0 ) {

+

(!pLineReader->

()) {

( ! pSeqAnnot || ! pSeqAnnot->

() ||

maxIdLength = args[

].AsInteger();

(maxIdLength != 0) {

( args[

] ) {

(args[

].AsString() ==

) {

(args[

].AsBoolean() ?

(std::exception&) {

= args[

].AsString();

==

) {

& filename )

( args[

] ) {

(!args[

]) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

( args[

] ) {

(args[

]) {

(args[

]) {

(args[

]) {

( args[

] ) {

(args[

]) {

( args[

] ) {

(args[

]) {

flagsStr = args[

].AsString();

( args[

] ) {

( args[

] ) {

list<string> stringFlags;

flagsStr = args[

].AsString();

list<string> stringFlags;

startingLocusTagNumber = 1;

startingFeatureId = 1;

(!args[

].AsBoolean() && !args[

].AsBoolean()) {

(args[

]) {

startingLocusTagNumber = tail;

, 0);

prefix = args[

].AsString();

edit::CFeatTableEdit fte(

annot, 0, prefix, startingLocusTagNumber, startingFeatureId,

.get());

fte.InferPartials();

fte.GenerateMissingParentFeatures(args[

].AsBoolean(), pLocationMerger);

(args[

].AsBoolean() && !fte.AnnotHasAllLocusTags()) {

(!prefix.empty()) {

fte.GenerateLocusTags();

,

);

fte.GenerateProteinAndTranscriptIds();

fte.ProcessCodonRecognized();

fte.EliminateBadQualifiers();

fte.SubmitFixProducts();

startingLocusTagNumber = fte.PendingLocusTagNumber();

startingFeatureId = fte.PendingFeatureId();

CLineErrorForMsg(

eDiagSev,

&

)

ostream & ostr,

& line_error)

line_error.

(ostr);

out_format = args[

].AsString();

unique_ptr<MSerial_Format> pOutFormat;

( out_format ==

) {

}

( out_format ==

) {

}

( out_format ==

) {

}

( out_format ==

) {

ostr << *pOutFormat << object;

strBuild = args[

].AsString();

strMapFile = args[

].AsString();

(strBuild.empty() && strMapFile.empty()) {

(!strMapFile.empty()) {

localOnly=

;

& args )

( args[

] ) {

( args[

] ) {

}

( args[

] ) {

iMaxErrorCount = args[

].AsInteger();

strMaxErrorLevel = args[

].AsString();

( strMaxErrorLevel ==

) {

( strMaxErrorLevel ==

) {

( iMaxErrorCount == -1 ) {

iMaxErrorCount, iMaxErrorLevel, *

));

->SetProgressOstream( &cerr );

(

argc,

* argv[])

list<string> split_args;

vector<const char*> new_argv;

(argc==2 && argv && argv[1] && strchr(argv[1],

))

argc = 1 + split_args.size();

new_argv.reserve(argc);

new_argv.push_back(argv[0]);

(

& s : split_args) {

new_argv.push_back(s.c_str());

std::cerr << s.c_str() <<

;

argv = new_argv.data();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

virtual int ReadStream(CNcbiIstream &is, EFinalize eFinalize=eFinalize_Yes)

Read an AGP file from the given input stream.

This class is used to turn an AGP file into a vector of Seq-entry's.

vector< CRef< objects::CSeq_entry > > TSeqEntryRefVec

This is the way the results will be returned Each Seq-entry contains just one Bioseq,...

TSeqEntryRefVec & GetResult(void)

This gets the results found, but don't call before finalizing.

class CAlnReader supports importing a large variety of text-based alignment formats into standard dat...

void Read(bool guess, bool generate_local_ids=false, objects::ILineErrorListener *pErrorListener=nullptr)

EReadFlags

Read the file This are the main functions.

void SetAlphabet(const string &value)

CRef< objects::CSeq_entry > GetSeqEntry(TFastaFlags fasta_flags=objects::CFastaReader::fAddMods, objects::ILineErrorListener *pErrorListener=nullptr)

CReaderBase implementation that reads BED data files, either a single object or all objects found.

virtual bool ReadTrackData(ILineReader &, CRawBedTrack &, ILineErrorListener *=nullptr)

virtual bool SetAutoSql(const string &)

CRef< CSeq_annot > ReadSeqAnnot(ILineReader &lr, ILineErrorListener *pErrors=nullptr) override

Read a single object from given line reader containing BED data.

Base class for reading FASTA sequences.

CRef< CSeq_annot > ReadSeqAnnot(ILineReader &lr, ILineErrorListener *pErrors) override

Read an object from a given line reader, render it as a single Seq-annot, if possible.

static void AddStringFlags(const list< string > &stringFlags, TFlags &baseFlags)

Class implements different ad-hoc unreliable file format identifications.

EFormat

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

@ eFiveColFeatureTable

Five-column feature table.

@ eGff2

GFF2, CGff2Reader, any GFF-like that doesn't fit the others.

@ eBed

UCSC BED file format, CBedReader.

@ eGtf

New GTF, CGtfReader.

@ eHgvs

HGVS, CHgvsParser.

@ eAgp

AGP format assembly, AgpRead.

@ eGff3

GFF3, CGff3Reader.

@ eGtf_POISENED

Old and Dead GFF/GTF style annotations.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eUnknown

unknown format

@ eGffAugustus

GFFish output of Augustus Gene Prediction.

@ eRmo

RepeatMasker Output.

@ eUCSCRegion

USCS Region file format.

@ eAlignment

Text alignment.

@ ePsl

PSL alignment format.

@ eBed15

UCSC BED15 or microarray format.

@ eWiggle

UCSC WIGGLE file format.

static EFormat Format(const string &path, EOnError onerror=eDefault)

Guess file format.

void ReadSeqAnnots(TAnnotList &, CNcbiIstream &, ILineErrorListener *=nullptr) override

Read all objects from given insput stream, returning them as a vector of Seq-annots.

shared_ptr< CGff3LocationMerger > GetLocationMerger()

IdMapper implementation using hardcoded values.

IdMapper implementation using an external configuration file.

size_t Count() const override

void StoreError(const ILineError &err)

void StoreMessage(const IObjtoolsMessage &message)

bool Next(const std::string &, string &)

void xProcessGff2(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessWiggle(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xDumpErrors(CNcbiOstream &)

unique_ptr< CMessageListenerBase > m_pErrors

void xSetMessageListener(const CArgs &)

void xSetMapper(const CArgs &)

void xWriteObject(const CArgs &, CSerialObject &, CNcbiOstream &)

void xProcessAgp(const CArgs &, CNcbiIstream &, CNcbiOstream &)

bool xProcessBed(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void WriteMessageImmediately(ostream &ostr, const ILineError &line_error_p)

void xProcessAlignment(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessRmo(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessDefault(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessFasta(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessBedRaw(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessGtf(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessGff3(const CArgs &, CNcbiIstream &, CNcbiOstream &)

unique_ptr< CObjtoolsListener > m_pEditErrors

void xProcessUCSCRegion(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xPostProcessAnnot(const CArgs &, CSeq_annot &, const CGff3LocationMerger *=nullptr)

CFormatGuess::EFormat m_uFormat

int Run() override

Run the application.

void xSetFormat(const CArgs &, CNcbiIstream &)

void Init() override

Initialize the application.

void xSetFlags(const CArgs &, const string &)

bool ShowingProgress() const

unique_ptr< CIdMapper > m_pMapper

bool xProcessSingleFile(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessNewick(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessWiggleRaw(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcessGvf(const CArgs &, CNcbiIstream &, CNcbiOstream &)

void xProcess5ColFeatTable(const CArgs &, CNcbiIstream &, CNcbiOstream &)

static AutoPtr< ILineError > sCreateSimpleMessage(EDiagSev eDiagSev, const string &msg)

bool PutMessage(const IObjtoolsMessage &message)

void PutProgress(const string &msg, const Uint8 bytesDone, const Uint8)

This is used for processing progress messages.

CMultiReaderApp & m_multi_reader_app

CMyMessageListenerCustomLevel(int level, CMultiReaderApp &multi_reader_app)

CMyMessageListenerCustom(int iMaxCount, int iMaxLevel, CMultiReaderApp &multi_reader_app)

bool PutMessage(const IObjtoolsMessage &message)

void PutProgress(const string &, const Uint8 bytesDone, const Uint8)

This is used for processing progress messages.

~CMyMessageListenerCustom()

bool PutError(const ILineError &err)

Store error in the container, and return true if error was stored fine, and return false if the calle...

CMultiReaderApp & m_multi_reader_app

void Dump(CNcbiOstream &ostr) const

void Dump(CNcbiOstream &ostr) const

static CRef< CSeq_id > AsSeqId(const string &rawId, long flags=0, bool localInts=true)

Convert a raw ID string to a Seq-id, based in given customization flags.

@ fNumericIdsAsLocal

numeric identifiers are local IDs

@ fAllIdsAsLocal

all identifiers are local IDs

list< CRef< CSeq_annot > > TAnnotList

void SetProgressReportInterval(unsigned int intv)

virtual void ReadSeqAnnots(TAnnots &annots, CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr)

Read all objects from given insput stream, returning them as a vector of Seq-annots.

static CReaderBase * GetReader(CFormatGuess::EFormat format, TReaderFlags flags=0, CReaderListener *=nullptr)

Allocate a CReaderBase derived reader object based on the given file format.

virtual void Write(CNcbiOstream &out) const override

virtual EDiagSev Severity() const

Implements a concrete class for reading RepeatMasker output from tabular form and rendering it as ASN...

CRef< CSeq_annot > ReadSeqAnnot(ILineReader &lr, ILineErrorListener *pMessageListener=0)

Read an object from a given line reader, render it as a single Seq-annot, if possible.

bool IsFtable(void) const

Base class for all serializable objects.

Simple implementation of ILineReader for i(o)streams.

CRef< CSerialObject > ReadObject(ILineReader &lr, ILineErrorListener *pErrors=nullptr) override

Read an object from a given line reader, render it as the most appropriate Genbank object.

virtual bool ReadTrackData(ILineReader &, CRawWiggleTrack &, ILineErrorListener *=nullptr)

Interface for testing cancellation request in a long lasting operation.

virtual void DumpAsXML(CNcbiOstream &out) const

virtual void Dump(CNcbiOstream &out) const

virtual EDiagSev Severity(void) const

@ eProblem_GeneralParsingError

vector< unsigned int > TVecOfLines

virtual EProblem Problem(void) const =0

CRef< objects::CBioTreeContainer > MakeDistanceSensitiveBioTreeContainer(const TPhyTreeNode *tree)

Conversion from TPhyTreeNode to CBioTreeContainer, potentially without dist feature key.

Operators to edit gaps in sequences.

static void cleanup(void)

static void fatal(const char *msg,...)

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const string & GetProgramDisplayName(void) const

Get the application's "display" name.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void SetVersion(const CVersionInfo &version)

Set the version number for the program.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ eDirectory

Name of file directory.

@ fBinary

Open file in binary mode.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Info

Informational message.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

virtual void ReportExtra(ostream &out) const

Report "non-standard" attributes.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

const string & GetMsg(void) const

Get message string.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

#define FORMAT(message)

Format message using iostreams library.

static string MakePath(const string &dir=kEmptyStr, const string &base=kEmptyStr, const string &ext=kEmptyStr)

Assemble a path from basic components.

static CRef< ILineReader > New(const string &filename)

Return a new ILineReader object corresponding to the given filename, taking "-" (but not "....

long TFlags

binary OR of EFlags

virtual CRef< CSeq_entry > ReadSeqEntry(ILineReader &lr, ILineErrorListener *pErrors)

Read an object from a given line reader, render it as a single Seq-entry, if possible.

static void AddStringFlags(const list< string > &stringFlags, TFlags &baseFlags)

virtual bool AtEOF(void) const =0

Indicates (negatively) whether there is any more input.

void SetMaxIDLength(Uint4 max_len)

If this is set, an exception will be thrown if a Sequence ID exceeds the given length.

@ fAddMods

Parse defline mods and add to SeqEntry.

@ fNoSplit

Don't split out ambiguous sequence regions.

@ fParseGaps

Make a delta sequence if gaps found.

@ fDisableParseRange

No ranges in seq-ids. Ranges part of seq-id instead.

void Reset(void)

Reset reference object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_CanEscape

Allow \... escaping.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

const TFtable & GetFtable(void) const

Get the variant data.

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

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

Lightweight interface for getting lines of data with minimal memory copying.

string s_AlnErrorToString(const CAlnError &error)

CMultiReaderMessageListener newStyleMessageListener

int main(int argc, const char *argv[])

constexpr bool empty(list< Ts... >) noexcept

#define NCBI_SC_VERSION_PROXY

#define NCBI_TEAMCITY_BUILD_NUMBER_PROXY

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

The NCBI C++/STL use hints.

TPhyTreeNode * ReadNewickTree(CNcbiIstream &is)

Newick format input.

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

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

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