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

NCBI C++ ToolKit: CMultiReaderApp Class Reference

Search Toolkit Book for CMultiReaderApp

void Init () override Initialize the application. More...
int Run () override Run the application. More...
bool xProcessSingleFile (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessDefault (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessWiggle (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessWiggleRaw (const CArgs &, CNcbiIstream &, CNcbiOstream &) bool xProcessBed (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessUCSCRegion (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessBedRaw (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessGtf (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessNewick (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessGff3 (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessGff2 (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessGvf (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessAlignment (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessAgp (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcess5ColFeatTable (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessFasta (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xProcessRmo (const CArgs &, CNcbiIstream &, CNcbiOstream &) void xSetFormat (const CArgs &, CNcbiIstream &) void xSetFlags (const CArgs &, const string &) void xSetFlags (const CArgs &, CNcbiIstream &) void xSetMapper (const CArgs &) void xSetMessageListener (const CArgs &) void xPostProcessAnnot (const CArgs &, CSeq_annot &, const CGff3LocationMerger *=nullptr) void xWriteObject (const CArgs &, CSerialObject &, CNcbiOstream &) void xDumpErrors (CNcbiOstream &) enum EAppNameType { eBaseName , eFullName , eRealName } enum EPreparseArgs { ePreparse_Continue , ePreparse_Exit } Result of PreparseArgs() More...
enum EDisableArgDesc { fDisableStdArgs = 0x01 } Disable argument descriptions. More...
enum EHideStdArgs {
  fHideLogfile = CArgDescriptions::fHideLogfile , fHideConffile = CArgDescriptions::fHideConffile , fHideVersion = CArgDescriptions::fHideVersion , fHideFullVersion = CArgDescriptions::fHideFullVersion ,
  fHideDryRun = CArgDescriptions::fHideDryRun , fHideHelp = CArgDescriptions::fHideHelp , fHideFullHelp = CArgDescriptions::fHideFullHelp , fHideXmlHelp = CArgDescriptions::fHideXmlHelp ,
  fHideAll = CArgDescriptions::fHideAll
} Which standard flag's descriptions should not be displayed in the usage message. More...
enum EStdioSetup {
  fNoSyncWithStdio = 0x01 , fDefault_CinBufferSize = 0x02 , fBinaryCin = 0x04 , fBinaryCout = 0x08 ,
  fDefault_SyncWithStdio = 0x00
} Flags to adjust standard I/O streams' behaviour. More...
enum EExitMode { eNoExits , eExceptionalExits , eAllExits } When to return a user-set exit code. More...
enum EAppFlags { fSkipSafeStaticDestroy = 1 << 0 } typedef int TDisableArgDesc Binary OR of "EDisableArgDesc". More...
typedef int THideStdArgs Binary OR of "EHideStdArgs". More...
typedef int TStdioSetupFlags Binary OR of "EStdioSetup". More...
typedef int TAppFlags virtual EPreparseArgs PreparseArgs (int argc, const char *const *argv) Check the command line arguments before parsing them. More...
void DisableArgDescriptions (TDisableArgDesc disable=fDisableStdArgs) void HideStdArgs (THideStdArgs hide_mask) Set the hide mask for the Hide Std Flags. More...
void SetStdioFlags (TStdioSetupFlags stdio_flags) Adjust the behavior of standard I/O streams. More...
void SetVersion (const CVersionInfo &version) Set the version number for the program. More...
void SetVersion (const CVersionInfo &version, const SBuildInfo &build_info) void SetVersionByBuild (int major) void SetFullVersion (CRef< CVersionAPI > version) Set version data for the program. More...
virtual void SetupArgDescriptions (CArgDescriptions *arg_desc) Setup the command line argument descriptions. More...
const CArgDescriptions * GetArgDescriptions (void) const Get argument descriptions (set by SetupArgDescriptions) More...
bool SetupDiag (EAppDiagStream diag) Setup the application diagnostic stream. More...
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf, CNcbiRegistry::TFlags reg_flags) Load settings from the configuration file to the registry. More...
virtual bool LoadConfig (CNcbiRegistry &reg, const string *conf) Load settings from the configuration file to the registry. More...
CNcbiRegistry & GetRWConfig (void) Get the application's cached configuration parameters, accessible for read-write for an application's internal use only. More...
void SetProgramDisplayName (const string &app_name) Set program's display name. More...
virtual void AppStart (void) Method to be called before application start. More...
virtual void AppStop (int exit_code) Method to be called before application exit. More...
void SetExitCode (int exit_code, EExitMode when=eExceptionalExits) Force the program to return a specific exit code later, either when it exits due to an exception or unconditionally. More...
void SetAppFlags (TAppFlags flags) void ExecuteOnExitActions () Should only be called from the destructors of classes derived from CNcbiApplicationAPI - if it is necessary to access their data members and virtual methods; or to dynamic_cast<> from the base app class. More...
void SetPhoneHomePolicy (IPhoneHomePolicy *policy, ENcbiOwnership ownership=eNoOwnership) Set Phone Home Policy. More...
IPhoneHomePolicy * GetPhoneHomePolicy () const Return pointer to current Phone Home Policy or NULL. More...
static CRWLock & GetInstanceLock (void) static string FindProgramExecutablePath (int argc, const char *const *argv, string *real_path=0) Find the application's executable file. More...

Definition at line 133 of file multireader.cpp.

◆ CMultiReaderApp() CMultiReaderApp::CMultiReaderApp ( ) inline ◆ Init() void CMultiReaderApp::Init ( void ) overrideprivatevirtual ◆ Run() int CMultiReaderApp::Run ( ) overrideprivatevirtual ◆ sCreateSimpleMessage() ◆ ShowingProgress() bool CMultiReaderApp::ShowingProgress ( ) const inline ◆ WriteMessageImmediately() void CMultiReaderApp::WriteMessageImmediately ( ostream & ostr, const ILineError & line_error_p ) ◆ xDumpErrors() ◆ xPostProcessAnnot()

Definition at line 1506 of file multireader.cpp.

References cleanup(), eDiag_Fatal, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::IsFtable(), m_pErrors, NCBI_THROW2, offset, sCreateSimpleMessage(), NStr::SplitInTwo(), NStr::StringToNonNegativeInt(), and WriteMessageImmediately().

Referenced by xProcessGff3(), and xProcessGtf().

◆ xProcess5ColFeatTable() ◆ xProcessAgp() ◆ xProcessAlignment()

Definition at line 1237 of file multireader.cpp.

References CAlnReader::eAlpha_Nucleotide, CAlnReader::eAlpha_Protein, CFastaReader::fAddMods, CAlnReader::fGenerateLocalIDs, flags, CAlnReader::fReadDefaults, CAlnReader::GetSeqEntry(), m_pErrors, CAlnReader::Read(), CAlnReader::SetAlphabet(), and xWriteObject().

Referenced by xProcessSingleFile().

◆ xProcessBed()

Definition at line 966 of file multireader.cpp.

References lr(), m_AnnotName, m_AnnotTitle, m_iFlags, m_pErrors, newStyleMessageListener, CBedReader::ReadSeqAnnot(), CRef< C, Locker >::Reset(), CBedReader::SetAutoSql(), CReaderBase::SetProgressReportInterval(), ShowingProgress(), and xWriteObject().

Referenced by xProcessSingleFile().

◆ xProcessBedRaw() ◆ xProcessDefault() ◆ xProcessFasta() ◆ xProcessGff2() ◆ xProcessGff3()

Definition at line 1036 of file multireader.cpp.

References CReadUtil::AsSeqId(), data, CGff3Reader::GetLocationMerger(), m_AnnotName, m_AnnotTitle, m_iFlags, m_pErrors, newStyleMessageListener, CGff2Reader::ReadSeqAnnots(), CReaderBase::SetProgressReportInterval(), ShowingProgress(), xPostProcessAnnot(), xProcessGff2(), and xWriteObject().

Referenced by xProcessGvf(), and xProcessSingleFile().

◆ xProcessGtf() ◆ xProcessGvf() ◆ xProcessNewick() ◆ xProcessRmo() ◆ xProcessSingleFile()

Definition at line 766 of file multireader.cpp.

References CObjtoolsMessage::Dump(), CFormatGuess::eAgp, CFormatGuess::eAlignment, CFormatGuess::eBed, eDiag_Fatal, CFormatGuess::eFasta, CFormatGuess::eFiveColFeatureTable, CFormatGuess::eGff2, CFormatGuess::eGff3, CFormatGuess::eGffAugustus, CFormatGuess::eGtf, CFormatGuess::eGtf_POISENED, CFormatGuess::eGvf, CFormatGuess::eNewick, CFormatGuess::eRmo, CFormatGuess::eUCSCRegion, CFormatGuess::eWiggle, CReaderBase::fAsRaw, FORMAT, CException::GetMsg(), m_iFlags, m_pErrors, m_uFormat, CException::ReportExtra(), sCreateSimpleMessage(), xDumpErrors(), xProcess5ColFeatTable(), xProcessAgp(), xProcessAlignment(), xProcessBed(), xProcessBedRaw(), xProcessDefault(), xProcessFasta(), xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), xProcessNewick(), xProcessRmo(), xProcessUCSCRegion(), xProcessWiggle(), xProcessWiggleRaw(), and xSetFlags().

Referenced by Run().

◆ xProcessUCSCRegion() ◆ xProcessWiggle() ◆ xProcessWiggleRaw() ◆ xSetFlags() [1/2]

Definition at line 1367 of file multireader.cpp.

References CFastaReader::AddStringFlags(), CFeature_table_reader::AddStringFlags(), CFormatGuess::eBed, CFormatGuess::eFasta, CFormatGuess::eFiveColFeatureTable, CFormatGuess::eGff3, CFormatGuess::eGtf, CFormatGuess::eUnknown, CFormatGuess::eWiggle, CFastaReader::fAddMods, CReaderBase::fAllIdsAsLocal, CWiggleReader::fAsByte, CWiggleReader::fAsGraph, CReaderBase::fAsRaw, NStr::fConvErr_NoThrow, CBedReader::fDirectedFeatureModel, CFastaReader::fDisableParseRange, CGff2Reader::fGenbankMode, CGtfReader::fGenerateChildXrefs, CGff3Reader::fGeneXrefs, CWiggleReader::fJoinSame, CFastaReader::fNoSplit, CReaderBase::fNumericIdsAsLocal, CFastaReader::fParseGaps, CGff2Reader::fRetainLocusIds, CBedReader::fThreeFeatFormat, m_AnnotName, m_AnnotTitle, m_bCheckOnly, m_bXmlMessages, m_iFlags, m_uFormat, NStr::Split(), NStr::StringToInt(), and xSetFormat().

◆ xSetFlags() [2/2] ◆ xSetFormat()

Definition at line 1268 of file multireader.cpp.

References CFormatGuess::eAgp, CFormatGuess::eAlignment, CFormatGuess::eBed, CFormatGuess::eBed15, CFormatGuess::eFasta, CFormatGuess::eFiveColFeatureTable, CFormatGuess::eGff2, CFormatGuess::eGff3, CFormatGuess::eGffAugustus, CFormatGuess::eGtf, CFormatGuess::eGvf, CFormatGuess::eHgvs, CFormatGuess::eNewick, CFormatGuess::ePsl, CFormatGuess::eUCSCRegion, CFormatGuess::eUnknown, CFormatGuess::eVcf, CFormatGuess::eWiggle, CFormatGuess::Format(), format, CNcbiApplicationAPI::GetProgramDisplayName(), m_uFormat, and NStr::StartsWith().

Referenced by xSetFlags().

◆ xSetMapper() void CMultiReaderApp::xSetMapper ( const CArgs & args ) private ◆ xSetMessageListener() void CMultiReaderApp::xSetMessageListener ( const CArgs & args ) private ◆ xWriteObject()

Definition at line 1613 of file multireader.cpp.

References m_bCheckOnly, m_pMapper, and NCBI_USER_THROW_FMT.

Referenced by xProcess5ColFeatTable(), xProcessAgp(), xProcessAlignment(), xProcessBed(), xProcessDefault(), xProcessFasta(), xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), xProcessNewick(), xProcessRmo(), xProcessUCSCRegion(), and xProcessWiggle().

◆ m_AnnotName string CMultiReaderApp::m_AnnotName private ◆ m_AnnotTitle string CMultiReaderApp::m_AnnotTitle private ◆ m_bCheckOnly bool CMultiReaderApp::m_bCheckOnly private ◆ m_bDumpStats ◆ m_bXmlMessages bool CMultiReaderApp::m_bXmlMessages private ◆ m_iFlags long CMultiReaderApp::m_iFlags private

Definition at line 187 of file multireader.cpp.

Referenced by Run(), xProcess5ColFeatTable(), xProcessAgp(), xProcessBed(), xProcessBedRaw(), xProcessDefault(), xProcessFasta(), xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), xProcessSingleFile(), xProcessUCSCRegion(), xProcessWiggle(), xProcessWiggleRaw(), and xSetFlags().

◆ m_pEditErrors ◆ m_pErrors

Definition at line 194 of file multireader.cpp.

Referenced by xDumpErrors(), xPostProcessAnnot(), xProcess5ColFeatTable(), xProcessAlignment(), xProcessBed(), xProcessDefault(), xProcessFasta(), xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), xProcessRmo(), xProcessSingleFile(), xProcessUCSCRegion(), xProcessWiggle(), xSetMapper(), and xSetMessageListener().

◆ m_pMapper unique_ptr<CIdMapper> CMultiReaderApp::m_pMapper private ◆ m_showingProgress bool CMultiReaderApp::m_showingProgress private ◆ m_uFormat

The documentation for this class was generated from the following file:

src/app/multireader/multireader.cpp

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