NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Private Attributes
CMultiReaderApp Class Reference

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+ Inheritance diagram for CMultiReaderApp:
+ Collaboration diagram for CMultiReaderApp:

List of all members.

Public Member Functions

 CMultiReaderApp ()

Private Member Functions

virtual void Init (void)
 Initialize the application.
virtual int Run (void)
 Run the application.
void xProcessDefault (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessWiggle (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessWiggleRaw (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessBed (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessUCSCRegion (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessBedRaw (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessGtf (const CArgs &, CNcbiIstream &, CNcbiOstream &)
void xProcessVcf (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 xSetFormat (const CArgs &, CNcbiIstream &)
void xSetFlags (const CArgs &, CNcbiIstream &)
void xSetMapper (const CArgs &)
void xSetMessageListener (const CArgs &)
void xPostProcessAnnot (const CArgs &, CSeq_annot &)
void xWriteObject (const CArgs &, CSerialObject &, CNcbiOstream &)
void xDumpErrors (CNcbiOstream &)

Private Attributes

CFormatGuess::EFormat m_uFormat
bool m_bCheckOnly
bool m_bDumpStats
int m_iFlags
string m_AnnotName
string m_AnnotTitle
bool m_bXMLErrors
auto_ptr< CIdMapperm_pMapper
CRef< CMessageListenerBasem_pErrors

Detailed Description

Definition at line 104 of file multireader.cpp.


Constructor & Destructor Documentation

Definition at line 109 of file multireader.cpp.

References CNcbiApplication::SetVersion().


Member Function Documentation

void CMultiReaderApp::Init ( void  ) [private, virtual]

Initialize the application.

The default behavior of this is "do nothing". If you have special initialization logic that needs to be peformed, then you must override this method with your own logic.

Reimplemented from CNcbiApplication.

Definition at line 183 of file multireader.cpp.

References CArgDescriptions::AddDefaultKey(), CArgDescriptions::AddFlag(), CArgDescriptions::AddKey(), CArgDescriptions::eInputFile, CArgDescriptions::eInteger, CArgDescriptions::eOutputFile, CArgDescriptions::eString, CNcbiApplication::GetArguments(), auto_ptr< X >::release(), CArgDescriptions::SetConstraint(), CArgDescriptions::SetCurrentGroup(), CNcbiApplication::SetupArgDescriptions(), and CArgDescriptions::SetUsageContext().

int CMultiReaderApp::Run ( void  ) [private, virtual]
void CMultiReaderApp::xDumpErrors ( CNcbiOstream ostr) [private]
void CMultiReaderApp::xPostProcessAnnot ( const CArgs args,
CSeq_annot annot 
) [private]

Definition at line 997 of file multireader.cpp.

References m_pErrors.

Referenced by xProcessGff3(), and xProcessGtf().

void CMultiReaderApp::xProcess5ColFeatTable ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessAgp ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessAlignment ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessBed ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 627 of file multireader.cpp.

References m_iFlags, m_pErrors, CBedReader::ReadSeqAnnot(), CRef< C, Locker >::Reset(), and xWriteObject().

Referenced by Run().

void CMultiReaderApp::xProcessBedRaw ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 645 of file multireader.cpp.

References CRawBedTrack::Dump(), m_iFlags, and CBedReader::ReadTrackData().

Referenced by Run().

void CMultiReaderApp::xProcessDefault ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessFasta ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessGff2 ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessGff3 ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessGtf ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessGvf ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]
void CMultiReaderApp::xProcessNewick ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 763 of file multireader.cpp.

References MakeBioTreeContainer(), ReadNewickTree(), and xWriteObject().

Referenced by Run().

void CMultiReaderApp::xProcessUCSCRegion ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 613 of file multireader.cpp.

References m_iFlags, m_pErrors, CUCSCRegionReader::ReadObject(), and xWriteObject().

Referenced by Run().

void CMultiReaderApp::xProcessVcf ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 746 of file multireader.cpp.

References m_iFlags, m_pErrors, CVcfReader::ReadSeqAnnots(), and xWriteObject().

Referenced by Run().

void CMultiReaderApp::xProcessWiggle ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 580 of file multireader.cpp.

References m_iFlags, m_pErrors, CWiggleReader::ReadSeqAnnots(), and xWriteObject().

Referenced by Run().

void CMultiReaderApp::xProcessWiggleRaw ( const CArgs args,
CNcbiIstream istr,
CNcbiOstream ostr 
) [private]

Definition at line 598 of file multireader.cpp.

References CRawWiggleTrack::Dump(), m_iFlags, and CWiggleReader::ReadTrackData().

Referenced by Run().

void CMultiReaderApp::xSetFlags ( const CArgs args,
CNcbiIstream istr 
) [private]
void CMultiReaderApp::xSetFormat ( const CArgs args,
CNcbiIstream istr 
) [private]
void CMultiReaderApp::xSetMapper ( const CArgs args) [private]

Definition at line 1048 of file multireader.cpp.

References m_pErrors, m_pMapper, and auto_ptr< X >::reset().

Referenced by Run().

void CMultiReaderApp::xSetMessageListener ( const CArgs args) [private]
void CMultiReaderApp::xWriteObject ( const CArgs args,
CSerialObject object,
CNcbiOstream ostr 
) [private]

Member Data Documentation

Definition at line 150 of file multireader.cpp.

Referenced by xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), and xSetFlags().

Definition at line 151 of file multireader.cpp.

Referenced by xProcessGff2(), xProcessGff3(), xProcessGtf(), xProcessGvf(), and xSetFlags().

Definition at line 147 of file multireader.cpp.

Referenced by xSetFlags(), and xWriteObject().

Definition at line 148 of file multireader.cpp.

Definition at line 152 of file multireader.cpp.

Referenced by xDumpErrors(), and xSetFlags().

Definition at line 154 of file multireader.cpp.

Referenced by xSetMapper(), and xWriteObject().

Definition at line 146 of file multireader.cpp.

Referenced by Run(), xProcessDefault(), xSetFlags(), and xSetFormat().


The documentation for this class was generated from the following file:
Modified on Fri Jul 11 17:23:21 2014 by modify_doxy.py rev. 426318