Importer Class Reference

#include <Importer.h>

Inheritance diagram for Importer:

Collaboration diagram for Importer:

Public Member Functions
	Importer (LineReader &Flatfile, DBwriter &DB_writer, const MetaTag *meta_description)
virtual	~Importer ()
void	import ()
void	warning (const char *msg)

Protected Member Functions
void	expectLine (string &line)
const MetaTag *	findTag (const string &tag)
virtual bool	readFeatureTableLine (string &line)=0
FeatureLinePtr	getFeatureTableLine ()
void	backFeatureTableLine (FeatureLinePtr &fline)
FeatureLinePtr	getUnwrappedFeatureTableLine ()
FeaturePtr	parseFeature ()
void	parseFeatureTable ()
virtual void	import_section ()=0
void	show_warnings (const string &import_of_what)
void	check_base_counters (const SequenceBuffer &seqData, const BaseCounter *headerCount)

Protected Attributes
DBwriter &	db_writer
LineReader &	flatfile
MetaTagTranslator	tagTranslator
FeatureLines	pushedFeatureLines
stringVector	warnings
long	expectedSeqLength

Detailed Description

Definition at line 58 of file Importer.h.

Constructor & Destructor Documentation

Importer::Importer	(	LineReader &	Flatfile,
		DBwriter &	DB_writer,
		const MetaTag *	meta_description
	)

Definition at line 121 of file Importer.cxx.

virtual Importer::~Importer ( )

inlinevirtual

Definition at line 88 of file Importer.h.

Member Function Documentation

void Importer::expectLine ( string &  line )

inlineprotected

Definition at line 67 of file Importer.h.

References LineReader::getLine(), and LineReader::lineError().

const MetaTag* Importer::findTag ( const string &  tag )

inlineprotected

Definition at line 68 of file Importer.h.

References MetaTagTranslator::get().

virtual bool Importer::readFeatureTableLine ( string &  line )

protectedpure virtual

Referenced by getFeatureTableLine().

FeatureLinePtr Importer::getFeatureTableLine ( )

protected

Definition at line 132 of file Importer.cxx.

References line, pushedFeatureLines, and readFeatureTableLine().

Referenced by getUnwrappedFeatureTableLine().

void Importer::backFeatureTableLine ( FeatureLinePtr &  fline )

inlineprotected

Definition at line 73 of file Importer.h.

Referenced by getUnwrappedFeatureTableLine(), and parseFeature().

FeatureLinePtr Importer::getUnwrappedFeatureTableLine ( )

protected

Definition at line 146 of file Importer.cxx.

References backFeatureTableLine(), FL_CONTINUED, FL_CONTINUED_QUOTE_CLOSED, FL_META_CONTINUED, FL_QUALIFIER, FL_QUALIFIER_NODATA, FL_QUALIFIER_QUOTE_OPENED, FL_QUALIFIER_QUOTED, FL_START, getFeatureTableLine(), gi_assert, and SmartPtr< T, C >::isNull().

Referenced by parseFeature().

FeaturePtr Importer::parseFeature ( )

protected

Definition at line 191 of file Importer.cxx.

References backFeatureTableLine(), FL_META_QUALIFIER, FL_START, getUnwrappedFeatureTableLine(), and SmartPtr< T, C >::isNull().

Referenced by parseFeatureTable().

void Importer::parseFeatureTable ( )

protected

Definition at line 211 of file Importer.cxx.

References db_writer, expectedSeqLength, SmartPtr< T, C >::isNull(), parseFeature(), and DBwriter::writeFeature().

virtual void Importer::import_section ( )

protectedpure virtual

Referenced by import().

void Importer::show_warnings ( const string &  import_of_what )

protected

Definition at line 222 of file Importer.cxx.

References GB_warningf(), and warnings.

void Importer::check_base_counters ( const SequenceBuffer &  seqData, const BaseCounter *  headerCount  )

protected

Definition at line 259 of file Importer.cxx.

References BC_ALL, BaseCounter::expectEqual(), SequenceBuffer::getBaseCounter(), BaseCounter::getCount(), gi_assert, NULp, and warning().

void Importer::import

(

)

Definition at line 234 of file Importer.cxx.

References LineReader::backLine(), expectedSeqLength, flatfile, LineReader::getLine(), DBerror::getMessage(), gi_assert, import_section(), line, LineReader::lineError(), pushedFeatureLines, and warnings.

Referenced by GI_importGenomeFile().

void Importer::warning

(

const char *

msg

)

Definition at line 128 of file Importer.cxx.

References warnings.

Referenced by check_base_counters(), and importerWarning().

Member Data Documentation

DBwriter& Importer::db_writer

protected

Definition at line 60 of file Importer.h.

Referenced by parseFeatureTable().

LineReader& Importer::flatfile

protected

Definition at line 61 of file Importer.h.

Referenced by import().

MetaTagTranslator Importer::tagTranslator

protected

Definition at line 62 of file Importer.h.

FeatureLines Importer::pushedFeatureLines

protected

Definition at line 63 of file Importer.h.

Referenced by getFeatureTableLine(), and import().

stringVector Importer::warnings

protected

Definition at line 64 of file Importer.h.

Referenced by import(), show_warnings(), and warning().

long Importer::expectedSeqLength

protected

Definition at line 65 of file Importer.h.

Referenced by import(), and parseFeatureTable().

---

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

• GENOM_IMPORT/Importer.h
• GENOM_IMPORT/Importer.cxx