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NCBI C++ ToolKit: CMicroArrayReader Class Reference
Search Toolkit Book for CMicroArrayReader
#include <objtools/readers/microarray_reader.hpp>
CMicroArrayReader (int=fDefaults, CReaderListener *=nullptr) virtual ~CMicroArrayReader () CRef< CSeq_annot > ReadSeqAnnot (ILineReader &, ILineErrorListener *=nullptr) override Read an object from a given line reader, render it as a single Seq-annot, if possible. More...
virtual ~CReaderBase () virtual CRef< CSerialObject > ReadObject (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr) Read an object from a given input stream, render it as the most appropriate Genbank object. More...
virtual CRef< CSerialObject > ReadObject (ILineReader &lr, ILineErrorListener *pErrors=nullptr) Read an object from a given line reader, render it as the most appropriate Genbank object. More...
virtual CRef< CSeq_annot > ReadSeqAnnot (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr) Read an object from a given input stream, render it as a single Seq-annot. More...
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. More...
virtual void ReadSeqAnnots (TAnnots &annots, ILineReader &lr, ILineErrorListener *pErrors=nullptr) Read all objects from given insput stream, returning them as a vector of Seq-annots. More...
virtual CRef< CSeq_entry > ReadSeqEntry (CNcbiIstream &istr, ILineErrorListener *pErrors=nullptr) Read an object from a given input stream, render it as a single Seq-entry, if possible. More...
virtual CRef< CSeq_entry > ReadSeqEntry (ILineReader &lr, ILineErrorListener *pErrors=nullptr) Read an object from a given line reader, render it as a single Seq-entry, if possible. More...
void SetProgressReportInterval (unsigned int intv) void SetCanceler (ICanceled *=nullptr) bool IsCanceled () const CRef< CSeq_annot > xCreateSeqAnnot () override void xGetData (ILineReader &, TReaderData &) override void xProcessData (const TReaderData &, CSeq_annot &) override virtual bool xProcessTrackLine (const string &) bool xProcessFeature (const string &, CSeq_annot &) void xSetFeatureLocation (CRef< CSeq_feat > &, const vector< string > &) void xSetFeatureDisplayData (CRef< CSeq_feat > &, const vector< string > &) CReaderBase (TReaderFlags flags=0, const string &name="", const string &title="", SeqIdResolver seqresolver=CReadUtil::AsSeqId, CReaderListener *pListener=nullptr) Protected constructor. Use GetReader() to get an actual reader object. More...
CReaderBase (const CReaderBase &)=delete CReaderBase (CReaderBase &&)=delete void xGuardedGetData (ILineReader &, TReaderData &, ILineErrorListener *) virtual void xGuardedProcessData (const TReaderData &, CSeq_annot &, ILineErrorListener *) virtual void xValidateAnnot (const CSeq_annot &) virtual bool xGetLine (ILineReader &, string &) virtual bool xUngetLine (ILineReader &) virtual bool xIsCommentLine (const CTempString &) virtual bool xIsTrackLine (const CTempString &) virtual bool xIsBrowserLine (const CTempString &) virtual bool xIsTrackTerminator (const CTempString &) virtual void xAssignTrackData (CSeq_annot &) virtual bool xParseBrowserLine (const CTempString &, CSeq_annot &) virtual bool xParseTrackLine (const CTempString &) virtual void xSetBrowserRegion (const CTempString &, CAnnot_descr &) virtual void xPostProcessAnnot (CSeq_annot &) virtual void xAddConversionInfo (CSeq_annot &, ILineErrorListener *) bool xParseComment (const CTempString &, CRef< CSeq_annot > &) virtual bool xReadInit () virtual bool xProgressInit (ILineReader &istr) bool xIsReportingProgress () const bool xIsOperationCanceled () const void xReportProgress (ILineErrorListener *=nullptr) void ProcessError (CObjReaderLineException &, ILineErrorListener *) void ProcessError (CLineError &, ILineErrorListener *) void ProcessWarning (CObjReaderLineException &, ILineErrorListener *) void ProcessWarning (CLineError &, ILineErrorListener *) void xProcessReaderMessage (CReaderMessage &, ILineErrorListener *) void xProcessLineError (const ILineError &, ILineErrorListener *) void xProcessUnknownException (const CException &)
Definition at line 46 of file microarray_reader.hpp.
◆ anonymous enum ◆ CMicroArrayReader() ◆ ~CMicroArrayReader() ◆ ReadSeqAnnot()
Read an object from a given line reader, render it as a single Seq-annot, if possible.
Return empty Seq-annot otherwise.
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Parameters
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lr line reader to read from. pErrors pointer to optional error container object.
Reimplemented from CReaderBase.
Definition at line 74 of file microarray_reader.cpp.
References CUser_object::AddField(), CSerialObject::Assign(), lr(), m_columncount, CReaderBase::ReadSeqAnnot(), CSeq_annot_Base::SetDesc(), CUser_object_Base::SetType(), CAnnotdesc_Base::SetUser(), and CReaderBase::xAssignTrackData().
◆ xCleanColumnValues() void CMicroArrayReader::xCleanColumnValues ( vector< string > & columns ) staticprotected ◆ xCreateSeqAnnot() ◆ xGetData() ◆ xProcessData() ◆ xProcessFeature() ◆ xProcessTrackLine() ◆ xSetFeatureDisplayData() ◆ xSetFeatureLocation() ◆ m_columncount vector<string>::size_type CMicroArrayReader::m_columncount protected ◆ m_currentId string CMicroArrayReader::m_currentId protected ◆ m_iExpScale int CMicroArrayReader::m_iExpScale protected ◆ m_iExpStep int CMicroArrayReader::m_iExpStep protected ◆ m_strExpNames string CMicroArrayReader::m_strExpNames protected ◆ m_usescore bool CMicroArrayReader::m_usescore protected
The documentation for this class was generated from the following files:
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