// ----------------------------------------------------------------------------
CRef< CSeq_annot >
CVcfReader::ReadSeqAnnot(
ILineReader& lr,
IErrorContainer* pErrorContainer )
// ----------------------------------------------------------------------------
{
CRef< CSeq_annot > annot( new CSeq_annot );
CRef< CAnnot_descr > desc( new CAnnot_descr );
annot->SetDesc( *desc );
annot->SetData().SetFtable();
m_Meta.Reset( new CAnnotdesc );
m_Meta->SetUser().SetType().SetStr( "vcf-meta-info" );
while ( ! lr.AtEOF() ) {
string line = *(++lr);
NStr::TruncateSpacesInPlace( line );
if ( x_ProcessMetaLine( line, annot ) ) {
continue;
}
if ( x_ProcessHeaderLine( line, annot ) ) {
continue;
}
if ( xProcessDataLine( line, annot ) ) {
continue;
}
// still here? not good!
cerr << "Unexpected line: " << line << endl;
}
return annot;
}
// ----------------------------------------------------------------------------
CRef< CSeq_annot >
CVcfReader::ReadSeqAnnot(
ILineReader& lr,
IMessageListener* pEC )
// ----------------------------------------------------------------------------
{
CRef< CSeq_annot > annot( new CSeq_annot );
CRef< CAnnot_descr > desc( new CAnnot_descr );
annot->SetDesc( *desc );
annot->SetData().SetFtable();
m_Meta.Reset( new CAnnotdesc );
m_Meta->SetUser().SetType().SetStr( "vcf-meta-info" );
while ( ! lr.AtEOF() ) {
m_uLineNumber++;
string line = *(++lr);
NStr::TruncateSpacesInPlace( line );
if (xProcessMetaLine(line, annot, pEC)) {
continue;
}
if (xProcessHeaderLine(line, annot)) {
continue;
}
if (xProcessDataLine(line, annot, pEC)) {
continue;
}
// still here? not good!
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Warning,
0,
"CVcfReader::ReadSeqAnnot: Unrecognized line or record type.",
ILineError::eProblem_GeneralParsingError) );
ProcessWarning(*pErr, pEC);
}
return annot;
}
