// ----------------------------------------------------------------------------
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>
CWiggleReader::ReadSeqAnnot(
ILineReader& lr,
IErrorContainer* pErrorContainer )
// ----------------------------------------------------------------------------
{
m_ChromId.clear();
m_Values.clear();
if (lr.AtEOF()) {
return CRef<CSeq_annot>();
}
while ( xGetLine(lr) ) {
CTempString s = xGetWord(pErrorContainer);
if ( s == "browser" ) {
xReadBrowser();
}
else if ( s == "track" ) {
xReadTrack(pErrorContainer);
}
else if ( s == "fixedStep" ) {
SFixedStepInfo fixedStepInfo;
xGetFixedStepInfo(fixedStepInfo, pErrorContainer);
if (!m_ChromId.empty() && fixedStepInfo.mChrom != m_ChromId) {
cerr << fixedStepInfo.mChrom << endl;
lr.UngetLine();
return xGetAnnot();
}
xReadFixedStepData(fixedStepInfo, lr, pErrorContainer);
}
else if ( s == "variableStep" ) {
SVarStepInfo varStepInfo;
xGetVarStepInfo(varStepInfo, pErrorContainer);
if (!m_ChromId.empty() && varStepInfo.mChrom != m_ChromId) {
lr.UngetLine();
return xGetAnnot();
}
xReadVariableStepData(varStepInfo, lr, pErrorContainer);
}
else {
xReadBedLine(s, pErrorContainer);
}
}
return xGetAnnot();
}
// ---------------------------------------------------------------------------
void
CVcfReader::ReadSeqAnnots(
vector< CRef<CSeq_annot> >& annots,
ILineReader& lr,
IMessageListener* pMessageListener )
// ----------------------------------------------------------------------------
{
while ( ! lr.AtEOF() ) {
CRef<CSeq_annot> pAnnot = ReadSeqAnnot( lr, pMessageListener );
if ( pAnnot ) {
annots.push_back( pAnnot );
}
}
}
// ---------------------------------------------------------------------------
void
CWiggleReader::ReadSeqAnnots(
vector< CRef<CSeq_annot> >& annots,
ILineReader& lr,
IErrorContainer* pErrorContainer )
// ----------------------------------------------------------------------------
{
while ( ! lr.AtEOF() ) {
CRef<CSeq_annot> pAnnot = ReadSeqAnnot( lr, pErrorContainer );
if ( pAnnot ) {
annots.push_back( pAnnot );
}
}
}
// ----------------------------------------------------------------------------
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;
}
// ----------------------------------------------------------------------------
CRef<CSeq_annot> CUCSCRegionReader::ReadSeqAnnot(
ILineReader& lr,
ILineErrorListener* pEC )
{
const size_t MAX_RECORDS = 100000;
CRef<CSeq_annot> annot;
CRef<CAnnot_descr> desc;
annot.Reset(new CSeq_annot);
desc.Reset(new CAnnot_descr);
annot->SetDesc(*desc);
CSeq_annot::C_Data::TFtable& tbl = annot->SetData().SetFtable();
int featureCount = 0;
while (!lr.AtEOF()) {
++m_uLineNumber;
CTempString line = *++lr;
if (NStr::TruncateSpaces_Unsafe(line).empty()) {
continue;
}
if (xParseComment(line, annot)) {
continue;
}
CTempString record_copy = NStr::TruncateSpaces_Unsafe(line);
// parse
vector<string> fields;
xSmartFieldSplit(fields, record_copy);
#if 0
try {
xCleanColumnValues(fields);
}
catch(CObjReaderLineException& err) {
ProcessError(err, pEC);
continue;
}
#endif
if (xParseFeature(fields, annot, pEC)) {
++featureCount;
continue;
}
if (tbl.size() >= MAX_RECORDS) {
break;
}
}
// Only return a valid object if there was at least one feature
if (0 == featureCount) {
return CRef<CSeq_annot>();
}
//x_AddConversionInfo(annot, pEC);
//x_AssignTrackData( annot );
#if 0
if(m_columncount >= 3) {
CRef<CUser_object> columnCountUser( new CUser_object() );
columnCountUser->SetType().SetStr( "NCBI_BED_COLUMN_COUNT" );
columnCountUser->AddField("NCBI_BED_COLUMN_COUNT", int ( m_columncount ) );
CRef<CAnnotdesc> userDesc( new CAnnotdesc() );
userDesc->SetUser().Assign( *columnCountUser );
annot->SetDesc().Set().push_back( userDesc );
}
#endif
return annot;
}