// ----------------------------------------------------------------------------
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
CGtfReader::ReadSeqAnnots(
TAnnots& annots,
ILineReader& lr,
ILineErrorListener* pEC)
// ----------------------------------------------------------------------------
{
xProgressInit(lr);
string line;
while (xGetLine(lr, line)) {
if (IsCanceled()) {
AutoPtr<CObjReaderLineException> pErr(
CObjReaderLineException::Create(
eDiag_Info,
0,
"Reader stopped by user.",
ILineError::eProblem_ProgressInfo));
ProcessError(*pErr, pEC);
annots.clear();
return;
}
xReportProgress(pEC);
try {
if (xIsTrackTerminator(line)) {
continue;
}
if (x_ParseBrowserLineGff(line, m_CurrentBrowserInfo)) {
continue;
}
if (xParseTrackLine(line, pEC)) {
continue;
}
if (x_ParseFeatureGff(line, annots, pEC)) {
continue;
}
}
catch(CObjReaderLineException& err) {
err.SetLineNumber(m_uLineNumber);
}
}
}
