LocusWithAlleles :: LocusWithAlleles (const RGString& inputLine) : RGPersistent (), mLineNumber (0), mMaxRFU (0) {
RGStringArray tokens;
RGStringArray delimiters;
RGString locusString (inputLine);
locusString.FindAndReplaceAllSubstrings ("\t\t", "\t");
RGStringTokenizer tokenizer (locusString);
tokenizer.AddDelimiter ("\t");
tokenizer.Split (tokens, delimiters);
int size = tokens.Length ();
int rfu;
double fit;
double residual;
LocusAllele* newAllele;
int i;
if (size >= 8) {
for (i=0; i<8; i++) {
if ((tokens [i].Length () == 0) || (tokens [i] == "\t"))
return;
}
mLineNumber = tokens [0].ConvertToInteger ();
mLocusName = tokens [1];
rfu = tokens [2].ConvertToInteger ();
residual = tokens [3].ConvertToDouble ();
fit = tokens [4].ConvertToDouble ();
newAllele = new LocusAllele (rfu, residual, fit);
InsertAllele (newAllele);
rfu = tokens [5].ConvertToInteger ();
residual = tokens [6].ConvertToDouble ();
fit = tokens [7].ConvertToDouble ();
newAllele = new LocusAllele (rfu, residual, fit);
InsertAllele (newAllele);
}
}
RGString LocusData :: FormXMLString () {
RGString Result;
if (AlleleStringIsEmpty ())
return Result;
RGTPtrDList<RGString> temp;
RGString sixTabs = "\t\t\t\t\t\t";
RGString sevenTabs = "\t\t\t\t\t\t\t";
RGString eightTabs = "\t\t\t\t\t\t\t\t";
Result << sixTabs << "<Locus>\n";
Result << sevenTabs << "<Name>" << (char*)mLocusName.GetData () << "</Name>\n";
RGString* nextAllele;
while (mAlleleList.entries () > 0) {
nextAllele = mAlleleList.RemoveFirst ();
nextAllele->FindAndReplaceAllSubstrings ("\"", "");
temp.append (nextAllele);
Result << sevenTabs << "<Allele>\n";
Result << eightTabs << "<Name>" << (char*)nextAllele->GetData () << "</Name>\n";
Result << eightTabs << "<BioID>0</BioID>\n";
Result << sevenTabs << "</Allele>\n";
}
Result << sixTabs << "</Locus>\n";
//cout << (char*) Result.GetData ();
while (temp.entries () > 0) {
nextAllele = temp.RemoveFirst ();
mAlleleList.append (nextAllele);
}
return Result;
}
void CoreBioComponent :: ReportXMLSmartSampleTableRowWithLinks (RGTextOutput& text, RGTextOutput& tempText) {
RGString type;
if (mIsNegativeControl)
type = "-Control";
else if (mIsPositiveControl)
type = "+Control";
else
type = "Sample";
RGString pResult;
RGString SimpleFileName (mName);
size_t startPos = 0;
size_t endPos;
size_t length = SimpleFileName.Length ();
if (SimpleFileName.FindLastSubstringCaseIndependent (DirectoryManager::GetDataFileType (), startPos, endPos)) {
if (endPos == length - 1)
SimpleFileName.ExtractAndRemoveLastCharacters (4);
}
SimpleFileName.FindAndReplaceAllSubstrings ("\\", "/");
startPos = endPos = 0;
if (SimpleFileName.FindLastSubstring ("/", startPos, endPos)) {
SimpleFileName.ExtractAndRemoveSubstring (0, startPos);
}
text << CLevel (1) << "\t\t<Sample>\n";
text << "\t\t\t<Name>" << xmlwriter::EscAscii (SimpleFileName, &pResult) << "</Name>\n";
text << "\t\t\t<SampleName>" << xmlwriter::EscAscii (mSampleName, &pResult) << "</SampleName>\n";
text << "\t\t\t<RunStart>" << mRunStart.GetData () << "</RunStart>\n";
text << "\t\t\t<Type>" << type.GetData () << "</Type>\n" << PLevel ();
int trigger = Notice::GetMessageTrigger ();
// int channelHighestLevel;
// bool channelAlerts = false;
int cbcHighestMsgLevel = GetHighestMessageLevelWithRestrictionSM ();
RGDListIterator it (*mSmartMessageReporters);
SmartMessageReporter* nextNotice;
bool includesExportInfo = false;
while (nextNotice = (SmartMessageReporter*) it ()) {
if (nextNotice->HasViableExportInfo ()) {
includesExportInfo = true;
break;
}
}
if (((cbcHighestMsgLevel > 0) && (cbcHighestMsgLevel <= trigger)) || includesExportInfo) {
// text << CLevel (1) << "\t\t\t<SampleAlerts>\n" << PLevel ();
// get message numbers and report
ReportXMLSmartNoticeObjects (text, tempText, " ");
// text << CLevel (1) << "\t\t\t</SampleAlerts>\n" << PLevel ();
}
mDataChannels [mLaneStandardChannel]->ReportXMLILSSmartNoticeObjects (text, tempText, " ");
int i;
//for (i=1; i<=mNumberOfChannels; i++) {
// //if (i == mLaneStandardChannel)
// // continue;
// channelHighestLevel = mDataChannels [i]->GetHighestMessageLevelWithRestrictionSM ();
// if ((channelHighestLevel > 0) && (channelHighestLevel <= trigger)) {
// channelAlerts = true;
// break;
// }
//}
// if (channelAlerts) {
text << CLevel (1) << "\t\t\t<ChannelAlerts>\n" << PLevel ();
for (i=1; i<=mNumberOfChannels; i++) {
if (i == mLaneStandardChannel)
continue;
mDataChannels [i]->ReportXMLSmartNoticeObjects (text, tempText, " ");
}
text << CLevel (1) << "\t\t\t</ChannelAlerts>\n" << PLevel ();
// }
mMarkerSet->ResetLocusList ();
Locus* nextLocus;
while (nextLocus = mMarkerSet->GetNextLocus ()) {
nextLocus->ReportXMLSmartSampleTableRowWithLinks (text, tempText, " ");
}
if (mIsPositiveControl)
text << CLevel (1) << "\t\t\t<PositiveControl>" << mPositiveControlName << "</PositiveControl>\n";
text << CLevel (1) << "\t\t</Sample>\n" << PLevel ();
}
