Boolean RGDirectory :: MoveDirectory (const RGString& oldName, const RGString& suffix, int MaxLevels) {
int i = 0;
RGString newName = oldName + suffix;
while (i < MaxLevels) {
if (!FileOrDirectoryExists (newName)) {
// FinalName = newName;
cout << "Attempting to move " << oldName.GetData () << " to " << newName.GetData () << endl;
return MoveFile (oldName.GetData (), newName.GetData ());
}
i++;
newName += suffix;
}
return FALSE;
}
int CopyVolumeFile (const RGString& inputFileName, const RGString& outputFileName) {
RGFile inputFile (inputFileName, "rt");
if (!inputFile.isValid ()) {
cout << "Could not read " << inputFileName.GetData () << " for default volume...exiting" << endl;
return -1;
}
RGString inputFileString;
inputFileString.ReadTextFile (inputFile);
RGTextOutput outputFile (outputFileName, FALSE);
if (!outputFile.FileIsValid ()) {
cout << "Could not create " << outputFileName.GetData () << "...exiting" << endl;
return -1;
}
outputFile << inputFileString;
return 0;
}
void Ladder :: OutputTo (RGTextOutput& xmlFile, LadderInputFile& inputFile) {
RGString link ("http://www.w3.org/2001/XMLSchema-instance");
xmlFile << "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
xmlFile << "<KitData xmlns:xsi=\"" << link.GetData () << "\" xsi:noNamespaceSchemaLocation=\"MarkerSet.xsd\">\n";
xmlFile << "\t<Version>" << inputFile.GetVersion () << "</Version>\n";
xmlFile << "\t<Kits>\n";
xmlFile << "\t\t<Set>\n";
xmlFile << "\t\t\t<Name>" << mMarkerSetName.GetData () << "</Name>\n";
xmlFile << "\t\t\t<NChannels>" << mNumberOfChannels << "</NChannels>\n";
xmlFile << "\t\t\t<ILS>\n";
if (inputFile.GenerateILSFamilies ()) {
xmlFile << "\t\t\t\t<LSBases>\n";
OutputILSFamilyListTo (xmlFile);
xmlFile << "\t\t\t\t</LSBases>\n";
}
else {
xmlFile << "\t\t\t<LS>\n";
OutputILSListTo (xmlFile);
xmlFile << "\t\t\t</LS>\n";
}
xmlFile << "\t\t\t\t<ChannelNo>" << mChannelForILS << "</ChannelNo>\n";
xmlFile << "\t\t\t</ILS>\n";
xmlFile << "\t\t\t<FileNameSuffix>" << mSuffix << "</FileNameSuffix>\n";
xmlFile << "\t\t\t<GenotypeSuffix>" << mSuffix << "</GenotypeSuffix>\n";
xmlFile << "\t\t\t<DirectorySearchString>" << mSuffix << "</DirectorySearchString>\n";
OutputChannelMapTo (xmlFile, inputFile);
list <Locus*>::const_iterator locusIterator;
Locus* nextLocus;
for (locusIterator = mLocusList.begin(); locusIterator != mLocusList.end(); locusIterator++) {
nextLocus = *locusIterator;
nextLocus->OutputTo (xmlFile);
}
xmlFile << "\t\t</Set>\n";
xmlFile << "\t</Kits>\n";
xmlFile << "</KitData>";
}
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;
}
int SmartNoticeWarehouse :: AddType (SmartNotice* NewType) {
RGPersistent* test = ClassTypes->Append (NewType);
int val;
if (SmartNoticeWarehouse::DebugFlag) {
RGString name (NewType->GetName ());
cout << "Adding class to notice list, Name = " << name.GetData () << endl;
}
if (test != NULL) {
val = ClassTypes->Entries ();
}
else {
val = 0;
}
return val;
}
int CoreBioComponent :: InitializeSM (SampleData& fileData, PopulationCollection* collection, const RGString& markerSetName, Boolean isGrid) {
//
// This is ladder and sample stage 1
//
mTime = fileData.GetCollectionStartTime ();
mDate = fileData.GetCollectionStartDate ();
mName = fileData.GetName ();
mRunStart = mDate.GetOARString () + mTime.GetOARString ();
mMarkerSet = collection->GetNamedPopulationMarkerSet (markerSetName);
Progress = 0;
smMarkerSetNameUnknown noNamedMarkerSet;
smNamedILSUnknown noNamedILS;
smChannelIsILS channelIsILS;
if (mMarkerSet == NULL) {
ErrorString = "*******COULD NOT FIND MARKER SET NAMED ";
ErrorString << markerSetName << " IN POPULATION COLLECTION********\n";
SetMessageValue (noNamedMarkerSet, true);
AppendDataForSmartMessage (noNamedMarkerSet, markerSetName);
return -1;
}
mLaneStandard = mMarkerSet->GetLaneStandard ();
mNumberOfChannels = mMarkerSet->GetNumberOfChannels ();
if ((mLaneStandard == NULL) || !mLaneStandard->IsValid ()) {
ErrorString = "Could not find named internal lane standard associated with marker set named ";
ErrorString << markerSetName << "\n";
cout << "Could not find named internal lane standard associated with marker set named " << (char*)markerSetName.GetData () << endl;
SetMessageValue (noNamedILS, true);
AppendDataForSmartMessage (noNamedILS, markerSetName);
return -1;
}
mDataChannels = new ChannelData* [mNumberOfChannels + 1];
int i;
const int* fsaChannelMap = mMarkerSet->GetChannelMap ();
for (i=0; i<=mNumberOfChannels; i++)
mDataChannels [i] = NULL;
mLaneStandardChannel = mMarkerSet->GetLaneStandardChannel ();
for (i=1; i<=mNumberOfChannels; i++) {
if (i == mLaneStandardChannel)
mDataChannels [i] = GetNewLaneStandardChannel (i, mLaneStandard);
else {
if (isGrid)
mDataChannels [i] = GetNewGridDataChannel (i, mLaneStandard);
else
mDataChannels [i] = GetNewDataChannel (i, mLaneStandard);
}
mDataChannels [i]->SetFsaChannel (fsaChannelMap [i]);
}
mLSData = mDataChannels [mLaneStandardChannel];
mLSData->SetMessageValue (channelIsILS, true);
mMarkerSet->ResetLocusList ();
Locus* nextLocus;
while (nextLocus = mMarkerSet->GetNextLocus ())
mDataChannels [nextLocus->GetLocusChannel ()]->AddLocus (nextLocus);
Progress = 1;
return 0;
}
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 ();
}
Locus* Bins :: AssembleLocusFromLineStrings () {
// uses current values in mLocusLineStrings
Locus* newLocus = new Locus ();
int nLines = mLocusLineStrings.Length ();
SplitLocusLine (mLocusLineStrings [0]); // This should give us the name field
RGString name = mLocusLineFieldString [1];
cout << "Locus name = " << name.GetData () << endl;
//cout << "Bins locus line 1: ";
int i;
int len = mLocusLineFieldString.Length ();
//for (i=0; i<len; i++) {
// cout << mLocusLineFieldString [i].GetData ();
// if (i < len - 1)
// cout << ", ";
//}
//cout << endl;
RGString firstAlleleName;
int firstLocusBP;
double firstILSBP;
double lastILSBP;
RGString firstExtendedAlleleName;
RGString lastExtendedAlleleName;
int lineForFirstAllele = 0;
for (i=1; i<nLines; i++) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4) {
cout << "Could not find first allele for locus " << name.GetData () << endl;
delete newLocus;
return NULL;
}
if (mLocusLineFieldString.Length () >= 5) {
if (mLocusLineFieldString [4] == "virtual") {
if (i == 1) {
firstExtendedAlleleName = mLocusLineFieldString [0];
}
continue;
}
}
firstAlleleName = mLocusLineFieldString [0];
firstILSBP = mLocusLineFieldString [1].ConvertToDouble ();
firstLocusBP = (int) floor (firstILSBP + 0.5);
lineForFirstAllele = i;
break;
}
if (firstExtendedAlleleName.Length () == 0)
firstExtendedAlleleName = firstAlleleName;
bool foundLastExtendedAllele = false;
for (i=nLines-1; i>lineForFirstAllele; i--) {
SplitLocusLine (mLocusLineStrings [i]);
if (mLocusLineFieldString.Length () < 4)
continue;
if (!foundLastExtendedAllele) {
lastExtendedAlleleName = mLocusLineFieldString [0];
foundLastExtendedAllele = true;
}
if ((mLocusLineFieldString.Length () >= 5) && (mLocusLineFieldString [4] == "virtual"))
continue;
lastILSBP = mLocusLineFieldString [1].ConvertToDouble ();
break;
}
if (lastExtendedAlleleName.Length () == 0) {
cout << "Could not locate last extended allele name for locus: " << name.GetData () << endl;
delete newLocus;
return NULL;
}
newLocus->SetFirstCoreAllele (firstAlleleName);
newLocus->SetFirstExtendedAllele (firstExtendedAlleleName);
newLocus->SetLastExtendedAllele (lastExtendedAlleleName);
newLocus->SetMinMaxSearchILSBP (firstILSBP, lastILSBP); // These will have to be adjusted later when core repeat number is known
newLocus->SetFirstCoreLocusBP (firstLocusBP);
newLocus->SetName (name);
// Need to add to Locus ability to compute first and last extended bp
return newLocus;
}
bool GenotypesForAMarkerSet :: AddCollectionToTables (const RGString& xmlString, const RGString& offLadderTag, const RGString& triallelesTag, const RGString& posTriTag) {
RGString XMLString (xmlString);
RGString positiveControlString;
RGString pControlsString;
RGString fullPathControlFileName = GenotypesForAMarkerSet::PathToStandardControlFile + "/LadderSpecifications/StandardPositiveControls.xml";
RGFile* allPositiveControls = new RGFile (fullPathControlFileName, "rt");
if (!allPositiveControls->isValid ()) {
cout << "Could not find positive controls file: " << (char*)fullPathControlFileName.GetData () << endl;
return false;
}
RGString posXMLString;
posXMLString.ReadTextFile (*allPositiveControls);
delete allPositiveControls;
RGXMLTagSearch nameSearch ("MarkerSetName", XMLString);
RGXMLTagSearch positiveControlsSearch ("PositiveControls", posXMLString);
RGXMLTagSearch oldPositiveControlsSearch ("PositiveControls", XMLString);
RGXMLTagSearch posCtrlSearch ("PositiveControl", pControlsString);
RGXMLTagSearch offLadderSearch (offLadderTag, XMLString);
RGXMLTagSearch trialleleSearch (triallelesTag, XMLString);
RGXMLTagSearch posTriSearch (posTriTag, XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
RGString collectionString;
RGString offLadderString;
RGString triString;
RGString posTriString;
size_t startPControls = 0;
size_t endPControls = 0;
bool returnValue = true;
RGString markerSetName;
IndividualGenotype* nextGenotype;
if (!nameSearch.FindNextTag (startOffset, endOffset, markerSetName))
return false;
if (mMarkerSetName.Length () == 0)
mMarkerSetName = markerSetName;
else if (mMarkerSetName != markerSetName)
return false;
startOffset = endOffset;
size_t startOffsetPos = 0;
size_t endOffsetPos = 0;
RGString temp;
if (oldPositiveControlsSearch.FindNextTag (startOffset, endOffset, temp))
startOffset = endOffset;
if (positiveControlsSearch.FindNextTag (startOffsetPos, endOffsetPos, pControlsString)) {
posCtrlSearch.ResetSearch ();
// cout << "Found positive controls in file" << endl;
while (posCtrlSearch.FindNextTag (startPControls, endPControls, positiveControlString)) {
// cout << "Found positive control..." << endl;
startPControls = endPControls;
nextGenotype = new IndividualGenotype (positiveControlString);
if (!nextGenotype->isValid ()) {
returnValue = false;
delete nextGenotype;
}
else {
if (!mGenotypes.Contains (nextGenotype)) {
mGenotypes.Insert (nextGenotype);
// cout << "Inserted genotype in list..." << endl;
}
else {
returnValue = false;
delete nextGenotype;
}
}
}
}
startOffset = endOffset;
if (offLadderSearch.FindNextTag (startOffset, endOffset, offLadderString)) {
if (mOffLadderAlleles == NULL) {
mOffLadderAlleles = new LocusCollection (offLadderString);
if (!mOffLadderAlleles->isValid ())
returnValue = false;
}
else {
if (!mOffLadderAlleles->AddLoci (offLadderString))
returnValue = false;
}
}
startOffset = endOffset;
if (trialleleSearch.FindNextTag (startOffset, endOffset, triString)) {
if (mSampleTriAlleles == NULL) {
mSampleTriAlleles = new LocusCollection (triString);
if (!mSampleTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mSampleTriAlleles->AddLoci (triString))
returnValue = false;
}
}
startOffset = endOffset;
if (posTriSearch.FindNextTag (startOffset, endOffset, posTriString)) {
if (mControlTriAlleles == NULL) {
mControlTriAlleles = new LocusCollection (posTriString);
if (!mControlTriAlleles->isValid ())
returnValue = false;
}
else {
if (!mControlTriAlleles->AddLoci (posTriString))
returnValue = false;
}
}
return returnValue;
}
int Ladder :: AmendLadderData (LadderInputFile* inFile, RGString& oldLadderString) {
RGString newLadderString;
// Parse oldLadder data into pieces for individual edits
RGString locusString;
RGString* newLocusString;
RGDList locusStrings;
size_t startPos = 0;
size_t endPos;
RGXMLTagSearch locusSearch ("Locus", oldLadderString);
RGXMLTagSearch searchRegionsSearch ("SearchRegions", oldLadderString);
RGString* ilsName = (RGString*)inFile->GetILSNameList ().First ();
endPos = 0;
oldLadderString.FindNextSubstring (0, "\t\t\t<Locus>", endPos);
RGString insertBase;
insertBase << "\t\t\t\t\t<ILSName>" << ilsName->GetData () << "</ILSName>\n";
insertBase << "\t\t\t\t</LSBases>";
RGString leadString = oldLadderString.ExtractSubstring (0, endPos - 1);
//cout << "Lead string = \n" << leadString.GetData () << endl;
endPos = 0;
leadString.FindAndReplaceNextSubstring ("\t\t\t\t</LSBases>", insertBase, endPos);
//cout << "Lead string = \n" << leadString.GetData () << endl;
newLadderString << leadString;
startPos = 0;
while (locusSearch.FindNextTag (startPos, endPos, locusString)) {
newLocusString = new RGString (locusString);
locusStrings.Append (newLocusString);
startPos = endPos;
}
if (mLocusList.size () != locusStrings.Entries ()) {
cout << "Number of loci in bins file does not match number of loci in ladder file" << endl;
return -152;
}
Locus* nextLocus;
RGString locusInsert;
RGString currentLocusString;
RGString nameString;
RGXMLTagSearch locusNameSearch ("Name", currentLocusString);
RGXMLTagSearch coreRepeatSearch ("CoreRepeatNumber", currentLocusString);
double minSearch;
double maxSearch;
RGString repeatString;
int repeatNumber;
while (locusStrings.Entries () > 0) {
newLocusString = (RGString*) locusStrings.GetFirst ();
currentLocusString = *newLocusString;
locusNameSearch.ResetSearch ();
coreRepeatSearch.ResetSearch ();
locusNameSearch.FindNextTag (0, endPos, nameString);
nextLocus = FindLocusByName (nameString);
if (nextLocus == NULL) {
cout << "Could not find locus named " << nameString.GetData () << ". Exiting..." << endl;
return -155;
}
if (!coreRepeatSearch.FindNextTag (0, endPos, repeatString))
repeatNumber = 4;
else
repeatNumber = repeatString.ConvertToInteger ();
locusInsert = "";
minSearch = nextLocus->GetMinSearchILSBP () - repeatNumber + 1;
maxSearch = nextLocus->GetMaxSearchILSBP () + repeatNumber -1;
locusInsert << "\t\t\t\t\t<Region>\n";
locusInsert << "\t\t\t\t\t\t<ILSName>" << ilsName->GetData () << "</ILSName>\n";
locusInsert << "\t\t\t\t\t\t<MinGrid>" << 0.01 * floor (100.0 * minSearch + 0.5) << "</MinGrid>\n";
locusInsert << "\t\t\t\t\t\t<MaxGrid>" << 0.01 * floor (100.0 * maxSearch + 0.5) << "</MaxGrid>\n";
locusInsert << "\t\t\t\t\t</Region>\n";
locusInsert << "\t\t\t\t</SearchRegions>";
endPos = 0;
currentLocusString.FindAndReplaceNextSubstring ("\t\t\t\t</SearchRegions>", locusInsert, endPos);
newLadderString << "\t\t\t<Locus>" << currentLocusString << "</Locus>\n";
delete newLocusString;
}
newLadderString << "\t\t</Set>\n";
newLadderString << "\t</Kits>\n";
newLadderString << "</KitData>\n";
RGString ladderPath = inFile->GetOutputConfigDirectoryPath () + "/" + inFile->GetLadderFileName ();
RGTextOutput ladderOutput (ladderPath, FALSE);
if (!ladderOutput.FileIsValid ()) {
cout << "Could not open ladder output file: " << ladderPath.GetData () << endl;
return -161;
}
ladderOutput << newLadderString;
cout << "Ladder update completed successfully..." << endl;
return 0;
}
Boolean RGDirectory :: MakeDirectory (const RGString& fullName)
{
return MakeDirectory(fullName.GetData());
}
RGDirectory :: RGDirectory (const RGString& fullName) {
direct = opendir (fullName.GetData ());
}
