bool LocusCollection :: AddLoci (const RGString& xmlString) {
RGString XMLString (xmlString);
RGBracketStringSearch locusSearch ("<Locus>", "</Locus>", XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
IndividualLocus* newLocus;
RGString locusString;
bool returnValue = true;
while (locusSearch.FindNextBracketedString (startOffset, endOffset, locusString)) {
startOffset = endOffset;
newLocus = new IndividualLocus (locusString);
if (!newLocus->isValid ())
returnValue = false;
else {
mLoci.Insert (newLocus);
mLociByName.Append (newLocus);
}
}
return returnValue;
}
SynonymList :: SynonymList (const RGString& tagName, const RGString& xmlString) : mIt (mList), mValid (true) {
RGString startTag = "<" + tagName + ">";
RGString endTag = "</" + tagName + ">";
RGString str (xmlString);
RGString txtSearchStr;
RGBracketStringSearch TagSearch (startTag, endTag, str);
RGBracketStringSearch TextSearch ("<text>", "</text>", txtSearchStr);
RGString textString;
size_t startPos = 0;
size_t endPos;
RGString* newString;
if (!TagSearch.FindNextBracketedString (startPos, endPos, txtSearchStr))
mValid = false;
else {
startPos = 0;
TextSearch .ResetSearch ();
while (TextSearch.FindNextBracketedString (startPos, endPos, textString)) {
startPos = endPos;
newString = new RGString (textString);
mList.Append (newString);
}
}
}
LocusCollection :: LocusCollection (const RGString& xmlString) : RGPersistent (), mLoci (31), mValid (true) {
RGString XMLString (xmlString);
RGBracketStringSearch locusSearch ("<Locus>", "</Locus>", XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
IndividualLocus* newLocus;
RGString locusString;
while (locusSearch.FindNextBracketedString (startOffset, endOffset, locusString)) {
startOffset = endOffset;
newLocus = new IndividualLocus (locusString);
if (!newLocus->isValid ())
mValid = false;
else {
mLoci.Insert (newLocus);
mLociByName.Append (newLocus);
}
}
if (mLoci.Entries () == 0)
mValid = false;
}
IndividualLocus :: IndividualLocus (const RGString& xmlString) : RGPersistent (), mAlleles (5), mValid (true) {
RGString XMLString (xmlString);
RGBracketStringSearch nameSearch ("<Name>", "</Name>", XMLString);
RGBracketStringSearch alleleSearch ("<Allele>", "</Allele>", XMLString);
size_t startOffset = 0;
size_t endOffset;
IndividualAllele* newAllele;
RGString alleleString;
if (!nameSearch.FindNextBracketedString (startOffset, endOffset, mName))
mValid = false;
startOffset = endOffset;
while (alleleSearch.FindNextBracketedString (startOffset, endOffset, alleleString)) {
startOffset = endOffset;
newAllele = new IndividualAllele (alleleString);
if (!newAllele->isValid ())
mValid = false;
else {
mAlleles.Insert (newAllele);
mAllelesByName.Append (newAllele);
}
}
if (mAlleles.Entries () == 0)
mValid = false;
}
IndividualAllele :: IndividualAllele (const RGString& xmlString) : RGPersistent (), mValid (true), mAssociatedPeak (NULL) {
RGString XMLString (xmlString);
RGBracketStringSearch nameSearch ("<Name>", "</Name>", XMLString);
// RGBracketStringSearch bioIDSearch ("<BioID>", "</BioID>", XMLString);
size_t startOffset = 0;
size_t endOffset = 0;
// RGString numberString;
if (!nameSearch.FindNextBracketedString (startOffset, endOffset, mName))
mName = xmlString;
/* if (!bioIDSearch.FindNextBracketedString (startOffset, endOffset, numberString))
mValid = false;
mBioID = numberString.ConvertToInteger ();*/
}
STRBaseAllele :: STRBaseAllele (const RGString& xmlInput) : BaseAllele (xmlInput) {
RGString Input (xmlInput);
RGBracketStringSearch BPToken ("<BP>", "</BP>", Input);
RGString bpString;
size_t EndPosition;
if (!BPToken.FindNextBracketedString (0, EndPosition, bpString)) {
BP = -1;
Valid = FALSE;
Msg << "Allele invalid...could not find BP string for allele named " << AlleleName << "\n";
// cout << "Allele invalid...could not find BP string...name: " << AlleleName << endl;
}
else
BP = bpString.ConvertToInteger ();
}
IndividualGenotype :: IndividualGenotype (const RGString& xmlString) : RGPersistent (), mValid (true) {
RGString XMLString (xmlString);
RGBracketStringSearch nameSearch ("<Name>", "</Name>", XMLString);
RGBracketStringSearch fileCriterionSearch ("<FileNameString>", "</FileNameString>", XMLString);
RGBracketStringSearch locusSearch ("<Loci>", "</Loci>", XMLString);
size_t startOffset = 0;
size_t endOffset = startOffset;
RGString locusString;
if (!nameSearch.FindNextBracketedString (startOffset, endOffset, mName))
mValid = false;
startOffset = endOffset;
if (fileCriterionSearch.FindNextBracketedString (startOffset, endOffset, mFileNameSearchString))
startOffset = endOffset;
else
mFileNameSearchString = mName;
if (!locusSearch.FindNextBracketedString (startOffset, endOffset, locusString))
mValid = false;
else {
mLoci = new LocusCollection (locusString);
if (!mLoci->isValid ())
mValid = false;
}
}
STRBaseLaneStandard :: STRBaseLaneStandard (const RGString& xmlString) : BaseLaneStandard (xmlString),
mCharacteristicArray (NULL), mDifferenceArray (NULL), mUnnormalizedDifferenceArray(0),
mNormsLeft (NULL), mNormsRight (NULL), mRelativeSizes (NULL),
mSize (0), mDifferenceSize (0), mOmissionSize (0), mOmissionArray (NULL), mNumberOfLargePeaks (0),
mLargeCharacteristicArray (NULL), mLargeDifferenceArray (NULL), mNumberOfLargeDifferences (0),
mFirstIntervalFraction (-1.0), mSmallestIntervalFraction (-1.0), mMaxRelativeHeight (-1),
mCorrelationAcceptanceThreshold (0.993), mCorrelationAutoAcceptanceThreshold (0.9975)
//
//, mLastHalfSize (0), mLastHalfCharacteristicArray (NULL), mLastHalfUnnormalizedDifferenceArray (NULL),
//mLastHalfRelativeSizes (NULL), mLastHalfDifferenceSize (0), mLastHalfNormsLeft (NULL), mLastHalfNormsRight (NULL)
{
RGString TextInput (xmlString);
RGBracketStringSearch CharacteristicsToken ("<Characteristics>", "</Characteristics>", TextInput);
RGString CharacteristicsString;
RGString HeightString;
RGBracketStringSearch HeightToken ("<RelativeHeights>", "</RelativeHeights>", TextInput);
RGBracketStringSearch OmissionSearch ("<Omissions>", "</Omissions>", TextInput);
RGBracketStringSearch AcceptanceThresholdSearch ("<CorrelationAcceptanceThreshold>", "</CorrelationAcceptanceThreshold>", TextInput);
RGBracketStringSearch AutoAcceptanceThresholdSearch ("<CorrelationAutoAcceptanceThreshold>", "</CorrelationAutoAcceptanceThreshold>", TextInput);
RGString OmissionString;
size_t endPosition;
RGString token;
RGString delim;
RGString numberString;
double minChar;
double maxChar;
RGDList tokens;
double value;
RGPDouble* valuePtr;
double previous;
double next;
double cumulative;
int i = 0;
double temp;
int k;
int j;
if (!CharacteristicsToken.FindNextBracketedString (0, endPosition, CharacteristicsString)) {
Msg << "Internal Lane Standard named " << Name << " could not find Characteristics token from string\n";
Msg << TextInput << "\n";
Valid = FALSE;
}
else {
RGStringTokenizer data (CharacteristicsString);
data.AddDelimiter (' ');
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddDelimiter (" ");
data.AddRemoveItem (',');
data.AddDelimiter ('\t');
data.AddDelimiter ('\n');
while (data.NextToken (token, delim)) {
if (token.Length () > 0) {
value = token.ConvertToDouble ();
valuePtr = new RGPDouble (value);
if (tokens.Entries () == 0) {
minChar = maxChar = value;
tokens.Append (valuePtr);
}
else if (value < minChar) {
minChar = value;
tokens.Prepend (valuePtr);
}
else if (value > maxChar) {
maxChar = value;
tokens.Append (valuePtr);
}
else
tokens.Insert (valuePtr);
}
}
mSize = (int)tokens.Entries ();
NCharacteristics = mSize;
mCharacteristicArray = new double [mSize];
mDifferenceSize = mSize - 1;
mDifferenceArray = new double [mDifferenceSize];
mUnnormalizedDifferenceArray = new double [mDifferenceSize];
mNormsLeft = new double [mDifferenceSize];
mNormsRight = new double [mDifferenceSize];
//mLastHalfSize = mSize / 2;
//if (2 * mLastHalfSize < mSize)
// mLastHalfSize += 1;
//mLastHalfDifferenceSize = mLastHalfSize - 1;
//mLastHalfCharacteristicArray = new double [mLastHalfSize];
//mLastHalfUnnormalizedDifferenceArray = new double [mLastHalfDifferenceSize];
//mLastHalfNormsLeft = new double [mLastHalfDifferenceSize];
//mLastHalfNormsRight = new double [mLastHalfDifferenceSize];
while (valuePtr = (RGPDouble*)tokens.GetFirst ()) {
mCharacteristicArray [i] = valuePtr->GetDouble ();
delete valuePtr;
i++;
}
//int displacement = mSize - mLastHalfSize; // +0, +1, -1?????
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfCharacteristicArray [i] = mCharacteristicArray [i + displacement];
previous = mCharacteristicArray [0];
for (i=0; i<mDifferenceSize; i++) {
next = mCharacteristicArray [i+1];
mUnnormalizedDifferenceArray [i] = mDifferenceArray [i] = next - previous;
previous = next;
}
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfUnnormalizedDifferenceArray [i] = mUnnormalizedDifferenceArray [i + displacement];
double norm = 0.0;
for (i=0; i<mDifferenceSize; i++)
norm += mDifferenceArray [i] * mDifferenceArray [i];
norm = sqrt (norm);
if (norm > 0.0) {
for (i=0; i<mDifferenceSize; i++)
mDifferenceArray [i] /= norm;
}
cumulative = 0.0;
for (i=0; i<mDifferenceSize; i++) {
temp = mUnnormalizedDifferenceArray [i];
cumulative += temp * temp;
mNormsLeft [i] = cumulative;
}
cumulative = 0.0;
for (i=mDifferenceSize-1; i>=0; i--) {
temp = mUnnormalizedDifferenceArray [i];
cumulative += temp * temp;
mNormsRight [i] = cumulative;
}
//cumulative = 0.0;
//for (i=0; i<mLastHalfDifferenceSize; i++) {
// temp = mLastHalfUnnormalizedDifferenceArray [i];
// cumulative += temp * temp;
// mLastHalfNormsLeft [i] = cumulative;
//}
//cumulative = 0.0;
//for (i=mLastHalfDifferenceSize-1; i>=0; i--) {
// temp = mLastHalfUnnormalizedDifferenceArray [i];
// cumulative += temp * temp;
// mLastHalfNormsRight [i] = cumulative;
//}
MaxCharacteristic = maxChar;
MinCharacteristic = minChar;
double width = mCharacteristicArray [mSize - 1] - mCharacteristicArray [0];
if (width > 0.0)
mFirstIntervalFraction = mUnnormalizedDifferenceArray [0] / width;
else
mFirstIntervalFraction = 1.0;
double temp = mUnnormalizedDifferenceArray [0];
double value;
for (i=0; i<mDifferenceSize; i++) {
value = mUnnormalizedDifferenceArray [i];
if (value < temp)
temp = value;
}
if (width > 0.0)
mSmallestIntervalFraction = temp / width;
else
mSmallestIntervalFraction = 1.0;
if (!HeightToken.FindNextBracketedString (0, endPosition, HeightString)) {
mRelativeSizes = NULL;
// mLastHalfRelativeSizes = NULL;
}
else {
RGStringTokenizer data2 (HeightString);
data2.AddDelimiter (' ');
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddDelimiter (" ");
data2.AddRemoveItem (',');
data2.AddDelimiter ('\t');
data2.AddDelimiter ('\n');
mRelativeSizes = new int [mSize];
for (k=0; k<mSize; k++)
mRelativeSizes [k] = -1;
k = 0;
while (data2.NextToken (token, delim)) {
if (token.Length () > 0) {
token.ToUpper ();
char first = token.GetFirstCharacter ();
switch (first) {
case 'H':
mRelativeSizes [k] = 5;
break;
case 'L':
mRelativeSizes [k] = 1;
break;
case 'M':
if (token.Length () == 1)
mRelativeSizes [k] = 3;
else if (token.GetLastCharacter () == 'H')
mRelativeSizes [k] = 4;
else
mRelativeSizes [k] = 2;
break;
default:
mRelativeSizes [k] = -1;
}
}
k++;
if (k >= mSize)
break;
}
//mLastHalfRelativeSizes = new int [mLastHalfSize];
//for (i=0; i<mLastHalfSize; i++)
// mLastHalfRelativeSizes [i] = mRelativeSizes [i + displacement];
int maxRelativeSize = 0;
int relativeSize;
for (j=0; j<mSize; j++) {
relativeSize = mRelativeSizes [j];
if (relativeSize > maxRelativeSize)
maxRelativeSize = relativeSize;
}
int numberOfHighsInILS = 0;
mMaxRelativeHeight = maxRelativeSize;
for (j=0; j<mSize; j++) {
if (mRelativeSizes [j] == maxRelativeSize)
numberOfHighsInILS++;
}
mNumberOfLargePeaks = numberOfHighsInILS;
mNumberOfLargeDifferences = numberOfHighsInILS - 1;
mLargeCharacteristicArray = new double [numberOfHighsInILS];
if (mNumberOfLargeDifferences > 0)
mLargeDifferenceArray = new double [mNumberOfLargeDifferences];
k = 0;
for (j=0; j<mSize; j++) {
if (mRelativeSizes [j] == maxRelativeSize) {
mLargeCharacteristicArray [k] = mCharacteristicArray [j];
k++;
}
}
if (mLargeDifferenceArray != NULL) {
for (j=0; j<mNumberOfLargeDifferences; j++)
mLargeDifferenceArray [j] = mLargeCharacteristicArray [j + 1] - mLargeCharacteristicArray [j];
}
}
if (OmissionSearch.FindNextBracketedString (0, endPosition, OmissionString)) {
RGStringTokenizer omissionData (OmissionString);
omissionData.AddDelimiter (' ');
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddDelimiter (" ");
omissionData.AddRemoveItem (',');
omissionData.AddDelimiter ('\t');
omissionData.AddDelimiter ('\n');
while (omissionData.NextToken (token, delim)) {
if (token.Length () > 0) {
value = token.ConvertToDouble ();
valuePtr = new RGPDouble (value);
if (tokens.Entries () == 0) {
minChar = maxChar = value;
tokens.Append (valuePtr);
}
else if (value < minChar) {
minChar = value;
tokens.Prepend (valuePtr);
}
else if (value > maxChar) {
maxChar = value;
tokens.Append (valuePtr);
}
else
tokens.Insert (valuePtr);
}
}
mOmissionSize = (int)tokens.Entries ();
if (mOmissionSize == 0)
return;
mOmissionArray = new double [mOmissionSize];
i = 0;
while (valuePtr = (RGPDouble*)tokens.GetFirst ()) {
mOmissionArray [i] = valuePtr->GetDouble ();
delete valuePtr;
i++;
}
}
}
cout << "ILS Name = " << Name.GetData () << endl;
if (!AcceptanceThresholdSearch.FindNextBracketedString (0, endPosition, numberString))
cout << "\tCould not find ILS acceptance threshold...using " << mCorrelationAcceptanceThreshold << endl;
else {
mCorrelationAcceptanceThreshold = numberString.ConvertToDouble ();
cout << "\tFrom ILS settings...ILS acceptance threshold = " << mCorrelationAcceptanceThreshold << endl;
}
if (!AutoAcceptanceThresholdSearch.FindNextBracketedString (0, endPosition, numberString))
cout << "\tCould not find ILS auto acceptance threshold...using default value = " << mCorrelationAutoAcceptanceThreshold << endl << endl;
else {
mCorrelationAutoAcceptanceThreshold = numberString.ConvertToDouble ();
cout << "\tFrom ILS settings...ILS auto acceptance threshold = " << mCorrelationAutoAcceptanceThreshold << endl << endl;
}
}
bool STRBaseLocus :: GetLadderSearchRegion (size_t& startIndex, RGString& input, const RGString& familyName) {
RGBracketStringSearch searchRegionsSearch ("<SearchRegions>", "</SearchRegions>", input);
RGString searchRegion;
RGString searchDetails;
RGBracketStringSearch individualRegionsSearch ("<Region>", "</Region>", searchRegion);
RGBracketStringSearch familyNameSearch ("<ILSName>", "</ILSName>", searchDetails);
RGBracketStringSearch minILSGridSearch ("<MinGrid>", "</MinGrid>", searchDetails);
RGBracketStringSearch maxILSGridSearch ("<MaxGrid>", "</MaxGrid>", searchDetails);
size_t start = startIndex;
size_t end;
size_t individualEnd;
bool foundData = false;
RGString searchName;
RGString number;
if (!searchRegionsSearch.FindNextBracketedString (start, end, searchRegion))
return false;
startIndex = end;
individualRegionsSearch.ResetSearch ();
start = 0;
while (individualRegionsSearch.FindNextBracketedString (start, end, searchDetails)) {
familyNameSearch.ResetSearch ();
if (!familyNameSearch.FindNextBracketedString (0, individualEnd, searchName))
return false;
if (searchName == familyName) {
minILSGridSearch.ResetSearch ();
maxILSGridSearch.ResetSearch ();
if (!minILSGridSearch.FindNextBracketedString (0, individualEnd, number))
return false;
LowerBoundGridLSBasePair = number.ConvertToDouble ();
if (!maxILSGridSearch.FindNextBracketedString (0, individualEnd, number))
return false;
UpperBoundGridLSBasePair = number.ConvertToDouble ();
return true;
}
start = end;
}
return false;
}
STRBaseLocus :: STRBaseLocus (const RGString& xmlInput) : BaseLocus (xmlInput), LowerBoundGridLSIndex (-1.0),
UpperBoundGridLSIndex (-1.0), MinimumGridTime (-1.0), MaximumGridTime (-1.0), LowerBoundGridLSBasePair (-1.0),
UpperBoundGridLSBasePair (-1.0), mNoExtension (false) {
mSampleLocusSpecificStutterThreshold = Locus::GetSampleStutterThreshold ();
mSampleLocusSpecificPlusStutterThreshold = Locus::GetSamplePlusStutterThreshold ();
mSampleLocusSpecificAdenylationThreshold = Locus::GetSampleAdenylationThreshold ();
mSampleLocusSpecificFractionalFilter = Locus::GetSampleFractionalFilter ();
mSampleLocusSpecificPullupFractionalFilter = Locus::GetSamplePullupFractionalFilter ();
mSampleLocusSpecificHeterozygousImbalanceThreshold = Locus::GetHeterozygousImbalanceLimit ();
mSampleLocusSpecificMinBoundForHomozygote = Locus::GetMinBoundForHomozygote ();
mLadderLocusSpecificStutterThreshold = Locus::GetGridStutterThreshold ();
mLadderLocusSpecificAdenylationThreshold = Locus::GetGridAdenylationThreshold ();
mLadderLocusSpecificFractionalFilter = Locus::GetGridFractionalFilter ();
mLadderLocusSpecificPullupFractionalFilter = Locus::GetGridPullupFractionalFilter ();
RGString Input (xmlInput);
RGBracketStringSearch MinToken ("<MinBP>", "</MinBP>", Input);
RGBracketStringSearch MaxToken ("<MaxBP>", "</MaxBP>", Input);
RGBracketStringSearch LowerGridIndex ("<MinGridLSIndex>", "</MinGridLSIndex>", Input);
RGBracketStringSearch UpperGridIndex ("<MaxGridLSIndex>", "</MaxGridLSIndex>", Input);
RGBracketStringSearch CoreRepeatSearch ("<CoreRepeatNumber>", "</CoreRepeatNumber>", Input);
RGBracketStringSearch LowerGridBasePair ("<MinGridLSBasePair>", "</MinGridLSBasePair>", Input);
RGBracketStringSearch UpperGridBasePair ("<MaxGridLSBasePair>", "</MaxGridLSBasePair>", Input);
RGBracketStringSearch NoExtensionSearch ("<NoExtension>", "</NoExtension>", Input);
RGXMLTagSearch yLinkedSearch ("YLinked", Input);
RGXMLTagSearch maxExpectedAllelesSearch ("MaxExpectedAlleles", Input);
RGXMLTagSearch minExpectedAllelesSearch ("MinExpectedAlleles", Input);
size_t EndPosition;
RGString BPString;
RGString extString;
bool lowerBoundFound = false;
bool upperBoundFound = false;
RGString trueString ("true");
RGString familyName = BaseLocus::GetILSFamilyName ();
// cout << "Current Family Name = " << familyName.GetData () << endl; // This was a test to make sure the family name is known at this point. Test succeeded 12/31/2015.
bool useILSFamilies = PopulationCollection::UseILSFamiliesInLadderFile (); // if true, use families; otherwise, use the old way.
bool isValid = true;
size_t StartPosition = 0;
if (NoExtensionSearch.FindNextBracketedString (0, EndPosition, extString)) {
if (extString.FindNextSubstringCaseIndependent (0, trueString, EndPosition))
mNoExtension = true;
else
mNoExtension = false;
}
if (!MinToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Base Pair token\n";
MinimumBP = -1;
}
else
MinimumBP = BPString.ConvertToInteger ();
if (!MaxToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Base Pair token\n";
MaximumBP = -1;
}
else
MaximumBP = BPString.ConvertToInteger ();
if (LowerGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSIndex = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSIndex = BPString.ConvertToDouble ();
upperBoundFound = true;
}
// test for ladder with ILS Family names here and, if found, use family name instead of the following four if's *******
if (useILSFamilies) {
isValid = GetLadderSearchRegion (StartPosition, Input, familyName);
if (!isValid) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find family-based search region\n";
}
}
else {
if (LowerGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSBasePair = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSBasePair = BPString.ConvertToDouble ();
upperBoundFound = true;
}
if (!lowerBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Grid Internal Lane Standard token, either index or base pair\n";
}
if (!upperBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Grid Internal Lane Standard token, either index or base pair\n";
}
}
if (!CoreRepeatSearch.FindNextBracketedString (0, EndPosition, BPString))
CoreRepeatNumber = 4;
else
CoreRepeatNumber = BPString.ConvertToInteger ();
if (!yLinkedSearch.FindNextTag (0, EndPosition, BPString))
mIsYLinked = false;
else {
if (BPString == "false")
mIsYLinked = false;
else
mIsYLinked = true;
}
if (!maxExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMaxExpectedAlleles = 2;
else
mMaxExpectedAlleles = BPString.ConvertToInteger ();
if (!minExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMinExpectedAlleles = 1;
else
mMinExpectedAlleles = BPString.ConvertToInteger ();
if (!Valid) {
Msg << "XML Input:\n" << Input << "\n";
}
}
STRBaseLocus :: STRBaseLocus (const RGString& xmlInput) : BaseLocus (xmlInput), LowerBoundGridLSIndex (-1.0),
UpperBoundGridLSIndex (-1.0), MinimumGridTime (-1.0), MaximumGridTime (-1.0), LowerBoundGridLSBasePair (-1.0),
UpperBoundGridLSBasePair (-1.0) {
mSampleLocusSpecificStutterThreshold = Locus::GetSampleStutterThreshold ();
mSampleLocusSpecificPlusStutterThreshold = Locus::GetSamplePlusStutterThreshold ();
mSampleLocusSpecificAdenylationThreshold = Locus::GetSampleAdenylationThreshold ();
mSampleLocusSpecificFractionalFilter = Locus::GetSampleFractionalFilter ();
mSampleLocusSpecificPullupFractionalFilter = Locus::GetSamplePullupFractionalFilter ();
mSampleLocusSpecificHeterozygousImbalanceThreshold = Locus::GetHeterozygousImbalanceLimit ();
mSampleLocusSpecificMinBoundForHomozygote = Locus::GetMinBoundForHomozygote ();
mLadderLocusSpecificStutterThreshold = Locus::GetGridStutterThreshold ();
mLadderLocusSpecificAdenylationThreshold = Locus::GetGridAdenylationThreshold ();
mLadderLocusSpecificFractionalFilter = Locus::GetGridFractionalFilter ();
mLadderLocusSpecificPullupFractionalFilter = Locus::GetGridPullupFractionalFilter ();
RGString Input (xmlInput);
RGBracketStringSearch MinToken ("<MinBP>", "</MinBP>", Input);
RGBracketStringSearch MaxToken ("<MaxBP>", "</MaxBP>", Input);
RGBracketStringSearch LowerGridIndex ("<MinGridLSIndex>", "</MinGridLSIndex>", Input);
RGBracketStringSearch UpperGridIndex ("<MaxGridLSIndex>", "</MaxGridLSIndex>", Input);
RGBracketStringSearch CoreRepeatSearch ("<CoreRepeatNumber>", "</CoreRepeatNumber>", Input);
RGBracketStringSearch LowerGridBasePair ("<MinGridLSBasePair>", "</MinGridLSBasePair>", Input);
RGBracketStringSearch UpperGridBasePair ("<MaxGridLSBasePair>", "</MaxGridLSBasePair>", Input);
RGXMLTagSearch yLinkedSearch ("YLinked", Input);
RGXMLTagSearch maxExpectedAllelesSearch ("MaxExpectedAlleles", Input);
RGXMLTagSearch minExpectedAllelesSearch ("MinExpectedAlleles", Input);
size_t EndPosition;
RGString BPString;
bool lowerBoundFound = false;
bool upperBoundFound = false;
if (!MinToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Base Pair token\n";
MinimumBP = -1;
}
else
MinimumBP = BPString.ConvertToInteger ();
if (!MaxToken.FindNextBracketedString (0, EndPosition, BPString)) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Base Pair token\n";
MaximumBP = -1;
}
else
MaximumBP = BPString.ConvertToInteger ();
if (LowerGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSIndex = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridIndex.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSIndex = BPString.ConvertToDouble ();
upperBoundFound = true;
}
if (LowerGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
LowerBoundGridLSBasePair = BPString.ConvertToDouble ();
lowerBoundFound = true;
}
if (UpperGridBasePair.FindNextBracketedString (0, EndPosition, BPString)) {
UpperBoundGridLSBasePair = BPString.ConvertToDouble ();
upperBoundFound = true;
}
if (!lowerBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Minimum Grid Internal Lane Standard token, either index or base pair\n";
}
if (!upperBoundFound) {
Valid = FALSE;
Msg << "Locus named " << LocusName << " could not find Maximum Grid Internal Lane Standard token, either index or base pair\n";
}
if (!CoreRepeatSearch.FindNextBracketedString (0, EndPosition, BPString))
CoreRepeatNumber = 4;
else
CoreRepeatNumber = BPString.ConvertToInteger ();
if (!yLinkedSearch.FindNextTag (0, EndPosition, BPString))
mIsYLinked = false;
else {
if (BPString == "false")
mIsYLinked = false;
else
mIsYLinked = true;
}
if (!maxExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMaxExpectedAlleles = 2;
else
mMaxExpectedAlleles = BPString.ConvertToInteger ();
if (!minExpectedAllelesSearch.FindNextTag (0, EndPosition, BPString))
mMinExpectedAlleles = 1;
else
mMinExpectedAlleles = BPString.ConvertToInteger ();
if (!Valid) {
Msg << "XML Input:\n" << Input << "\n";
}
}
