bool InterchannelLinkage :: RecalculatePrimarySignalSM (SmartNotice& primaryTarget, SmartNotice& primaryReplace) {
// Add notice objects for test and replacement on removal
if (mSecondarySignals.Entries () <= 1)
return false;
if (mPrimarySignal != NULL)
return true;
DataSignal* nextSignal;
RGDListIterator it (mSecondarySignals);
DataSignal* maxSignal = NULL;
double maxPeak = 0.0;
double thisPeak;
while (nextSignal = (DataSignal*) it ()) {
thisPeak = nextSignal->Peak ();
if (thisPeak > maxPeak) {
maxPeak = thisPeak;
maxSignal = nextSignal;
}
}
if (maxSignal == NULL)
return false;
mPrimarySignal = maxSignal;
mPrimarySignal->SetMessageValue (primaryTarget, false);
mPrimarySignal->SetMessageValue (primaryReplace, true);
it.Reset ();
mPrimarySignal->RemoveAllCrossChannelSignalLinks ();
while (nextSignal = (DataSignal*) it ()) {
if (nextSignal != mPrimarySignal) {
nextSignal->SetPrimaryCrossChannelSignalLink (mPrimarySignal);
mPrimarySignal->AddCrossChannelSignalLink (nextSignal);
}
}
return true;
}
void DataSignal :: WriteSmartTableArtifactInfoToXML (RGTextOutput& text, RGTextOutput& tempText, const RGString& indent, const RGString& bracketTag, const RGString& locationTag) {
int peak;
Endl endLine;
RGString suffix;
RGString label;
SmartMessageReporter* notice;
int i;
RGString virtualAllele;
SmartMessageReporter* nextNotice;
text.SetOutputLevel (1);
int msgNum;
smAcceptedOLLeft acceptedOLLeft;
smAcceptedOLRight acceptedOLRight;
int reportedMessageLevel = GetHighestMessageLevelWithRestrictionSM ();
//bool hasThreeLoci;
//bool needLocus0;
if ((!DontLook ()) && (NumberOfSmartNoticeObjects () != 0)) {
bool firstNotice = true;
peak = (int) floor (Peak () + 0.5);
virtualAllele = GetVirtualAlleleName ();
text << indent << "<" << bracketTag << ">" << endLine; // Should be <Artifact>
text << indent << "\t<Id>" << GetSignalID () << "</Id>" << endLine;
text << indent << "\t<Level>" << reportedMessageLevel << "</Level>" << endLine;
text << indent << "\t<RFU>" << peak << "</RFU>" << endLine;
text << indent << "\t<" << locationTag << ">" << GetApproximateBioID () << "</" << locationTag << ">" << endLine;
text << indent << "\t<PeakArea>" << TheoreticalArea () << "</PeakArea>" << endLine;
text << indent << "\t<Time>" << GetMean () << "</Time>" << endLine;
text << indent << "\t<Fit>" << GetCurveFit () << "</Fit>" << endLine;
if (!mAllowPeakEdit)
text << indent << "\t<AllowPeakEdit>false</AllowPeakEdit>" << endLine;
RGDListIterator it (*mSmartMessageReporters);
i = 0;
while (notice = (SmartMessageReporter*) it ()) {
if (!notice->GetDisplayOsirisInfo ())
continue;
if (firstNotice) {
label = indent + "\t<Label>";
firstNotice = false;
}
if (i > 0)
label << " ";
label += notice->GetMessage ();
label += notice->GetMessageData ();
i++;
}
if (i > 0) {
label << "</Label>";
text << label << endLine;
}
// Now add list of notices...
it.Reset ();
while (nextNotice = (SmartMessageReporter*) it ()) {
msgNum = Notice::GetNextMessageNumber ();
nextNotice->SetMessageCount (msgNum);
text << indent << "\t<MessageNumber>" << msgNum << "</MessageNumber>" << endLine;
tempText << "\t\t<Message>\n";
tempText << "\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
tempText << "\t\t\t<Text>" << nextNotice->GetMessage () << nextNotice->GetMessageData () << "</Text>\n";
if (nextNotice->HasViableExportInfo ()) {
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Hidden>false</Hidden>\n";
else
tempText << "\t\t\t<Hidden>true</Hidden>\n";
if (!nextNotice->IsCritical ())
tempText << "\t\t\t<Critical>false</Critical>\n";
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Enabled>true</Enabled>\n";
else
tempText << "\t\t\t<Enabled>false</Enabled>\n";
if (!nextNotice->IsEditable ())
tempText << "\t\t\t<Editable>false</Editable>\n";
if (nextNotice->GetDisplayExportInfo ())
tempText << "\t\t\t<DisplayExportInfo>true</DisplayExportInfo>\n";
else
tempText << "\t\t\t<DisplayExportInfo>false</DisplayExportInfo>\n";
if (!nextNotice->GetDisplayOsirisInfo ())
tempText << "\t\t\t<DisplayOsirisInfo>false</DisplayOsirisInfo>\n";
tempText << "\t\t\t<MsgName>" << nextNotice->GetMessageName () << "</MsgName>\n";
//tempText << "\t\t\t<ExportProtocolList>";
//tempText << "\t\t\t" << nextNotice->GetExportProtocolInformation ();
//tempText << "\t\t\t</ExportProtocolList>\n";
}
tempText << "\t\t</Message>\n";
}
// Now add list of alleles
//hasThreeLoci = (mLocus != NULL) && (mLeftLocus != NULL) && (mRightLocus != NULL);
//if (mLocus != NULL) {
// if ((mLeftLocus == NULL) && (mRightLocus == NULL))
// needLocus0 = true;
// else
// needLocus0 = false;
//}
//else
// needLocus0 = false;
//needLocus0 = (!hasThreeLoci) && ((mLocus != mLeftLocus) || (mLocus != mRightLocus));
if (mLocus != NULL) {
//testing
RGString locusName = mLocus->GetLocusName ();
suffix = GetAlleleName (0);
if ((suffix.Length () > 0) || (virtualAllele.Length () > 0)) {
text << indent << "\t<Allele>" << endLine;
if (suffix.Length () > 0)
text << indent << "\t\t<Name>" << suffix << "</Name>" << endLine;
else
text << indent << "\t\t<Name>" << virtualAllele << "</Name>" << endLine;
if (mOffGrid)
suffix = "true";
else if (mAcceptedOffGrid)
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (0) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>0</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mLeftLocus != NULL) && (mLeftLocus != mLocus)) {
if (mAlleleNameLeft.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameLeft << "</Name>" << endLine;
if (mIsOffGridLeft)
suffix = "true";
else if (GetMessageValue (acceptedOLLeft))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (-1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mLeftLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>-1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
if ((mRightLocus != NULL) && (mRightLocus != mLocus)) {
if (mAlleleNameRight.Length () > 0) {
text << indent << "\t<Allele>" << endLine;
text << indent << "\t\t<Name>" << mAlleleNameRight << "</Name>" << endLine;
if (mIsOffGridRight)
suffix = "true";
else if (GetMessageValue (acceptedOLRight))
suffix = "accepted";
else
suffix = "false";
text << indent << "\t\t<OffLadder>" << suffix << "</OffLadder>" << endLine;
text << indent << "\t\t<BPS>" << GetBioID (1) << "</BPS>" << endLine;
text << indent << "\t\t<Locus>" << mRightLocus->GetLocusName () << "</Locus>" << endLine;
text << indent << "\t\t<Location>1</Location>" << endLine;
text << indent << "\t</Allele>" << endLine;
}
}
text << indent << "</" + bracketTag << ">" << endLine;
}
text.ResetOutputLevel ();
}
bool InterchannelLinkage :: RecalculatePrimarySignalBasedOnValiditySM () {
// Add notice objects for test and replacement on removal
//
// This is sample stage 1 and 3
//
smPrimaryInterchannelLink primaryLink;
smNotInterchannelLink notInterchannelLink;
if ((mPrimarySignal != NULL) && mPrimarySignal->cannotBePrimary ()) {
// mSecondarySignals.InsertWithNoReferenceDuplication (mPrimarySignal);
mPrimarySignal->SetMessageValue (primaryLink, false);
//mPrimarySignal->RemoveCrossChannelSignalLinkSM ();
//mPrimarySignal->SetMessageValue (notInterchannelLink, true);
mPrimarySignal = NULL;
}
if (mSecondarySignals.Entries () <= 1) {
RemoveAllBasedOnValiditySM ();
return true;
}
if (mPrimarySignal != NULL)
return false;
DataSignal* nextSignal;
RGDListIterator it (mSecondarySignals);
DataSignal* maxSignal = NULL;
double maxPeak = 0.0;
double thisPeak;
while (nextSignal = (DataSignal*) it ()) {
if (nextSignal->cannotBePrimary ())
continue;
thisPeak = nextSignal->Peak ();
if (thisPeak > maxPeak) {
maxPeak = thisPeak;
maxSignal = nextSignal;
}
}
if (maxSignal == NULL) {
RemoveAllBasedOnValiditySM ();
return true;
}
mPrimarySignal = maxSignal;
mPrimarySignal->SetMessageValue (primaryLink, true);
it.Reset ();
mPrimarySignal->RemoveAllCrossChannelSignalLinksSM (); //???????????????????????????????????????
while (nextSignal = (DataSignal*) it ()) {
if (nextSignal != mPrimarySignal) {
nextSignal->SetPrimaryCrossChannelSignalLink (mPrimarySignal);
nextSignal->AddCrossChannelSignalLink (nextSignal);
nextSignal->SetMessageValue (primaryLink, false);
}
}
return true;
}
bool InterchannelLinkage :: RecalculatePrimarySignalSM () {
// Add notice objects for test and replacement on removal
//
// This is sample stage 1 and 3
//
smPrimaryInterchannelLink primaryLink;
smPullUp pullup;
if (mSecondarySignals.Entries () <= 1)
return false;
if (mPrimarySignal != NULL)
return true;
DataSignal* nextSignal;
RGDListIterator it (mSecondarySignals);
DataSignal* maxSignal = NULL;
double maxPeak = 0.0;
double thisPeak;
while (nextSignal = (DataSignal*) it ()) {
thisPeak = nextSignal->Peak ();
if (thisPeak > maxPeak) {
maxPeak = thisPeak;
maxSignal = nextSignal;
}
}
if (maxSignal == NULL)
return false;
mPrimarySignal = maxSignal;
mPrimarySignal->SetMessageValue (primaryLink, true);
mPrimarySignal->SetMessageValue (pullup, false);
it.Reset ();
mPrimarySignal->RemoveAllCrossChannelSignalLinksSM (); //???????????????????????????????????????
list<int> pChannels;
double ratio;
int nextChannel = mPrimarySignal->GetChannel ();
while (nextSignal = (DataSignal*) it ()) {
if (nextSignal != mPrimarySignal) {
nextSignal->SetPrimaryCrossChannelSignalLink (mPrimarySignal);
mPrimarySignal->AddCrossChannelSignalLink (nextSignal);
nextSignal->SetMessageValue (primaryLink, false);
nextSignal->SetMessageValue (pullup, true);
ratio = 0.01 * floor (10000.0 * (nextSignal->Peak () / mPrimarySignal->Peak ()) + 0.5);
nextSignal->AppendDataForSmartMessage (pullup, nextChannel);
nextSignal->AppendDataForSmartMessage (pullup, ratio);
pChannels.push_back (nextSignal->GetChannel ());
//mPrimarySignal->AppendDataForSmartMessage (primaryLink, nextSignal->GetChannel ());
}
}
pChannels.sort ();
while (!pChannels.empty ()) {
nextChannel = pChannels.front ();
mPrimarySignal->AppendDataForSmartMessage (primaryLink, nextChannel);
pChannels.pop_front ();
}
return true;
}
Boolean STRBaseLocus :: ExtractGridSignals (RGDList& channelSignalList, const LaneStandard* ls, RGDList& locusDataSignalList, ChannelData* lsData, Locus* locus) {
int lsSize = ls->GetNumberOfCharacteristics ();
int i1;
int i2;
double c1;
double c2;
Notice* newNotice;
if (lsSize < 0) {
Msg << "Number of characteristics not available for Locus named " << LocusName << "\n";
newNotice = new SetupErrorNumberPeaksUnavailableForLocus;
locus->AddNoticeToList (newNotice);
return FALSE;
}
if (LowerBoundGridLSBasePair < 0.0) {
i1 = (int) floor (LowerBoundGridLSIndex);
if (i1 < 0) {
Msg << "Internal Lane Standard lower bound index for Grid is out of bounds for Locus named " << LocusName << "\n";
return FALSE;
}
i2 = i1 + 1;
c2 = LowerBoundGridLSIndex - i1;
c1 = 1.0 - c2;
MinimumGridTime = c1 * ls->GetLaneStandardTimeForCharacteristicNumber (i1) +
c2 * ls->GetLaneStandardTimeForCharacteristicNumber (i2);
// cout << "Not using base pairs for minimum of locus " << LocusName << endl;
}
else
MinimumGridTime = lsData->GetTimeForSpecifiedID (LowerBoundGridLSBasePair);
if (UpperBoundGridLSBasePair < 0.0) {
i1 = (int) floor (UpperBoundGridLSIndex);
if (i1 < 0) {
Msg << "Internal Lane Standard upper bound index for Grid is out of bounds for Locus named " << LocusName << "\n";
return FALSE;
}
i2 = i1 + 1;
c2 = UpperBoundGridLSIndex - i1;
c1 = 1.0 - c2;
MaximumGridTime = c1 * ls->GetLaneStandardTimeForCharacteristicNumber (i1) +
c2 * ls->GetLaneStandardTimeForCharacteristicNumber (i2);
// cout << "Not using base pairs for maximum of locus " << LocusName << endl;
}
else
MaximumGridTime = lsData->GetTimeForSpecifiedID (UpperBoundGridLSBasePair);
RGDListIterator it (channelSignalList);
DataSignal* nextSignal;
double nextMean;
locusDataSignalList.Clear ();
// Assume channelSignalList is in increasing order by signal means
while (nextSignal = (DataSignal*) it ()) {
nextMean = nextSignal->GetMean ();
if (nextMean >= MinimumGridTime) {
if (nextMean <= MaximumGridTime) {
it.RemoveCurrentItem ();
locusDataSignalList.Append (nextSignal);
}
else
break;
}
}
if (locusDataSignalList.Entries () < mLocusSize) {
Msg << "Locus named " << LocusName << " could not find the required number of unanalyzed peaks in range\n";
newNotice = new LocusHasTooFewPeaks;
locus->AddNoticeToList (newNotice);
return FALSE;
}
return TRUE;
}
bool CoreBioComponent :: ReportXMLSmartNoticeObjects (RGTextOutput& text, RGTextOutput& tempText, const RGString& delim) {
if (NumberOfSmartNoticeObjects () > 0) {
int msgLevel = GetHighestMessageLevelWithRestrictionSM ();
RGDListIterator it (*mSmartMessageReporters);
SmartMessageReporter* nextNotice;
text.SetOutputLevel (msgLevel);
tempText.SetOutputLevel (1);
int msgNum;
int triggerLevel = Notice::GetMessageTrigger ();
bool includesExportInfo = false;
bool viable;
while (nextNotice = (SmartMessageReporter*) it ()) {
if (nextNotice->HasViableExportInfo ()) {
includesExportInfo = true;
break;
}
}
if (!text.TestCurrentLevel () && !includesExportInfo) {
text.ResetOutputLevel ();
tempText.ResetOutputLevel ();
return FALSE;
}
text.ResetOutputLevel ();
text << CLevel (1) << "\t\t\t<SampleAlerts>\n" << PLevel ();
it.Reset ();
text.SetOutputLevel (1);
while (nextNotice = (SmartMessageReporter*) it ()) {
viable = nextNotice->HasViableExportInfo ();
msgLevel = nextNotice->GetMessagePriority ();
if (((msgLevel > 0) && (msgLevel <= triggerLevel)) || viable) {
msgNum = Notice::GetNextMessageNumber ();
nextNotice->SetMessageCount (msgNum);
text << "\t\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
tempText << "\t\t<Message>\n";
tempText << "\t\t\t<MessageNumber>" << msgNum << "</MessageNumber>\n";
tempText << "\t\t\t<Text>" << nextNotice->GetMessage () << nextNotice->GetMessageData () << "</Text>\n";
if (viable) {
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Hidden>false</Hidden>\n";
else
tempText << "\t\t\t<Hidden>true</Hidden>\n";
if (!nextNotice->IsCritical ())
tempText << "\t\t\t<Critical>false</Critical>\n";
if (nextNotice->IsEnabled ())
tempText << "\t\t\t<Enabled>true</Enabled>\n";
else
tempText << "\t\t\t<Enabled>false</Enabled>\n";
if (!nextNotice->IsEditable ())
tempText << "\t\t\t<Editable>false</Editable>\n";
if (nextNotice->GetDisplayExportInfo ())
tempText << "\t\t\t<DisplayExportInfo>true</DisplayExportInfo>\n";
else
tempText << "\t\t\t<DisplayExportInfo>false</DisplayExportInfo>\n";
if (!nextNotice->GetDisplayOsirisInfo ())
tempText << "\t\t\t<DisplayOsirisInfo>false</DisplayOsirisInfo>\n";
tempText << "\t\t\t<MsgName>" << nextNotice->GetMessageName () << "</MsgName>\n";
//tempText << "\t\t\t<ExportProtocolList>";
//tempText << "\t\t\t" << nextNotice->GetExportProtocolInformation ();
//tempText << "\t\t\t</ExportProtocolList>\n";
}
tempText << "\t\t</Message>\n";
}
}
text.ResetOutputLevel ();
text << CLevel (1) << "\t\t\t</SampleAlerts>\n" << PLevel ();
tempText.ResetOutputLevel ();
}
else
return false;
return true;
}
void RGHashTable :: ResizeTable (int size) {
RGPersistent* next;
unsigned hash;
unsigned index;
int i;
if (NumberOfLists < size) {
RGDList** NewArray = new RGDList* [size];
for (i=0; i<size; i++) {
if (i < NumberOfLists)
NewArray [i] = ListArray [i];
else
NewArray [i] = new RGDList;
}
delete[] ListArray;
ListArray = NewArray;
for (i=0; i<NumberOfLists; i++) {
if (ListArray [i]->Entries() > 0) {
RGDListIterator* it = new RGDListIterator (*ListArray [i]);
while (next = (*it)()) {
hash = next->HashNumber (size);
index = hash%size;
if (index != i) {
it->RemoveCurrentItem ();
ListArray [index]->Insert (next);
}
}
delete it;
}
}
NumberOfLists = size;
}
else if ((NumberOfLists > size) && (size > 0)) {
RGDList** NewArray = new RGDList* [size];
for (int i=0; i<NumberOfLists; i++) {
if (i < size)
NewArray [i] = ListArray [i];
if (ListArray [i]->Entries() > 0) {
RGDListIterator* it = new RGDListIterator (*ListArray [i]);
while (next = (*it)()) {
hash = next->HashNumber (size);
index = hash%size;
if (index != i) {
it->RemoveCurrentItem ();
ListArray [index]->Insert (next);
}
}
delete it;
}
if (i >= size)
delete ListArray [i];
}
delete[] ListArray;
ListArray = NewArray;
NumberOfLists = size;
}
}
