int Ladder :: MergeLocusIntoLadder (const Locus* locus) {
// This combines info and then computes the rest
Locus* matchingLocus = FindLocusByName (locus->GetName ());
if (matchingLocus == NULL) {
cout << "Could not find locus matching name: " << locus->GetName ().GetData () << endl;
return -1;
}
matchingLocus->SetFirstCoreLocusBP (locus->GetFirstCoreLocusBP ());
matchingLocus->SetFirstExtendedAllele (locus->GetFirstExtendedAllele ());
matchingLocus->SetLastExtendedAllele (locus->GetLastExtendedAllele ());
matchingLocus->ComputeAllBPs ();
matchingLocus->SetMinMaxSearchILSBP (locus->GetMinSearchILSBP (), locus->GetMaxSearchILSBP ());
matchingLocus->AdjustSearchRegion ();
matchingLocus->SetMerged ();
return 0;
}
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;
}