//***************************************************************************************************************
-RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileName){
+RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
m = MothurOut::getInstance();
- m->openOutputFile(chimeraReportFileName, chimeraReportFile);
numRefSeqs = refs.size();
referenceSeqs.resize(numRefSeqs);
alignLength = referenceSeqs[0].length();
- chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
-// chimeraReportFile << "leftParentTri,middleParentTri,rightParentTri\tbreakPointTriA,breakPointTriB\tminMismatchToTrimera\tdistToBestMera\tnMera" << endl;
}
+//***************************************************************************************************************
+int RefChimeraTest::printHeader(ofstream& chimeraReportFile){
+ try {
+ chimeraReportFile << "queryName\tbestRef\tbestSequenceMismatch\tleftParentChi,rightParentChi\tbreakPointChi\tminMismatchToChimera\tdistToBestMera\tnumParents" << endl;
+ return 0;
+ }catch(exception& e) {
+ m->errorOut(e, "RefChimeraTest", "execute");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-int RefChimeraTest::analyzeQuery(string queryName, string querySeq){
+int RefChimeraTest::analyzeQuery(string queryName, string querySeq, ofstream& chimeraReportFile){
vector<vector<int> > left(numRefSeqs);
vector<int> singleLeft, bestLeft;