//***************************************************************************************************************
-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;
for(int i=0;i<numRefSeqs;i++){
int lDiffs = 0;
+
for(int l=0;l<alignLength;l++){
// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
- if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
lDiffs++;
}
left[i][l] = lDiffs;
int index = 0;
for(int l=alignLength-1;l>=0;l--){
// if(querySeq[l] != '.' && querySeq[l] != referenceSeqs[i][l]){
- if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l]){
+ if(querySeq[l] != '.' && referenceSeqs[i][l] != '.' && querySeq[l] != referenceSeqs[i][l] && referenceSeqs[i][l] != 'N'){
rDiffs++;
}
right[i][index++] = rDiffs;
}
+
if(lDiffs < bestSequenceMismatch){
bestSequenceMismatch = lDiffs;
bestRefSeq = i;
for(int i=0;i<alignLength;i++){
// if(querySeq[i] != '.' && chimeraRefSeq[i] != '.'){
- if(chimeraRefSeq[i] != '.'){
- if(querySeq[i] == '-' && chimeraRefSeq[i] == '-'){ /* do nothing */ }
+ if(chimeraRefSeq[i] != '.' && querySeq[i] != '.'){
+ if(querySeq[i] == '-' && chimeraRefSeq[i] == '-' && chimeraRefSeq[i] != 'N'){ /* do nothing */ }
else if(querySeq[i] == chimeraRefSeq[i]){
match++;
}