paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / refchimeratest.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 28e6728907470c85b97538b097180e0db71170dc..2f397e8f71ec0b8a1d47338b1f12cfc552642ed2 100644 (file)
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -14,11 +14,10 @@ int MAXINT = numeric_limits<int>::max();
 
 //***************************************************************************************************************
 
-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);
@@ -30,14 +29,22 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, string chimeraReportFileN
        
        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;