Working on seq.error changes

[mothur.git] / refchimeratest.cpp

diff --git a/refchimeratest.cpp b/refchimeratest.cpp
index 2f397e8f71ec0b8a1d47338b1f12cfc552642ed2..ab55ca454bde78e547330f081a1d8781a52d9753 100644 (file)
--- a/refchimeratest.cpp
+++ b/refchimeratest.cpp
@@ -14,7 +14,7 @@ int MAXINT = numeric_limits<int>::max();
 
 //***************************************************************************************************************
 
-RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
+RefChimeraTest::RefChimeraTest(vector<Sequence>& refs, bool aligned) : aligned(aligned){
 
        m = MothurOut::getInstance();
 
@@ -29,7 +29,6 @@ RefChimeraTest::RefChimeraTest(vector<Sequence>& refs){
        
        alignLength = referenceSeqs[0].length();
 
-
 }
 //***************************************************************************************************************
 
@@ -61,28 +60,12 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq, ofstream& ch
        int leftParentBi, rightParentBi, breakPointBi;
        int minMismatchToChimera = getChimera(left, right, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight);
        
-//     int minMismatchToTrimera = MAXINT;
-//     int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
-       
        int nMera = 0;
        string chimeraRefSeq = "";
        
        if(bestSequenceMismatch - minMismatchToChimera >= 3){// || (minMismatchToChimera == 0 && bestSequenceMismatch != 0)){
-       
                nMera = 2;
                chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
-               
-//             minMismatchToTrimera = getTrimera(left, right, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight);
-//
-//             if(minMismatchToChimera - minMismatchToTrimera <= 3){
-//                     nMera = 2;
-//                     chimeraRefSeq = stitchBimera(leftParentBi, rightParentBi, breakPointBi);
-//             }
-//             else{                   
-//                     nMera = 3;
-//                     chimeraRefSeq = stitchTrimera(leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB);
-//             }
-               
        }
        else{
                nMera = 1;
@@ -92,20 +75,10 @@ int RefChimeraTest::analyzeQuery(string queryName, string querySeq, ofstream& ch
        
        double distToChimera = calcDistToChimera(querySeq, chimeraRefSeq);
        
-//     double loonIndex = calcLoonIndex(querySeq, referenceSeqs[leftParentBi], referenceSeqs[rightParentBi], breakPointBi, binMatrix);         
-       
        chimeraReportFile << queryName << '\t' << referenceNames[bestMatch] << '\t' << bestSequenceMismatch << '\t';
        chimeraReportFile << referenceNames[leftParentBi] << ',' << referenceNames[rightParentBi] << '\t' << breakPointBi << '\t';
        chimeraReportFile << minMismatchToChimera << '\t';
-       
-//     if(nMera == 1){
-//             chimeraReportFile << "NA" << '\t' << "NA" << '\t' << "NA";
-//     }
-//     else{
-//             chimeraReportFile << referenceNames[leftParentTri] << ',' << referenceNames[middleParentTri] << ',' << referenceNames[rightParentTri] << '\t' << breakPointTriA << ',' << breakPointTriB << '\t' << minMismatchToTrimera;       
-//     }
-       
-       chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
+    chimeraReportFile << '\t' << distToChimera << '\t' << nMera << endl;
                
        return nMera;
 }
@@ -121,8 +94,6 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
                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] && referenceSeqs[i][l] != 'N'){
                                lDiffs++;
                        }
@@ -132,7 +103,6 @@ int RefChimeraTest::getMismatches(string& querySeq, vector<vector<int> >& left,
                int rDiffs = 0;
                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] && referenceSeqs[i][l] != 'N'){
                                rDiffs++;
                        }