some alterations to chimera.slayer

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index eaaaa8789961d4938a1aba793fb32e7ac331a105..b3cb991299fbf29d595318e613f8654cc7f3426f 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -88,7 +88,8 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
 
                vector<Sequence*> temp = refSeqs;
                temp.push_back(query);
-               
+                       
+                       
                verticalFilter(temp);
 
                vector< vector<score_struct> > matrix = buildScoreMatrix(query->getAligned().length(), refSeqs.size()); //builds and initializes
@@ -204,7 +205,7 @@ int Maligner::computeChimeraPenalty() {
                
                int numAllowable = ((1.0 - (1.0/minDivR)) * query->getNumBases());
 
-//             if(numAllowable < 2){   numAllowable = 2;       }
+//             if(numAllowable < 1){   numAllowable = 1;       }
                
                int penalty = int(numAllowable + 1) * misMatchPenalty;
 
@@ -314,7 +315,7 @@ void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequenc
                        if ((!isalpha(queryAligned[0])) && (!isalpha(subjectAligned[0]))) {
                                ms[i][0].score = 0;
 //                             ms[i][0].mismatches = 0;
-                       }else if (queryAligned[0] == subjectAligned[0]) {
+                       }else if (queryAligned[0] == subjectAligned[0] || subjectAligned[0] == 'N') {
                                ms[i][0].score = matchScore;
 //                             ms[i][0].mismatches = 0;
                        }else{
@@ -335,6 +336,7 @@ void Maligner::fillScoreMatrix(vector<vector<score_struct> >& ms, vector<Sequenc
                                if ((!isalpha(queryAligned[j])) && (!isalpha(subjectAligned[j]))) {
                                        //leave the same
                                }else if ((toupper(queryAligned[j]) == 'N') || (toupper(subjectAligned[j]) == 'N')) {
+                                       matchMisMatchScore = matchScore;
                                        //leave the same
                                }else if (queryAligned[j] == subjectAligned[j]) {
                                        matchMisMatchScore = matchScore;
@@ -421,11 +423,10 @@ vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> >
                        }
                }
                        
-//             cout << highestScore << '\t' << highestStruct.size() << endl;   
+//             cout << endl << highestScore << '\t' << highestStruct.size() << '\t' << highestStruct[0].row << endl;   
                
                vector<trace_struct> maxTrace;
                double maxPercentIdenticalQueryAntiChimera = 0;
-               int maxIndex = -1;
                
                for(int i=0;i<highestStruct.size();i++){
                        
@@ -453,11 +454,7 @@ vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> >
 //                     for(int j=0;j<trace.size();j++){
 //                             cout << trace[j].col << '\t' << trace[j].oldCol << '\t' << refSeqs[trace[j].row]->getName() << endl;
 //                     }
-                       
-//                     Need to do something with this in a bit...
-//                     if (trace.size() > 1) {         chimera = "yes";        }
-//                     else { chimera = "no";  }
-                       
+                                               
                        int traceStart = path[0].col;
                        int traceEnd = path[path.size()-1].col; 
 //                     cout << "traceStart/End\t" << traceStart << '\t' << traceEnd << endl;
@@ -475,10 +472,9 @@ vector<trace_struct> Maligner::extractHighestPath(vector<vector<score_struct> >
                        if(percentIdenticalQueryAntiChimera > maxPercentIdenticalQueryAntiChimera){
                                maxPercentIdenticalQueryAntiChimera = percentIdenticalQueryAntiChimera;
                                maxTrace = trace;
-                               maxIndex = i;
                        }
                }
-//             cout << maxPercentIdenticalQueryAntiChimera << '\t' << maxIndex << endl;
+//             cout << maxPercentIdenticalQueryAntiChimera << endl;
                return maxTrace;
                
        }