fixed bug in windows summary.seqs and summary.qual paralellization. paralellized...

[mothur.git] / summaryqualcommand.h

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index 1ec3cf1891893227d07d256cecd15f742ee9d127..d7aa39a5c60fa927c057cc86660b8062c6a5ab5d 100644 (file)
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -58,9 +58,9 @@ private:
 // This is passed by void pointer so it can be any data type
 // that can be passed using a single void pointer (LPVOID).
 struct seqSumQualData {
-       vector<int>* position;
-       vector<int>* averageQ;
-       vector< vector<int> >* scores; 
+       vector<int> position;
+       vector<int> averageQ;
+       vector< vector<int> > scores; 
        string filename, namefile; 
        unsigned long long start;
        unsigned long long end;
@@ -69,10 +69,7 @@ struct seqSumQualData {
        map<string, int> nameMap;
        
        ~seqSumQualData(){}
-       seqSumQualData(vector<int>* p, vector<int>* a, vector< vector<int> >* s, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
-               position = p;
-               averageQ = a;
-               scores = s;
+       seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
                filename = f;
                m = mout;
                start = st;
@@ -122,20 +119,20 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
                                vector<int> thisScores = current.getQualityScores();
                                
                                //resize to num of positions setting number of seqs with that size to 1
-                               if (pDataArray->position->size() < thisScores.size()) { pDataArray->position->resize(thisScores.size(), 0); }
-                               if (pDataArray->averageQ->size() < thisScores.size()) { pDataArray->averageQ->resize(thisScores.size(), 0); }
-                               if (pDataArray->scores->size() < thisScores.size()) { 
-                                       pDataArray->scores->resize(thisScores.size()); 
-                                       for (int i = 0; i < pDataArray->scores->size(); i++) { pDataArray->scores->at(i).resize(41, 0); }
+                               if (pDataArray->position.size() < thisScores.size()) { pDataArray->position.resize(thisScores.size(), 0); }
+                               if (pDataArray->averageQ.size() < thisScores.size()) { pDataArray->averageQ.resize(thisScores.size(), 0); }
+                               if (pDataArray->scores.size() < thisScores.size()) { 
+                                       pDataArray->scores.resize(thisScores.size()); 
+                                       for (int i = 0; i < pDataArray->scores.size(); i++) { pDataArray->scores.at(i).resize(41, 0); }
                                }
                                
                                //increase counts of number of seqs with this position
                                //average is really the total, we will average in execute
                                for (int i = 0; i < thisScores.size(); i++) { 
-                                       pDataArray->position->at(i) += num; 
-                                       pDataArray->averageQ->at(i) += (thisScores[i] * num); //weighting for namesfile
+                                       pDataArray->position.at(i) += num; 
+                                       pDataArray->averageQ.at(i) += (thisScores[i] * num); //weighting for namesfile
                                        if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
-                                       else { pDataArray->scores->at(i)[thisScores[i]] += num; }  
+                                       else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
                                }
                                
                                count += num;