fixes while testing 1.33.0

[mothur.git] / summaryqualcommand.h

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index bbd103c1d14f7b40badd9654152aec0fd2b47a10..b9edc5148ca5f7a834433815204b40f9ea317db4 100644 (file)
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -25,7 +25,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "summary.qual";                        }
        string getCommandCategory()             { return "Sequence Processing";         }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
        string getDescription()         { return "summarize the quality of a set of sequences"; }
        
@@ -34,7 +36,7 @@ public:
        
 private:
        bool abort;
-       string qualfile, outputDir, namefile;
+       string qualfile, outputDir, namefile, countfile;
        vector<string> outputNames;
        map<string, int> nameMap;
        int processors;
@@ -61,20 +63,21 @@ struct seqSumQualData {
        vector<int> position;
        vector<int> averageQ;
        vector< vector<int> > scores; 
-       string filename, namefile; 
+       string filename; 
        unsigned long long start;
        unsigned long long end;
-       int count;
+       int count, numSeqs;
        MothurOut* m;
+    bool hasNameMap;
        map<string, int> nameMap;
        
        ~seqSumQualData(){}
-       seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+       seqSumQualData(string f, MothurOut* mout, unsigned long long st, unsigned long long en, bool n, map<string, int> nam) {
                filename = f;
                m = mout;
                start = st;
                end = en;
-               namefile = n;
+               hasNameMap = n;
                nameMap = nam;
                count = 0;
        }
@@ -98,7 +101,8 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
                        in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
                }
                
-               int count = 0;
+               pDataArray->count = 0;
+        pDataArray->numSeqs = 0;
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
                                
                        if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
@@ -108,7 +112,7 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
                        if (current.getName() != "") {
                        
                                int num = 1;
-                               if (pDataArray->namefile != "") {
+                               if (pDataArray->hasNameMap) {
                                        //make sure this sequence is in the namefile, else error 
                                        map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
                                        
@@ -135,11 +139,11 @@ static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
                                        else { pDataArray->scores.at(i)[thisScores[i]] += num; }  
                                }
                                
-                               count += num;
+                               pDataArray->numSeqs += num;
+                pDataArray->count++;
                        }
                }
                
-               pDataArray->count = count;
                in.close();
                
                return 0;