added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / summaryqualcommand.h

diff --git a/summaryqualcommand.h b/summaryqualcommand.h
index 31390b4296ff7659fdfb2946d3f37ff33b2877b7..ac65938bc23075fc7db7cb40b9ce6d05d0d5d64e 100644 (file)
--- a/summaryqualcommand.h
+++ b/summaryqualcommand.h
@@ -35,7 +35,7 @@ public:
        
 private:
        bool abort;
-       string qualfile, outputDir, namefile;
+       string qualfile, outputDir, namefile, countfile;
        vector<string> outputNames;
        map<string, int> nameMap;
        int processors;
@@ -62,20 +62,21 @@ 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;
        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;
        }
@@ -109,7 +110,7 @@ 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());