working on chimera.slayer

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 58d637ec9698fa33d7c522c27cbc539595d42e5f..3f4eb4ef9f430ed9191f7de78e41df3427c4bec4 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -45,10 +45,10 @@ struct data_struct {
 struct data_results {
        vector<data_struct> results;
        string flag;
-       map<int, int> spotMap;
        Sequence trimQuery;
+       //results malignerResults;
        
-       data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+       data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
        data_results() {}
 };
 /***********************************************************************/
@@ -137,7 +137,7 @@ class Chimera {
        public:
        
                Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  }
-               virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
+               virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i];  } };
                virtual bool getUnaligned()                             {       return unaligned;                       }
                virtual int getLength()                                 {   return length;      }
                virtual vector<Sequence*> readSeqs(string);
@@ -162,6 +162,7 @@ class Chimera {
        protected:
                
                vector<Sequence*> templateSeqs;
+               vector<Sequence*> filteredTemplateSeqs;
                bool filter, unaligned; 
                int length; 
                string seqMask, filterString, outputDir, templateFileName;