added checks for ^C to quit command instead of program

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 8c00aecf720433bec4610968bc1c227bc93d5a03..ef62b5357981272c93cd2c9869c5b507f0c1daaa 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -88,10 +88,10 @@ class Chimera {
 
        public:
        
-               Chimera(){};
-               Chimera(string);
-               Chimera(string, bool, string);
-               Chimera(string, string);
+               Chimera(){ m = MothurOut::getInstance(); }
+               Chimera(string) { m = MothurOut::getInstance(); }
+               Chimera(string, bool, string) { m = MothurOut::getInstance(); }
+               Chimera(string, string) { m = MothurOut::getInstance(); }
                virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
                virtual void setFilter(bool f)                  {       filter = f;                     }
                virtual void setCorrection(bool c)              {       correction = c;         }
@@ -117,7 +117,7 @@ class Chimera {
                
                virtual void setCons(string){};
                virtual void setQuantiles(string){};
-               virtual void doPrep(){};
+               virtual int doPrep(){ return 0; }
                virtual vector<Sequence*> readSeqs(string);
                virtual vector< vector<float> > readQuantiles();
                virtual void setMask(string);
@@ -127,7 +127,7 @@ class Chimera {
                virtual void printHeader(ostream&){};
                virtual int getChimeras(Sequence*){ return 0; }
                virtual int getChimeras(){ return 0; }
-               virtual void print(ostream&, ostream&){};       
+               virtual int print(ostream&, ostream&){ return 0; }
                
                
        protected:
@@ -138,6 +138,7 @@ class Chimera {
                float divR;
                string seqMask, quanfile, filterString, name, outputDir, templateFileName;
                Sequence* getSequence(string);  //find sequence from name       
+               MothurOut* m;
 };
 
 /***********************************************************************/