added modify names parameter to set.dir

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index c60b1302f9802af48e3d34f847ab67e8d425cf52..456b735df524ff3eed9c2688be95f8537c0d0c86 100644 (file)
--- a/ccode.h
+++ b/ccode.h
@@ -24,17 +24,20 @@
 class Ccode : public Chimera {
        
        public:
-               Ccode(string, string);  
+               Ccode(string, string, bool, string, int, int, string);  //fasta, template, filter, mask, window, numWanted, outputDir
                ~Ccode();
                
                int getChimeras(Sequence* query);
-               void print(ostream&);
-               void printHeader(ostream&);             
+               Sequence print(ostream&, ostream&);
+               
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
        private:
        
                Dist* distCalc;
                DeCalculator* decalc;
-               int iters;
+               int iters, window, numWanted;
                string fastafile, mapInfo;
                
                Sequence* querySeq;
@@ -75,6 +78,12 @@ class Ccode : public Chimera {
                int getDiff(string, string);  //return number of mismatched bases, a gap to base is not counted as a mismatch
                float getT(int); 
                float getF(int); 
+               
+               #ifdef USE_MPI
+               int printMapping(string&);
+               MPI_File outMap;
+               #endif
+
 };
 
 /***********************************************************/