added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index afc77cce5d9c003bc94ad16f970819a8f5c4680e..91ef84517053c22129c0257daddf11dbcf50d041 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);
                int print(ostream&, ostream&);
-               void printHeader(ostream&);             
+               
+               #ifdef USE_MPI
+               int 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
+
 };
 
 /***********************************************************/