X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ccode.h;h=dcd48797da324699218114a5dfd1b64be4ac8dd3;hp=afc77cce5d9c003bc94ad16f970819a8f5c4680e;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3

diff --git a/ccode.h b/ccode.h
index afc77cc..dcd4879 100644
--- a/ccode.h
+++ b/ccode.h
@@ -15,7 +15,7 @@
 #include "decalc.h"
 
 /***********************************************************/
-//This class was created using the algorythms described in the 
+//This class was created using the algorithms described in the 
 // "Evaluating putative chimeric sequences from PCR-amplified products" paper 
 //by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
 
@@ -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&);		
+		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
+
 };
 
 /***********************************************************/