pat's differences before v.1.8

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index 6322292c12534fc44838255ed6490da4292bbf46..52592f9c8e19ef4ef80e26b62199e3c9daf489d8 100644 (file)
--- a/ccode.h
+++ b/ccode.h
@@ -14,6 +14,7 @@
 #include "dist.h"
 #include "decalc.h"
 
+/***********************************************************/
 //This class was created using the algorythms described in the 
 // "Evaluating putative chimeric sequences from PCR-amplified products" paper 
 //by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
@@ -23,10 +24,10 @@
 class Ccode : public Chimera {
        
        public:
-               Ccode(string, string);  
+               Ccode(string, string, string);  
                ~Ccode();
                
-               void getChimeras();
+               int getChimeras();
                void print(ostream&);
                
                void setCons(string c)          {}
@@ -42,7 +43,6 @@ class Ccode : public Chimera {
                
                
                vector<linePair*> lines;
-               vector<linePair*> templateLines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
                vector< map<int, int> > spotMap;
@@ -83,7 +83,11 @@ class Ccode : public Chimera {
                float getF(int); 
                
                void createProcessesClosest();
-               
+               void createProcessesRemoveBad();
+               void createProcessesAverages();
+               void createProcessesVariances();
+               void createProcessesDetermine();
+                               
 };
 
 /***********************************************************/