added name option to read.tree for use in unifrac and parimony commands

[mothur.git] / ccode.h

diff --git a/ccode.h b/ccode.h
index 2888aea3b7cc8bf2e063c078b7abbaae43f1d62c..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;