added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index da908ce07571a54148f561e28c16b94e8b09f68b..f893d63ed9c57e7d53d84843cb3b647cc9dd89d6 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -114,6 +114,7 @@ class Chimera {
                virtual void setTemplateSeqs(vector<Sequence*> t)       {       templateSeqs = t;       }
                virtual bool getUnaligned()                             {       return unaligned;                       }
                virtual void setTemplateFile(string t)  {   templateFileName = t;       }
+               virtual int getLength()                                 {   return length;      }
                
                virtual void setCons(string){};
                virtual void setQuantiles(string){};
@@ -127,14 +128,14 @@ class Chimera {
                virtual void printHeader(ostream&){};
                virtual int getChimeras(Sequence*){ return 0; }
                virtual int getChimeras(){ return 0; }
-               virtual void print(ostream&){}; 
+               virtual void print(ostream&, ostream&){};       
                
                
        protected:
                
                vector<Sequence*> templateSeqs;
                bool filter, correction, svg, unaligned;
-               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
+               int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, length;
                float divR;
                string seqMask, quanfile, filterString, name, outputDir, templateFileName;
                Sequence* getSequence(string);  //find sequence from name