changes while testing

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index 1df4d6b2122d88318193a74d906e601e9cd214a1..e187bfc60d8d504d80561d4347f9a838f1ddabee 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -146,7 +146,7 @@ class Chimera {
 
        public:
        
-               Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  }
+               Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false;  byGroup = false; }
                virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i];  } };
                virtual bool getUnaligned()                             {       return unaligned;                       }
                virtual int getLength()                                 {   return length;      }
@@ -165,7 +165,7 @@ class Chimera {
                
                #ifdef USE_MPI
                virtual Sequence print(MPI_File&, MPI_File&){  Sequence temp; return temp; }
-               virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results){  Sequence temp; return temp; }
+               virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&){  Sequence temp; return temp; }
                virtual int print(MPI_File&, MPI_File&, string){  return 0; }
                #endif
                
@@ -174,7 +174,7 @@ class Chimera {
                
                vector<Sequence*> templateSeqs;
                vector<Sequence*> filteredTemplateSeqs;
-               bool filter, unaligned; 
+               bool filter, unaligned, byGroup; 
                int length; 
                string seqMask, filterString, outputDir, templateFileName; 
                Sequence* getSequence(string);  //find sequence from name