added parameter to chimera.uchime

[mothur.git] / chimera.h

diff --git a/chimera.h b/chimera.h
index e37d9f9af93cdbc808a6eb7bc7fe7f1ebe4df20a..3f4eb4ef9f430ed9191f7de78e41df3427c4bec4 100644 (file)
--- a/chimera.h
+++ b/chimera.h
@@ -45,10 +45,10 @@ struct data_struct {
 struct data_results {
        vector<data_struct> results;
        string flag;
-       map<int, int> spotMap;
        Sequence trimQuery;
+       //results malignerResults;
        
-       data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), spotMap(s), trimQuery(t) {}
+       data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
        data_results() {}
 };
 /***********************************************************************/
@@ -77,6 +77,7 @@ struct score_struct {
        int score;
        int row;
        int col;
+//     int mismatches;
 };
 /***********************************************************************/
 struct trace_struct {
@@ -135,8 +136,8 @@ class Chimera {
 
        public:
        
-               Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
-               virtual ~Chimera(){     for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  } };
+               Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = 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;      }
                virtual vector<Sequence*> readSeqs(string);
@@ -153,6 +154,7 @@ class Chimera {
                
                #ifdef USE_MPI
                virtual Sequence* print(MPI_File&, MPI_File&){  return 0; }
+               virtual Sequence* print(MPI_File&, MPI_File&, data_results, data_results){  return NULL; }
                virtual int print(MPI_File&, MPI_File&, string){  return 0; }
                #endif
                
@@ -160,6 +162,7 @@ class Chimera {
        protected:
                
                vector<Sequence*> templateSeqs;
+               vector<Sequence*> filteredTemplateSeqs;
                bool filter, unaligned; 
                int length; 
                string seqMask, filterString, outputDir, templateFileName;