added modify names parameter to set.dir

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index 0ba851a9d6906b48a44b66d311882e0a88c8c400..cc23c2e9e8b0b794339a0dfa8fa91bae50f28c00 100644 (file)
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -25,15 +25,17 @@
 class ChimeraCheckRDP : public Chimera {
        
        public:
-               ChimeraCheckRDP(string, string);        
+               ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir      
                ~ChimeraCheckRDP();
                
                int getChimeras(Sequence*);
-               void print(ostream&, ostream&);
-               void doPrep();
+               Sequence print(ostream&, ostream&);
                
-       private:
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
                
+       private:
                
                Sequence* querySeq;
                AlignmentDB* templateDB;
@@ -43,6 +45,9 @@ class ChimeraCheckRDP : public Chimera {
                vector<sim>  IS;  //IS is the vector of IS values for each window for query
                string fastafile;
                map<string, string> names;
+               string name;
+               bool svg;
+               int kmerSize, increment;
                
                vector<sim> findIS();
                int calcKmers(map<int, int>, map<int, int>);