added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / chimeracheckrdp.h

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index f54faab045bf65f0c71797dd64ce5e25c045d0ca..f17c7b16d9124074548c391300a0e7d99d2c07b8 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*);
                int print(ostream&, ostream&);
-               int doPrep();
                
-       private:
+               #ifdef USE_MPI
+               int 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>);