fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 87439a327e9e83acf1db63375a3f1173e7829b3a..3e76297b038b9eeafab2c04e5428a2091814a07d 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -19,7 +19,6 @@
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
-
 class ChimeraSlayer : public Chimera {
        
        public:
@@ -30,11 +29,14 @@ class ChimeraSlayer : public Chimera {
                
                int getChimeras(Sequence*);
                Sequence* print(ostream&, ostream&);
+               Sequence* print(ostream&, ostream&, data_results, data_results);
                void printHeader(ostream&);
                int doPrep();
+               data_results getResults() { return printResults; }
                
                #ifdef USE_MPI
                Sequence* print(MPI_File&, MPI_File&);
+               Sequence* print(MPI_File&, MPI_File&, data_results, data_results);
                #endif
                
        private:
@@ -47,13 +49,16 @@ class ChimeraSlayer : public Chimera {
                map<string, vector<string> > nameMapRank;  //sequence name to rank so you can construct a template of the abundant sequences if the user uses itself as template
                
                vector<data_struct>  chimeraResults;
+               data_results printResults;
                string chimeraFlags, searchMethod, fastafile, includeAbunds;
                bool realign, trimChimera;
                int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
                float divR;
        
                void printBlock(data_struct, string, ostream&);
+               void printBlock(data_results, data_results, bool, bool, string, ostream&);
                string getBlock(data_struct, string);
+               string getBlock(data_results, data_results, bool, bool, string);
                int readNameFile(string);
                vector<Sequence*> getTemplate(Sequence*);