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

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 58e1656e6b995ae97d879863c0f2becc092ef9d1..3ce4cce4b40cbe331b260f08552fa34bad010d3d 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,7 +15,7 @@
 #include "maligner.h"
 #include "slayer.h"
 
-/***********************************************************************/
+//***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
 
@@ -23,7 +23,7 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, bool, string);    
+               ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
@@ -31,6 +31,10 @@ class ChimeraSlayer : public Chimera {
                void printHeader(ostream&);
                int doPrep();
                
+               #ifdef USE_MPI
+               int print(MPI_File&, MPI_File&);
+               #endif
+               
        private:
                Sequence* querySeq;
                DeCalculator* decalc;
@@ -43,8 +47,11 @@ class ChimeraSlayer : public Chimera {
                vector<data_struct>  chimeraResults;
                string chimeraFlags, searchMethod, fastafile;
                bool realign;
+               int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+               float divR;
        
                void printBlock(data_struct, ostream&);
+               string getBlock(data_struct);
                
 };