fixed indicator command bug

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index f8006c41382919b311e8fd8b590f31e9b8bfaad1..e4615ee8787d481dfad122bd8120ae35e130cdb6 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
 /***********************************************************************/
 
@@ -23,12 +23,17 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, bool);    
+               ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
-               void print(ostream&);
+               int print(ostream&, ostream&);
                void printHeader(ostream&);
+               int doPrep();
+               
+               #ifdef USE_MPI
+               int print(MPI_File&, MPI_File&);
+               #endif
                
        private:
                Sequence* querySeq;
@@ -36,13 +41,18 @@ class ChimeraSlayer : public Chimera {
                Maligner* maligner;
                Slayer* slayer;
                map<int, int>  spotMap;
+               Database* databaseRight;
+               Database* databaseLeft;
                
                vector<data_struct>  chimeraResults;
-               string chimeraFlags, searchMethod;
-               string fastafile;
+               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&);
+               void printBlock(data_struct, string, ostream&);
+               string getBlock(data_struct, string);
+               
 };
 
 /************************************************************************/