added pearson coefficient metric to pcoa

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 3ce4cce4b40cbe331b260f08552fa34bad010d3d..fbe880fde4ed0723dff1e3ec8e982942360e993a 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -15,6 +15,8 @@
 #include "maligner.h"
 #include "slayer.h"
 
+
+
 //***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
@@ -24,6 +26,8 @@ class ChimeraSlayer : public Chimera {
        
        public:
                ChimeraSlayer(string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+               ChimeraSlayer(string, string, string, string, string, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
@@ -38,20 +42,21 @@ class ChimeraSlayer : public Chimera {
        private:
                Sequence* querySeq;
                DeCalculator* decalc;
-               Maligner* maligner;
-               Slayer* slayer;
                map<int, int>  spotMap;
                Database* databaseRight;
                Database* databaseLeft;
+               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;
-               string chimeraFlags, searchMethod, fastafile;
+               string chimeraFlags, searchMethod, fastafile, includeAbunds;
                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);
+               void printBlock(data_struct, string, ostream&);
+               string getBlock(data_struct, string);
+               int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence*);
                
 };