added template=self capability to chimers.slayer, worked on corr.axes and added accno...

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 6d57474829e51f44a9eca05021c937ba537cb610..b6cae49f0709922ac9067ef1d39effab77d3d5be 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, int, int, int, int, float, int, int, int, int, int, int, int, int, bool);
+
                ~ChimeraSlayer();
                
                int getChimeras(Sequence*);
@@ -41,6 +45,7 @@ class ChimeraSlayer : public Chimera {
                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;
@@ -50,6 +55,8 @@ class ChimeraSlayer : public Chimera {
        
                void printBlock(data_struct, string, ostream&);
                string getBlock(data_struct, string);
+               int readNameFile(string);
+               vector<Sequence*> getTemplate(Sequence*);
                
 };