added parse.list command

[mothur.git] / chimeraslayer.h

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 5343ec2a58c8a043ae23ac7a58dbeae56744c1b6..14a22beed74f0d0fe6dbea9e5d255117d3187008 100644 (file)
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,32 +23,29 @@
 class ChimeraSlayer : public Chimera {
        
        public:
-               ChimeraSlayer(string, string);  
+               ChimeraSlayer(string, bool, string);    
                ~ChimeraSlayer();
                
-               int getChimeras();
-               void print(ostream&);
-               
-               void setCons(string){};
-               void setQuantiles(string q) {};
-               
+               int getChimeras(Sequence*);
+               void print(ostream&, ostream&);
+               void printHeader(ostream&);
+               void doPrep();
                
        private:
+               Sequence* querySeq;
                DeCalculator* decalc;
                Maligner* maligner;
                Slayer* slayer;
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-               vector< map<int, int> > spotMap;
+               map<int, int>  spotMap;
+               Database* databaseRight;
+               Database* databaseLeft;
                
-               vector< vector<data_struct> > chimeraResults;
-               vector<string> chimeraFlags;
-                               
-               string fastafile, templateFile;
+               vector<data_struct>  chimeraResults;
+               string chimeraFlags, searchMethod, fastafile;
+               bool realign;
+       
+               void printBlock(data_struct, ostream&);
                
-               Sequence* getSequence(string);  //find sequence from name
-               void printBlock(data_struct, ostream&, int i);
 };
 
 /************************************************************************/