added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 181be2ca4410c32a4ab0222adbe8e5e2c138e1de..516c682da3d9123cc07f9e6e143dd7fdc7d519c4 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -14,6 +14,7 @@
 #include "dist.h"
 #include "decalc.h"
 
+/***********************************************************/
 //This class was created using the algorythms described in the 
 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper 
 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
@@ -26,7 +27,7 @@ class Pintail : public Chimera {
                Pintail(string, string);        
                ~Pintail();
                
-               void getChimeras();
+               int getChimeras();
                void print(ostream&);
                
                void setCons(string c)          { consfile = c;  }
@@ -35,17 +36,10 @@ class Pintail : public Chimera {
                
        private:
        
-               struct linePair {
-                       int start;
-                       int end;
-                       linePair(int i, int j) : start(i), end(j) {}
-                       linePair(){}
-               };
-
                Dist* distcalculator;
                DeCalculator* decalc;
                int iters;
-               string fastafile, templateFile, consfile, quanfile;
+               string fastafile, templateFile, consfile;
                
                
                vector<linePair*> lines;
@@ -77,7 +71,6 @@ class Pintail : public Chimera {
                
                
                vector<float> readFreq();
-               vector< vector<float> > readQuantiles();
                vector<Sequence*> findPairs(int, int);
                        
                void createProcessesSpots();
@@ -85,8 +78,6 @@ class Pintail : public Chimera {
                void createProcesses();
                void createProcessesQuan();
                
-               vector<float> makeCompliant;  //used by decalc->getQuantiles so pintail and mallard can use same function, it contains the highest de value for each seq in the template
-               
 };
 
 /***********************************************************/