fixed bug with aligner in database class, worked on chimeras

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 8c0dce4d4b802910cfad2f398871a9ba497bbe83..8afc75469ef4ad8405f2ff54db8293d1cf010e6d 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -12,6 +12,7 @@
 
 #include "chimera.h"
 #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 
@@ -42,9 +43,11 @@ class Pintail : public Chimera {
                };
 
                Dist* distcalculator;
+               DeCalculator* decalc;
                int iters;
                string fastafile, templateFile, consfile, quanfile;
                
+               
                vector<linePair*> lines;
                vector<linePair*> templateLines;
                vector<Sequence*> querySeqs;
@@ -69,22 +72,13 @@ class Pintail : public Chimera {
                vector<float> DE;                                       //DE[0] is the deviaation for queryseqs[0]...
                vector<float> probabilityProfile;
                vector< vector<float> > quantiles;  //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
+               vector< set<int> > h;
+               
                
-               void trimSeqs(Sequence*, Sequence, map<int, int>&);
                vector<float> readFreq();
                vector< vector<float> > readQuantiles();
-               vector< vector<float> > getQuantiles(int, int);
-               vector<float> calcFreq(vector<Sequence*>);
-               
                vector<Sequence> findPairs(int, int);
-               vector<int> findWindows(Sequence*, int, int, int&);
-               vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
-               vector<float>  calcExpected(vector<float>, float);
-               vector<float>  findQav(vector<int>, int);  
-               float calcDE(vector<float>, vector<float>);
-               float calcDist(Sequence*, Sequence, int, int);
-               float getCoef(vector<float>, vector<float>);
-       
+                       
                void createProcessesSpots();
                void createProcesses();
                void createProcessesQuan();