changed sequence class so that when constructor is called aligned and unaligned value...

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 797c99e1543ace2df4a142015a17fe56eaf4f033..289af65b68cb2f37ddf3c392cf9c67572dd5560b 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -28,7 +28,8 @@ class Pintail : public Chimera {
                void getChimeras();
                void print(ostream&);
                
-               void setCons(string c) { consfile = c;  }
+               void setCons(string c)          { consfile = c;  }
+               void setQuantiles(string q) { quanfile = q;  }
                
                
        private:
@@ -41,7 +42,8 @@ class Pintail : public Chimera {
 
                Dist* distcalculator;
                int iters;
-               string fastafile, templateFile, consfile;
+               string fastafile, templateFile, consfile, quanfile;
+               
                vector<linePair*> lines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
@@ -53,31 +55,38 @@ class Pintail : public Chimera {
                vector<float> deviation;  //deviation[0] is the percentage of mismatched pairs over the whole seq between querySeqs[0] and its best match.
                vector< vector<int> > windows;  // windows[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
                                                                                //this is needed so you can move by bases and not just spots in the alignment
-               vector< map<int, int> >  trim;  //trim[0] is the start and end position of trimmed querySeqs[0].  Used to find the variability over each sequence window.
                                                                                
                vector<int> windowSizes;    //windowSizes[0] = window size of querySeqs[0]
                
+               vector< map<int, int> > trimmed;    //trimmed[0] = start and stop of trimmed sequences for querySeqs[0]
+               map<int, int>::iterator it;
+               
                vector< vector<float> > Qav;    //Qav[0] is the vector of average variablility for queryseqs[0]... 
                vector<float>  seqCoef;                         //seqCoef[0] is the coeff for queryseqs[0]...
                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<Sequence*> readSeqs(string);
-               void trimSeqs(Sequence*, Sequence&, int);
+               map<int, int> trimSeqs(Sequence*, Sequence, int);
                vector<float> readFreq();
-               vector< vector<float> > findQav(int, int);  
+               vector< vector<float> > readQuantiles();
+               vector< vector<float> > getQuantiles(int, int);
                vector<float> calcFreq(vector<Sequence*>);
-               vector<float> getCoef(int, int);
+               
                
                vector<Sequence> findPairs(int, int);
-               vector< vector<int> > findWindows(int, int);
-               vector< vector<float> > calcObserved(int, int);
-               vector< vector<float> > calcExpected(int, int);
-               vector<float> calcDE(int, int);
-               vector<float> calcDist(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();