fixed bugs in venn and aligner

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 7c0f81bca5659a0f3fa56357dd70fe5498570334..797c99e1543ace2df4a142015a17fe56eaf4f033 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -22,12 +22,14 @@
 class Pintail : public Chimera {
        
        public:
-               Pintail(string);        
+               Pintail(string, string);        
                ~Pintail();
                
                void getChimeras();
                void print(ostream&);
                
+               void setCons(string c) { consfile = c;  }
+               
                
        private:
        
@@ -37,41 +39,47 @@ class Pintail : public Chimera {
                        linePair(int i, int j) : start(i), end(j) {}
                };
 
-       
-               Dist* distCalculator;
-               string fastafile;
+               Dist* distcalculator;
                int iters;
+               string fastafile, templateFile, consfile;
                vector<linePair*> lines;
                vector<Sequence*> querySeqs;
                vector<Sequence*> templateSeqs;
                
-               map<Sequence*, Sequence*> bestfit;  //maps a query sequence to its most similiar sequence in the template
-               map<Sequence*, Sequence*>::iterator itBest;
+               vector<Sequence> bestfit;  //bestfit[0] matches queryseqs[0]...
                
-               map<Sequence*, vector<float> > obsDistance;  //maps a query sequence to its observed distance at each window
-               map<Sequence*, vector<float> > expectedDistance;  //maps a query sequence to its expected distance at each window
-               map<Sequence*, vector<float> >::iterator itObsDist;
-               map<Sequence*, vector<float> >::iterator itExpDist;
+               vector< vector<float> > obsDistance;  //obsDistance[0] is the vector of observed distances for queryseqs[0]... 
+               vector< vector<float> > expectedDistance;  //expectedDistance[0] is the vector of expected distances for queryseqs[0]... 
+               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<float> averageProbability;                       //Qav
-               map<Sequence*, float> seqCoef;                          //maps a sequence to its coefficient
-               map<Sequence*, float> DE;                                       //maps a sequence to its deviation
-               map<Sequence*, float>::iterator itCoef; 
+               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<Sequence*> readSeqs(string);
-               vector<float> findQav(vector<float>);
+               void trimSeqs(Sequence*, Sequence&, int);
+               vector<float> readFreq();
+               vector< vector<float> > findQav(int, int);  
                vector<float> calcFreq(vector<Sequence*>);
-               map<Sequence*, float> getCoef(vector<float>);
+               vector<float> getCoef(int, int);
                
-               void findPairs(int, int);
-               void calcObserved(int, int);
-               void calcExpected(int, int);
-               void calcDE(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);
        
-               void createProcessesPairs();
-               void createProcessesObserved();
-               void createProcessesExpected();
-               void createProcessesDE();
+               void createProcessesSpots();
+               void createProcesses();
+               
+               
                
 };