working on chimeras

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 26154b2403176e14691fd86248a9edc4ac03a085..ed52c3aa0d010c70bd99bb045ac3715a5d8cb94e 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -24,10 +24,10 @@
 class Pintail : public Chimera {
        
        public:
-               Pintail(string, string, string);        
+               Pintail(string, string);        
                ~Pintail();
                
-               int getChimeras();
+               int getChimeras(Sequence*);
                void print(ostream&);
                
                void setCons(string c)          { consfile = c;  }
@@ -39,44 +39,39 @@ class Pintail : public Chimera {
                Dist* distcalculator;
                DeCalculator* decalc;
                int iters;
-               string fastafile, templateFile, consfile;
+               string fastafile, consfile;
                
-               
-               vector<linePair*> lines;
                vector<linePair*> templateLines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
-               
-               vector<Sequence*> bestfit;  //bestfit[0] matches queryseqs[0]...
+               Sequence*querySeq;
+                               
+               Sequence* bestfit;  //closest match to query in template
                
-               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> > windowsForeachQuery;  // windowsForeachQuery[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
+               vector<float>  obsDistance;  //obsDistance is the vector of observed distances for query 
+               vector<float>  expectedDistance;  //expectedDistance is the vector of expected distances for query
+               float deviation;  //deviation is the percentage of mismatched pairs over the whole seq between query and its best match.
+               vector<int>  windowsForeachQuery;  // windowsForeachQuery is a vector containing the starting spot in query aligned sequence for each window.
                                                                                //this is needed so you can move by bases and not just spots in the alignment
                                                                                
-               vector<int> windowSizes;                        //windowSizes[0] = window size of querySeqs[0]
+               int windowSizes;                        //windowSizes = window size of query
                vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
                
-               vector< map<int, int> > trimmed;    //trimmed[0] = start and stop of trimmed sequences for querySeqs[0]
+               map<int, int> trimmed;    //trimmed = start and stop of trimmed sequences for query
                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>  Qav;     //Qav is the vector of average variablility for query
+               float  seqCoef;         //seqCoef is the coeff for query
+               float DE;                       //DE is the deviaation for query
                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< vector<quanMember> > quantilesMembers;  //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;
+               set<int>  h;
                
                
                vector<float> readFreq();
-               vector<Sequence*> findPairs(int, int);
+               Sequence* findPairs(Sequence*);
                        
-               void createProcessesSpots();
-               void createProcessesPairs();
-               void createProcesses();
                void createProcessesQuan();
+               void doPrep();
                
 };