added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index 59d4feeec7fa3743a059b331db524b0df3fe48cf..7164842106d7b61d36883b351167163aeb4e878a 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -24,7 +24,7 @@
 class Pintail : public Chimera {
        
        public:
-               Pintail(string, string);        
+               Pintail(string, string, bool, int, string, string, string, int, int, string); //fastafile, templatefile, filter, processors, mask, conservation, quantile, window, increment, outputDir)        
                ~Pintail();
                
                int getChimeras(Sequence*);
@@ -33,13 +33,16 @@ class Pintail : public Chimera {
                void setCons(string c)          { consfile = c;  }
                void setQuantiles(string q) { quanfile = q;  }
                
+               #ifdef USE_MPI
+               int print(MPI_File&, MPI_File&);
+               #endif
                
        private:
        
                Dist* distcalculator;
                DeCalculator* decalc;
-               int iters;
-               string fastafile, consfile;
+               int iters, window, increment, processors;
+               string fastafile, quanfile, consfile;
                
                vector<linePair*> templateLines;
                Sequence* querySeq;
@@ -52,7 +55,7 @@ class Pintail : public Chimera {
                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
                                                                                
-               int windowSizes;                        //windowSizes = window size of query
+               int  windowSizes;                       //windowSizes = window size of query
                vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
                
                map<int, int> trimmed;    //trimmed = start and stop of trimmed sequences for query
@@ -67,12 +70,13 @@ class Pintail : public Chimera {
                set<int>  h;
                string mergedFilterString;
                
-               
+               vector< vector<float> > readQuantiles();
                vector<float> readFreq();
                Sequence* findPairs(Sequence*);
                        
                void createProcessesQuan();
                int doPrep();
+               void printQuanFile(string, string);
                
 };