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[mothur.git] / pintail.h

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+#ifndef PINTAIL_H
+#define PINTAIL_H
+
+/*
+ *  pintail.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/9/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#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 
+//by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
+
+/***********************************************************/
+
+class Pintail : public Chimera {
+       
+       public:
+               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*);
+               Sequence print(ostream&, ostream&);
+               
+               void setCons(string c)          { consfile = c;  }
+               void setQuantiles(string q) { quanfile = q;  }
+               
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
+               
+       private:
+       
+               Dist* distcalculator;
+               DeCalculator* decalc;
+               int iters, window, increment, processors;
+               string fastafile, quanfile, consfile;
+               
+               vector<linePair*> templateLines;
+               Sequence* querySeq;
+                               
+               Sequence* bestfit;  //closest match to query in template
+               
+               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
+                                                                               
+               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
+               map<int, int>::iterator it;
+               
+               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<float> > 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...
+               set<int>  h;
+               string mergedFilterString;
+               
+               vector< vector<float> > readQuantiles();
+               vector<float> readFreq();
+               Sequence* findPairs(Sequence*);
+                       
+               void createProcessesQuan();
+               int doPrep();
+               void printQuanFile(string, string);
+               
+};
+
+/***********************************************************/
+
+#endif
+