moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
deleted file mode 100644 (file)
index 92c3998..0000000
--- a/pintail.h
+++ /dev/null
@@ -1,86 +0,0 @@
-#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
-