optimizing classify.seqs calculating of template probabilities.

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d92df1a4045adbabd768210a628353d9b61383b3..d19a396410f2e2c9850f9b20a93d65c03000bac2 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,15 +12,13 @@
  /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
+#include "readmatrix.hpp"
+#include "formatmatrix.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -38,37 +36,52 @@ class GetOTURepCommand : public Command {
 
 public:
        GetOTURepCommand(string);
-       ~GetOTURepCommand();
-       int execute();
-       void help();
+       GetOTURepCommand();
+       ~GetOTURepCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.oturep";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.oturep"; }
+       string getDescription()         { return "gets a representative sequence for each OTU"; }
 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
 private:
-       GlobalData* globaldata;
-       SparseMatrix* matrix;
        ListVector* list;
-       ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, listfile, namesfile, groupfile, label, sorted;
+       ReadMatrix* readMatrix;
+       FormatMatrix* formatMatrix;
+       NameAssignment* nameMap;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
        ofstream out;
-       ifstream in, inNames;
-       bool groupError;
-
-       bool abort, allLines;
+       ifstream in, inNames, inRow;
+       bool abort, allLines, groupError, large, weighted;
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
-
+       map<string, string> nameFileMap;
+       vector<string> outputNames, Groups;
+       map<string, string> outputNameFiles;
+       float cutoff;
+       int precision;
        vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
                                                                        // for all distances related to a certain sequence
-
+       vector<int> rowPositions;
 
        void readNamesFile();
+       void readNamesFile(bool);
        int process(ListVector*);
-       string findRep(int, string&, ListVector*, int&);        // returns the name of the "representative" sequence of given bin, 
-                                                                       // fills a string containing the groups in that bin if a groupfile is given,
-                                                                       // and returns the number of sequences in the given bin
-
+       SeqMap getMap(int);
+       string findRep(vector<string>);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+       int processNames(string, string);
+       int processFastaNames(string, string);
 };
 
 #endif