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

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
deleted file mode 100644 (file)
index 4168000..0000000
--- a/getoturepcommand.h
+++ /dev/null
@@ -1,88 +0,0 @@
-#ifndef GETOTUREPCOMMAND_H
-#define GETOTUREPCOMMAND_H
-/*
- *  getoturepcommand.h
- *  Mothur
- *
- *  Created by Sarah Westcott on 4/6/09.
- *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
- 
- /* The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin. */
-
-#include "command.hpp"
-#include "listvector.hpp"
-#include "inputdata.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 {
-               string name;
-               int     bin;
-               int size;
-               string group;
-               
-               repStruct(){}
-               repStruct(string n, int b, int s, string g) : name(n), bin(b), size(s), group(g) {}
-               ~repStruct() {}
-};
-
-class GetOTURepCommand : public Command {
-
-public:
-       GetOTURepCommand(string);
-       GetOTURepCommand();
-       ~GetOTURepCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "get.oturep";                          }
-       string getCommandCategory()             { return "OTU-Based Approaches";        }
-       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:
-       ListVector* list;
-       InputData* input;
-       FastaMap* fasta;
-       GroupMap* groupMap;
-       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, 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*);
-       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
-