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[mothur.git] / getoturepcommand.h

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+#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
+