changing command name classify.shared to classifyrf.shared

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index f413d4f51f2a9c45e3a5d17dd0243a825eb71679..ca3439d809f96f6eff93dcf3948abd1a8274a7f5 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,53 +12,79 @@
  /* 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"
+#include "counttable.h"
 
-class GlobalData;
+typedef map<int, float> SeqMap;
 
-typedef list<PCell>::iterator MatData;
+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();
-       int execute();
-       void help();    
+       GetOTURepCommand(string);
+       GetOTURepCommand();
+       ~GetOTURepCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.oturep";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       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, line, label;
+       ReadMatrix* readMatrix;
+       FormatMatrix* formatMatrix;
+       NameAssignment* nameMap;
+    CountTable ct;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;
        ofstream out;
-       ifstream in, inNames;
-       bool groupError;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it4;
-       bool abort, allLines;
-       set<int> lines; //hold lines to be used
+       ifstream in, inNames, inRow;
+       bool abort, allLines, groupError, large, weighted, hasGroups;
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
-       map<int, string>::iterator it;
-       map<int, string>::iterator it2;
-       map<string, int>::iterator it3;
-       
-       void readNamesFile();
-       int process(ListVector*);
-       string FindRep(int, string&, ListVector*); // returns name of "representative" sequence of given bin. //and fill a string containing the groups in that bin if a groupfile is given
+       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(FastaMap*&);
+       void readNamesFile(bool);
+       int process(ListVector*);
+       SeqMap getMap(int);
+       string findRep(vector<string>, string);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+    string findRepAbund(vector<string>, string);
+       int processNames(string, string);
+       int processFastaNames(string, string, FastaMap*&);
+    int readDist();
 };
 
 #endif