changing command name classify.shared to classifyrf.shared

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 8099a3998c1a63de92d9c72b2c5419c08e2f96ff..ca3439d809f96f6eff93dcf3948abd1a8274a7f5 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -12,16 +12,14 @@
  /* 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 "listvector.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "fastamap.h"
 #include "groupmap.h"
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
+#include "counttable.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -39,26 +37,37 @@ 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 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;
        ListVector* list;
-       ReadOTUFile* read;
-       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;
+    CountTable ct;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups, method;
        ofstream out;
        ifstream in, inNames, inRow;
-       bool abort, allLines, groupError, large;
+       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<string, string> nameFileMap;
        vector<string> outputNames, Groups;
        map<string, string> outputNameFiles;
        float cutoff;
@@ -67,13 +76,15 @@ private:
                                                                        // for all distances related to a certain sequence
        vector<int> rowPositions;
 
-       void readNamesFile();
+       void readNamesFile(FastaMap*&);
+       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
+       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