changing command name classify.shared to classifyrf.shared

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d8f8f0905ba3c3e8c09dfb8ec83ec34f817db89e..ca3439d809f96f6eff93dcf3948abd1a8274a7f5 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,8 +18,8 @@
 #include "groupmap.h"
 #include "readmatrix.hpp"
 #include "formatmatrix.h"
+#include "counttable.h"
 
-typedef list<PCell>::iterator MatData;
 typedef map<int, float> SeqMap;
 
 struct repStruct {
@@ -43,7 +43,12 @@ public:
        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()); }  
@@ -51,16 +56,15 @@ public:
        
 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;
+    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, weighted;
+       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;
@@ -72,12 +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