changing command name classify.shared to classifyrf.shared

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 390632975afc85aac5b714c7194c81e74d58e16e..ca3439d809f96f6eff93dcf3948abd1a8274a7f5 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -43,8 +43,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.oturep";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
-       string getOutputFileNameTag(string, string);
+       
        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"; }
 
@@ -55,14 +56,12 @@ public:
        
 private:
        ListVector* list;
-       InputData* input;
-       FastaMap* fasta;
        GroupMap* groupMap;
        ReadMatrix* readMatrix;
        FormatMatrix* formatMatrix;
        NameAssignment* nameMap;
     CountTable ct;
-       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, countfile, columnfile, distFile, format, outputDir, groups;
+       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, hasGroups;
@@ -77,13 +76,14 @@ 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>, 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);
+       int processFastaNames(string, string, FastaMap*&);
     int readDist();
 };