changed random forest output filename

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
index fda603c1fd46323a3af168cd7ba32777a1fbf5a9..f67c36584a58a14556032ce2374bda17925c6aaa 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -25,8 +25,12 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "get.groups";                          }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
+       string getDescription()         { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -34,7 +38,10 @@ public:
        
 private:
        set<string> names;
-       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
+                                                                                  //then the other files need to change the unique name in their file to match.
+                                                                                  //only add the names that need to be changed to keep the map search quick
+       string accnosfile, countfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;
        GroupMap* groupMap;
@@ -42,10 +49,12 @@ private:
        int readFasta();
        int readName();
        int readGroup();
-       void readAccnos();
+    int readCount();
        int readList();
        int readTax();
        int fillNames();
+       int readShared();
+    int readDesign();
        
 };