added code to check path for uchime and catchall executables

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
index 7c4c92fff02ae6f577ca92a736fb7b14711cb302..224f4f07ea1c45d3e734d8f6406e8a17f40fd1fd 100644 (file)
--- a/getgroupscommand.h
+++ b/getgroupscommand.h
@@ -21,19 +21,27 @@ public:
        GetGroupsCommand(string);       
        GetGroupsCommand();
        ~GetGroupsCommand(){}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.groups";                          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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()); }  
+       
        
 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, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
        bool abort;
        vector<string> outputNames, Groups;
-       map<string, vector<string> > outputTypes;
        GroupMap* groupMap;
        
        int readFasta();
@@ -43,6 +51,8 @@ private:
        int readList();
        int readTax();
        int fillNames();
+       int readShared();
+    int readDesign();
        
 };