paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 5b7c43ed65808f7038b3c46cb96f3b7a32b8849a..ca84bf2fad3e11e60808daa15230b5674a4a7849 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -18,20 +18,23 @@ class GetLineageCommand : public Command {
        
                GetLineageCommand(string);
                GetLineageCommand();
-               ~GetLineageCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+               ~GetLineageCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.lineage";                         }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
-               vector<string> outputNames;
+               vector<string> outputNames, listOfTaxons;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
-               map<string, vector<string> > outputTypes;
                
                int readFasta();
                int readName();