fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index c590ec640dbbfec2f9cbc886041aadfe614fd719..a4ffea9c529829da3c3f08cfbc41c5e3bdf5ddcf 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -19,17 +19,20 @@ class RemoveLineageCommand : public Command {
                RemoveLineageCommand(string);
                RemoveLineageCommand();
                ~RemoveLineageCommand(){};
-               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 "remove.lineage";                      }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
+               string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                set<string> names;
-               vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
+               vector<string> outputNames, listOfTaxons;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
@@ -39,7 +42,7 @@ class RemoveLineageCommand : public Command {
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
+               vector< map<string, float> > getTaxons(string);
 };
 
 #endif