added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 9fdca48db66da3e0ddf5c603949c7380e61155b0..a4ffea9c529829da3c3f08cfbc41c5e3bdf5ddcf 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -24,13 +24,15 @@ class RemoveLineageCommand : public Command {
                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;
+               vector<string> outputNames, listOfTaxons;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
@@ -40,7 +42,6 @@ class RemoveLineageCommand : public Command {
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
                vector< map<string, float> > getTaxons(string);
 };