added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 310a66a5a90ea24acf34d7a94d8f7ff7df5a154d..a756d24f583be82eac03634ebcd8496c4fd687b6 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -23,25 +23,27 @@ class RemoveLineageCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "remove.lineage";                      }
                string getCommandCategory()             { return "Phylotype Analysis";          }
-               string getHelpString(); 
+               string getOutputFileNameTag(string, string);
+       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, listOfTaxons;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
                vector< map<string, float> > getTaxons(string);
 };