added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index d18fc23076d83a8a3d4083ce2423af47cfd08e2f..a5caec8e4c3e0f04ec7744489c3f27c0a495e38d 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -17,13 +17,23 @@ class RemoveLineageCommand : public Command {
        public:
        
                RemoveLineageCommand(string);
+               RemoveLineageCommand();
                ~RemoveLineageCommand(){};
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "remove.lineage";                      }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
+               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;
+               vector<string> outputNames, listOfTaxons;
                string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
                bool abort, dups;
                
@@ -33,7 +43,7 @@ class RemoveLineageCommand : public Command {
                int readAlign();
                int readList();
                int readTax();  
-               string removeConfidences(string);
+               vector< map<string, float> > getTaxons(string);
 };
 
 #endif