added shared, constaxonomy and label parameter to get.lineage and remove.lineage...

[mothur.git] / removelineagecommand.h

diff --git a/removelineagecommand.h b/removelineagecommand.h
index c590ec640dbbfec2f9cbc886041aadfe614fd719..8bfa5f15be3502e93e878d7ddfadc1870628be39 100644 (file)
--- a/removelineagecommand.h
+++ b/removelineagecommand.h
@@ -11,6 +11,9 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
+
 
 class RemoveLineageCommand : public Command {
        
@@ -19,27 +22,40 @@ 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 getOutputPattern(string);   
+               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;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               vector<string> outputNames, listOfTaxons;
+               string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
                bool abort, dups;
+        vector<SharedRAbundVector*> lookup;
+        ListVector* list;
                
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
                int readList();
-               int readTax();  
-               string removeConfidences(string);
+               int readTax();
+        int readShared();
+        int readConsTax();
+        int readConsList();
+        int getShared();
+        int getListVector();
+               vector< map<string, float> > getTaxons(string);
 };
 
 #endif