changing command name classify.shared to classifyrf.shared

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
index 0d07ac6193f37807a25247df864f762e67369d58..4cee8b6459e3089b4d69e015b2bb4b2edb22c9eb 100644 (file)
--- a/getlineagecommand.h
+++ b/getlineagecommand.h
@@ -11,29 +11,52 @@
  */
  
 #include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
 
 class GetLineageCommand : public Command {
        
        public:
        
                GetLineageCommand(string);
-               ~GetLineageCommand(){};
-               int execute();
-               void help();    
+               GetLineageCommand();
+               ~GetLineageCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.lineage";                         }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
                
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
+               string getDescription()         { return "gets 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;
-               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               vector<string> outputNames, listOfTaxons;
+               string fastafile, namefile, groupfile, alignfile, countfile, listfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
                bool abort, dups;
+        vector<SharedRAbundVector*> lookup;
+        ListVector* list;
                
                int readFasta();
                int readName();
+        int readCount();
                int readGroup();
                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