X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removelineagecommand.h;h=8bfa5f15be3502e93e878d7ddfadc1870628be39;hp=02a4440e79ec4a7e996b58a7b9209b30cc933dcd;hb=d3e27ba055f6765044b885cded5302d9cece161a;hpb=a4f05f09c250323132a4b9427f41a3ededaec634

diff --git a/removelineagecommand.h b/removelineagecommand.h
index 02a4440..8bfa5f1 100644
--- 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 +22,39 @@ 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);
 };