X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=1a6365dac35b9e18669f8827c4054268b9123d9e;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hp=de1e3d9d6aff8595a098cf8bf2fd6c1d5c79ec9f;hpb=89f19f9c6ab89c2f6c7c6921a328ae87bce6f8e3;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index de1e3d9..1a6365d 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -19,25 +19,32 @@ class RemoveSeqsCommand : public Command {
 		RemoveSeqsCommand(string);	
 		RemoveSeqsCommand();
 		~RemoveSeqsCommand(){}
-		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.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
 		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+		string getDescription()		{ return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		set<string> names;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
+        map<string, string> uniqueMap;
 		
 		int readFasta();
 		int readName();
 		int readGroup();
+        int readCount();
 		int readAlign();
-		void readAccnos();
 		int readList();
 		int readTax();
 		int readQual();