X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=7aaff172800c43b160fe62b2b49c2035e08502f8;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=8238c649489e3dff52371fa06ab8e2f49b93258f;hpb=14edc148cb299c5624f72bb681375b704aa74f43;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 8238c64..7aaff17 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -17,23 +17,38 @@ class RemoveSeqsCommand : public Command {
 	public:
 	
 		RemoveSeqsCommand(string);	
-		~RemoveSeqsCommand(){};
-		int execute();
-		void help();	
+		RemoveSeqsCommand();
+		~RemoveSeqsCommand(){}
+	
+		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, outputDir;
+		string accnosfile, fastafile, fastqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
 		vector<string> outputNames;
+        map<string, string> uniqueMap;
 		
 		int readFasta();
+        int readFastq();
 		int readName();
 		int readGroup();
+        int readCount();
 		int readAlign();
-		void readAccnos();
 		int readList();
 		int readTax();
+		int readQual();
 		
 };