X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.h;h=df96e4514bc84787ad901e137bbc794588681705;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=8321212fff48bb240c54f1a1df4516b393f7216f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 8321212..df96e45 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -19,19 +19,23 @@ 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 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, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
 		vector<string> outputNames;
-		map<string, vector<string> > outputTypes;
 		
 		int readFasta();
 		int readName();
@@ -40,6 +44,7 @@ class RemoveSeqsCommand : public Command {
 		void readAccnos();
 		int readList();
 		int readTax();
+		int readQual();
 		
 };