X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeseqscommand.h;h=1a6365dac35b9e18669f8827c4054268b9123d9e;hp=8321212fff48bb240c54f1a1df4516b393f7216f;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 8321212..1a6365d 100644
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -19,27 +19,35 @@ 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, 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();
 		
 };