X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=listseqscommand.h;h=b8a79c06035825fd92050a1e0c610ac6b77bd122;hp=889b3733df47f346be5a3fd9dd327a0660913c61;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/listseqscommand.h b/listseqscommand.h
index 889b373..b8a79c0 100644
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -19,17 +19,23 @@ class ListSeqsCommand : public Command {
 		ListSeqsCommand(string);
 		ListSeqsCommand();	
 		~ListSeqsCommand(){}
-		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 "list.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
 		
+	string getHelpString();	
+    string getOutputPattern(string);	
+		string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
+		string getDescription()		{ return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		vector<string> names, outputNames;
-		map<string, vector<string> > outputTypes;
-		string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
+		string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
 		bool abort;
 		
 		int readFasta();
@@ -38,6 +44,7 @@ class ListSeqsCommand : public Command {
 		int readAlign();
 		int readList();
 		int readTax();
+        int readCount();
 		
 };