X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=623c3c1e8f400f4262414a5cf546143d698840e7;hb=77ac47e1ea0b5a0c6f55eb25e6bc7d7494ed3ad2;hp=305c6e34dd0fcf1a66e434b797ea3a5af991dfd0;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 305c6e3..623c3c1 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -17,20 +17,21 @@ class SeqSummaryCommand : public Command {
 public:
 	SeqSummaryCommand(string);
 	SeqSummaryCommand();
-	~SeqSummaryCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~SeqSummaryCommand(){}
 	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getHelpString();	
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 private:
 	bool abort;
-	string fastafile, outputDir;
+	string fastafile, outputDir, namefile;
 	int processors;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
+	map<string, int> nameMap;
 	
 	struct linePair {
 		unsigned long int start;