X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=4561d28614c62686c42e29a9747b84d853537fd0;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=ea93b5a1c4e0427cc43157a5d77f995bb3f2308b;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index ea93b5a..4561d28 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -18,20 +18,24 @@ class GetSeqsCommand : public Command {
 	
 		GetSeqsCommand(string);
 		GetSeqsCommand();
-		~GetSeqsCommand(){};
-		vector<string> getRequiredParameters();
-		vector<string> getValidParameters();
-		vector<string> getRequiredFiles();
-		map<string, vector<string> > getOutputFiles() { return outputTypes; }
-		int execute();
-		void help();	
-		
+		~GetSeqsCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "get.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
+		string getHelpString();	
+		string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+		string getDescription()		{ return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+		int execute(); 
+		void help() { m->mothurOut(getHelpString()); }	
+	
+	
 	private:
 		set<string> names;
 		vector<string> outputNames;
-		string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+		string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
-		map<string, vector<string> > outputTypes;
 		
 		int readFasta();
 		int readName();
@@ -40,6 +44,8 @@ class GetSeqsCommand : public Command {
 		int readAccnos();
 		int readList();
 		int readTax();
+		int readQual();
+		int compareAccnos();
 		
 };