X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;fp=getseqscommand.h;h=4561d28614c62686c42e29a9747b84d853537fd0;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
new file mode 100644
index 0000000..4561d28
--- /dev/null
+++ b/getseqscommand.h
@@ -0,0 +1,53 @@
+#ifndef GETSEQSCOMMAND_H
+#define GETSEQSCOMMAND_H
+
+/*
+ *  getseqscommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+class GetSeqsCommand : public Command {
+	
+	public:
+	
+		GetSeqsCommand(string);
+		GetSeqsCommand();
+		~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, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		bool abort, dups;
+		
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readAccnos();
+		int readList();
+		int readTax();
+		int readQual();
+		int compareAccnos();
+		
+};
+
+#endif
+