X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=c71b5f2804a71190c6919f0dc80bf80d32f15508;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=b574afe38734a789fa39985090012cff358d2e95;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index b574afe..c71b5f2 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,22 +17,41 @@ class GetSeqsCommand : public Command {
 	public:
 	
 		GetSeqsCommand(string);
-		~GetSeqsCommand(){};
-		int execute();
-		void help();	
-		
+		GetSeqsCommand();
+		~GetSeqsCommand(){}
+	
+		vector<string> setParameters();
+		string getCommandName()			{ return "get.seqs";				}
+		string getCommandCategory()		{ return "Sequence Processing";		}
+		string getOutputFileNameTag(string, string);
+	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, outputDir;
-		bool abort;
+		string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		bool abort, dups;
+    
+        //for debug
+        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
 		
 		int readFasta();
 		int readName();
 		int readGroup();
 		int readAlign();
-		int readAccnos();
 		int readList();
+		int readTax();
+		int readQual();
+		int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
 		
 };