X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=c71b5f2804a71190c6919f0dc80bf80d32f15508;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=809109c486de9f00b39091b863da8a23dfc95a96;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 809109c..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.
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
-		void readAccnos();
-		void readList();
+		int readFasta();
+		int readName();
+		int readGroup();
+		int readAlign();
+		int readList();
+		int readTax();
+		int readQual();
+		int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
 		
 };