X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getseqscommand.h;h=c5b6ca4141afc00c12b646ea34604b898b1c4131;hp=ea93b5a1c4e0427cc43157a5d77f995bb3f2308b;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/getseqscommand.h b/getseqscommand.h
index ea93b5a..c5b6ca4 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -18,28 +18,42 @@ 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 getOutputPattern(string);	
+		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, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
 		bool abort, dups;
-		map<string, vector<string> > outputTypes;
+        map<string, string> uniqueMap;
+        //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 readCount();
 		int readAlign();
-		int readAccnos();
 		int readList();
 		int readTax();
+		int readQual();
+		int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
 		
 };