X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.h;h=c5b6ca4141afc00c12b646ea34604b898b1c4131;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=47f56f75c52f6ec3bf11128fa06ea14295571649;hpb=b9456b1087ade74251792e039f4e5021dbf32349;p=mothur.git

diff --git a/getseqscommand.h b/getseqscommand.h
index 47f56f7..c5b6ca4 100644
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -6,7 +6,7 @@
  *  Mothur
  *
  *  Created by Sarah Westcott on 7/8/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
  
@@ -16,21 +16,44 @@ class GetSeqsCommand : public Command {
 	
 	public:
 	
-		GetSeqsCommand(string);	
-		~GetSeqsCommand(){};
-		int execute();
-		void help();	
+		GetSeqsCommand(string);
+		GetSeqsCommand();
+		~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;
-		string accnosfile, fastafile, namefile, groupfile, alignfile;
-		bool abort;
+		vector<string> outputNames;
+		string accnosfile, accnosfile2, fastafile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+		bool abort, dups;
+        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.
 		
-		void readFasta();
-		void readName();
-		void readGroup();
-		void readAlign();
-		void readAccnos();
+		int readFasta();
+		int readName();
+		int readGroup();
+        int readCount();
+		int readAlign();
+		int readList();
+		int readTax();
+		int readQual();
+		int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
 		
 };