X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=7d4cb50023eb6312b652a8368d2d862882b3ffd4;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=b6bda8faa00a274369e7a23803440025c241e612;hpb=cd37904452dc95b183ff313ff05720c562902487;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b6bda8f..7d4cb50 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -19,16 +19,26 @@
 class DeconvoluteCommand : public Command {
 
 public:
-	DeconvoluteCommand(string);	
-	~DeconvoluteCommand() { delete fastamap; };
-	int execute();
-	void help();	
+	DeconvoluteCommand(string);
+	DeconvoluteCommand();
+	~DeconvoluteCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "unique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+    string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+	string getDescription()		{ return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
 	
 private:
-	FastaMap* fastamap;
-	ifstream in;
-	ofstream out, outFasta;
-	string filename, outputFileName, outFastafile;
+	string inFastaName, oldNameMapFName, outputDir;
+	vector<string> outputNames;
 
 	bool abort;
 };