X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deconvolutecommand.h;h=e514bdae70f7e0b51854b40baacf44d2b0174c8a;hp=0b6eb5e1f8fbce6e0f9ba9c5cccaee56739990dc;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 0b6eb5e..e514bda 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -11,7 +11,7 @@
 
 #include "command.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 /* The unique.seqs command reads a fasta file, finds the duplicate sequences and outputs a names file
 	containing 2 columns.  The first being the groupname and the second the list of identical sequence names. */ 
@@ -20,23 +20,29 @@
 class DeconvoluteCommand : public Command {
 
 public:
-	DeconvoluteCommand(string);	
-	~DeconvoluteCommand() { delete fastamap; };
-	int execute();
-	void help();	
+	DeconvoluteCommand(string);
+	DeconvoluteCommand();
+	~DeconvoluteCommand() {}
 	
-private:
-	GlobalData* globaldata;
-	FastaMap* fastamap;
-	ifstream in;
-	ofstream out, outFasta;
-	string filename, outputFileName, outFastafile;
-	OptionParser* parser;
-	map<string, string> parameters;
-	map<string, string>::iterator it;
-	bool abort;
+	vector<string> setParameters();
+	string getCommandName()			{ return "unique.seqs";		}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+    
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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:
+	string inFastaName, oldNameMapFName, outputDir, countfile;
+	vector<string> outputNames;
 
+	bool abort;
 };
 
 #endif