X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=deconvolutecommand.h;h=88b7a382d4c175a14c243d21e97a7580cba9c32d;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=2ccc20a633b882475099132269eb0142cf55adcf;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 2ccc20a..88b7a38 100644
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,32 +9,32 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
-#include "utilities.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
 
-/* The deconvolute command reads a fasta file, finds the duplicate sequences and outputs a names file
+/* 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. */ 
 
-using namespace std;
 
 class DeconvoluteCommand : public Command {
 
 public:
-	DeconvoluteCommand() {};	
-	~DeconvoluteCommand() { delete fastamap; };
-	int execute();	
+	DeconvoluteCommand(string);
+	DeconvoluteCommand();
+	~DeconvoluteCommand() {}
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
 	
 private:
-	GlobalData* globaldata;
-	FastaMap* fastamap;
-	ifstream in;
-	ofstream out, outFasta;
-	string filename, outputFileName, outFastafile;
+	string inFastaName, oldNameMapFName, outputDir;
+	vector<string> outputNames;
+	map<string, vector<string> > outputTypes;
 
+	bool abort;
 };
 
 #endif