broke up globaldata and moved error checking and help into commands

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 2ccc20a633b882475099132269eb0142cf55adcf..0b6eb5e1f8fbce6e0f9ba9c5cccaee56739990dc 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -9,24 +9,21 @@
  *
  */
 
-#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(string);     
        ~DeconvoluteCommand() { delete fastamap; };
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -34,6 +31,11 @@ private:
        ifstream in;
        ofstream out, outFasta;
        string filename, outputFileName, outFastafile;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+
 
 };