merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index c80bb360533a8b08e819d820d72f431f722c9e1b..b6bda8faa00a274369e7a23803440025c241e612 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -10,29 +10,27 @@
  */
 
 #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;
        FastaMap* fastamap;
        ifstream in;
        ofstream out, outFasta;
        string filename, outputFileName, outFastafile;
 
+       bool abort;
 };
 
 #endif