worked on hcluster. made .single command run using a sharedfile. and various other...

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index 0b6eb5e1f8fbce6e0f9ba9c5cccaee56739990dc..635e53fe455ab05eacdb2a19e09837b30ef4c955 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -11,7 +11,6 @@
 
 #include "command.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
 
 /* 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. */ 
@@ -21,22 +20,14 @@ class DeconvoluteCommand : public Command {
 
 public:
        DeconvoluteCommand(string);     
-       ~DeconvoluteCommand() { delete fastamap; };
+       ~DeconvoluteCommand() { };
        int execute();
        void help();    
        
 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;
-
+       string inFastaName, oldNameMapFName;
 
+       bool abort;
 };
 
 #endif