sped up align.seqs appending of files

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index c80bb360533a8b08e819d820d72f431f722c9e1b..88b7a382d4c175a14c243d21e97a7580cba9c32d 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -10,29 +10,31 @@
  */
 
 #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