working on pam

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index fe5c0db5587d9909fdad12d1f65cb916f5901043..e514bdae70f7e0b51854b40baacf44d2b0174c8a 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -11,27 +11,38 @@
 
 #include "command.hpp"
 #include "fastamap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
-/* 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> setParameters();
+       string getCommandName()                 { return "unique.seqs";         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+    
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Unique.seqs"; }
+       string getDescription()         { return "creates a fasta containing the unique sequences as well as a namesfile with the names each sequence represents"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       FastaMap* fastamap;
-       ifstream in;
-       ofstream out, outFasta;
-       string filename, outputFileName, outFastafile;
+       string inFastaName, oldNameMapFName, outputDir, countfile;
+       vector<string> outputNames;
 
+       bool abort;
 };
 
 #endif