added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index b6bda8faa00a274369e7a23803440025c241e612..7d4cb50023eb6312b652a8368d2d862882b3ffd4 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -19,16 +19,26 @@
 class DeconvoluteCommand : public Command {
 
 public:
-       DeconvoluteCommand(string);     
-       ~DeconvoluteCommand() { delete fastamap; };
-       int execute();
-       void help();    
+       DeconvoluteCommand(string);
+       DeconvoluteCommand();
+       ~DeconvoluteCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "unique.seqs";         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+    string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+       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:
-       FastaMap* fastamap;
-       ifstream in;
-       ofstream out, outFasta;
-       string filename, outputFileName, outFastafile;
+       string inFastaName, oldNameMapFName, outputDir;
+       vector<string> outputNames;
 
        bool abort;
 };