broke up globaldata and moved error checking and help into commands

[mothur.git] / deconvolutecommand.h

diff --git a/deconvolutecommand.h b/deconvolutecommand.h
index aaed841ed8012a274cb96c3153463b4c1b0a2bc0..0b6eb5e1f8fbce6e0f9ba9c5cccaee56739990dc 100644 (file)
--- a/deconvolutecommand.h
+++ b/deconvolutecommand.h
@@ -20,9 +20,10 @@
 class DeconvoluteCommand : public Command {
 
 public:
-       DeconvoluteCommand() {};        
+       DeconvoluteCommand(string);     
        ~DeconvoluteCommand() { delete fastamap; };
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -30,6 +31,11 @@ private:
        ifstream in;
        ofstream out, outFasta;
        string filename, outputFileName, outFastafile;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+
 
 };