added count.groups command and paralellized align.seqs for windows

[mothur.git] / countgroupscommand.h

diff --git a/countgroupscommand.h b/countgroupscommand.h
new file mode 100644 (file)
index 0000000..2532a80
--- /dev/null
+++ b/countgroupscommand.h
@@ -0,0 +1,42 @@
+#ifndef COUNTGROUPSCOMMAND_H
+#define COUNTGROUPSCOMMAND_H
+
+/*
+ *  countgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 8/9/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+class CountGroupsCommand : public Command {
+       
+public:
+       
+       CountGroupsCommand(string);
+       CountGroupsCommand();   
+       ~CountGroupsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "count.groups";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Count.groups"; }
+       string getDescription()         { return "counts the number of sequences in each group"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       string sharedfile, groupfile, outputDir, groups, accnosfile;
+       bool abort;
+       vector<string> Groups;
+       
+       void readAccnos();
+};
+
+#endif