added get.groups and remove.groups commands

[mothur.git] / removegroupscommand.h

diff --git a/removegroupscommand.h b/removegroupscommand.h
new file mode 100644 (file)
index 0000000..896697a
--- /dev/null
+++ b/removegroupscommand.h
@@ -0,0 +1,51 @@
+#ifndef REMOVEGROUPSCOMMAND_H
+#define REMOVEGROUPSCOMMAND_H
+
+/*
+ *  removegroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class RemoveGroupsCommand : public Command {
+       
+public:
+       
+       RemoveGroupsCommand(string);    
+       RemoveGroupsCommand();
+       ~RemoveGroupsCommand(){}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+       
+private:
+       set<string> names;
+       string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+       bool abort;
+       vector<string> outputNames, Groups;
+       map<string, vector<string> > outputTypes;
+       GroupMap* groupMap;
+       
+       int readFasta();
+       int readName();
+       int readGroup();
+       void readAccnos();
+       int readList();
+       int readTax();
+       int fillNames();
+       
+};
+
+#endif
+
+