added get.groups and remove.groups commands

[mothur.git] / getgroupscommand.h

diff --git a/getgroupscommand.h b/getgroupscommand.h
new file mode 100644 (file)
index 0000000..7c4c92f
--- /dev/null
+++ b/getgroupscommand.h
@@ -0,0 +1,52 @@
+#ifndef GETGROUPSCOMMAND_H
+#define GETGROUPSCOMMAND_H
+
+/*
+ *  getgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class GetGroupsCommand : public Command {
+       
+public:
+       
+       GetGroupsCommand(string);       
+       GetGroupsCommand();
+       ~GetGroupsCommand(){}
+       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
+
+
+