added calcs to tree.shared. working on remove.rare command

[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
new file mode 100644 (file)
index 0000000..7db54b4
--- /dev/null
+++ b/removerarecommand.h
@@ -0,0 +1,50 @@
+#ifndef REMOVERARECOMMAND_H
+#define REMOVERARECOMMAND_H
+
+/*
+ *  removerarecommand.h
+ *  mothur
+ *
+ *  Created by westcott on 1/21/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "listvector.hpp"
+
+class RemoveRareCommand : public Command {
+       
+public:
+       
+       RemoveRareCommand(string);      
+       RemoveRareCommand();
+       ~RemoveRareCommand(){}
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       int execute();
+       void help();    
+       
+private:
+       string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+       int nseqs, allLines;
+       bool abort, byGroup;
+       vector<string> outputNames, Groups;
+       set<string> labels;
+       map<string, vector<string> > outputTypes;
+       
+       int processSabund();
+       int processRabund();
+       int processList();
+       int processShared();
+       
+};
+
+#endif
+
+
+
+