added summary.tax command and fixed bug with root level totals in tax.summary file

[mothur.git] / summarytaxcommand.h

diff --git a/summarytaxcommand.h b/summarytaxcommand.h
new file mode 100644 (file)
index 0000000..acef7ee
--- /dev/null
+++ b/summarytaxcommand.h
@@ -0,0 +1,40 @@
+#ifndef SUMMARYTAXCOMMAND_H
+#define SUMMARYTAXCOMMAND_H
+
+/*
+ *  summarytaxcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/23/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+/**************************************************************************************************/
+
+class SummaryTaxCommand : public Command {
+       public:
+               SummaryTaxCommand(string);
+               SummaryTaxCommand();
+               ~SummaryTaxCommand(){}
+               
+               vector<string> setParameters();
+               string getCommandName()                 { return "summary.tax";                 }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
+               string getDescription()         { return "summarize the taxonomies of a set of sequences"; }
+               
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+               
+       private:
+               bool abort;
+               string taxfile, outputDir, namefile, groupfile, refTaxonomy;
+               vector<string> outputNames;
+               map<string, int> nameMap;
+};
+
+#endif