added filter.shared command. fixed lci and uci for thetayc calc

[mothur.git] / filtersharedcommand.h

diff --git a/filtersharedcommand.h b/filtersharedcommand.h
new file mode 100644 (file)
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+++ b/filtersharedcommand.h
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+//
+//  filtersharedcommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 1/4/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_filtersharedcommand_h
+#define Mothur_filtersharedcommand_h
+
+#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
+
+
+class FilterSharedCommand : public Command {
+    
+public:
+       FilterSharedCommand(string);
+       FilterSharedCommand();
+       ~FilterSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "filter.shared";       }
+       string getCommandCategory()             { return "OTU-Based Approaches";                }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Filter.shared"; }
+       string getDescription()         { return "remove OTUs based on various criteria"; }
+    
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:       
+       bool abort, pickedGroups, allLines, makeRare;
+       set<string> labels; //holds labels to be used
+       string groups, label, outputDir, sharedfile;
+       vector<string> Groups, outputNames;
+       int minAbund, minTotal;
+    float minPercent;
+    
+    int processShared(vector<SharedRAbundVector*>&);
+       
+};
+
+
+
+#endif