added classify.otu command

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
new file mode 100644 (file)
index 0000000..0ac0288
--- /dev/null
+++ b/classifyotucommand.h
@@ -0,0 +1,49 @@
+#ifndef CLASSIFYOTUSCOMMAND_H
+#define CLASSIFYOTUSCOMMAND_H
+
+/*
+ *  classifyotucommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 6/1/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+#include "listvector.hpp"
+#include "inputdata.h"
+
+
+class ClassifyOtuCommand : public Command {
+
+public:
+       ClassifyOtuCommand(string);
+       ~ClassifyOtuCommand();
+       int execute();
+       void help();
+
+private:
+
+       ListVector* list;
+       InputData* input;
+       string listfile, namefile, taxfile, label, outputDir;
+       bool abort, allLines, probs;
+       int cutoff;
+       set<string> labels; //holds labels to be used
+       vector<string> outputNames;
+       map<string, string> nameMap;
+       map<string, string> taxMap;
+
+       int readNamesFile();
+       int readTaxonomyFile();
+       void removeConfidences(string&);
+       int process(ListVector*);
+       string findConcensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
+       
+                                                                                               
+};
+
+#endif
+
+