added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / classifysharedcommand.h

diff --git a/classifysharedcommand.h b/classifysharedcommand.h
new file mode 100755 (executable)
index 0000000..93c6286
--- /dev/null
+++ b/classifysharedcommand.h
@@ -0,0 +1,54 @@
+//
+//  classifysharedcommand.h
+//  Mothur
+//
+//  Created by Abu Zaher Md. Faridee on 8/13/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__classifysharedcommand__
+#define __Mothur__classifysharedcommand__
+
+#include "command.hpp"
+#include "inputdata.h"
+
+class ClassifySharedCommand : public Command {
+public:
+  ClassifySharedCommand();
+  ClassifySharedCommand(string);
+  ~ClassifySharedCommand() {};
+  
+  vector<string> setParameters();
+  string getCommandName()                      { return "classify.shared";     }
+   string getCommandCategory()         { return "OTU-Based Approaches";                }
+  string getOutputFileNameTag(string, string);
+  string getHelpString();
+  string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
+  string getDescription()              { return "description"; }
+  int execute();
+  
+  void help() { m->mothurOut(getHelpString()); }
+
+private:
+    bool abort;
+    string outputDir;
+    vector<string> outputNames, Groups;
+  
+    string sharedfile, designfile, otupersplit, splitcriteria;
+    set<string> labels;
+    bool allLines;
+  
+    int processors;
+    bool useTiming;
+
+    GroupMap designMap;
+  
+    int numDecisionTrees;
+    string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
+    bool doPruning, discardHighErrorTrees;
+    double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
+    
+    void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
+};
+
+#endif /* defined(__Mothur__classifysharedcommand__) */