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

[mothur.git] / randomforest.hpp

diff --git a/randomforest.hpp b/randomforest.hpp
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+//
+//  randomforest.hpp
+//  rrf-fs-prototype
+//
+//  Created by Abu Zaher Faridee on 7/20/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#ifndef rrf_fs_prototype_randomforest_hpp
+#define rrf_fs_prototype_randomforest_hpp
+
+#include "macros.h"
+#include "abstractrandomforest.hpp"
+#include "decisiontree.hpp"
+
+class RandomForest: public AbstractRandomForest {
+    
+public:
+    
+    // DONE
+    RandomForest(const vector <vector<int> > dataSet,const int numDecisionTrees, const string);
+    
+    
+    //NOTE:: if you are going to dynamically cast, aren't you undoing the advantage of abstraction. Why abstract at all?
+    //could cause maintenance issues later if other types of Abstract decison trees are created that cannot be cast as a decision tree.
+    virtual ~RandomForest() {
+        for (vector<AbstractDecisionTree*>::iterator it = decisionTrees.begin(); it != decisionTrees.end(); it++) {
+            // we know that this is decision tree, so we can do a dynamic_case<DecisionTree*> here
+            DecisionTree* decisionTree = dynamic_cast<DecisionTree*>(*it);
+            // calling the destructor by deleting
+            delete decisionTree;
+        }
+    }
+    
+    int calcForrestErrorRate();
+    int calcForrestVariableImportance(string);
+    int populateDecisionTrees();
+    int updateGlobalOutOfBagEstimates(DecisionTree* decisionTree);
+    
+private:
+    MothurOut* m;
+    
+};
+
+#endif