changing command name classify.shared to classifyrf.shared

[mothur.git] / randomforest.hpp

diff --git a/randomforest.hpp b/randomforest.hpp
old mode 100755 (executable)
new mode 100644 (file)
index 30eb438..67d4372
--- a/randomforest.hpp
+++ b/randomforest.hpp
@@ -6,8 +6,8 @@
 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
 //
 
-#ifndef rrf_fs_prototype_randomforest_hpp
-#define rrf_fs_prototype_randomforest_hpp
+#ifndef RF_RANDOMFOREST_HPP
+#define RF_RANDOMFOREST_HPP
 
 #include "macros.h"
 #include "forest.h"
@@ -17,25 +17,34 @@ class RandomForest: public Forest {
     
 public:
     
-    // DONE
-    RandomForest(const vector <vector<int> > dataSet,const int numDecisionTrees, const string);
+    RandomForest(const vector <vector<int> > dataSet,
+                 const int numDecisionTrees,
+                 const string treeSplitCriterion,
+                 const bool doPruning,
+                 const float pruneAggressiveness,
+                 const bool discardHighErrorTrees,
+                 const float highErrorTreeDiscardThreshold,
+                 const string optimumFeatureSubsetSelectionCriteria,
+                 const float featureStandardDeviationThreshold);
     
     
     //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;
-//        }
-//    }
+    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);
+    int printConfusionMatrix(map<int, string> intToTreatmentMap);
+    int getMissclassifications(string, map<int, string> intToTreatmentMap, vector<string> names);
     
 private:
     MothurOut* m;