Revert to previous commit

[mothur.git] / consensus.h

diff --git a/consensus.h b/consensus.h
new file mode 100644 (file)
index 0000000..faa4e42
--- /dev/null
+++ b/consensus.h
@@ -0,0 +1,61 @@
+#ifndef CONCENSUS_H
+#define CONCENSUS_H
+/*
+ *  consensus.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 4/29/09.
+ *  Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
+ *
+ */
+
+
+#include "tree.h"
+#include "treemap.h"
+
+//NOTE: This class assumes all leaf nodes have 1 member.  
+//      Mothur does allow for names files with trees which would make a tree with multiple members at one leaf.  
+//      This class is currently only called internally by commands that have leaf node containing only 1 member.
+//      But if in the future, this changes things will need to be reworked in getSets and buildConsensus.
+
+
+class Consensus {
+       
+public:
+       Consensus() { m = MothurOut::getInstance(); }   
+       ~Consensus() {}
+       
+    Tree* getTree(vector<Tree*>&);
+               
+private:
+    MothurOut* m;
+    Tree* consensusTree;
+    
+    vector<string> treeSet;            //set containing all members of the tree to start recursion.  filled in getSets().
+       map< vector<string>, int > nodePairs;  //<map of possible combinations these combos are the pcounts or descendants info, to how many times they occured
+                                                                               // ie. combos FI and EGK would create nodePairs[vector containing F and I] = 1; nodePairs[vector containing E, G and K] = 1
+                                                                               // if you saw the combo FI again in another tree you would then update nodePairs[vector containing F and I] = 2;
+                                                                               // requires vectors to be sorted to find key.
+       map< vector<string>, vector< vector<string> > > bestSplit;  //maps a group to its best split
+       map< vector<string>, int > nodePairsInitialRate;
+       map< vector<string>, int > nodePairsInTree;
+       map<string, int>::iterator it;
+       map< vector<string>, int>::iterator it2;
+       string outputFile, notIncluded, filename;
+       int numNodes, numLeaves, count, numTrees;  //count is the next available spot in the tree vector
+       vector<string> outputNames;
+                                                                               
+       int getSets(vector<Tree*>&);
+       int getSubgroupRating(vector<string>);
+       vector<string> getSmallest(map< vector<string>, int>);
+       vector<string> getNextAvailableSet(vector<string>, vector<string>&);  
+       vector<string> getRestSet(vector<string>, vector<string>);
+       bool isSubset(vector<string>, vector<string>); 
+       int findSpot(string); 
+       int buildConsensusTree(vector<string>);
+    int printSetsInfo();
+       
+};
+
+#endif
+