moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / consensus.h

diff --git a/consensus.h b/consensus.h
deleted file mode 100644 (file)
index faa4e42..0000000
--- a/consensus.h
+++ /dev/null
@@ -1,61 +0,0 @@
-#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
-