Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / UPGMA / UPGMAAlgorithm.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/UPGMAAlgorithm.h b/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/UPGMAAlgorithm.h
deleted file mode 100644 (file)
index f6f1bac..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/UPGMAAlgorithm.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#ifndef __UPGMAALGORITHM_H
-#define __UPGMAALGORITHM_H
-
-#include "Node.h" 
-#include <limits>
-#include "../../general/clustalw.h"
-#include "../AlignmentSteps.h"
-#include "RootedGuideTree.h"
-#include <list>
-#include <memory>
-
-namespace clustalw
-{
-
-using namespace std;
-
-class UPGMAAlgorithm
-{
-    public:
-        bool overwriteMatrix; 
-
-        UPGMAAlgorithm();
-        auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree, 
-                                    DistMatrix* distMat, SeqInfo* seqInfo,
-                                    bool overwrite, ofstream* tree = 0);
-        void setVerbose(bool _verbose){verbose = _verbose;}                            
-                  
-    private:
-        Node **initialiseNodes(double *distanceMatrix, int firstSeq);
-
-        Node *doUPGMA(Node **nodes, ofstream* tree);
-        void printAllNodes(Node** nodes);
-        void addAlignmentStep(vector<int>* group1, vector<int>* group2);
-        Node** getNodeWithMinDist(Node** clusters);
-        void recomputeNodeToJoin1DistMatRow(Node* nodeToJoin1, double** nodeToJoin2DistIter);
-        void computeAllOtherDistsToNewNode(Node* nodeToJoin1, Node* nodeToJoin2,
-                                                   double** nodeToJoin2DistIter);
-        void computeDistsUpToNodeToJoin2(Node* nToJoin1, Node* nToJoin2, 
-                                         double** nodeToJoin2DistIter);
-        void computeDistsForNodesAfterNode2(Node* nToJoin2);
-        void movePtrPastUnusedDistances(double** ptrToDist)
-        {            
-            while(**ptrToDist < 0)
-            {
-                (*ptrToDist)++;
-            }
-        }
-        double calcNewDist(double dist1, double dist2);                             
-        //vector<Node*>::iterator getIterToNodeWithMinDist(vector<Node*>* nodesLeft);
-        
-        auto_ptr<AlignmentSteps> progSteps;
-        int numSeqs; 
-        bool verbose;
-        int orderNode1, orderNode2, orderNewNode;
-};
-
-}
-
-#endif