Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/Tree.h b/website/archive/binaries/mac/src/clustalw/src/tree/Tree.h
deleted file mode 100644 (file)
index bd30b64..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/tree/Tree.h
+++ /dev/null
@@ -1,72 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifndef TREE_H
-#define TREE_H
-
-#include <vector>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "../alignment/Alignment.h"
-#include "AlignmentSteps.h"
-#include <memory>
-namespace clustalw
-{
-
-class Tree
-{
-    public:
-        /* Functions */
-        void calcSeqWeights(int firstSeq, int lastSeq, vector<int>* sweight);
-        int readTree(Alignment* alignPtr, const string& treeFileName, int firstSeq, 
-                     int lastSeq);
-        auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
-        int calcSimilarities(Alignment* alignPtr, DistMatrix* distMat);
-        void clearTree(TreeNode* p);
-        /* Attributes */
-
-    private:
-        /* Functions */
-        void createTree(TreeNode* ptree, TreeNode* parent, ifstream* file);
-        void createNode(TreeNode* pptr, TreeNode* parent);
-        TreeNode* insertNode(TreeNode* pptr);
-        void clearTreeNodes(TreeNode* p);
-        TreeNode* reRoot(TreeNode* ptree, int nseqs);
-        TreeNode* insertRoot(TreeNode* p, float diff);
-        float calcRootMean(TreeNode* root, float *maxDist);
-        float calcMean(TreeNode* nptr, float *maxDist, int nSeqs);
-        void orderNodes();
-        int calcWeight(int leaf);
-        void skipSpace(ifstream* file);
-        void groupSeqs(TreeNode* p, int *nextGroups, int nSeqs, AlignmentSteps* stepsPtr);
-        void markGroup1(TreeNode* p, int *groups, int n);
-        void markGroup2(TreeNode* p, int *groups, int n);
-        TreeNode* avail();
-        void setInfo(TreeNode* p, TreeNode* parent, int pleaf, string pname, float
-                     pdist);
-        void debugPrintAllNodes(int nseqs);
-            
-        /* Attributes */
-        AlignmentSteps progSteps;
-        char charFromFile;
-        ifstream file;
-        TreeNode** lptr;
-        TreeNode** olptr;
-        TreeNode** nptr;
-        TreeNode** ptrs;
-        int nnodes;
-        int ntotal;
-        bool rootedTree;
-        TreeNode* seqTree;
-        TreeNode* root;
-        int* groups;
-        int numSeq;
-        int numSets;
-        const static int MAXERRS = 10;
-};
-
-}
-#endif