Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / UPGMA / RootedGuideTree.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedGuideTree.cpp b/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedGuideTree.cpp
deleted file mode 100644 (file)
index 3a841dd..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/tree/UPGMA/RootedGuideTree.cpp
+++ /dev/null
@@ -1,164 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include <iostream>
-#include "RootedGuideTree.h"
-#include "../../general/userparams.h"
-using namespace std;
-
-namespace clustalw
-{
-
-RootedGuideTree::RootedGuideTree()
- : root(0){ }
-
-RootedGuideTree::RootedGuideTree(Node* r)
- : root(r) { }
-
-RootedGuideTree::~RootedGuideTree()
-{
-    root->makeEmpty();
-}
-
-void RootedGuideTree::setRoot(Node* r)
-{
-    makeEmpty();
-    
-    root = r;
-}
- 
-void RootedGuideTree::makeEmpty()
-{
-    root->makeEmpty();
-}
-
-void RootedGuideTree::orderNodes()
-{
-    calcOrderNode(root);
-}
-
-int RootedGuideTree::calcOrderNode(Node* node)
-{
-    if(node != 0)
-    {
-        if(node->getLeft() == 0 && node->getRight() == 0) // Leaf Node
-        {
-            node->setOrder(1);
-            return 1;
-        }
-        else // Internal node
-        {
-            node->setOrder(calcOrderNode(node->getLeft()) + calcOrderNode(node->getRight()));
-            return node->getOrder();            
-        }
-    }
-    return 0;
-}
-
-void RootedGuideTree::calcSeqWeights(int firstSeq, int lastSeq, vector<int>* seqWeights)
-{
-    if((int)seqWeights->size() < lastSeq - 1)
-    {
-        seqWeights->resize(lastSeq - 1);
-    }
-    
-    int i = 0, _nSeqs = 0;
-    int temp = 0, sum = 0;
-    //
-    // If there are more than three sequences....
-    //
-    _nSeqs = lastSeq - firstSeq;
-    if ((_nSeqs >= 2) && (userParameters->getDistanceTree() == true) && 
-        (userParameters->getNoWeights() == false))
-    {
-        //
-        // Calculate sequence weights based on Phylip tree.
-        //
-        orderNodes();
-        calcWeights(seqWeights);
-
-        //
-        // Normalise the weights, such that the sum of the weights = INT_SCALE_FACTOR
-        //
-
-        sum = 0;
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            sum += (*seqWeights)[i];
-        }
-
-        if (sum == 0)
-        {
-            for (i = firstSeq; i < lastSeq; i++)
-            {
-                (*seqWeights)[i] = 1;
-            }
-            sum = i;
-        }
-
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            (*seqWeights)[i] = ((*seqWeights)[i] * INT_SCALE_FACTOR) / sum;
-            if ((*seqWeights)[i] < 1)
-            {
-                (*seqWeights)[i] = 1;
-            }
-        }
-    }
-    else
-    {
-        //
-        // Otherwise, use identity weights.
-        //
-        temp = INT_SCALE_FACTOR / _nSeqs;
-        // AW 2009-07-09: goes wrong if we have more than
-        // INT_SCALE_FACTOR seqs. if so, set to 1, just as above
-        // same as in Tree.cpp
-        if (temp < 1)
-            temp = 1;
-
-        
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            (*seqWeights)[i] = temp;
-        }
-    }
-}
-
-void RootedGuideTree::calcWeights(vector<int>* seqWeights)
-{
-    vector<float> weights;
-    int sizeSeqWeights = seqWeights->size();
-    weights.resize(sizeSeqWeights, 0.0);
-    
-    doWeightCalc(0.0, &weights, root);
-
-    for(int i = 0; i < sizeSeqWeights; i++)
-    {
-        (*seqWeights)[i] = static_cast<int>(weights[i] * 100);        
-    }
-}
-
-void RootedGuideTree::doWeightCalc(float weightSoFar, vector<float>* weights, Node* t)
-{
-    if(t != 0)
-    {
-        if(t->getLeft() == 0 && t->getRight() == 0) // Leaf Node
-        {
-            (*weights)[t->getSeqNum() - 1] = weightSoFar;
-        }
-        else // Internal node
-        {
-            float w = weightSoFar + (t->getHeight() / t->getOrder());
-            doWeightCalc(w, weights, t->getLeft());
-            doWeightCalc(w, weights, t->getRight());            
-        }
-    }
-}
-
-}