source: branches/nameserver/GDE/MUSCLE/src/phyfromclust.cpp

#include "muscle.h"
#include "tree.h"
#include "clust.h"

void Tree::InitCache(unsigned uCacheCount)
        {
        m_uCacheCount = uCacheCount;

        m_uNeighbor1 = new unsigned[m_uCacheCount];
        m_uNeighbor2 = new unsigned[m_uCacheCount];
        m_uNeighbor3 = new unsigned[m_uCacheCount];

        m_Ids = new unsigned[m_uCacheCount];

        m_dEdgeLength1 = new double[m_uCacheCount];
        m_dEdgeLength2 = new double[m_uCacheCount];
        m_dEdgeLength3 = new double[m_uCacheCount];
        m_dHeight = new double[m_uCacheCount];

        m_bHasEdgeLength1 = new bool[m_uCacheCount];
        m_bHasEdgeLength2 = new bool[m_uCacheCount];
        m_bHasEdgeLength3 = new bool[m_uCacheCount];
        m_bHasHeight = new bool[m_uCacheCount];

        m_ptrName = new char *[m_uCacheCount];

        for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)
                {
                m_uNeighbor1[uNodeIndex] = NULL_NEIGHBOR;
                m_uNeighbor2[uNodeIndex] = NULL_NEIGHBOR;
                m_uNeighbor3[uNodeIndex] = NULL_NEIGHBOR;
                m_bHasEdgeLength1[uNodeIndex] = false;
                m_bHasEdgeLength2[uNodeIndex] = false;
                m_bHasEdgeLength3[uNodeIndex] = false;
                m_bHasHeight[uNodeIndex] = false;
                m_dEdgeLength1[uNodeIndex] = dInsane;
                m_dEdgeLength2[uNodeIndex] = dInsane;
                m_dEdgeLength3[uNodeIndex] = dInsane;
                m_dHeight[uNodeIndex] = dInsane;
                m_ptrName[uNodeIndex] = 0;
                m_Ids[uNodeIndex] = uInsane;
                }
        }

void Tree::FromClust(Clust &C)
        {
        Clear();

        m_uNodeCount = C.GetNodeCount();
        InitCache(m_uNodeCount);

// Cluster is always rooted. An unrooted cluster
// is represented by a pseudo-root, which we fix later.
        m_bRooted = true;
        const unsigned uRoot = C.GetRootNodeIndex();
        m_uRootNodeIndex = uRoot;
        m_uNeighbor1[uRoot] = NULL_NEIGHBOR;
        m_bHasEdgeLength1[uRoot] = false;

        for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)
                {
                if (C.IsLeaf(uNodeIndex))
                        {
                        const char *ptrName = C.GetNodeName(uNodeIndex);
                        m_ptrName[uNodeIndex] = strsave(ptrName);
                        m_Ids[uNodeIndex] = C.GetNodeId(uNodeIndex);
                        continue;
                        }

                const unsigned uLeft = C.GetLeftIndex(uNodeIndex);
                const unsigned uRight = C.GetRightIndex(uNodeIndex);

                const double dLeftLength = C.GetLength(uLeft);
                const double dRightLength = C.GetLength(uRight);

                m_uNeighbor2[uNodeIndex] = uLeft;
                m_uNeighbor3[uNodeIndex] = uRight;

                m_dEdgeLength1[uLeft] = dLeftLength;
                m_dEdgeLength1[uRight] = dRightLength;

                m_uNeighbor1[uLeft] = uNodeIndex;
                m_uNeighbor1[uRight] = uNodeIndex;

                m_bHasEdgeLength1[uLeft] = true;
                m_bHasEdgeLength1[uRight] = true;

                m_dEdgeLength2[uNodeIndex] = dLeftLength;
                m_dEdgeLength3[uNodeIndex] = dRightLength;

                m_bHasEdgeLength2[uNodeIndex] = true;
                m_bHasEdgeLength3[uNodeIndex] = true;
                }
        Validate();
        }