binaries/src/muscle/phyfromclust.cpp

   1 #include "muscle.h"\r
   2 #include "tree.h"\r
   3 #include "clust.h"\r
   4 \r
   5 void Tree::InitCache(unsigned uCacheCount)\r
   6         {\r
   7         m_uCacheCount = uCacheCount;\r
   8 \r
   9         m_uNeighbor1 = new unsigned[m_uCacheCount];\r
  10         m_uNeighbor2 = new unsigned[m_uCacheCount];\r
  11         m_uNeighbor3 = new unsigned[m_uCacheCount];\r
  12 \r
  13         m_Ids = new unsigned[m_uCacheCount];\r
  14 \r
  15         m_dEdgeLength1 = new double[m_uCacheCount];\r
  16         m_dEdgeLength2 = new double[m_uCacheCount];\r
  17         m_dEdgeLength3 = new double[m_uCacheCount];\r
  18         m_dHeight = new double[m_uCacheCount];\r
  19 \r
  20         m_bHasEdgeLength1 = new bool[m_uCacheCount];\r
  21         m_bHasEdgeLength2 = new bool[m_uCacheCount];\r
  22         m_bHasEdgeLength3 = new bool[m_uCacheCount];\r
  23         m_bHasHeight = new bool[m_uCacheCount];\r
  24 \r
  25         m_ptrName = new char *[m_uCacheCount];\r
  26 \r
  27         for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)\r
  28                 {\r
  29                 m_uNeighbor1[uNodeIndex] = NULL_NEIGHBOR;\r
  30                 m_uNeighbor2[uNodeIndex] = NULL_NEIGHBOR;\r
  31                 m_uNeighbor3[uNodeIndex] = NULL_NEIGHBOR;\r
  32                 m_bHasEdgeLength1[uNodeIndex] = false;\r
  33                 m_bHasEdgeLength2[uNodeIndex] = false;\r
  34                 m_bHasEdgeLength3[uNodeIndex] = false;\r
  35                 m_bHasHeight[uNodeIndex] = false;\r
  36                 m_dEdgeLength1[uNodeIndex] = dInsane;\r
  37                 m_dEdgeLength2[uNodeIndex] = dInsane;\r
  38                 m_dEdgeLength3[uNodeIndex] = dInsane;\r
  39                 m_dHeight[uNodeIndex] = dInsane;\r
  40                 m_ptrName[uNodeIndex] = 0;\r
  41                 m_Ids[uNodeIndex] = uInsane;\r
  42                 }\r
  43         }\r
  44 \r
  45 void Tree::FromClust(Clust &C)\r
  46         {\r
  47         Clear();\r
  48 \r
  49         m_uNodeCount = C.GetNodeCount();\r
  50         InitCache(m_uNodeCount);\r
  51 \r
  52 // Cluster is always rooted. An unrooted cluster\r
  53 // is represented by a pseudo-root, which we fix later.\r
  54         m_bRooted = true;\r
  55         const unsigned uRoot = C.GetRootNodeIndex();\r
  56         m_uRootNodeIndex = uRoot;\r
  57         m_uNeighbor1[uRoot] = NULL_NEIGHBOR;\r
  58         m_bHasEdgeLength1[uRoot] = false;\r
  59 \r
  60         for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)\r
  61                 {\r
  62                 if (C.IsLeaf(uNodeIndex))\r
  63                         {\r
  64                         const char *ptrName = C.GetNodeName(uNodeIndex);\r
  65                         m_ptrName[uNodeIndex] = strsave(ptrName);\r
  66                         m_Ids[uNodeIndex] = C.GetNodeId(uNodeIndex);\r
  67                         continue;\r
  68                         }\r
  69 \r
  70                 const unsigned uLeft = C.GetLeftIndex(uNodeIndex);\r
  71                 const unsigned uRight = C.GetRightIndex(uNodeIndex);\r
  72 \r
  73                 const double dLeftLength = C.GetLength(uLeft);\r
  74                 const double dRightLength = C.GetLength(uRight);\r
  75 \r
  76                 m_uNeighbor2[uNodeIndex] = uLeft;\r
  77                 m_uNeighbor3[uNodeIndex] = uRight;\r
  78 \r
  79                 m_dEdgeLength1[uLeft] = dLeftLength;\r
  80                 m_dEdgeLength1[uRight] = dRightLength;\r
  81 \r
  82                 m_uNeighbor1[uLeft] = uNodeIndex;\r
  83                 m_uNeighbor1[uRight] = uNodeIndex;\r
  84 \r
  85                 m_bHasEdgeLength1[uLeft] = true;\r
  86                 m_bHasEdgeLength1[uRight] = true;\r
  87 \r
  88                 m_dEdgeLength2[uNodeIndex] = dLeftLength;\r
  89                 m_dEdgeLength3[uNodeIndex] = dRightLength;\r
  90 \r
  91                 m_bHasEdgeLength2[uNodeIndex] = true;\r
  92                 m_bHasEdgeLength3[uNodeIndex] = true;\r
  93                 }\r
  94         Validate();\r
  95         }\r