website/archive/binaries/mac/src/muscle/phytofile.cpp

   1 #include "muscle.h"\r
   2 #include "tree.h"\r
   3 #include "textfile.h"\r
   4 \r
   5 unsigned Tree::GetAnyNonLeafNode() const\r
   6         {\r
   7         for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)\r
   8                 if (!IsLeaf(uNodeIndex))\r
   9                         return uNodeIndex;\r
  10         return NULL_NEIGHBOR;\r
  11         }\r
  12 \r
  13 void Tree::ToFile(TextFile &File) const\r
  14         {\r
  15         if (IsRooted())\r
  16                 {\r
  17                 ToFileNodeRooted(File, m_uRootNodeIndex);\r
  18                 File.PutString(";\n");\r
  19                 return;\r
  20                 }\r
  21 \r
  22 // Unrooted.\r
  23         unsigned uNodeIndex = GetAnyNonLeafNode();\r
  24 \r
  25         File.PutString("(\n");\r
  26         ToFileNodeUnrooted(File, m_uNeighbor1[uNodeIndex], uNodeIndex);\r
  27         File.PutString(",\n");\r
  28         ToFileNodeUnrooted(File, m_uNeighbor2[uNodeIndex], uNodeIndex);\r
  29         File.PutString(",\n");\r
  30         ToFileNodeUnrooted(File, m_uNeighbor3[uNodeIndex], uNodeIndex);\r
  31         File.PutString(");\n");\r
  32         }\r
  33 \r
  34 void Tree::ToFileNodeUnrooted(TextFile &File, unsigned uNodeIndex, unsigned uParent) const\r
  35         {\r
  36         assert(!IsRooted());\r
  37 \r
  38         bool bGroup = !IsLeaf(uNodeIndex);\r
  39         if (bGroup)\r
  40                 File.PutString("(\n");\r
  41 \r
  42         if (IsLeaf(uNodeIndex))\r
  43                 File.PutString(GetName(uNodeIndex));\r
  44         else\r
  45                 {\r
  46                 ToFileNodeUnrooted(File, GetFirstNeighbor(uNodeIndex, uParent), uNodeIndex);\r
  47                 File.PutString(",\n");\r
  48                 ToFileNodeUnrooted(File, GetSecondNeighbor(uNodeIndex, uParent), uNodeIndex);\r
  49                 }\r
  50 \r
  51         if (bGroup)\r
  52                 File.PutString(")");\r
  53 \r
  54         if (HasEdgeLength(uNodeIndex, uParent))\r
  55                 File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));\r
  56         File.PutString("\n");\r
  57         }\r
  58 \r
  59 void Tree::ToFileNodeRooted(TextFile &File, unsigned uNodeIndex) const\r
  60         {\r
  61         assert(IsRooted());\r
  62 \r
  63         bool bGroup = !IsLeaf(uNodeIndex) || IsRoot(uNodeIndex);\r
  64         if (bGroup)\r
  65                 File.PutString("(\n");\r
  66 \r
  67         if (IsLeaf(uNodeIndex))\r
  68                 File.PutString(GetName(uNodeIndex));\r
  69         else\r
  70                 {\r
  71                 ToFileNodeRooted(File, GetLeft(uNodeIndex));\r
  72                 File.PutString(",\n");\r
  73                 ToFileNodeRooted(File, GetRight(uNodeIndex));\r
  74                 }\r
  75 \r
  76         if (bGroup)\r
  77                 File.PutString(")");\r
  78 \r
  79         if (!IsRoot(uNodeIndex))\r
  80                 {\r
  81                 unsigned uParent = GetParent(uNodeIndex);\r
  82                 if (HasEdgeLength(uNodeIndex, uParent))\r
  83                         File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));\r
  84                 }\r
  85         File.PutString("\n");\r
  86         }\r