Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / phytofile.cpp

diff --git a/website/archive/binaries/mac/src/muscle/phytofile.cpp b/website/archive/binaries/mac/src/muscle/phytofile.cpp
deleted file mode 100644 (file)
index 76fb368..0000000
--- a/website/archive/binaries/mac/src/muscle/phytofile.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-#include "muscle.h"\r
-#include "tree.h"\r
-#include "textfile.h"\r
-\r
-unsigned Tree::GetAnyNonLeafNode() const\r
-       {\r
-       for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)\r
-               if (!IsLeaf(uNodeIndex))\r
-                       return uNodeIndex;\r
-       return NULL_NEIGHBOR;\r
-       }\r
-\r
-void Tree::ToFile(TextFile &File) const\r
-       {\r
-       if (IsRooted())\r
-               {\r
-               ToFileNodeRooted(File, m_uRootNodeIndex);\r
-               File.PutString(";\n");\r
-               return;\r
-               }\r
-\r
-// Unrooted.\r
-       unsigned uNodeIndex = GetAnyNonLeafNode();\r
-\r
-       File.PutString("(\n");\r
-       ToFileNodeUnrooted(File, m_uNeighbor1[uNodeIndex], uNodeIndex);\r
-       File.PutString(",\n");\r
-       ToFileNodeUnrooted(File, m_uNeighbor2[uNodeIndex], uNodeIndex);\r
-       File.PutString(",\n");\r
-       ToFileNodeUnrooted(File, m_uNeighbor3[uNodeIndex], uNodeIndex);\r
-       File.PutString(");\n");\r
-       }\r
-\r
-void Tree::ToFileNodeUnrooted(TextFile &File, unsigned uNodeIndex, unsigned uParent) const\r
-       {\r
-       assert(!IsRooted());\r
-\r
-       bool bGroup = !IsLeaf(uNodeIndex);\r
-       if (bGroup)\r
-               File.PutString("(\n");\r
-\r
-       if (IsLeaf(uNodeIndex))\r
-               File.PutString(GetName(uNodeIndex));\r
-       else\r
-               {\r
-               ToFileNodeUnrooted(File, GetFirstNeighbor(uNodeIndex, uParent), uNodeIndex);\r
-               File.PutString(",\n");\r
-               ToFileNodeUnrooted(File, GetSecondNeighbor(uNodeIndex, uParent), uNodeIndex);\r
-               }\r
-\r
-       if (bGroup)\r
-               File.PutString(")");\r
-\r
-       if (HasEdgeLength(uNodeIndex, uParent))\r
-               File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));\r
-       File.PutString("\n");\r
-       }\r
-\r
-void Tree::ToFileNodeRooted(TextFile &File, unsigned uNodeIndex) const\r
-       {\r
-       assert(IsRooted());\r
-\r
-       bool bGroup = !IsLeaf(uNodeIndex) || IsRoot(uNodeIndex);\r
-       if (bGroup)\r
-               File.PutString("(\n");\r
-\r
-       if (IsLeaf(uNodeIndex))\r
-               File.PutString(GetName(uNodeIndex));\r
-       else\r
-               {\r
-               ToFileNodeRooted(File, GetLeft(uNodeIndex));\r
-               File.PutString(",\n");\r
-               ToFileNodeRooted(File, GetRight(uNodeIndex));\r
-               }\r
-\r
-       if (bGroup)\r
-               File.PutString(")");\r
-\r
-       if (!IsRoot(uNodeIndex))\r
-               {\r
-               unsigned uParent = GetParent(uNodeIndex);\r
-               if (HasEdgeLength(uNodeIndex, uParent))\r
-                       File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent));\r
-               }\r
-       File.PutString("\n");\r
-       }\r