Mac binaries

[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
new file mode 100644 (file)
index 0000000..76fb368
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/phytofile.cpp
@@ -0,0 +1,86 @@
+#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