Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/physeq.cpp b/website/archive/binaries/mac/src/muscle/physeq.cpp
deleted file mode 100644 (file)
index 522f8b1..0000000
--- a/website/archive/binaries/mac/src/muscle/physeq.cpp
+++ /dev/null
@@ -1,128 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include "textfile.h"\r
-\r
-const int BLOCKSIZE = 60;\r
-\r
-static char FixChar(char c)\r
-       {\r
-       switch (c)\r
-               {\r
-       case '(':\r
-       case ')':\r
-       case '[':\r
-       case ']':\r
-       case ':':\r
-       case ';':\r
-       case ',':\r
-               return '_';\r
-               }\r
-       if (!isprint(c))\r
-               return '_';\r
-       return c;\r
-       }\r
-\r
-static void FixName(char Name[])\r
-       {\r
-       while (char c = *Name)\r
-               *Name++ = FixChar(c);\r
-       }\r
-\r
-void MSA::ToPhySequentialFile(TextFile &File) const\r
-       {\r
-       const unsigned SeqCount = GetSeqCount();\r
-       const unsigned ColCount = GetColCount();\r
-\r
-       File.PutFormat("%d %d\n", SeqCount, ColCount);\r
-\r
-       if (0 == ColCount)\r
-               return;\r
-\r
-       for (unsigned Seq = 0; Seq < SeqCount; ++Seq)\r
-               {\r
-               char Name[11];\r
-               const char *ptrName = GetSeqName(Seq);\r
-               size_t n = strlen(ptrName);\r
-               if (n > 10)\r
-                       n = 10;\r
-               memcpy(Name, ptrName, n);\r
-               Name[n] = 0;\r
-               FixName(Name);\r
-               File.PutFormat("%-10.10s", Name);\r
-\r
-               int BlockIndex = 0;\r
-               int Col = 0;\r
-               for (;;)\r
-                       {\r
-                       const unsigned MaxCols = (BlockIndex == 0) ? (BLOCKSIZE - 10) : BLOCKSIZE;\r
-                       for (unsigned ColsThisBlock = 0; ColsThisBlock < MaxCols; ++ColsThisBlock)\r
-                               {\r
-                               if (Col == ColCount)\r
-                                       break;\r
-                               if (ColsThisBlock%10 == 0 && (BlockIndex == 0 || ColsThisBlock > 0))\r
-                                       File.PutChar(' ');\r
-                               char c = GetChar(Seq, Col);\r
-                               if (isalpha(c))\r
-                                       c = toupper(c);\r
-                               File.PutChar(c);\r
-                               ++Col;\r
-                               }\r
-                       File.PutChar('\n');\r
-                       if (Col == ColCount)\r
-                               break;\r
-                       ++BlockIndex;\r
-                       }\r
-               }\r
-       }\r
-\r
-void MSA::ToPhyInterleavedFile(TextFile &File) const\r
-       {\r
-       const unsigned SeqCount = GetSeqCount();\r
-       const unsigned ColCount = GetColCount();\r
-\r
-       File.PutFormat("%d %d\n", SeqCount, ColCount);\r
-\r
-       if (0 == ColCount)\r
-               return;\r
-\r
-       int Col = 0;\r
-       for (;;)\r
-               {\r
-               const unsigned ColBlockStart = Col;\r
-               const unsigned MaxCols = (ColBlockStart == 0) ? (BLOCKSIZE - 10) : BLOCKSIZE;\r
-\r
-               for (unsigned Seq = 0; Seq < SeqCount; ++Seq)\r
-                       {\r
-                       if (0 == ColBlockStart)\r
-                               {\r
-                               char Name[11];\r
-                               const char *ptrName = GetSeqName(Seq);\r
-                               size_t n = strlen(ptrName);\r
-                               if (n > 10)\r
-                                       n = 10;\r
-                               memcpy(Name, ptrName, n);\r
-                               Name[n] = 0;\r
-                               FixName(Name);\r
-                               File.PutFormat("%-10.10s", Name);\r
-                               }\r
-\r
-                       Col = ColBlockStart;\r
-                       for (unsigned ColsThisBlock = 0; ColsThisBlock < MaxCols; ++ColsThisBlock)\r
-                               {\r
-                               if (Col == ColCount)\r
-                                       break;\r
-                               if (ColsThisBlock%10 == 0 && (0 == ColBlockStart || ColsThisBlock > 0))\r
-                                       File.PutChar(' ');\r
-                               char c = GetChar(Seq, Col);\r
-                               if (isalpha(c))\r
-                                       c = toupper(c);\r
-                               File.PutChar(c);\r
-                               ++Col;\r
-                               }\r
-                       File.PutChar('\n');\r
-                       }\r
-               if (Col == ColCount)\r
-                       break;\r
-               File.PutChar('\n');\r
-               }\r
-       }\r