Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/msf.cpp b/website/archive/binaries/mac/src/muscle/msf.cpp
deleted file mode 100644 (file)
index 251064a..0000000
--- a/website/archive/binaries/mac/src/muscle/msf.cpp
+++ /dev/null
@@ -1,121 +0,0 @@
-#include "muscle.h"\r
-#include <stdio.h>\r
-#include <ctype.h>\r
-#include "msa.h"\r
-#include "textfile.h"\r
-\r
-const int MAX_NAME = 63;\r
-\r
-const unsigned uCharsPerLine = 50;\r
-const unsigned uCharsPerBlock = 10;\r
-\r
-// Truncate at first white space or MAX_NAME, whichever comes\r
-// first, then pad with blanks up to PadLength.\r
-static const char *GetPaddedName(const char *Name, int PadLength)\r
-       {\r
-       static char PaddedName[MAX_NAME+1];\r
-       memset(PaddedName, ' ', MAX_NAME);\r
-       size_t n = strcspn(Name, " \t");\r
-       memcpy(PaddedName, Name, n);\r
-       PaddedName[PadLength] = 0;\r
-       return PaddedName;\r
-       }\r
-\r
-static const char *strfind(const char *s, const char *t)\r
-       {\r
-       size_t n = strcspn(s, t);\r
-       if (0 == n)\r
-               return 0;\r
-       return s + n;\r
-       }\r
-\r
-// GCG checksum code kindly provided by Eric Martel.\r
-unsigned MSA::GetGCGCheckSum(unsigned uSeqIndex) const\r
-       {\r
-       unsigned CheckSum = 0;\r
-       const unsigned uColCount = GetColCount();\r
-       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-               {\r
-               unsigned c = (unsigned) GetChar(uSeqIndex, uColIndex);\r
-               CheckSum += c*(uColIndex%57 + 1);\r
-               CheckSum %= 10000;              \r
-               }\r
-       return CheckSum;\r
-       }\r
-\r
-static void MSFFixGaps(MSA &a)\r
-       {\r
-       const int SeqCount = a.GetSeqCount();\r
-       const int ColCount = a.GetColCount();\r
-       for (int SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex)\r
-               {\r
-               for (int ColIndex = 0; ColIndex < ColCount; ++ColIndex)\r
-                       if (a.IsGap(SeqIndex, ColIndex))\r
-                               a.SetChar(SeqIndex, ColIndex, '.');\r
-               }\r
-       }\r
-\r
-void MSA::ToMSFFile(TextFile &File, const char *ptrComment) const\r
-       {\r
-// Cast away const, yuck\r
-       SetMSAWeightsMuscle((MSA &) *this);\r
-       MSFFixGaps((MSA &) *this);\r
-\r
-       File.PutString("PileUp\n");\r
-       \r
-       if (0 != ptrComment)\r
-               File.PutFormat("Comment: %s\n", ptrComment);\r
-       else\r
-               File.PutString("\n");\r
-\r
-       char seqtype = (g_Alpha == ALPHA_DNA || g_Alpha == ALPHA_RNA) ? 'N' : 'A';\r
-       File.PutFormat("  MSF: %u  Type: %c  Check: 0000  ..\n\n",\r
-         GetColCount(), seqtype);\r
-\r
-       int iLongestNameLength = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-               {\r
-               const char *Name = GetSeqName(uSeqIndex);\r
-               const char *PaddedName = GetPaddedName(Name, MAX_NAME);\r
-               int iLength = (int) strcspn(PaddedName, " \t");\r
-               if (iLength > iLongestNameLength)\r
-                       iLongestNameLength = iLength;\r
-               }\r
-               \r
-       for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-               {\r
-               const char *Name = GetSeqName(uSeqIndex);\r
-               const char *PaddedName = GetPaddedName(Name, iLongestNameLength);\r
-               File.PutFormat(" Name: %s", PaddedName);\r
-               File.PutFormat("  Len: %u  Check: %5u  Weight: %g\n",\r
-                 GetColCount(), GetGCGCheckSum(uSeqIndex), GetSeqWeight(uSeqIndex));\r
-               }\r
-       File.PutString("\n//\n");\r
-       if (0 == GetColCount())\r
-               return;\r
-\r
-       unsigned uLineCount = (GetColCount() - 1)/uCharsPerLine + 1;\r
-       for (unsigned uLineIndex = 0; uLineIndex < uLineCount; ++uLineIndex)\r
-               {\r
-               File.PutString("\n");\r
-               unsigned uStartColIndex = uLineIndex*uCharsPerLine;\r
-               unsigned uEndColIndex = uStartColIndex + uCharsPerLine - 1;\r
-               if (uEndColIndex >= GetColCount())\r
-                       uEndColIndex = GetColCount() - 1;\r
-               for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-                       {\r
-                       const char *Name = GetSeqName(uSeqIndex);\r
-                       const char *PaddedName = GetPaddedName(Name, iLongestNameLength);\r
-                       File.PutFormat("%s   ", PaddedName);\r
-                       for (unsigned uColIndex = uStartColIndex; uColIndex <= uEndColIndex;\r
-                         ++uColIndex)\r
-                               {\r
-                               if (0 == uColIndex%uCharsPerBlock)\r
-                                       File.PutString(" ");\r
-                               char c = GetChar(uSeqIndex, uColIndex);\r
-                               File.PutFormat("%c", c);\r
-                               }\r
-                       File.PutString("\n");\r
-                       }\r
-               }\r
-       }\r