Mac binaries

[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
new file mode 100644 (file)
index 0000000..251064a
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/msf.cpp
@@ -0,0 +1,121 @@
+#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