Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/writescorefile.cpp b/website/archive/binaries/mac/src/muscle/writescorefile.cpp
deleted file mode 100644 (file)
index 17f7a81..0000000
--- a/website/archive/binaries/mac/src/muscle/writescorefile.cpp
+++ /dev/null
@@ -1,69 +0,0 @@
-#include "muscle.h"\r
-#include "msa.h"\r
-#include <errno.h>\r
-\r
-extern float VTML_SP[32][32];\r
-extern float NUC_SP[32][32];\r
-\r
-static double GetColScore(const MSA &msa, unsigned uCol)\r
-       {\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       unsigned uPairCount = 0;\r
-       double dSum = 0.0;\r
-       for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1)\r
-               {\r
-               if (msa.IsGap(uSeq1, uCol))\r
-                       continue;\r
-               unsigned uLetter1 = msa.GetLetterEx(uSeq1, uCol);\r
-               if (uLetter1 >= g_AlphaSize)\r
-                       continue;\r
-               for (unsigned uSeq2 = uSeq1 + 1; uSeq2 < uSeqCount; ++uSeq2)\r
-                       {\r
-                       if (msa.IsGap(uSeq2, uCol))\r
-                               continue;\r
-                       unsigned uLetter2 = msa.GetLetterEx(uSeq2, uCol);\r
-                       if (uLetter2 >= g_AlphaSize)\r
-                               continue;\r
-                       double Score;\r
-                       switch (g_Alpha)\r
-                               {\r
-                       case ALPHA_Amino:\r
-                               Score = VTML_SP[uLetter1][uLetter2];\r
-                               break;\r
-                       case ALPHA_DNA:\r
-                       case ALPHA_RNA:\r
-                               Score = NUC_SP[uLetter1][uLetter2];\r
-                               break;\r
-                       default:\r
-                               Quit("GetColScore: invalid alpha=%d", g_Alpha);\r
-                               }\r
-                       dSum += Score;\r
-                       ++uPairCount;\r
-                       }\r
-               }\r
-       if (0 == uPairCount)\r
-               return 0;\r
-       return dSum / uPairCount;\r
-       }\r
-\r
-void WriteScoreFile(const MSA &msa)\r
-       {\r
-       FILE *f = fopen(g_pstrScoreFileName, "w");\r
-       if (0 == f)\r
-               Quit("Cannot open score file '%s' errno=%d", g_pstrScoreFileName, errno);\r
-\r
-       const unsigned uColCount = msa.GetColCount();\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       for (unsigned uCol = 0; uCol < uColCount; ++uCol)\r
-               {\r
-               double Score = GetColScore(msa, uCol);\r
-               fprintf(f, "%10.3f  ", Score);\r
-               for (unsigned uSeq = 0; uSeq < uSeqCount; ++uSeq)\r
-                       {\r
-                       char c = msa.GetChar(uSeq, uCol);\r
-                       fprintf(f, "%c", c);\r
-                       }\r
-               fprintf(f, "\n");\r
-               }\r
-       fclose(f);\r
-       }\r