Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / msadistmafft.h

diff --git a/website/archive/binaries/mac/src/muscle/msadistmafft.h b/website/archive/binaries/mac/src/muscle/msadistmafft.h
new file mode 100644 (file)
index 0000000..56772e1
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/msadistmafft.h
@@ -0,0 +1,24 @@
+#ifndef MSADistMAFFT_h\r
+#define MSADistMAFFT_h\r
+\r
+#include "msadist.h"\r
+#include <math.h>\r
+\r
+extern double PctIdToMAFFTDist(double dPctId);\r
+\r
+class MSADistMAFFT : public MSADist\r
+       {\r
+public:\r
+       virtual double ComputeDist(const MSA &msa, unsigned uSeqIndex1,\r
+         unsigned uSeqIndex2)\r
+               {\r
+               double dPctId = msa.GetPctIdentityPair(uSeqIndex1, uSeqIndex2);\r
+               //if (dPctId < 0.05)\r
+               //      dPctId = 0.05;\r
+               //double dDist = -log(dPctId);\r
+               //return dDist;\r
+               return PctIdToMAFFTDist(dPctId);\r
+               }\r
+       };\r
+\r
+#endif // MSADistMAFFT_h\r