Mac binaries

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

diff --git a/website/archive/binaries/mac/src/muscle/aligntwomsas.cpp b/website/archive/binaries/mac/src/muscle/aligntwomsas.cpp
new file mode 100644 (file)
index 0000000..d428c93
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/aligntwomsas.cpp
@@ -0,0 +1,41 @@
+#include "muscle.h"\r
+#include "msa.h"\r
+#include "profile.h"\r
+#include "pwpath.h"\r
+#include "textfile.h"\r
+#include "timing.h"\r
+\r
+SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,\r
+  bool bLockLeft, bool bLockRight)\r
+       {\r
+       const unsigned uLengthA = msa1.GetColCount();\r
+       const unsigned uLengthB = msa2.GetColCount();\r
+\r
+       ProfPos *PA = ProfileFromMSA(msa1);\r
+       ProfPos *PB = ProfileFromMSA(msa2);\r
+\r
+       if (bLockLeft)\r
+               {\r
+               PA[0].m_scoreGapOpen = MINUS_INFINITY;\r
+               PB[0].m_scoreGapOpen = MINUS_INFINITY;\r
+               }\r
+\r
+       if (bLockRight)\r
+               {\r
+               PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;\r
+               PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;\r
+               }\r
+\r
+       float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0\r
+       if (r < 1)\r
+               r = 1/r;\r
+\r
+       SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);\r
+\r
+       AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);\r
+\r
+       delete[] PA;\r
+       delete[] PB;\r
+\r
+       return Score;\r
+       }\r