removing chime source files from mother project.

[mothur.git] / globalalign2.cpp

diff --git a/globalalign2.cpp b/globalalign2.cpp
deleted file mode 100644 (file)
index 6bb35a9..0000000
--- a/globalalign2.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-//#if  UCHIMES\r
-\r
-#include "dp.h"\r
-#include "seq.h"\r
-\r
-static AlnParams g_AP;\r
-static bool g_APInitDone = false;\r
-\r
-bool GlobalAlign(const SeqData &Query, const SeqData &Target, PathData &PD)\r
-       {\r
-       if (!g_APInitDone)\r
-               {\r
-               g_AP.InitFromCmdLine(true);\r
-               g_APInitDone = true;\r
-               }\r
-\r
-       ViterbiFast(Query.Seq, Query.L, Target.Seq, Target.L, g_AP, PD);\r
-       return true;\r
-       }\r
-\r
-bool GlobalAlign(const SeqData &Query, const SeqData &Target, string &Path)\r
-       {\r
-       PathData PD;\r
-       GlobalAlign(Query, Target, PD);\r
-       Path = string(PD.Start);\r
-       return true;\r
-       }\r
-\r
-bool GlobalAlign(const SeqData &Query, const SeqData &Target, const AlnParams &/*AP*/,\r
-  const AlnHeuristics &AH, HSPFinder &/*HF*/, float /*MinFractId*/, float &/*HSPId*/, PathData &PD)\r
-       {\r
-       PD.Clear();\r
-       string Path;\r
-       bool Found = GlobalAlign(Query, Target, Path);\r
-       if (!Found)\r
-               return false;\r
-       unsigned n = SIZE(Path);\r
-       PD.Alloc(n+1);\r
-       memcpy(PD.Front, Path.c_str(), n);\r
-       PD.Start = PD.Front;\r
-       PD.Start[n] = 0;\r
-       return true;\r
-       }\r
-\r
-//#endif // UCHIMES\r