added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / alnparams.h

diff --git a/uchime_src/alnparams.h b/uchime_src/alnparams.h
new file mode 100644 (file)
index 0000000..4037912
--- /dev/null
+++ b/uchime_src/alnparams.h
@@ -0,0 +1,59 @@
+#ifndef alnparams_h\r
+#define alnparams_h\r
+\r
+struct HSPData;\r
+\r
+// Gap penalty scores are negative\r
+// (i.e., are scores, not penalties).\r
+struct AlnParams\r
+       {\r
+       const char *SubstMxName;\r
+       const float * const *SubstMx;\r
+\r
+       bool Nucleo;\r
+       bool NucleoSet;\r
+\r
+// Local gaps\r
+       float LocalOpen;\r
+       float LocalExt;\r
+\r
+// Global internal gaps\r
+       float OpenA;\r
+       float OpenB;\r
+\r
+       float ExtA;\r
+       float ExtB;\r
+\r
+// Global terminal gaps\r
+       float LOpenA;\r
+       float LOpenB;\r
+       float ROpenA;\r
+       float ROpenB;\r
+\r
+       float LExtA;\r
+       float LExtB;\r
+       float RExtA;\r
+       float RExtB;\r
+\r
+       void Clear();\r
+       void SetLocal(float Open, float Ext);\r
+       void Init2(const float * const *Mx, float Open, float Ext);\r
+       void Init4(const float * const *Mx, float Open, float Ext, float TermOpen, float TermExt);\r
+       void Init(const AlnParams &AP, const HSPData &HSP, unsigned LA, unsigned LB);\r
+       void InitFromCmdLine(bool Nucleo);\r
+       void SetMxFromCmdLine(bool Nucleo);\r
+       void SetPenalties(const string &OpenStr, const string &ExtStr);\r
+       float GetLocalOpen() const;\r
+       float GetLocalExt() const;\r
+       bool GetIsNucleo() const;\r
+\r
+       bool Is2() const;\r
+       bool Is4() const;\r
+       const char *GetType() const;\r
+\r
+       void LogMe() const;\r
+       };\r
+\r
+const float OBVIOUSLY_WRONG_PENALTY = 1000.0;\r
+\r
+#endif // alnparams_h\r