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

[mothur.git] / uchime_src / alnheuristics.h

diff --git a/uchime_src/alnheuristics.h b/uchime_src/alnheuristics.h
new file mode 100644 (file)
index 0000000..9a8d283
--- /dev/null
+++ b/uchime_src/alnheuristics.h
@@ -0,0 +1,29 @@
+#ifndef alnheuristics_h\r
+#define alnheuristics_h\r
+\r
+struct AlnParams;\r
+\r
+struct AlnHeuristics\r
+       {\r
+       unsigned BandRadius;\r
+       unsigned HSPFinderWordLength;\r
+       float SeedT;\r
+\r
+       float XDropG;                   //  GappedBlast default\r
+       float XDropU;                   //  UngappedBlast default\r
+       float XDropUG;                  //  UngappedBlast called by GappedBlast\r
+\r
+       unsigned MinGlobalHSPLength;\r
+\r
+       AlnHeuristics();\r
+       void InitFromCmdLine(const AlnParams &AP);\r
+       void InitGlobalFull();\r
+\r
+       bool IsGlobalFull() const\r
+               {\r
+               return MinGlobalHSPLength == 0 && BandRadius == 0;\r
+               }\r
+\r
+       };\r
+\r
+#endif // alnheuristics_h\r