--- /dev/null
+#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