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

[mothur.git] / uchime_src / seq.h

diff --git a/uchime_src/seq.h b/uchime_src/seq.h
new file mode 100644 (file)
index 0000000..9014641
--- /dev/null
+++ b/uchime_src/seq.h
@@ -0,0 +1,38 @@
+#ifndef seq_h\r
+#define seq_h\r
+\r
+struct ORFData;\r
+\r
+struct SeqData\r
+       {\r
+       const char *Label;\r
+       const byte *Seq;\r
+       unsigned L;\r
+       unsigned Index;\r
+\r
+// RevComp means that SeqData.Seq is reverse-complemented relative\r
+// to the sequence in the input file (query or db). Coordinates in\r
+// a hit (e.g., AlnData) will be relative to SeqData.Seq, so both\r
+// the sequence and the coordinates should be r.c.'d for output.\r
+       bool RevComp;\r
+       bool Nucleo;\r
+       const ORFData *ORFParent;\r
+\r
+       SeqData()\r
+               {\r
+               Clear();\r
+               }\r
+\r
+       void Clear()\r
+               {\r
+               Label = 0;\r
+               Seq = 0;\r
+               L = 0;\r
+               Index = UINT_MAX;\r
+               RevComp = false;\r
+               Nucleo = false;\r
+               ORFParent = 0;\r
+               }\r
+       };\r
+\r
+#endif // seq_h\r