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

[mothur.git] / uchime_src / dp.h

diff --git a/uchime_src/dp.h b/uchime_src/dp.h
new file mode 100644 (file)
index 0000000..c771538
--- /dev/null
+++ b/uchime_src/dp.h
@@ -0,0 +1,164 @@
+#ifndef dp_h\r
+#define dp_h\r
+\r
+#define SAVE_FAST      0\r
+\r
+#include "myutils.h"\r
+#include "mx.h"\r
+#include "seqdb.h"\r
+#include "diagbox.h"\r
+#include "path.h"\r
+#include "alnparams.h"\r
+#include "alnheuristics.h"\r
+#include "hspfinder.h"\r
+\r
+typedef void (*OnPathFn)(const string &Path, bool Full);\r
+\r
+enum XType\r
+       {\r
+       XType_Full=1,\r
+       XType_Fwd=2,\r
+       XType_Bwd=3,\r
+       };\r
+\r
+// public\r
+float ViterbiBrute(const byte *A, unsigned LA, const byte *B, unsigned LB, \r
+  unsigned DiagLo, unsigned DiagHi, const AlnParams &AP, PathData &PD);\r
+\r
+float ViterbiSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, PathData &PD);\r
+\r
+float ViterbiSimpleBand(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, unsigned DiagLo, unsigned DiagHi, PathData &PD);\r
+\r
+float ViterbiFast(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, PathData &PD);\r
+\r
+float ViterbiFastBand(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  unsigned DiagLo, unsigned DiagHi, const AlnParams &AP, PathData &PD);\r
+\r
+float ViterbiFastMainDiag(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  unsigned BandRadius, const AlnParams &AP, PathData &PD);\r
+\r
+float XDropFwdSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);\r
+\r
+float XDropBwdSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);\r
+\r
+float XDropFwdFast(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);\r
+\r
+float XDropBwdFast(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, float XDrop, unsigned &Leni, unsigned &Lenj, PathData &PD);\r
+\r
+void XDropAlign(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  unsigned AncLoi, unsigned AncLoj, unsigned AncLen, const AlnParams &AP,\r
+  float XDrop, HSPData &HSP, PathData &PD);\r
+\r
+float SWSimple(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, unsigned &Loi, unsigned &Leni, unsigned &Lenj,\r
+  unsigned &Hij, PathData &PD);\r
+\r
+float SWFast(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, unsigned &Loi, unsigned &Leni, unsigned &Lenj,\r
+  unsigned &Hij, PathData &PD);\r
+\r
+void SWFast2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,\r
+  HSPData &HSP, PathData &PD);\r
+\r
+void SWSimple2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,\r
+  HSPData &HSP, PathData &PD);\r
+\r
+float SWUngapped(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const float * const *SubstMx, unsigned &LoA, unsigned &LoB, unsigned &Len);\r
+\r
+void SWUngapped2(const SeqData &SA, const SeqData &SB, const AlnParams &AP,\r
+  HSPData &HSP);\r
+\r
+float SWFastNTB(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP);\r
+\r
+void GlobalAlignBand(const byte *A, unsigned LA, const byte *B, unsigned LB,\r
+  const AlnParams &AP, unsigned BandRadius, PathData &PD);\r
+\r
+bool GlobalAlign(const SeqData &Query, const SeqData &Target, const AlnParams &AP,\r
+  const AlnHeuristics &AH, HSPFinder &HF, float MinFractId, float &HSPFractId,\r
+  PathData &PD);\r
+\r
+bool GlobalAlign(const SeqData &Query, const SeqData &Target, string &Path);\r
+\r
+void GetBruteMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+void GetSimpleDPMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+void GetSimpleBandMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+void GetXDropFwdSimpleDPMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+#if    SAVE_FAST\r
+void GetFastMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+void GetFastBandMxs(Mx<float> **M, Mx<float> **D, Mx<float> **I);\r
+#endif\r
+\r
+// private\r
+void TraceBackBit(unsigned LA, unsigned LB, char State, PathData &PD);\r
+void TraceBackBitSW(unsigned LA, unsigned LB, unsigned Besti, unsigned Bestj,\r
+  unsigned &Leni, unsigned &Lenj, PathData &PD);\r
+void EnumPaths(unsigned L1, unsigned L2, bool SubPaths, OnPathFn OnPath);\r
+void AllocBit(unsigned LA, unsigned LB);\r
+\r
+const byte TRACEBITS_DM = 0x01;\r
+const byte TRACEBITS_IM = 0x02;\r
+const byte TRACEBITS_MD = 0x04;\r
+const byte TRACEBITS_MI = 0x08;\r
+const byte TRACEBITS_SM = 0x10;\r
+const byte TRACEBITS_UNINIT = ~0x1f;\r
+\r
+extern Mx<byte> g_Mx_TBBit;\r
+extern float *g_DPRow1;\r
+extern float *g_DPRow2;\r
+extern byte **g_TBBit;\r
+\r
+static inline void Max_xM(float &Score, float MM, float DM, float IM, byte &State)\r
+       {\r
+       Score = MM;\r
+       State = 'M';\r
+\r
+       if (DM > Score)\r
+               {\r
+               Score = DM;\r
+               State = 'D';\r
+               }\r
+       if (IM > Score)\r
+               {\r
+               Score = IM;\r
+               State = 'I';\r
+               }\r
+       }\r
+\r
+static inline void Max_xD(float &Score, float MD, float DD, byte &State)\r
+       {\r
+       if (MD >= DD)\r
+               {\r
+               Score = MD;\r
+               State = 'M';\r
+               }\r
+       else\r
+               {\r
+               Score = DD;\r
+               State = 'D';\r
+               }\r
+       }\r
+\r
+static inline void Max_xI(float &Score, float MI, float II, byte &State)\r
+       {\r
+       if (MI >= II)\r
+               {\r
+               Score = MI;\r
+               State = 'M';\r
+               }\r
+       else\r
+               {\r
+               Score = II;\r
+               State = 'I';\r
+               }\r
+       }\r
+\r
+#endif // dp_h\r