removing chime source files from mother project.

[mothur.git] / tracebackbit.cpp

diff --git a/tracebackbit.cpp b/tracebackbit.cpp
deleted file mode 100644 (file)
index 94159cd..0000000
--- a/tracebackbit.cpp
+++ /dev/null
@@ -1,180 +0,0 @@
-#include "dp.h"
-
-#define TRACE  0
-
-Mx<byte> g_Mx_TBBit;
-byte **g_TBBit;
-float *g_DPRow1;
-float *g_DPRow2;
-static float *g_DPBuffer1;
-static float *g_DPBuffer2;
-
-static unsigned g_CacheLB;
-
-void AllocBit(unsigned LA, unsigned LB)
-       {
-       g_Mx_TBBit.Alloc("TBBit", LA+1, LB+1);
-       g_TBBit = g_Mx_TBBit.GetData();
-       if (LB > g_CacheLB)
-               {
-               MYFREE(g_DPBuffer1, g_CacheLB, AllocBit);
-               MYFREE(g_DPBuffer2, g_CacheLB, AllocBit);
-
-               g_CacheLB = LB + 128;
-
-       // Allow use of [-1]
-               //g_DPBuffer1 = myalloc<float>(g_CacheLB+3);
-               //g_DPBuffer2 = myalloc<float>(g_CacheLB+3);
-               g_DPBuffer1 = MYALLOC(float, g_CacheLB+3, AllocBit);
-               g_DPBuffer2 = MYALLOC(float, g_CacheLB+3, AllocBit);
-               g_DPRow1 = g_DPBuffer1 + 1;
-               g_DPRow2 = g_DPBuffer2 + 1;
-               }
-       }
-
-void TraceBackBit(unsigned LA, unsigned LB, char State, PathData &PD)
-       {
-       PD.Alloc(LA+LB);
-
-       StartTimer(TraceBackBit);
-       char *PathPtr = PD.Back;
-       *PathPtr = 0;
-
-       byte **TB = g_TBBit;
-
-#if    TRACE
-       Log("\n");
-       Log("TraceBackBit\n");
-#endif
-
-       size_t i = LA;
-       size_t j = LB;
-       for (;;)
-               {
-#if    TRACE
-               Log("i=%3d  j=%3d  state=%c\n", (int) i, (int) j, State);
-#endif
-               if (i == 0 && j == 0)
-                       break;
-
-               --PathPtr;
-               *PathPtr = State;
-
-               byte t;
-               switch (State)
-                       {
-               case 'M':
-                       asserta(i > 0 && j > 0);
-                       t = TB[i-1][j-1];
-                       if (t & TRACEBITS_DM)
-                               State = 'D';
-                       else if (t & TRACEBITS_IM)
-                               State = 'I';
-                       else
-                               State = 'M';
-                       --i;
-                       --j;
-                       break;
-               case 'D':
-                       asserta(i > 0);
-                       t = TB[i-1][j];
-                       if (t & TRACEBITS_MD)
-                               State = 'M';
-                       else
-                               State = 'D';
-                       --i;
-                       break;
-
-               case 'I':
-                       asserta(j > 0);
-                       t = TB[i][j-1];
-                       if (t & TRACEBITS_MI)
-                               State = 'M';
-                       else
-                               State = 'I';
-                       --j;
-                       break;
-
-               default:
-                       Die("TraceBackBit, invalid state %c", State);
-                       }
-               }
-       PD.Start = PathPtr;
-       EndTimer(TraceBackBit);
-       }
-
-void TraceBackBitSW(unsigned LA, unsigned LB, unsigned Besti, unsigned Bestj,
-  unsigned &Leni, unsigned &Lenj, PathData &PD)
-       {
-       PD.Alloc(LA+LB);
-
-       StartTimer(TraceBackBitSW);
-       char *PathPtr = PD.Back;
-       *PathPtr = 0;
-
-       byte **TB = g_TBBit;
-
-#if    TRACE
-       Log("\n");
-       Log("TraceBackBitSW\n");
-#endif
-
-       unsigned i = Besti;
-       unsigned j = Bestj;
-       char State = 'M';
-       for (;;)
-               {
-#if    TRACE
-               Log("i=%3d  j=%3d  state=%c\n", (int) i, (int) j, State);
-#endif
-               --PathPtr;
-               *PathPtr = State;
-
-               byte t;
-               switch (State)
-                       {
-               case 'M':
-                       asserta(i > 0 && j > 0);
-                       t = TB[i-1][j-1];
-                       if (t & TRACEBITS_DM)
-                               State = 'D';
-                       else if (t & TRACEBITS_IM)
-                               State = 'I';
-                       else if (t & TRACEBITS_SM)
-                               {
-                               Leni = Besti - i + 1;
-                               Lenj = Bestj - j + 1;
-                               PD.Start = PathPtr;
-                               EndTimer(TraceBackBitSW);
-                               return;
-                               }
-                       else
-                               State = 'M';
-                       --i;
-                       --j;
-                       break;
-               case 'D':
-                       asserta(i > 0);
-                       t = TB[i-1][j];
-                       if (t & TRACEBITS_MD)
-                               State = 'M';
-                       else
-                               State = 'D';
-                       --i;
-                       break;
-
-               case 'I':
-                       asserta(j > 0);
-                       t = TB[i][j-1];
-                       if (t & TRACEBITS_MI)
-                               State = 'M';
-                       else
-                               State = 'I';
-                       --j;
-                       break;
-
-               default:
-                       Die("TraceBackBitSW, invalid state %c", State);
-                       }
-               }
-       }