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

[mothur.git] / uchime_src / path.cpp

diff --git a/uchime_src/path.cpp b/uchime_src/path.cpp
new file mode 100644 (file)
index 0000000..9340344
--- /dev/null
+++ b/uchime_src/path.cpp
@@ -0,0 +1,151 @@
+#include "myutils.h"\r
+#include "path.h"\r
+#include "timing.h"\r
+\r
+#define TRACE  0\r
+\r
+const unsigned PathMagic = 0x9A783A16;\r
+\r
+struct PathBuffer\r
+       {\r
+       unsigned Magic;\r
+       char *Buffer;\r
+       unsigned Size;\r
+       bool InUse;\r
+       };\r
+\r
+static PathBuffer **g_PathBuffers;\r
+static unsigned g_PathBufferSize;\r
+\r
+static char *AllocBuffer(unsigned Size)\r
+       {\r
+       if (Size == 0)\r
+               return 0;\r
+\r
+// Is a free buffer that is big enough?\r
+       for (unsigned i = 0; i < g_PathBufferSize; ++i)\r
+               {\r
+               PathBuffer *PB = g_PathBuffers[i];\r
+               asserta(PB->Magic == PathMagic);\r
+               if (!PB->InUse)\r
+                       {\r
+                       if (PB->Size >= Size)\r
+                               {\r
+                               PB->InUse = true;\r
+                               return PB->Buffer;\r
+                               }\r
+                       if (PB->Buffer == 0)\r
+                               {\r
+                               unsigned Size2 = Size + 1024;\r
+                               PB->Buffer = MYALLOC(char, Size2, Path);\r
+                               PB->Size = Size2;\r
+                               PB->InUse = true;\r
+                               return PB->Buffer;\r
+                               }\r
+                       }\r
+               }\r
+\r
+// No available buffer, must expand g_PathBuffers[]\r
+       unsigned NewPathBufferSize = g_PathBufferSize + 1024;\r
+       PathBuffer **NewPathBuffers = MYALLOC(PathBuffer *, NewPathBufferSize, Path);\r
+       \r
+       for (unsigned i = 0; i < g_PathBufferSize; ++i)\r
+               NewPathBuffers[i] = g_PathBuffers[i];\r
+\r
+       for (unsigned i = g_PathBufferSize; i < NewPathBufferSize; ++i)\r
+               {\r
+               PathBuffer *PB = MYALLOC(PathBuffer, 1, Path);\r
+               PB->Magic = PathMagic;\r
+               PB->Buffer = 0;\r
+               PB->Size = 0;\r
+               PB->InUse = false;\r
+               NewPathBuffers[i] = PB;\r
+               }\r
+\r
+       PathBuffer *PB = NewPathBuffers[g_PathBufferSize];\r
+\r
+       MYFREE(g_PathBuffers, g_PathBufferSize, Path);\r
+       g_PathBuffers = NewPathBuffers;\r
+       g_PathBufferSize = NewPathBufferSize;\r
+\r
+       asserta(!PB->InUse && PB->Buffer == 0);\r
+\r
+       unsigned Size2 = Size + 1024;\r
+       PB->Buffer = MYALLOC(char, Size2, Path);\r
+       PB->Size = Size2;\r
+       PB->InUse = true;\r
+       return PB->Buffer;\r
+       }\r
+\r
+static void FreeBuffer(char *Buffer)\r
+       {\r
+       if (Buffer == 0)\r
+               return;\r
+\r
+       for (unsigned i = 0; i < g_PathBufferSize; ++i)\r
+               {\r
+               PathBuffer *PB = g_PathBuffers[i];\r
+               if (PB->Buffer == Buffer)\r
+                       {\r
+                       asserta(PB->InUse);\r
+                       PB->InUse = false;\r
+                       return;\r
+                       }\r
+               }\r
+\r
+       Die("FreeBuffer, not found");\r
+       }\r
+\r
+void PathData::Alloc(unsigned MaxLen)\r
+       {\r
+       if (MaxLen < Bytes)\r
+               return;\r
+\r
+       StartTimer(PathAlloc);\r
+       if (Bytes > 0)\r
+               {\r
+               FreeBuffer(Front);\r
+               }\r
+\r
+       Bytes = MaxLen + 1;\r
+       Front = AllocBuffer(Bytes);\r
+       Back = Front + Bytes - 1;\r
+       Start = 0;\r
+       EndTimer(PathAlloc);\r
+       }\r
+\r
+void PathData::Free()\r
+       {\r
+       FreeBuffer(Front);\r
+       Front = 0;\r
+       Start = 0;\r
+       Back = 0;\r
+       }\r
+\r
+void PathData::Copy(const PathData &rhs)\r
+       {\r
+       Alloc(rhs.Bytes);\r
+       strcpy(Front, rhs.Front);\r
+       Start = Front + (rhs.Start - rhs.Front);\r
+       }\r
+\r
+void PathData::FromStr(const char *PathStr)\r
+       {\r
+       asserta(PathStr != 0);\r
+       unsigned NeededBytes = (unsigned) strlen(PathStr) + 1;\r
+       Alloc(NeededBytes);\r
+       strcpy(Front, PathStr);\r
+       Start = Front;\r
+       }\r
+\r
+void LogPathStats()\r
+       {\r
+       Log("\n");\r
+       unsigned Bytes = 0;\r
+       for (unsigned i = 0; i < g_PathBufferSize; ++i)\r
+               {\r
+               const PathBuffer *PB = g_PathBuffers[i];\r
+               Bytes += PB->Size;\r
+               }\r
+       Log("%u paths allocated, total memory %u bytes\n", g_PathBufferSize, Bytes);\r
+       }\r