+++ /dev/null
-#ifndef mx_h\r
-#define mx_h\r
-\r
-#include <list>\r
-#include <limits.h>\r
-#include <math.h>\r
-#include "timing.h"\r
-#include "myutils.h"\r
-\r
-const int OPT_LOG = 0x01;\r
-const int OPT_EXP = 0x02;\r
-const int OPT_ZERO_BASED = 0x04;\r
-const float MINUS_INFINITY = -9e9f;\r
-const float UNINIT = -8e8f;\r
-\r
-struct SeqData;\r
-\r
-template<class T> const char *TypeToStr(T t)\r
- {\r
- Die("Unspecialised TypeToStr() called");\r
- ureturn(0);\r
- }\r
-\r
-template<> inline const char *TypeToStr<unsigned short>(unsigned short f)\r
- {\r
- static char s[16];\r
-\r
- sprintf(s, "%12u", f);\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<short>(short f)\r
- {\r
- static char s[16];\r
-\r
- sprintf(s, "%12d", f);\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<int>(int f)\r
- {\r
- static char s[16];\r
-\r
- sprintf(s, "%5d", f);\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<float>(float f)\r
- {\r
- static char s[16];\r
-\r
- if (f == UNINIT)\r
- sprintf(s, "%12.12s", "?");\r
- else if (f < MINUS_INFINITY/2)\r
- sprintf(s, "%12.12s", "*");\r
- else if (f == 0.0f)\r
- sprintf(s, "%12.12s", ".");\r
- else if (f >= -1e5 && f <= 1e5)\r
- sprintf(s, "%12.5f", f);\r
- else\r
- sprintf(s, "%12.4g", f);\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<double>(double f)\r
- {\r
- static char s[16];\r
-\r
- if (f < -1e9)\r
- sprintf(s, "%12.12s", "*");\r
- else if (f == 0.0f)\r
- sprintf(s, "%12.12s", ".");\r
- else if (f >= -1e-5 && f <= 1e5)\r
- sprintf(s, "%12.5f", f);\r
- else\r
- sprintf(s, "%12.4g", f);\r
- return s;\r
- }\r
-\r
-static inline const char *FloatToStr(float f, string &s)\r
- {\r
- s = TypeToStr<float>(f);\r
- return s.c_str();\r
- }\r
-\r
-template<> inline const char *TypeToStr<char>(char c)\r
- {\r
- static char s[2];\r
- s[0] = c;\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<byte>(byte c)\r
- {\r
- static char s[2];\r
- s[0] = c;\r
- return s;\r
- }\r
-\r
-template<> inline const char *TypeToStr<bool>(bool tof)\r
- {\r
- static char s[2];\r
- s[0] = tof ? 'T' : 'F';\r
- return s;\r
- }\r
-\r
-struct SeqDB;\r
-\r
-struct MxBase\r
- {\r
-private:\r
- MxBase(const MxBase &rhs);\r
- MxBase &operator=(const MxBase &rhs);\r
-\r
-public:\r
- char m_Name[32];\r
- char m_Alpha[32];\r
- char m_Alpha2[32];\r
- unsigned m_RowCount;\r
- unsigned m_ColCount;\r
- unsigned m_AllocatedRowCount;\r
- unsigned m_AllocatedColCount;\r
- const SeqDB *m_SeqDB;\r
- unsigned m_IdA;\r
- unsigned m_IdB;\r
- const SeqData *m_SA;\r
- const SeqData *m_SB;\r
-\r
- static list<MxBase *> *m_Matrices;\r
- //static MxBase *Get(const string &Name);\r
- //static float **Getf(const string &Name);\r
- //static double **Getd(const string &Name);\r
- //static char **Getc(const string &Name);\r
-\r
- static unsigned m_AllocCount;\r
- static unsigned m_ZeroAllocCount;\r
- static unsigned m_GrowAllocCount;\r
- static double m_TotalBytes;\r
- static double m_MaxBytes;\r
-\r
- static void OnCtor(MxBase *Mx);\r
- static void OnDtor(MxBase *Mx);\r
-\r
- MxBase()\r
- {\r
- m_AllocatedRowCount = 0;\r
- m_AllocatedColCount = 0;\r
- m_RowCount = 0;\r
- m_ColCount = 0;\r
- m_IdA = UINT_MAX;\r
- m_IdB = UINT_MAX;\r
- m_SeqDB = 0;\r
- OnCtor(this);\r
- }\r
- virtual ~MxBase()\r
- {\r
- OnDtor(this);\r
- }\r
-\r
- virtual unsigned GetTypeSize() const = 0;\r
- virtual unsigned GetBytes() const = 0;\r
-\r
- void Clear()\r
- {\r
- FreeData();\r
- m_AllocatedRowCount = 0;\r
- m_AllocatedColCount = 0;\r
- m_RowCount = 0;\r
- m_ColCount = 0;\r
- m_IdA = UINT_MAX;\r
- m_IdB = UINT_MAX;\r
- m_SA = 0;\r
- m_SB = 0;\r
- }\r
-\r
- bool Empty() const\r
- {\r
- return m_RowCount == 0;\r
- }\r
-\r
- virtual void AllocData(unsigned RowCount, unsigned ColCount) = 0;\r
- virtual void FreeData() = 0;\r
- virtual const char *GetAsStr(unsigned i, unsigned j) const = 0;\r
-\r
- void SetAlpha(const char *Alpha)\r
- {\r
- unsigned n = sizeof(m_Alpha);\r
- strncpy(m_Alpha, Alpha, n);\r
- m_Alpha[n] = 0;\r
- }\r
-\r
- void Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqDB *DB, unsigned IdA, unsigned IdB,\r
- const SeqData *SA, const SeqData *SB);\r
-\r
- void Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqDB *DB = 0, unsigned IdA = UINT_MAX, unsigned IdB = UINT_MAX);\r
-\r
- void Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqData *SA, const SeqData *SB);\r
-\r
- static void LogAll()\r
- {\r
- Log("\n");\r
- if (m_Matrices == 0)\r
- {\r
- Log("MxBase::m_Matrices=0\n");\r
- return;\r
- }\r
- Log("\n");\r
- Log("AllRows AllCols Sz MB Name\n");\r
- Log("------- ------- ---- -------- ----\n");\r
- double TotalMB = 0;\r
- for (list<MxBase *>::const_iterator p = m_Matrices->begin();\r
- p != m_Matrices->end(); ++p)\r
- {\r
- const MxBase *Mx = *p;\r
- if (Mx == 0)\r
- continue;\r
- //if (Mx->m_RowCount != 0 || ShowEmpty)\r
- // Mx->LogMe(WithData);\r
- unsigned ar = Mx->m_AllocatedRowCount;\r
- if (ar == 0)\r
- continue;\r
- unsigned ac = Mx->m_AllocatedColCount;\r
- unsigned sz = Mx->GetTypeSize();\r
- double MB = (double) ar*(double) ac*(double) sz/1e6;\r
- TotalMB += MB;\r
- Log("%7u %7u %4u %8.2f %s\n", ar, ac, sz, MB, Mx->m_Name);\r
- }\r
- Log(" --------\n");\r
- Log("%7.7s %7.7s %4.4s %8.2f\n", "", "", "", TotalMB);\r
- }\r
-\r
- void LogMe(bool WithData = true, int Opts = 0) const;\r
- static void LogCounts();\r
- };\r
-\r
-template<class T> struct Mx : public MxBase\r
- {\r
-// Disable unimplemented stuff\r
-private:\r
- Mx(Mx &rhs);\r
- Mx &operator=(Mx &rhs);\r
- // const Mx &operator=(const Mx &rhs) const;\r
-\r
-public:\r
- T **m_Data;\r
-\r
- Mx()\r
- {\r
- m_Data = 0;\r
- }\r
- \r
- ~Mx()\r
- {\r
- FreeData();\r
- }\r
-\r
- virtual void AllocData(unsigned RowCount, unsigned ColCount)\r
- {\r
- if (opt_logmemgrows)\r
- Log("MxBase::AllocData(%u,%u) %s bytes, Name=%s\n",\r
- RowCount, ColCount, IntToStr(GetBytes()), m_Name);\r
- // m_Data = myalloc<T *>(RowCount);\r
- m_Data = MYALLOC(T *, RowCount, Mx);\r
- for (unsigned i = 0; i < RowCount; ++i)\r
- // m_Data[i] = myalloc<T>(ColCount);\r
- m_Data[i] = MYALLOC(T, ColCount, Mx);\r
- AddBytes("Mx_AllocData", RowCount*sizeof(T *) + RowCount*ColCount*sizeof(T));\r
-\r
- m_AllocatedRowCount = RowCount;\r
- m_AllocatedColCount = ColCount;\r
- }\r
-\r
- virtual void FreeData()\r
- {\r
- for (unsigned i = 0; i < m_AllocatedRowCount; ++i)\r
- MYFREE(m_Data[i], m_AllocatedColCount, Mx);\r
- MYFREE(m_Data, m_AllocatedRowCount, Mx);\r
- SubBytes("Mx_AllocData",\r
- m_AllocatedRowCount*sizeof(T *) + m_AllocatedRowCount*m_AllocatedColCount*sizeof(T));\r
-\r
- m_Data = 0;\r
- m_RowCount = 0;\r
- m_ColCount = 0;\r
- m_AllocatedRowCount = 0;\r
- m_AllocatedColCount = 0;\r
- }\r
-\r
- T **GetData()\r
- {\r
- return (T **) m_Data;\r
- }\r
-\r
- T Get(unsigned i, unsigned j) const\r
- {\r
- assert(i < m_RowCount);\r
- assert(j < m_ColCount);\r
- return m_Data[i][j];\r
- }\r
-\r
- void Put(unsigned i, unsigned j, T x) const\r
- {\r
- assert(i < m_RowCount);\r
- assert(j < m_ColCount);\r
- m_Data[i][j] = x;\r
- }\r
-\r
- T GetOffDiagAvgs(vector<T> &Avgs) const\r
- {\r
- if (m_RowCount != m_ColCount)\r
- Die("GetOffDiagAvgs, not symmetrical");\r
- Avgs.clear();\r
- T Total = T(0);\r
- for (unsigned i = 0; i < m_RowCount; ++i)\r
- {\r
- T Sum = T(0);\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- {\r
- if (j == i)\r
- continue;\r
- Sum += m_Data[i][j];\r
- }\r
- T Avg = Sum/(m_RowCount-1);\r
- Total += Avg;\r
- Avgs.push_back(Avg);\r
- }\r
- return m_RowCount == 0 ? T(0) : Total/m_RowCount;\r
- }\r
-\r
- unsigned GetTypeSize() const\r
- {\r
- return sizeof(T);\r
- }\r
-\r
- virtual unsigned GetBytes() const\r
- {\r
- return m_AllocatedRowCount*m_AllocatedColCount*GetTypeSize() +\r
- m_AllocatedRowCount*sizeof(T *);\r
- }\r
-\r
- const char *GetAsStr(unsigned i, unsigned j) const\r
- {\r
- return TypeToStr<T>(Get(i, j));\r
- }\r
-\r
- const T *const *const GetData() const\r
- {\r
- return (const T *const *) m_Data;\r
- }\r
-\r
- void Copy(const Mx<T> &rhs)\r
- {\r
- Alloc("Copy", rhs.m_RowCount, rhs.m_ColCount, rhs.m_SeqDB, rhs.m_IdA, rhs.m_IdB);\r
- const T * const *Data = rhs.GetData();\r
- for (unsigned i = 0; i < m_RowCount; ++i)\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- m_Data[i][j] = Data[i][j];\r
- }\r
-\r
- void Assign(T v)\r
- {\r
- for (unsigned i = 0; i < m_RowCount; ++i)\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- m_Data[i][j] = v;\r
- }\r
-\r
- bool Eq(const Mx &rhs, bool Bwd = false) const\r
- {\r
- if (rhs.m_ColCount != m_ColCount)\r
- return false;\r
- if (rhs.m_RowCount != m_RowCount)\r
- return false;\r
- const T * const*d = rhs.GetData();\r
- int i1 = Bwd ? m_RowCount : 0;\r
- int j1 = Bwd ? m_ColCount : 0;\r
- int i2 = Bwd ? -1 : m_RowCount;\r
- int j2 = Bwd ? -1 : m_ColCount;\r
- for (int i = i1; i != i2; Bwd ? --i : ++i)\r
- for (int j = j1; j != j2; Bwd ? --j : ++j)\r
- {\r
- float x = m_Data[i][j];\r
- float y = d[i][j];\r
- if (x < -1e10 && y < -1e10)\r
- continue;\r
- if (!feq(x, y))\r
- {\r
- Warning("%s[%d][%d] = %g, %s = %g",\r
- m_Name, i, j, x, rhs.m_Name, y);\r
- return false;\r
- }\r
- }\r
- return true;\r
- }\r
-\r
- bool EqMask(const Mx &rhs, const Mx<bool> &Mask) const\r
- {\r
- if (rhs.m_ColCount != m_ColCount)\r
- return false;\r
- if (rhs.m_RowCount != m_RowCount)\r
- return false;\r
-\r
- if (Mask.m_ColCount != m_ColCount)\r
- return false;\r
- if (Mask.m_RowCount != m_RowCount)\r
- return false;\r
-\r
- const T * const*d = rhs.GetData();\r
- bool Bwd = false;\r
- int i1 = Bwd ? m_RowCount : 0;\r
- int j1 = Bwd ? m_ColCount : 0;\r
- int i2 = Bwd ? -1 : m_RowCount;\r
- int j2 = Bwd ? -1 : m_ColCount;\r
- for (int i = i1; i != i2; Bwd ? --i : ++i)\r
- for (int j = j1; j != j2; Bwd ? --j : ++j)\r
- {\r
- if (!Mask.m_Data[i][j])\r
- continue;\r
- float x = m_Data[i][j];\r
- float y = d[i][j];\r
- if (x < -1e10 && y < -1e10)\r
- continue;\r
- if (!feq(x, y))\r
- {\r
- Warning("%s[%d][%d] = %g, %s = %g",\r
- m_Name, i, j, x, rhs.m_Name, y);\r
- return false;\r
- }\r
- }\r
- return true;\r
- }\r
-\r
- void Init(T v)\r
- {\r
- for (unsigned i = 0; i < m_RowCount; ++i)\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- m_Data[i][j] = v;\r
- }\r
- };\r
-\r
-void WriteMx(const string &Name, Mx<float> &Mxf);\r
-\r
-template<class T> void ReserveMx(Mx<T> &Mxf, unsigned N = UINT_MAX)\r
- {\r
- if (Mxf.m_AllocatedRowCount > 0)\r
- return;\r
- extern unsigned g_MaxInputSeqLength;\r
- if (N == UINT_MAX)\r
- N = g_MaxInputSeqLength+1;\r
- Mxf.Alloc("(Reserved)", N, N);\r
- }\r
-\r
-#endif // mx_h\r
projects / mothur.git / blobdiff