+++ /dev/null
-#include "myutils.h"\r
-#include "mx.h"\r
-#include "seqdb.h"\r
-#include "seq.h"\r
-\r
-char ProbToChar(float p);\r
-\r
-list<MxBase *> *MxBase::m_Matrices = 0;\r
-unsigned MxBase::m_AllocCount;\r
-unsigned MxBase::m_ZeroAllocCount;\r
-unsigned MxBase::m_GrowAllocCount;\r
-double MxBase::m_TotalBytes;\r
-double MxBase::m_MaxBytes;\r
-\r
-static const char *LogizeStr(const char *s)\r
- {\r
- double d = atof(s);\r
- d = log(d);\r
- return TypeToStr<float>(float(d));\r
- }\r
-\r
-static const char *ExpizeStr(const char *s)\r
- {\r
- double d = atof(s);\r
- d = exp(d);\r
- return TypeToStr<float>(float(d));\r
- }\r
-\r
-void MxBase::OnCtor(MxBase *Mx)\r
- {\r
- if (m_Matrices == 0)\r
- m_Matrices = new list<MxBase *>;\r
- asserta(m_Matrices != 0);\r
- m_Matrices->push_front(Mx);\r
- }\r
-\r
-void MxBase::OnDtor(MxBase *Mx)\r
- {\r
- if (m_Matrices == 0)\r
- {\r
- Warning("MxBase::OnDtor, m_Matrices = 0");\r
- return;\r
- }\r
- for (list<MxBase*>::iterator p = m_Matrices->begin();\r
- p != m_Matrices->end(); ++p)\r
- {\r
- if (*p == Mx)\r
- {\r
- m_Matrices->erase(p);\r
- if (m_Matrices->empty())\r
- delete m_Matrices;\r
- return;\r
- }\r
- }\r
- Warning("MxBase::OnDtor, not found");\r
- }\r
-\r
-//float **MxBase::Getf(const string &Name)\r
-// {\r
-// Mx<float> *m = (Mx<float> *) Get(Name);\r
-// asserta(m->GetTypeSize() == sizeof(float));\r
-// return m->GetData();\r
-// }\r
-//\r
-//double **MxBase::Getd(const string &Name)\r
-// {\r
-// Mx<double> *m = (Mx<double> *) Get(Name);\r
-// asserta(m->GetTypeSize() == sizeof(double));\r
-// return m->GetData();\r
-// }\r
-//\r
-//char **MxBase::Getc(const string &Name)\r
-// {\r
-// Mx<char> *m = (Mx<char> *) Get(Name);\r
-// asserta(m->GetTypeSize() == sizeof(char));\r
-// return m->GetData();\r
-// }\r
-\r
-void MxBase::Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqDB *DB, unsigned IdA, unsigned IdB)\r
- {\r
- Alloc(Name, RowCount, ColCount, DB, IdA, IdB, 0, 0);\r
- }\r
-\r
-void MxBase::Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqData *SA, const SeqData *SB)\r
- {\r
- Alloc(Name, RowCount, ColCount, 0, UINT_MAX, UINT_MAX, SA, SB);\r
- }\r
-\r
-void MxBase::Alloc(const char *Name, unsigned RowCount, unsigned ColCount,\r
- const SeqDB *DB, unsigned IdA, unsigned IdB, const SeqData *SA, const SeqData *SB)\r
- {\r
- StartTimer(MxBase_Alloc);\r
-\r
- ++m_AllocCount;\r
- if (m_AllocatedRowCount == 0)\r
- ++m_ZeroAllocCount;\r
-\r
- if (DB != 0)\r
- {\r
- asserta(IdA != UINT_MAX);\r
- asserta(IdB != UINT_MAX);\r
- asserta(RowCount >= DB->GetSeqLength(IdA) + 1);\r
- asserta(ColCount >= DB->GetSeqLength(IdB) + 1);\r
- }\r
- if (RowCount > m_AllocatedRowCount || ColCount > m_AllocatedColCount)\r
- {\r
- if (m_AllocatedRowCount > 0)\r
- {\r
- if (opt_logmemgrows)\r
- Log("MxBase::Alloc grow %s %u x %u -> %u x %u, %s bytes\n",\r
- Name, m_AllocatedRowCount, m_AllocatedColCount,\r
- RowCount, ColCount,\r
- IntToStr(GetBytes()));\r
- ++m_GrowAllocCount;\r
- }\r
-\r
- m_TotalBytes -= GetBytes();\r
-\r
- PauseTimer(MxBase_Alloc);\r
- StartTimer(MxBase_FreeData);\r
- FreeData();\r
- EndTimer(MxBase_FreeData);\r
- StartTimer(MxBase_Alloc);\r
-\r
- unsigned N = max(RowCount + 16, m_AllocatedRowCount);\r
- unsigned M = max(ColCount + 16, m_AllocatedColCount);\r
- N = max(N, M);\r
-\r
- PauseTimer(MxBase_Alloc);\r
- StartTimer(MxBase_AllocData);\r
- AllocData(N, N);\r
- EndTimer(MxBase_AllocData);\r
- StartTimer(MxBase_Alloc);\r
-\r
- m_TotalBytes += GetBytes();\r
- if (m_TotalBytes > m_MaxBytes)\r
- m_MaxBytes = m_TotalBytes;\r
- }\r
- \r
- unsigned n = sizeof(m_Name)-1;\r
- strncpy(m_Name, Name, n);\r
- m_Name[n] = 0;\r
- m_RowCount = RowCount;\r
- m_ColCount = ColCount;\r
- m_SeqDB = DB;\r
- m_IdA = IdA;\r
- m_IdB = IdB;\r
- m_SA = SA;\r
- m_SB = SB;\r
-\r
- EndTimer(MxBase_Alloc);\r
- }\r
-\r
-void MxBase::LogMe(bool WithData, int Opts) const\r
- {\r
- Log("\n");\r
- if (Opts & OPT_EXP)\r
- Log("Exp ");\r
- else if (Opts & OPT_LOG)\r
- Log("Log ");\r
- bool ZeroBased = ((Opts & OPT_ZERO_BASED) != 0);\r
- Log("%s(%p) Rows %u/%u, Cols %u/%u",\r
- m_Name, this,\r
- m_RowCount, m_AllocatedRowCount,\r
- m_ColCount, m_AllocatedColCount);\r
- if (m_SeqDB != 0 && m_IdA != UINT_MAX)\r
- Log(", A=%s", m_SeqDB->GetLabel(m_IdA));\r
- else if (m_SA != 0)\r
- Log(", A=%s", m_SA->Label);\r
- if (m_SeqDB != 0 && m_IdB != UINT_MAX)\r
- Log(", B=%s", m_SeqDB->GetLabel(m_IdB));\r
- else if (m_SB != 0)\r
- Log(", B=%s", m_SB->Label);\r
- Log("\n");\r
- if (!WithData || m_RowCount == 0 || m_ColCount == 0)\r
- return;\r
-\r
- const char *z = GetAsStr(0, 0);\r
- unsigned Width = strlen(z);\r
- unsigned Mod = 1;\r
- for (unsigned i = 0; i < Width; ++i)\r
- Mod *= 10;\r
-\r
- if (m_Alpha[0] != 0)\r
- {\r
- Log("// Alphabet=%s\n", m_Alpha);\r
- Log("// ");\r
- unsigned n = strlen(m_Alpha);\r
- for (unsigned j = 0; j < n; ++j)\r
- Log(" %*c", Width, m_Alpha[j]);\r
- Log("\n");\r
- for (unsigned i = 0; i < n; ++i)\r
- {\r
- Log("/* %c */ {", m_Alpha[i]);\r
- unsigned ci = m_Alpha[i];\r
- for (unsigned j = 0; j < n; ++j)\r
- {\r
- unsigned cj = m_Alpha[j];\r
- Log("%s,", GetAsStr(ci, cj));\r
- }\r
- Log("}, // %c\n", m_Alpha[i]);\r
- }\r
- return;\r
- }\r
- else if (m_Alpha2[0] != 0)\r
- {\r
- unsigned n = strlen(m_Alpha2);\r
- Log("// Alphabet=%s\n", m_Alpha2);\r
- Log("// ");\r
- for (unsigned j = 0; j < n; ++j)\r
- Log(" %*c", Width, m_Alpha2[j]);\r
- Log("\n");\r
- for (unsigned i = 0; i < n; ++i)\r
- {\r
- Log("/* %c */ {", m_Alpha2[i]);\r
- unsigned ci = m_Alpha2[i];\r
- for (unsigned j = 0; j < n; ++j)\r
- Log("%s,", GetAsStr(i, j));\r
- Log("}, // %c\n", m_Alpha2[i]);\r
- }\r
- return;\r
- }\r
-\r
- const byte *A = 0;\r
- const byte *B = 0;\r
- if (m_SeqDB != 0 && m_IdA != UINT_MAX)\r
- A = m_SeqDB->GetSeq(m_IdA);\r
- else if (m_SA != 0)\r
- A = m_SA->Seq;\r
- if (m_SeqDB != 0 && m_IdB != UINT_MAX)\r
- B = m_SeqDB->GetSeq(m_IdB);\r
- else if (m_SB != 0)\r
- B = m_SB->Seq;\r
-\r
- if (B != 0)\r
- {\r
- if (A != 0)\r
- Log(" ");\r
- Log("%5.5s", "");\r
- if (ZeroBased)\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- Log("%*c", Width, B[j]);\r
- else\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- Log("%*c", Width, j == 0 ? ' ' : B[j-1]);\r
- Log("\n");\r
- }\r
-\r
- if (A != 0)\r
- Log(" ");\r
- Log("%5.5s", "");\r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- Log("%*u", Width, j%Mod);\r
- Log("\n");\r
-\r
- for (unsigned i = 0; i < m_RowCount; ++i)\r
- {\r
- if (A != 0)\r
- {\r
- if (ZeroBased)\r
- Log("%c ", A[i]);\r
- else\r
- Log("%c ", i == 0 ? ' ' : A[i-1]);\r
- }\r
- Log("%4u ", i);\r
- \r
- for (unsigned j = 0; j < m_ColCount; ++j)\r
- {\r
- const char *s = GetAsStr(i, j);\r
- if (Opts & OPT_LOG)\r
- s = LogizeStr(s);\r
- else if (Opts & OPT_EXP)\r
- s = ExpizeStr(s);\r
- Log("%s", s);\r
- }\r
- Log("\n");\r
- }\r
- }\r
-static unsigned g_MatrixFileCount;\r
-\r
-void MxBase::LogCounts()\r
- {\r
- Log("\n");\r
- Log("MxBase::LogCounts()\n");\r
- Log(" What N\n");\r
- Log("---------- ----------\n");\r
- Log(" Allocs %10u\n", m_AllocCount);\r
- Log("ZeroAllocs %10u\n", m_ZeroAllocCount);\r
- Log(" Grows %10u\n", m_GrowAllocCount);\r
- Log(" Bytes %10.10s\n", MemBytesToStr(m_TotalBytes));\r
- Log(" Max bytes %10.10s\n", MemBytesToStr(m_MaxBytes));\r
- }\r
projects / mothur.git / blobdiff