--- /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