CTime
CSeqDB::GetDate(const string & dbname,
ESeqType seqtype)
{
vector<string> vols;
CSeqDB::FindVolumePaths(dbname, seqtype, vols);
string fmt = "b d, Y H:m P";
CTime retv;
char date[128];
ITERATE(vector<string>, vol, vols)
{
string fn = *vol + ((seqtype == CSeqDB::eProtein)? ".pin" : ".nin");
ifstream f(fn.c_str(), ios::in|ios::binary);
char s[4]; // size of next chunk
if (f.is_open())
{
f.seekg(8, ios::beg);
f.read(s, 4);
Uint4 offset = SeqDB_GetStdOrd((Uint4 *) s);
f.seekg(offset, ios::cur);
f.read(s, 4);
offset = SeqDB_GetStdOrd((Uint4 *) s);
f.read(date, offset);
CTime d(string(date), fmt);
if (retv.IsEmpty() || d > retv)
{
retv = d;
}
}
}
TIndx CSeqDBRawFile::ReadSwapped(CSeqDBMemLease & lease,
TIndx offset,
string * value,
CSeqDBLockHold & locked) const
{
Uint4 len = 0;
m_Atlas.Lock(locked);
if (! lease.Contains(offset, offset + sizeof(len))) {
m_Atlas.GetRegion(lease, m_FileName, offset, offset + sizeof(len));
}
len = SeqDB_GetStdOrd((Int4 *) lease.GetPtr(offset));
offset += sizeof(len);
if (! lease.Contains(offset, offset + len)) {
m_Atlas.GetRegion(lease, m_FileName, offset, offset + sizeof(len));
}
value->assign(lease.GetPtr(offset), (int) len);
return offset + len;
}
TIndx CSeqDBRawFile::ReadSwapped(CSeqDBMemLease & lease,
TIndx offset,
Uint4 * value,
CSeqDBLockHold & locked) const
{
m_Atlas.Lock(locked);
if (! lease.Contains(offset, offset + sizeof(*value))) {
m_Atlas.GetRegion(lease, m_FileName, offset, offset + sizeof(*value));
}
*value = SeqDB_GetStdOrd((Uint4 *) lease.GetPtr(offset));
return offset + sizeof(*value);
}
/// Return the offset field (in host order)
Int4 GetOffset() const
{
return SeqDB_GetStdOrd(& m_Offset);
}
/// Return the taxonomic identifier field (in host order)
Int4 GetTaxId()const
{
return SeqDB_GetStdOrd(& m_Taxid);
}
CTaxDBFileInfo::CTaxDBFileInfo()
: m_AllTaxidCount(0),
m_IndexPtr(NULL),
m_DataPtr(NULL),
m_DataFileSize(0),
m_MissingDB(false)
{
// It is reasonable for this database to not exist.
m_IndexFN = SeqDB_ResolveDbPath("taxdb.bti");
if (m_IndexFN.size()) {
m_DataFN = m_IndexFN;
m_DataFN[m_DataFN.size()-1] = 'd';
}
if (! (m_IndexFN.size() &&
m_DataFN.size() &&
CFile(m_IndexFN).Exists() &&
CFile(m_DataFN).Exists())) {
m_MissingDB = true;
return;
}
// Size for header data plus one taxid object.
Uint4 data_start = (4 + // magic
4 + // taxid count
16); // 4 reserved fields
Uint4 idx_file_len = (Uint4) CFile(m_IndexFN).GetLength();
if (idx_file_len < (data_start + sizeof(CSeqDBTaxId))) {
m_MissingDB = true;
return;
}
m_IndexFileMap.reset(new CMemoryFile(m_IndexFN));
m_IndexFileMap->Map();
// Last check-up of the database validity
Uint4 * magic_num_ptr = (Uint4 *)m_IndexFileMap->GetPtr();
const unsigned TAX_DB_MAGIC_NUMBER = 0x8739;
if (TAX_DB_MAGIC_NUMBER != SeqDB_GetStdOrd(magic_num_ptr ++)) {
m_MissingDB = true;
m_IndexFileMap.reset();
ERR_POST("Error: Tax database file has wrong magic number.");
return;
}
m_AllTaxidCount = SeqDB_GetStdOrd(magic_num_ptr ++);
// Skip the four reserved fields
magic_num_ptr += 4;
int taxid_array_size = int((idx_file_len - data_start)/sizeof(CSeqDBTaxId));
if (taxid_array_size != m_AllTaxidCount) {
m_MissingDB = true;
m_IndexFileMap.reset();
ERR_POST("SeqDB: Taxid metadata indicates (" << m_AllTaxidCount
<< ") entries but file has room for (" << taxid_array_size
<< ").");
if (taxid_array_size < m_AllTaxidCount) {
m_AllTaxidCount = taxid_array_size;
}
return;
}
m_DataFileMap.reset(new CMemoryFile(m_DataFN));
m_DataPtr = (char *) (m_DataFileMap->GetPtr());
m_DataFileSize = m_DataFileMap->GetSize();
m_IndexPtr = (CSeqDBTaxId*) magic_num_ptr;
}