CIgAnnotationInfo::CIgAnnotationInfo(CConstRef<CIgBlastOptions> &ig_opt)
{
vector<string> lines;
// read domain info from pdm or ndm file
const string suffix = (ig_opt->m_IsProtein) ? ".pdm." : ".ndm.";
string fn(SeqDB_ResolveDbPath(ig_opt->m_IgDataPath + "/" + ig_opt->m_Origin + "/"
+ ig_opt->m_Origin + suffix + ig_opt->m_DomainSystem));
if (fn == "") {
NCBI_THROW(CBlastException, eInvalidArgument,
"Domain annotation data file could not be found in [internal_data] directory");
}
s_ReadLinesFromFile(fn, lines);
int index = 0;
ITERATE(vector<string>, l, lines) {
vector<string> tokens;
NStr::Tokenize(*l, " \t\n\r", tokens, NStr::eMergeDelims);
if (!tokens.empty()) {
m_DomainIndex[tokens[0]] = index;
for (int i=1; i<11; ++i) {
m_DomainData.push_back(NStr::StringToInt(tokens[i]));
}
index += 10;
m_DomainChainType[tokens[0]] = tokens[11];
int frame = NStr::StringToInt(tokens[12]);
if (frame != -1) {
m_FrameOffset[tokens[0]] = frame;
}
}
}
void
CCmdLineBlastXML2ReportData::x_InitCommon(
const CSearchResults & results,
CConstRef<CBlastOptions> opts)
{
if(opts.Empty()) {
NCBI_THROW(CException, eUnknown, "blastxml2: Empty blast options");
}
if(m_Scope.Empty()) {
NCBI_THROW(CException, eUnknown, "blastxml2: Empty scope");
}
x_FillScoreMatrix(m_Options->GetMatrixName());
string resolved = SeqDB_ResolveDbPath("taxdb.bti");
if(!resolved.empty()) {
m_TaxDBFound = true;
}
m_isIterative = opts->IsIterativeSearch();
}
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;
}
