Elf_Half elfio::load_sections( std::istream &stream ) {
Elf_Half entry_size = header->get_section_entry_size();
Elf_Half num = header->get_sections_num();
Elf64_Off offset = header->get_sections_offset();
for ( Elf_Half i = 0; i < num; ++i ) {
section* sec = create_section();
sec->load( stream, (std::streamoff)offset + i * entry_size );
sec->set_index( i );
// To mark that the section is not permitted to reassign address
// during layout calculation
sec->set_address( sec->get_address() );
}
Elf_Half shstrndx = get_section_name_str_index();
if ( SHN_UNDEF != shstrndx ) {
string_section_accessor str_reader( sections[shstrndx] );
for ( Elf_Half i = 0; i < num; ++i ) {
Elf_Word offset = sections[i]->get_name_string_offset();
const char* p = str_reader.get_string( offset );
if ( p != 0 ) {
sections[i]->set_name( p );
}
}
}
return num;
}
bool
generic_get_symbol( Elf_Xword index,
std::string& name, Elf64_Addr& value,
Elf_Xword& size,
unsigned char& bind, unsigned char& type,
Elf_Half& section_index,
unsigned char& other ) const
{
bool ret = false;
if ( index < get_symbols_num() ) {
const T* pSym = reinterpret_cast<const T*>(
symbol_section->get_data() +
index * symbol_section->get_entry_size() );
const endianess_convertor& convertor = elf_file.get_convertor();
section* string_section = elf_file.sections[get_string_table_index()];
string_section_accessor str_reader( string_section );
const char* pStr = str_reader.get_string( convertor( pSym->st_name ) );
if ( 0 != pStr ) {
name = pStr;
}
value = convertor( pSym->st_value );
size = convertor( pSym->st_size );
bind = ELF_ST_BIND( pSym->st_info );
type = ELF_ST_TYPE( pSym->st_info );
section_index = convertor( pSym->st_shndx );
other = pSym->st_other;
ret = true;
}
return ret;
}
void FMIndex::loadSGABWT(const std::string& filename)
{
FMIndexBuilder builder(filename, m_smallSampleRate, m_largeSampleRate);
size_t n = 0;
// Load the compressed string from the file
std::ifstream str_reader(builder.getStringFilename().c_str());
n = builder.getNumStringBytes();
m_string.resize(n);
str_reader.read(reinterpret_cast<char*>(&m_string[0]), n);
// Load the small markers from the file
std::ifstream sm_reader(builder.getSmallMarkerFilename().c_str());
n = builder.getNumSmallMarkers();
m_smallMarkers.resize(n);
sm_reader.read(reinterpret_cast<char*>(&m_smallMarkers[0]), sizeof(SmallMarker) * n);
// Load the large markers from the file
std::ifstream lm_reader(builder.getLargeMarkerFilename().c_str());
n = builder.getNumLargeMarkers();
m_largeMarkers.resize(n);
lm_reader.read(reinterpret_cast<char*>(&m_largeMarkers[0]), sizeof(LargeMarker) * n);
m_numStrings = builder.getNumStrings();
m_numSymbols = builder.getNumSymbols();
AlphaCount64 totals = builder.getSymbolCounts();
assert(totals.get('$') +
totals.get('A') +
totals.get('C') +
totals.get('G') +
totals.get('T') == m_numSymbols);
m_predCount.set('$', 0);
m_predCount.set('A', totals.get('$'));
m_predCount.set('C', m_predCount.get('A') + totals.get('A'));
m_predCount.set('G', m_predCount.get('C') + totals.get('C'));
m_predCount.set('T', m_predCount.get('G') + totals.get('G'));
assert(m_predCount.get('T') + totals.get('T') == m_numSymbols);
m_decoder = builder.getDecoder();
printInfo();
}
