Block getWordBlock(std::string word, std::fstream& f, bool createIfReauired = false) {
seekRW(f, 0);
BlockOffset currentOffset = 0;
Block b {readBlockFromFile(f)};
for(auto c : word) {
unsigned int i = char2int(c);
if (b.offsets[i] == 0 ) {
if (!createIfReauired) {
b.data=0;
return b;
}
BlockOffset off = f.tellp();
Block newBlock {};
seekRW(f, 0, f.end);
BlockOffset newCurrent = b.offsets[i] = writeBlockToFile(newBlock, f);
seekRW(f, off);
writeBlockToFile(b, f);
seekRW(f, newCurrent);
currentOffset = newCurrent;
b = newBlock;
} else {
currentOffset = b.offsets[i];
seekRW(f, currentOffset);
b = readBlockFromFile(f);
}
}
return b;
}
std::fstream& initializeFile(std::fstream& f, std::string fn) {
f.close();
f.open( fn ,f.in | f.out | f.binary );
if (!f.is_open()) {
f.open( fn , f.out | f.binary );
Block b {};
writeBlockToFile(b, f);
f.close();
f.open( fn ,f.in | f.out | f.binary );
}
return f;
}
static void saveSequence(IOAdapter* io, const DNASequence& sequence, U2OpStatus& os) {
writeHeaderToFile( io, sequence.getName( ), os );
CHECK_OP( os, );
const char *seq = sequence.seq.constData( );
const int len = sequence.seq.length( );
for ( int i = 0; i < len; i += SAVE_LINE_LEN ) {
const int chunkSize = qMin( SAVE_LINE_LEN, len - i );
writeBlockToFile( io, seq + i, chunkSize, os );
CHECK_OP( os, );
}
}
static void saveSequence( IOAdapter* io, const U2SequenceObject *sequence, U2OpStatus& os ) {
writeHeaderToFile( io, sequence->getSequenceName( ), os );
CHECK_OP( os, );
const int len = sequence->getSequenceLength( );
for ( int i = 0; i < len; i += SAVE_LINE_LEN ) {
int chunkSize = qMin( SAVE_LINE_LEN, len - i );
const QByteArray chunkContent = sequence->getSequenceData( U2Region( i, chunkSize ), os );
CHECK_OP( os, );
writeBlockToFile( io, chunkContent.constData( ), chunkSize, os );
CHECK_OP( os, );
}
}
FileID addWord(std::string word, std::fstream& f, bool createIfReauired = true) {
Block b = getWordBlock(word, f, createIfReauired);
FileID fid {b.data};
if (!createIfReauired) return fid;
if (fid == 0)
fid = getNextID();
b.data = fid;
writeBlockToFile(b, f);
return fid;
}
