private boolean loadIndex(long dataIndexVersion) throws IOException {
mIndexPos = 0;
mIndexedSequenceFileNumber = -1;
mIndex =
DataFileIndex.loadDataFileIndex(
dataIndexVersion, new File(mDir, mIndexFile), mDataFilePrefix);
if (mIndex.getTotalNumberSequences() != mNumberSequences) {
throw new CorruptSdfException(mDir);
}
return true;
}
/**
* Alternative to other one with similar name
*
* @param directory directory containing SDF
* @param indexFile index file
* @param loadNames should we load names
* @param loadFullNames should we load full names
* @param region region to restrict to
* @throws IOException IO exception occurs
*/
CompressedMemorySequencesReader2(
File directory,
IndexFile indexFile,
boolean loadNames,
boolean loadFullNames,
LongRange region)
throws IOException {
mIndexFile = indexFile;
mRegion = SequencesReaderFactory.resolveRange(indexFile, region);
mStart = mRegion.getStart();
mEnd = mRegion.getEnd();
mNumberSequences = mEnd - mStart;
mData =
DataInMemory.loadDelayQuality(
directory,
indexFile,
DataFileIndex.loadSequenceDataFileIndex(indexFile.dataIndexVersion(), directory),
mStart,
mEnd);
if (mNumberSequences > Integer.MAX_VALUE) {
throw new IllegalArgumentException(
"Too many sequences in region: " + region + ", maximum is: " + Integer.MAX_VALUE);
}
mDirectory = directory;
if (loadNames && mIndexFile.hasNames()) {
loadNames();
loadNameSuffixes(loadFullNames, mIndexFile.hasSequenceNameSuffixes());
}
final StringBuilder sb = new StringBuilder("CMSR2 statistics");
sb.append(LS);
this.infoString(sb);
Diagnostic.userLog(sb.toString());
}
protected void loadNext() {
final long value;
value = mIndex.numberSequences(mIndexPos++);
mIndexedSequenceFileNumber++;
mCurrentLower = mCurrentUpper;
mCurrentUpper += value;
}
/**
* Creates a the stream manager
*
* @param dir Directory containing sequence data
* @param numbersequences Number of sequences in directory
* @param indexFile Name of file containing index
* @param dataPrefix Filename prefix for data
* @param pointerPrefix Filename prefix for pointers
* @param dataIndexVersion the version with which to interpret the data
* @param opener file opener implementation
* @throws IOException If an I/O Error occurs
*/
AbstractStreamManager(
final File dir,
final long numbersequences,
final String indexFile,
final String dataPrefix,
final String pointerPrefix,
long dataIndexVersion,
DataFileOpener opener)
throws IOException {
mDir = dir;
mNumberSequences = numbersequences;
mIndexFile = indexFile;
mDataFilePrefix = dataPrefix;
loadIndex(dataIndexVersion);
mData = new DataRollingFile(mDir, dataPrefix, mIndex.numberEntries(), mIndex, opener);
mPointers = new RollingFile(mDir, pointerPrefix, mIndex.numberEntries());
}
@Override
SeekableStream openFileInternal(File f, int fileNum) throws IOException {
return mOpener.openRandomAccess(f, mDataIndex.dataSize(fileNum));
}
