/**
* Load the names if they haven't already been loaded.
*
* @throws IOException if an I/O related error occurs
*/
private void loadNames() throws IOException {
mNames = new PrereadNames(mDirectory, mRegion, false);
if (mIndexFile.getVersion() >= IndexFile.SEPARATE_CHECKSUM_VERSION
&& mRegion.getStart() == 0
&& mRegion.getEnd() == mIndexFile.getNumberSequences()) {
if (mNames.calcChecksum() != mIndexFile.getNameChecksum()) {
throw new CorruptSdfException(
"Sequence names failed checksum - SDF may be corrupt: \"" + mDirectory + "\"");
} else {
Diagnostic.developerLog("Sequence names passed checksum");
}
}
}
private void loadNameSuffixes(boolean attemptLoad, boolean suffixExists) throws IOException {
mNameSuffixes =
attemptLoad && suffixExists
? new PrereadNames(mDirectory, mRegion, true)
: new EmptyStringPrereadNames(mEnd - mStart);
if (attemptLoad && suffixExists) {
if (mRegion.getStart() == 0 && mRegion.getEnd() == mIndexFile.getNumberSequences()) {
if (mNameSuffixes.calcChecksum() != mIndexFile.getNameSuffixChecksum()) {
throw new CorruptSdfException(
"Sequence name suffixes failed checksum - SDF may be corrupt: \""
+ mDirectory
+ "\"");
} else {
Diagnostic.developerLog("Sequence name suffixes passed checksum");
}
}
}
}
void infoString(final StringBuilder sb) {
sb.append("Memory Usage: ").append(mNumberSequences).append(" sequences").append(LS);
long totalBytes = mData.infoString(sb);
if (mNames != null) {
sb.append("\t\t")
.append(StringUtils.commas(mNames.bytes()))
.append("\t")
.append(StringUtils.commas(mNames.length()))
.append("\tNames")
.append(LS);
totalBytes += mNames.bytes();
}
if (mNameSuffixes != null) {
sb.append("\t\t")
.append(StringUtils.commas(mNameSuffixes.bytes()))
.append("\t")
.append(StringUtils.commas(mNameSuffixes.length()))
.append("\tSuffixes")
.append(LS);
totalBytes += mNameSuffixes.bytes();
}
sb.append("\t\t").append(StringUtils.commas(totalBytes)).append("\t\tTotal bytes").append(LS);
}
@Override
public String nameSuffix(long sequenceIndex) {
return mNameSuffixes.name(sequenceIndex);
}
