SharedProteinResources(
final ProteinScoringMatrix matrix,
final SequencesReader template,
final SequencesReader query,
boolean readNames)
throws IOException {
mProteinScoringMatrix = matrix;
mTemplateReader = template;
mQueryReader = query;
if (query != null) {
mWorkSpace = new byte[(int) query.maxLength()];
mWorkSpaceProtein = new byte[mWorkSpace.length / 3];
if (query.numberSequences() > Integer.MAX_VALUE) {
throw new IllegalArgumentException("Number of reads exceeds " + Integer.MAX_VALUE);
}
} else {
mWorkSpace = null;
mWorkSpaceProtein = null;
}
if (mTemplateReader != null) {
mTemplateNames = mTemplateReader.names();
} else {
mTemplateNames = null;
}
if (readNames && mQueryReader != null) {
mReadNames = query.names();
} else {
mReadNames = null;
}
}
int queryLength(final int id) throws IOException {
if (mQueryReader == null) {
return -1;
} else {
return mQueryReader.length(id);
}
}
int templateLength(final int id) throws IOException {
if (mTemplateReader == null) {
return -1;
} else {
return mTemplateReader.length(id);
}
}
long totalTemplateLength() {
if (mTemplateReader == null) {
return -1;
} else {
return mTemplateReader.totalLength();
}
}
/**
* Return the query, resulting array may contain rubbish entries at the end. Assumes the caller
* knows what it is doing!
*
* @param id read id
* @param frame read frame
* @return amino acid sequence
* @exception IOException if an I/O error occurs.
*/
byte[] query(final int id, final int frame) throws IOException {
if (mQueryReader == null) {
return EMPTY;
} else if (mQueryReader.type() == SequenceType.DNA) {
// In this situation, use precomputed array to store intermediate nt version
final int length = mQueryReader.read(id, mWorkSpace);
// Convert to protein in situ
final Frame frames = ProteinOutputProcessor.FRAMES_MAPPING[frame + 3];
final int limit = (length - Math.abs(frame) + 1) / 3;
for (int j = 0, i = 0; j < limit; j++, i += 3) {
mWorkSpaceProtein[j] = frames.code(mWorkSpace, length, i);
}
return mWorkSpaceProtein;
} else {
return mQueryReader.read(id);
}
}
byte[] template(final int id) throws IOException {
if (id != mCachedTemplateId) {
if (mTemplateReader == null) {
mCachedTemplate = EMPTY;
} else {
mCachedTemplate = mTemplateReader.read(id);
}
mCachedTemplateId = id;
}
return mCachedTemplate;
}
private static BufferedReader getReferenceReader(SequencesReader genome, DefaultFallback fallback)
throws IOException {
final BufferedReader r;
final File ref = new File(genome.path(), REFERENCE_FILE);
if (ref.exists()) {
final InputStreamReader isr =
new InputStreamReader(new BufferedInputStream(new FileInputStream(ref)));
r = new BufferedReader(isr);
} else if (fallback == DefaultFallback.DIPLOID) {
r = new BufferedReader(new StringReader(REFERENCE_DEFAULT_DIPLOID));
} else if (fallback == DefaultFallback.HAPLOID) {
r = new BufferedReader(new StringReader(REFERENCE_DEFAULT_HAPLOID));
} else {
if (genome.path() != null) {
throw new IOException("No reference file contained in: " + genome.path().getPath());
} else {
throw new IOException("No reference file found");
}
}
return r;
}
/**
* Test if reference file exists
*
* @param sr sequences reader
* @return true if it exists
*/
public static boolean hasReferenceFile(SequencesReader sr) {
return new File(sr.path(), REFERENCE_FILE).exists();
}
