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;
}
}
