/**
* Convert {@link TraceData} value object into {@link TraceSequence} object with the given
* depositor and {@link Entry}.
*
* @param traceData TraceData object to convert.
* @param depositor Depositor email.
* @param entry Entry to associate.
* @return TraceSequence object.
*/
public static TraceSequence traceDataToTraceSequence(
TraceData traceData, String depositor, Entry entry) {
TraceSequence resultTraceSequence = new TraceSequence();
if (traceData == null) {
return resultTraceSequence;
}
resultTraceSequence.setFilename(traceData.getFilename());
resultTraceSequence.setSequence(traceData.getSequence());
resultTraceSequence.setEntry(entry);
resultTraceSequence.setDepositor(depositor);
TraceSequenceAlignment traceSequenceAlignment = new TraceSequenceAlignment();
resultTraceSequence.setTraceSequenceAlignment(traceSequenceAlignment);
if (traceData.getScore() >= 0) {
traceSequenceAlignment.setScore(traceData.getScore());
traceSequenceAlignment.setStrand(traceData.getStrand());
traceSequenceAlignment.setQueryStart(traceData.getQueryStart());
traceSequenceAlignment.setQueryEnd(traceData.getQueryEnd());
traceSequenceAlignment.setSubjectStart(traceData.getSubjectStart());
traceSequenceAlignment.setSubjectEnd(traceData.getSubjectEnd());
traceSequenceAlignment.setQueryAlignment(traceData.getQueryAlignment());
traceSequenceAlignment.setSubjectAlignment(traceData.getSubjectAlignment());
}
return resultTraceSequence;
}
