public ArrayList<TraceSequenceAnalysis> getTraceSequences(String userId, long entryId) {
Entry entry = dao.get(entryId);
if (entry == null) return null;
authorization.expectRead(userId, entry);
List<TraceSequence> sequences = DAOFactory.getTraceSequenceDAO().getByEntry(entry);
ArrayList<TraceSequenceAnalysis> analysisArrayList = new ArrayList<>();
if (sequences == null) return analysisArrayList;
AccountController accountController = new AccountController();
for (TraceSequence traceSequence : sequences) {
TraceSequenceAnalysis analysis = traceSequence.toDataTransferObject();
AccountTransfer accountTransfer = new AccountTransfer();
String depositor = traceSequence.getDepositor();
boolean canEdit = canEdit(userId, depositor, entry);
analysis.setCanEdit(canEdit);
Account account = accountController.getByEmail(traceSequence.getDepositor());
if (account != null) {
accountTransfer.setFirstName(account.getFirstName());
accountTransfer.setLastName(account.getLastName());
accountTransfer.setEmail(account.getEmail());
accountTransfer.setId(account.getId());
}
analysis.setDepositor(accountTransfer);
analysisArrayList.add(analysis);
}
return analysisArrayList;
}
public boolean deleteTraceSequence(String userId, long entryId, long traceId) {
Entry entry = dao.get(entryId);
if (entry == null) return false;
TraceSequenceDAO traceSequenceDAO = DAOFactory.getTraceSequenceDAO();
TraceSequence traceSequence = traceSequenceDAO.get(traceId);
if (traceSequence == null || !canEdit(userId, traceSequence.getDepositor(), entry))
return false;
try {
new SequenceAnalysisController().removeTraceSequence(traceSequence);
} catch (Exception e) {
Logger.error(e);
return false;
}
return true;
}
/**
* 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;
}
/**
* Convert {@link TraceSequence} to {@link TraceData} value object.
*
* @param traceSequence TraceSequence to convert.
* @return TraceData object.
*/
public static TraceData traceSequenceToTraceData(TraceSequence traceSequence) {
TraceData resultTraceData = new TraceData();
if (traceSequence == null) {
return resultTraceData;
}
resultTraceData.setFilename(traceSequence.getFilename());
resultTraceData.setSequence(traceSequence.getSequence());
if (traceSequence.getTraceSequenceAlignment() != null) {
resultTraceData.setScore(traceSequence.getTraceSequenceAlignment().getScore());
resultTraceData.setStrand(traceSequence.getTraceSequenceAlignment().getStrand());
resultTraceData.setQueryStart(traceSequence.getTraceSequenceAlignment().getQueryStart());
resultTraceData.setQueryEnd(traceSequence.getTraceSequenceAlignment().getQueryEnd());
resultTraceData.setSubjectStart(traceSequence.getTraceSequenceAlignment().getSubjectStart());
resultTraceData.setSubjectEnd(traceSequence.getTraceSequenceAlignment().getSubjectEnd());
resultTraceData.setQueryAlignment(
traceSequence.getTraceSequenceAlignment().getQueryAlignment());
resultTraceData.setSubjectAlignment(
traceSequence.getTraceSequenceAlignment().getSubjectAlignment());
}
return resultTraceData;
}