private Map<Long, JobInput> inputs = new LinkedHashMap<>();
private Map<Long, Integer> exceptionCount = new HashMap<>();
private Map<Long, JobInput> inputs = new LinkedHashMap<>();
private Map<Long, Integer> exceptionCount = new HashMap<>();
private final int MAX_RETRY = 5;
public AlignmentWorker(AlignmentView msa, List<ArgumentI> args,
private final int MAX_RETRY = 5;
public AlignmentWorker(AlignmentView msa, List<ArgumentI> args,
- String alnTitle, boolean submitGaps, boolean preserveOrder,
- AlignViewport viewport)
+ String alnTitle, boolean submitGaps, boolean preserveOrder,
+ AlignViewport viewport)
{
JobInput input = JobInput.create(conmsa[i], 2, submitGaps);
WSJob job = new WSJob(service.getProviderName(), service.getName(),
{
JobInput input = JobInput.create(conmsa[i], 2, submitGaps);
WSJob job = new WSJob(service.getProviderName(), service.getName(),
Cache.log.error(format("Polling job %s failed.", job), e);
listeners.firePollException(job, e);
int count = exceptionCount.getOrDefault(job.getUid(),
Cache.log.error(format("Polling job %s failed.", job), e);
listeners.firePollException(job, e);
int count = exceptionCount.getOrDefault(job.getUid(),
}
exceptionCount.put(job.getUid(), count);
} catch (OutOfMemoryError e)
{
job.setStatus(WSJobStatus.BROKEN);
Cache.log.error(
}
exceptionCount.put(job.getUid(), count);
} catch (OutOfMemoryError e)
{
job.setStatus(WSJobStatus.BROKEN);
Cache.log.error(
width = Integer.max(width, emptySeq.getLength());
// pad shorter sequences with gaps
String gapSeq = String.join("",
width = Integer.max(width, emptySeq.getLength());
// pad shorter sequences with gaps
String gapSeq = String.join("",
}
SequenceI[] result = seqs.toArray(new SequenceI[0]);
AlignmentOrder msaOrder = new AlignmentOrder(result);
}
SequenceI[] result = seqs.toArray(new SequenceI[0]);
AlignmentOrder msaOrder = new AlignmentOrder(result);
final Map<String, ? extends Map> sequenceNames;
private JobInput(int numSequences, List<SequenceI> inputSequences,
final Map<String, ? extends Map> sequenceNames;
private JobInput(int numSequences, List<SequenceI> inputSequences,
- List<SequenceI> emptySequences,
- @SuppressWarnings("rawtypes") Map<String, ? extends Map> names)
+ List<SequenceI> emptySequences,
+ @SuppressWarnings("rawtypes") Map<String, ? extends Map> names)
{
this.inputSequences = Collections.unmodifiableList(inputSequences);
this.emptySequences = Collections.unmodifiableList(emptySequences);
{
this.inputSequences = Collections.unmodifiableList(inputSequences);
this.emptySequences = Collections.unmodifiableList(emptySequences);