{
alseqs[i] = seqs[i];
if (seqs[i].getDatasetSequence() != null)
+ {
ds[i] = seqs[i].getDatasetSequence();
+ }
else
+ {
ds[i] = seqs[i];
+ }
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
{
if (dbSources == null)
{
- throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ sequence.getDBRef(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
if (uprefs != null && uprefs.length > 0)
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[]
- { dbSource });
+ entry.getDBRef(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
sequence.getSequenceAsString()).toUpperCase();
int absStart = entrySeq.indexOf(nonGapped);
- int mapStart = entry.getStart();
- jalview.datamodel.Mapping mp;
+ Mapping mp;
+ final int sequenceStart = sequence.getStart();
if (absStart == -1)
{
// Is local sequence contained in dataset sequence?
// absStart = 0;
// create valid mapping between matching region of local sequence and
// the mapped sequence
- mp = new Mapping(null, new int[]
- { sequence.getStart() + absStart,
- sequence.getStart() + absStart + entrySeq.length() - 1 },
- new int[]
- { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ mp = new Mapping(null, new int[] { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+ { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+ 1, 1);
updateRefFrame = false; // mapping is based on current start/end so
// don't modify start and end
}
if (sequence.getSequenceFeatures() != null)
{
SequenceFeature[] sf = sequence.getSequenceFeatures();
- int start = sequence.getStart();
+ int start = sequenceStart;
int end = sequence.getEnd();
int startShift = 1 - absStart - start; // how much the features
// are
+ " from " + dbSource + " sequence : " + entry.getName());
sequence.transferAnnotation(entry, mp);
// unknownSequences.remove(sequence);
- int absEnd = absStart + nonGapped.length();
- absStart += 1;
+ absStart += entry.getStart();
+ int absEnd = absStart + nonGapped.length() - 1;
if (!trimDatasetSeqs)
{
// insert full length sequence from record