*/
public DBRefFetcher(SequenceI[] seqs,
IProgressIndicator progressIndicatorFrame,
- DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
+ DbSourceProxy[] sources, FeatureSettings featureSettings,
+ boolean isNucleotide)
{
listeners = new ArrayList<FetchFinishedListenerI>();
this.progressWindow = progressIndicatorFrame;
{
progressWindow.setProgressBar(
MessageManager.getString("status.fetching_db_refs"),
- startTime);
+ startTime);
}
try
{
// Still queries to make for current seqIndex
StringBuffer queryString = new StringBuffer("");
int numq = 0;
- int nqSize = (maxqlen > queries.size()) ? queries
- .size() : maxqlen;
+ int nqSize = (maxqlen > queries.size()) ? queries.size()
+ : maxqlen;
while (queries.size() > 0 && numq < nqSize)
{
output.setText(sb.toString());
Desktop.addInternalFrame(output,
- MessageManager.getString("label.sequences_updated"),
- 600, 300);
+ MessageManager.getString("label.sequences_updated"), 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
* @param warningMessages
* a list of messages to add to
*/
- boolean transferReferences(Vector<SequenceI> sdataset,
- String dbSource,
+ boolean transferReferences(Vector<SequenceI> sdataset, String dbSource,
AlignmentI retrievedAl, boolean trimDatasetSeqs,
List<String> warningMessages)
{
// taking into account all accessionIds and names in the file
Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
// look for corresponding accession ids
- DBRefEntry[] entryRefs = DBRefUtils.selectRefs(retrievedSeq.getDBRefs(),
- new String[] { dbSource });
+ DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
+ retrievedSeq.getDBRefs(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
*/
mp = new Mapping(null, new int[] { sequenceStart + absStart,
sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
- { retrievedSeq.getStart(), retrievedSeq.getStart() + entrySeq.length() - 1 },
- 1, 1);
+ { retrievedSeq.getStart(),
+ retrievedSeq.getStart() + entrySeq.length() - 1 }, 1, 1);
updateRefFrame = false;
}
else
}
System.out.println("Adding dbrefs to " + sequence.getName()
- + " from " + dbSource + " sequence : " + retrievedSeq.getName());
+ + " from " + dbSource + " sequence : "
+ + retrievedSeq.getName());
sequence.transferAnnotation(retrievedSeq, mp);
absStart += retrievedSeq.getStart();