*/
public DBRefFetcher(SequenceI[] seqs,
IProgressIndicator progressIndicatorFrame,
*/
public DBRefFetcher(SequenceI[] seqs,
IProgressIndicator progressIndicatorFrame,
{
progressWindow.setProgressBar(
MessageManager.getString("status.fetching_db_refs"),
{
progressWindow.setProgressBar(
MessageManager.getString("status.fetching_db_refs"),
output.setText(sb.toString());
Desktop.addInternalFrame(output,
output.setText(sb.toString());
Desktop.addInternalFrame(output,
// The above is the dataset, we must now find out the index
// of the viewed sequence
// The above is the dataset, we must now find out the index
// of the viewed sequence
AlignmentI retrievedAl, boolean trimDatasetSeqs,
List<String> warningMessages)
{
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
// 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 });
*/
mp = new Mapping(null, new int[] { sequenceStart + absStart,
sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
*/
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);
sequence.transferAnnotation(retrievedSeq, mp);
absStart += retrievedSeq.getStart();
sequence.transferAnnotation(retrievedSeq, mp);
absStart += retrievedSeq.getStart();