private SequenceI[] alseqs;
/**
- * when true - retrieved sequences will be trimmed to cover longest derived alignment sequence
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
*/
- private boolean trimDsSeqs=true;
+ private boolean trimDsSeqs = true;
public DBRefFetcher()
{
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
- // set default behaviour for transferring excess sequence data to the dataset
+ // set default behaviour for transferring excess sequence data to the
+ // dataset
trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
if (sources == null)
{
{
if (dbSources == null)
{
- throw new Error("Implementation error. Must initialise dbSources");
+ throw new Error(MessageManager.getString("error.implementation_error_must_init_dbsources"));
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar("Fetching db refs", startTime);
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"), startTime);
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
if (retrieved != null)
{
transferReferences(sdataset, dbsource.getDbSource(),
- retrieved,trimDsSeqs);
+ retrieved, trimDsSeqs);
}
}
else
} // all databases have been queries.
if (sbuffer.length() > 0)
{
- output.setText(MessageManager.getString("label.your_sequences_have_been_verified")
+ output.setText(MessageManager
+ .getString("label.your_sequences_have_been_verified")
+ sbuffer.toString());
- Desktop.addInternalFrame(output, MessageManager.getString("label.sequence_names_updated"), 600, 300);
+ Desktop.addInternalFrame(output,
+ MessageManager.getString("label.sequence_names_updated"),
+ 600, 300);
// The above is the dataset, we must now find out the index
// of the viewed sequence
}
- af.setProgressBar(MessageManager.getString("label.dbref_search_completed"), startTime);
+ af.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
// promptBeforeBlast();
running = false;
/**
* Verify local sequences in seqRefs against the retrieved sequence database
* records.
- * @param trimDatasetSeqs
+ *
+ * @param trimDatasetSeqs
*
*/
void transferReferences(Vector sdataset, String dbSource,
AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
// file)
{
- System.out.println("trimming ? "+trimDatasetSeqs);
+ System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
return;
// unknownSequences.remove(sequence);
int absEnd = absStart + nonGapped.length();
absStart += 1;
- if (!trimDatasetSeqs) {
+ if (!trimDatasetSeqs)
+ {
// insert full length sequence from record
sequence.setSequence(entry.getSequenceAsString());
sequence.setStart(entry.getStart());
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
- if (trimDatasetSeqs) {
+ if (trimDatasetSeqs)
+ {
// just fix start/end
sequence.setStart(absStart);
sequence.setEnd(absEnd);