import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
import jalview.gui.CutAndPasteTransfer;
import jalview.gui.Desktop;
+import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
import jalview.util.MessageManager;
*/
public class DBRefFetcher implements Runnable
{
+ public interface FetchFinishedListenerI
+ {
+ void finished();
+ }
+
+ private List<FetchFinishedListenerI> listeners;
+
SequenceI[] dataset;
- IProgressIndicator af;
+ IProgressIndicator progressWindow;
CutAndPasteTransfer output = new CutAndPasteTransfer();
*/
private boolean trimDsSeqs = true;
- public DBRefFetcher()
- {
- }
-
- /**
- * Creates a new SequenceFeatureFetcher object and fetches from the currently
- * selected set of databases.
- *
- * @param seqs
- * fetch references for these sequences
- * @param af
- * the parent alignframe for progress bar monitoring.
- */
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
- {
- this(seqs, af, null);
- }
-
/**
- * Creates a new SequenceFeatureFetcher object and fetches from the currently
- * selected set of databases.
+ * Creates a new DBRefFetcher object and fetches from the currently selected
+ * set of databases, if this is null then it fetches based on feature settings
*
* @param seqs
- * fetch references for these sequences
- * @param af
- * the parent alignframe for progress bar monitoring.
+ * fetch references for these SequenceI array
+ * @param progressIndicatorFrame
+ * the frame for progress bar monitoring
* @param sources
- * array of database source strings to query references from
+ * array of DbSourceProxy to query references form
+ * @param featureSettings
+ * FeatureSettings to get alternative DbSourceProxy from
+ * @param isNucleotide
+ * indicates if the array of SequenceI are Nucleotides or not
*/
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af,
- DbSourceProxy[] sources)
+ public DBRefFetcher(SequenceI[] seqs,
+ IProgressIndicator progressIndicatorFrame,
+ DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
{
- this.af = af;
+ listeners = new ArrayList<FetchFinishedListenerI>();
+ this.progressWindow = progressIndicatorFrame;
alseqs = new SequenceI[seqs.length];
SequenceI[] ds = new SequenceI[seqs.length];
for (int i = 0; i < seqs.length; i++)
{
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!
- sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+ sfetcher = jalview.gui.SequenceFetcher
+ .getSequenceFetcherSingleton(progressIndicatorFrame);
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
String[] defdb = null, otherdb = sfetcher
.getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
- Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ Vector dasselsrc = (featureSettings != null) ? featureSettings
.getSelectedSources() : new jalview.gui.DasSourceBrowser()
.getSelectedSources();
Enumeration<jalviewSourceI> en = dasselsrc.elements();
}
}
// select appropriate databases based on alignFrame context.
- if (af.getViewport().getAlignment().isNucleotide())
+ if (isNucleotide)
{
defdb = DBRefSource.DNACODINGDBS;
}
}
/**
+ * Add a listener to be notified when sequence fetching is complete
+ *
+ * @param l
+ */
+ public void addListener(FetchFinishedListenerI l)
+ {
+ listeners.add(l);
+ }
+
+ /**
* retrieve all the das sequence sources and add them to the list of db
* sources to retrieve from
*/
/**
* DOCUMENT ME!
*/
+ @Override
public void run()
{
if (dbSources == null)
}
running = true;
long startTime = System.currentTimeMillis();
- af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ if (progressWindow != null)
+ {
+ progressWindow.setProgressBar(
+ MessageManager.getString("status.fetching_db_refs"),
startTime);
+ }
try
{
if (Cache.getDefault("DBREFFETCH_USEPICR", false))
// TODO: introduce multithread multisource queries and logic to remove a
// query from other sources if any source for a database returns a
// record
- if (dbsource.getDbSourceProperties().containsKey(
- DBRefSource.MULTIACC))
- {
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
- DBRefSource.MULTIACC)).intValue();
- }
- else
- {
- maxqlen = 1;
- }
+ maxqlen = dbsource.getMaximumQueryCount();
+
while (queries.size() > 0 || seqIndex < currSeqs.length)
{
if (queries.size() > 0)
{
SequenceI sequence = dataset[seqIndex];
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(),
+ sequence.getDBRefs(),
new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
// });
// check for existing dbrefs to use
// of the viewed sequence
}
+ if (progressWindow != null)
+ {
+ progressWindow.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
+ }
- af.setProgressBar(
- MessageManager.getString("label.dbref_search_completed"),
- startTime);
- // promptBeforeBlast();
-
+ for (FetchFinishedListenerI listener : listeners)
+ {
+ listener.finished();
+ }
running = false;
-
}
/**
Vector sequenceMatches = new Vector();
// look for corresponding accession ids
DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
- entry.getDBRef(), new String[] { dbSource });
+ entry.getDBRefs(), new String[] { dbSource });
if (entryRefs == null)
{
System.err
// no existing references
// TODO: test for legacy where uniprot or EMBL refs exist but no
// mappings are made (but content matches retrieved set)
- boolean updateRefFrame = sequence.getDBRef() == null
- || sequence.getDBRef().length == 0;
+ boolean updateRefFrame = sequence.getDBRefs() == null
+ || sequence.getDBRefs().length == 0;
// TODO:
// verify sequence against the entry sequence
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
for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
{
nseq.addElement(sequencesArray[i]);
- DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+ DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
jalview.datamodel.Mapping map = null;
for (int r = 0; (dbr != null) && r < dbr.length; r++)
{