*/
package jalview.ws;
+import java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Cache;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
import uk.ac.ebi.picr.model.UPEntry;
import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
CutAndPasteTransfer output = new CutAndPasteTransfer();
- boolean running = false;
-
/**
* picr client instance
*/
*/
public void fetchDBRefs(boolean waitTillFinished)
{
- // TODO can we not simply write
- // if (waitTillFinished) { run(); } else { new Thread(this).start(); }
-
- Thread thread = new Thread(this);
- thread.start();
- running = true;
-
if (waitTillFinished)
{
- while (running)
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- }
- }
+ run();
+ }
+ else
+ {
+ new Thread(this).start();
}
}
*/
void addSeqId(SequenceI seq, String key)
{
- key = key.toUpperCase();
+ key = key.toUpperCase(Locale.ROOT);
Vector<SequenceI> seqs;
if (seqRefs.containsKey(key))
throw new Error(MessageManager
.getString("error.implementation_error_must_init_dbsources"));
}
- running = true;
long startTime = System.currentTimeMillis();
if (progressWindow != null)
{
DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
- upref.getAccessionId().toUpperCase());
+ upref.getAccessionId().toUpperCase(Locale.ROOT));
}
}
else
"Validated ID against PICR... (for what its worth):"
+ token);
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
else
{
// System.out.println("Not querying source with
// token="+token+"\n");
addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
+ queries.addElement(token.toUpperCase(Locale.ROOT));
}
}
}
{
listener.finished();
}
- running = false;
}
/**
DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
- if (seqRefs.containsKey(accessionId.toUpperCase()))
+ if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
{
Vector<SequenceI> seqs = seqRefs.get(accessionId);
for (int jj = 0; jj < seqs.size(); jj++)
// sequenceMatches now contains the set of all sequences associated with
// the returned db record
final String retrievedSeqString = retrievedSeq.getSequenceAsString();
- String entrySeq = retrievedSeqString.toUpperCase();
+ String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
for (int m = 0; m < sequenceMatches.size(); m++)
{
sequence = sequenceMatches.elementAt(m);
boolean remoteEnclosesLocal = false;
String nonGapped = AlignSeq
.extractGaps("-. ", sequence.getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int absStart = entrySeq.indexOf(nonGapped);
if (absStart == -1)
{
String ngAlsq = AlignSeq
.extractGaps("-. ",
alseqs[alsq].getSequenceAsString())
- .toUpperCase();
+ .toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase().indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(