*/
package jalview.gui;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.io.IdentifyFile;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
}
}
if (sfetch == null
- || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
- || lastDasSourceRegistry != (jalview.bin.Cache
- .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ || dasRegistry != Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (Cache
+ .getDasSourceRegistry().getDasRegistryURL() + Cache
.getDasSourceRegistry().getLocalSourceString())
.hashCode())
{
guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
- dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry = Cache.getDasSourceRegistry();
dasRegistry.refreshSources();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
frame = new JInternalFrame();
frame.setContentPane(this);
- if (new jalview.util.Platform().isAMac())
+ if (Platform.isAMac())
{
Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
}
boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
for (DbSourceProxy dbs : database.getSelectedSources())
{
- if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ if (dbs instanceof DasSequenceSource)
{
enablePunct = false;
break;
error += "Please select the source database\n";
}
// TODO: make this transformation more configurable
- com.stevesoft.pat.Regex empty;
+ Regex empty;
if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
- empty = new com.stevesoft.pat.Regex(
+ empty = new Regex(
// replace commas and spaces with a semicolon
"(\\s|[,; ])+", ";");
}
else
{
// just turn spaces and semicolons into single semicolons
- empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ empty = new Regex("(\\s|[; ])+", ";");
}
textArea.setText(empty.replaceAll(textArea.getText()));
// see if there's anthing to search with
- if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ if (!new Regex("[A-Za-z0-9_.]").search(textArea
.getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
} catch (Exception e)
{
- jalview.bin.Cache.log.info("Error retrieving " + item
+ Cache.log.info("Error retrieving " + item
+ " from " + proxy.getDbName(), e);
nextfetch.add(item);
}
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
false));
} catch (Exception ex)
{