import java.util.ArrayList;
import java.util.Enumeration;
+import java.util.List;
import java.util.StringTokenizer;
import java.util.Vector;
{
this.ap = ap;
this.al = al;
- output.setText(MessageManager
- .getString("label.wswublast_client_credits"));
+ output.setText(
+ MessageManager.getString("label.wswublast_client_credits"));
- Desktop.addInternalFrame(output, MessageManager
- .getString("label.blasting_for_unidentified_sequence"), 800,
- 300);
+ Desktop.addInternalFrame(output, MessageManager.getString(
+ "label.blasting_for_unidentified_sequence"), 800, 300);
for (int i = 0; i < ids.size(); i++)
{
{
identitiesFound = true;
- int value = Integer.parseInt(data.substring(
- data.indexOf("(") + 1, data.indexOf("%")));
+ int value = Integer.parseInt(data
+ .substring(data.indexOf("(") + 1, data.indexOf("%")));
if (value >= maxFound)
{
}
}
- DBRefEntry[] entries = oldseq.getDBRefs();
- if (entries != null)
+ List<DBRefEntry> entries = oldseq.getDBRefs();
+ // BH 2019.01.25 check for 0-length was missing here
+ if (entries != null && entries.size() > 0)
{
oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
- jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
- .getAccessionId()));
+ jalview.datamodel.DBRefSource.UNIPROT, "0",
+ entries.get(0).getAccessionId()));
}
}
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, false);
}
for (int i = 0; i < 9; i++)
{
- java.net.URL url = getClass().getResource(
- "/images/dna" + (i + 1) + ".gif");
+ java.net.URL url = getClass()
+ .getResource("/images/dna" + (i + 1) + ".gif");
if (url != null)
{
output.setFrameIcon(imageIcon[imageIndex]);
output.setTitle(MessageManager.formatMessage(
"label.blasting_for_unidentified_sequence_jobs_running",
- new String[] { Integer.valueOf(jobsRunning).toString() }));
+ new String[]
+ { Integer.valueOf(jobsRunning).toString() }));
} catch (Exception ex)
{
}