import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
}
if (jal.getProperties() != null)
{
- Enumeration en = jal.getProperties().keys();
- while (en.hasMoreElements())
+ for (Entry<Object, Object> prop : jal.getProperties().entrySet())
{
- String key = en.nextElement().toString();
+ String key = prop.getKey().toString();
SequenceSetProperties ssp = new SequenceSetProperties();
ssp.setKey(key);
- ssp.setValue(jal.getProperties().get(key).toString());
+ ssp.setValue(prop.getValue().toString());
// vamsasSet.addSequenceSetProperties(ssp);
vamsasSet.getSequenceSetProperties().add(ssp);
}
{
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
- .startsWith(pdbId.toLowerCase())))
+ if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+ && entry.getId().toLowerCase(Locale.ROOT)
+ .startsWith(pdbId.toLowerCase(Locale.ROOT))))
{
/*
* not interested in a binding to a different PDB entry here
dbref.setSource(ref.getSource());
dbref.setVersion(ref.getVersion());
dbref.setAccessionId(ref.getAccessionId());
+ dbref.setCanonical(ref.isCanonical());
if (ref instanceof GeneLocus)
{
dbref.setLocus(true);
for (int i = 0; i < colours.length; i++)
{
Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
col.setRGB(jalview.util.Format.getHexString(colours[i]));
// jbucs.addColour(col);
jbucs.getColour().add(col);
entryCount++;
}
} while (jarentry != null);
+ jin.close();
resolveFrefedSequences();
} catch (IOException ex)
{
{
entry.setMap(addMapping(dr.getMapping()));
}
+ entry.setCanonical(dr.isCanonical());
datasetSequence.addDBRef(entry);
}
}