*/
package jalview.io;
-import java.util.Locale;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
-import com.google.common.collect.Lists;
-
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
private static final int MAX_REFS_PER_SOURCE = 4;
- private static final int MAX_SOURCES = 40;
+ private static final int MAX_SOURCES = 5;
private static String linkImageURL;
{
return 1;
}
+
String s1 = ref1.getSource();
String s2 = ref2.getSource();
boolean s1Primary = DBRefSource.isPrimarySource(s1);
boolean s2Primary = DBRefSource.isPrimarySource(s2);
+ if (ref1.isCanonical() && !ref2.isCanonical())
+ {
+ return -1;
+ }
+ if (!ref1.isCanonical() && ref2.isCanonical())
+ {
+ return 1;
+ }
if (s1Primary && !s2Primary)
{
return -1;
}
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"problem when creating links from " + urlstring);
x.printStackTrace();
}
UrlLink urlLink = new UrlLink(link);
if (!urlLink.isValid())
{
- System.err.println(urlLink.getInvalidMessage());
+ jalview.bin.Console.errPrintln(urlLink.getInvalidMessage());
return null;
}
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- List<DBRefEntry> dbrefs,dbrefset = ds.getDBRefs();
+ List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
if (dbrefset == null)
{
// PATCH for JAL-3980 defensive copy
dbrefs = new ArrayList<DBRefEntry>();
-
+
dbrefs.addAll(dbrefset);
-
+
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;