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JAL-629 Change --open to --append and --opennew to --open. Make --open(new) part...
[jalview.git]
/
src
/
jalview
/
io
/
SequenceAnnotationReport.java
diff --git
a/src/jalview/io/SequenceAnnotationReport.java
b/src/jalview/io/SequenceAnnotationReport.java
index
7fc04e1
..
95bd1cc
100644
(file)
--- a/
src/jalview/io/SequenceAnnotationReport.java
+++ b/
src/jalview/io/SequenceAnnotationReport.java
@@
-20,17
+20,14
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.util.Locale;
import java.util.ArrayList;
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.Collection;
import java.util.Comparator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map;
-import com.google.common.collect.Lists;
-
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.api.FeatureColourI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
@@
-539,7
+536,7
@@
public class SequenceAnnotationReport
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
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)
{
if (dbrefset == null)
{
@@
-549,9
+546,9
@@
public class SequenceAnnotationReport
// PATCH for JAL-3980 defensive copy
dbrefs = new ArrayList<DBRefEntry>();
// PATCH for JAL-3980 defensive copy
dbrefs = new ArrayList<DBRefEntry>();
-
+
dbrefs.addAll(dbrefset);
dbrefs.addAll(dbrefset);
-
+
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;