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Merge branch 'develop' into JAL-1705_trialMerge
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
diff --git
a/src/jalview/datamodel/Sequence.java
b/src/jalview/datamodel/Sequence.java
index
ac2f9c1
..
7b05649
100755
(executable)
--- a/
src/jalview/datamodel/Sequence.java
+++ b/
src/jalview/datamodel/Sequence.java
@@
-265,11
+265,10
@@
public class Sequence extends ASequence implements SequenceI
}
if (seq.getAllPDBEntries() != null)
{
}
if (seq.getAllPDBEntries() != null)
{
- Vector ids = seq.getAllPDBEntries();
- Enumeration e = ids.elements();
- while (e.hasMoreElements())
+ Vector<PDBEntry> ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
{
{
- this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+ this.addPDBId(new PDBEntry(pdb));
}
}
}
}
}
}
@@
-289,6
+288,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
+ // TODO add to dataset sequence instead if there is one?
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
@@
-931,6
+931,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public void addDBRef(DBRefEntry entry)
{
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO add to dataset sequence instead if there is one?
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
@@
-964,6
+965,7
@@
public class Sequence extends ASequence implements SequenceI
@Override
public void setDatasetSequence(SequenceI seq)
{
@Override
public void setDatasetSequence(SequenceI seq)
{
+ // TODO check for circular reference before setting?
datasetSequence = seq;
}
datasetSequence = seq;
}