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Merge branch 'develop' into bug/JAL-1803_JAL-2157
[jalview.git]
/
src
/
jalview
/
datamodel
/
xdb
/
embl
/
EmblEntry.java
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
8688720
..
3ba36ca
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-49,8
+49,7
@@
import java.util.regex.Pattern;
* Castor binding file
*
* For example:
* Castor binding file
*
* For example:
- * http://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=ena_sequence&id=J03321
- * &format=emblxml
+ * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
*
* @see embl_mapping.xml
*/
*
* @see embl_mapping.xml
*/
@@
-188,6
+187,10
@@
public class EmblEntry
public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
SequenceI dna = makeSequence(sourceDb);
public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)
{
SequenceI dna = makeSequence(sourceDb);
+ if (dna == null)
+ {
+ return null;
+ }
dna.setDescription(description);
DBRefEntry retrievedref = new DBRefEntry(sourceDb,
getSequenceVersion(), accession);
dna.setDescription(description);
DBRefEntry retrievedref = new DBRefEntry(sourceDb,
getSequenceVersion(), accession);
@@
-239,6
+242,12
@@
public class EmblEntry
*/
SequenceI makeSequence(String sourceDb)
{
*/
SequenceI makeSequence(String sourceDb)
{
+ if (sequence == null)
+ {
+ System.err.println("No sequence was returned for ENA accession "
+ + accession);
+ return null;
+ }
SequenceI dna = new Sequence(sourceDb + "|" + accession,
sequence.getSequence());
return dna;
SequenceI dna = new Sequence(sourceDb + "|" + accession,
sequence.getSequence());
return dna;