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Merge branch 'develop' into features/JAL-2295setChimeraAttributes
[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
3ba36ca
..
4d09bdc
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-48,8
+48,7
@@
import java.util.regex.Pattern;
* Data model for one entry returned from an EMBL query, as marshalled by a
* Castor binding file
*
* Data model for one entry returned from an EMBL query, as marshalled by a
* Castor binding file
*
- * For example:
- * http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
+ * For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
*
* @see embl_mapping.xml
*/
*
* @see embl_mapping.xml
*/
@@
-200,7
+199,6
@@
public class EmblEntry
retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
new int[] { 1, dna.getLength() }, 1, 1));
retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
new int[] { 1, dna.getLength() }, 1, 1));
-
/*
* transform EMBL Database refs to canonical form
*/
/*
* transform EMBL Database refs to canonical form
*/
@@
-298,7
+296,8
@@
public class EmblEntry
if (qname.equals("translation"))
{
// remove all spaces (precompiled String.replaceAll(" ", ""))
if (qname.equals("translation"))
{
// remove all spaces (precompiled String.replaceAll(" ", ""))
- translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll("");
+ translation = SPACE_PATTERN.matcher(q.getValues()[0]).replaceAll(
+ "");
}
else if (qname.equals("protein_id"))
{
}
else if (qname.equals("protein_id"))
{
@@
-469,13
+468,14
@@
public class EmblEntry
*/
String source = DBRefUtils.getCanonicalName(ref.getSource());
ref.setSource(source);
*/
String source = DBRefUtils.getCanonicalName(ref.getSource());
ref.setSource(source);
- DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(), ref.getVersion(), ref
- .getAccessionId());
+ DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
+ ref.getVersion(), ref.getAccessionId());
if (source.equals(DBRefSource.UNIPROT))
{
String proteinSeqName = DBRefSource.UNIPROT + "|"
+ ref.getAccessionId();
if (source.equals(DBRefSource.UNIPROT))
{
String proteinSeqName = DBRefSource.UNIPROT + "|"
+ ref.getAccessionId();
- if (dnaToProteinMapping != null && dnaToProteinMapping.getTo() != null)
+ if (dnaToProteinMapping != null
+ && dnaToProteinMapping.getTo() != null)
{
if (mappingUsed)
{
{
if (mappingUsed)
{