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JAL-2005 added (stable) sort methods parameterised by
[jalview.git]
/
src
/
jalview
/
ws
/
DasSequenceFeatureFetcher.java
diff --git
a/src/jalview/ws/DasSequenceFeatureFetcher.java
b/src/jalview/ws/DasSequenceFeatureFetcher.java
index
808d9a0
..
d7ba24d
100644
(file)
--- a/
src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/
src/jalview/ws/DasSequenceFeatureFetcher.java
@@
-181,7
+181,7
@@
public class DasSequenceFeatureFetcher
int refCount = 0;
for (int i = 0; i < sequences.length; i++)
{
int refCount = 0;
for (int i = 0; i < sequences.length; i++)
{
- DBRefEntry[] dbref = sequences[i].getDBRef();
+ DBRefEntry[] dbref = sequences[i].getDBRefs();
if (dbref != null)
{
for (int j = 0; j < dbref.length; j++)
if (dbref != null)
{
for (int j = 0; j < dbref.length; j++)
@@
-238,6
+238,7
@@
public class DasSequenceFeatureFetcher
class FetchSeqFeatures implements Runnable
{
class FetchSeqFeatures implements Runnable
{
+ @Override
public void run()
{
startFetching();
public void run()
{
startFetching();
@@
-247,10
+248,15
@@
public class DasSequenceFeatureFetcher
class FetchDBRefs implements Runnable
{
class FetchDBRefs implements Runnable
{
+ @Override
public void run()
{
running = true;
public void run()
{
running = true;
- new DBRefFetcher(sequences, af).fetchDBRefs(true);
+ boolean isNuclueotide = af.getViewport().getAlignment()
+ .isNucleotide();
+ new jalview.ws.DBRefFetcher(sequences, af, null, af.featureSettings,
+ isNuclueotide).fetchDBRefs(true);
+
startFetching();
setGuiFetchComplete();
}
startFetching();
setGuiFetchComplete();
}
@@
-638,7
+644,7
@@
public class DasSequenceFeatureFetcher
return null;
}
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
return null;
}
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[] {
+ seq.getDBRefs(), new String[] {
// jalview.datamodel.DBRefSource.PDB,
jalview.datamodel.DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
// jalview.datamodel.DBRefSource.PDB,
jalview.datamodel.DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord