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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
b1c987e
..
7745b74
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-32,6
+32,7
@@
import jalview.gui.Desktop;
import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
import jalview.gui.FeatureSettings;
import jalview.gui.IProgressIndicator;
import jalview.gui.OOMWarning;
+import jalview.gui.Preferences;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
import jalview.ws.seqfetcher.DbSourceProxy;
@@
-134,7
+135,7
@@
public class DBRefFetcher implements Runnable
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
}
this.dataset = ds;
// TODO Jalview 2.5 lots of this code should be in the gui package!
- sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
+ sfetcher = SequenceFetcher.getInstance();
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
// set default behaviour for transferring excess sequence data to the
// dataset
trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
@@
-302,7
+303,7
@@
public class DBRefFetcher implements Runnable
}
try
{
}
try
{
- if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+ if (Cache.getDefault(Preferences.DBREFFETCH_USEPICR, false))
{
picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
{
picrClient = new AccessionMapperServiceLocator()
.getAccessionMapperPort();
@@
-785,7
+786,9
@@
public class DBRefFetcher implements Runnable
{
int n;
if (sequencesArray == null || (n = sequencesArray.length) == 0)
{
int n;
if (sequencesArray == null || (n = sequencesArray.length) == 0)
- return sequencesArray;
+ {
+ return sequencesArray;
+ }
ArrayList<SequenceI> nseq = new ArrayList<>();
for (int i = 0;i < n; i++)
{
ArrayList<SequenceI> nseq = new ArrayList<>();
for (int i = 0;i < n; i++)
{