JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 7745b74..b1c987e 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -32,7 +32,6 @@ import jalview.gui.Desktop;
 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;
@@ -135,7 +134,7 @@ public class DBRefFetcher implements Runnable
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
-    sfetcher = SequenceFetcher.getInstance();
+    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton();
     // set default behaviour for transferring excess sequence data to the
     // dataset
     trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
@@ -303,7 +302,7 @@ public class DBRefFetcher implements Runnable
     }
     try
     {
-      if (Cache.getDefault(Preferences.DBREFFETCH_USEPICR, false))
+      if (Cache.getDefault("DBREFFETCH_USEPICR", false))
       {
         picrClient = new AccessionMapperServiceLocator()
                 .getAccessionMapperPort();
@@ -786,9 +785,7 @@ public class DBRefFetcher implements Runnable
   {
        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++)
     {