JAL-1942 small tidy (formatting, explict imports, typed list, spelling)

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

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index d7ba24d..5f9b2d9 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -22,11 +22,13 @@ package jalview.ws;
 
 import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
@@ -186,8 +188,7 @@ public class DasSequenceFeatureFetcher
       {
         for (int j = 0; j < dbref.length; j++)
         {
-          if (dbref[j].getSource().equals(
-                  jalview.datamodel.DBRefSource.UNIPROT))
+          if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
           {
             refCount++;
             break;
@@ -252,10 +253,10 @@ public class DasSequenceFeatureFetcher
     public void run()
     {
       running = true;
-      boolean isNuclueotide = af.getViewport().getAlignment()
+      boolean isNucleotide = af.getViewport().getAlignment()
               .isNucleotide();
-      new jalview.ws.DBRefFetcher(sequences, af, null, af.featureSettings,
-              isNuclueotide).fetchDBRefs(true);
+      new DBRefFetcher(sequences, af, null, af.featureSettings,
+              isNucleotide).fetchDBRefs(true);
 
       startFetching();
       setGuiFetchComplete();
@@ -286,7 +287,7 @@ public class DasSequenceFeatureFetcher
       {
         jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
                 new jalviewSourceI[0]);
-        String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+        String active = Cache.getDefault("DAS_ACTIVE_SOURCE",
                 "uniprot");
         StringTokenizer st = new StringTokenizer(active, "\t");
         selectedSources = new Vector();
@@ -643,10 +644,10 @@ public class DasSequenceFeatureFetcher
     {
       return null;
     }
-    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+    DBRefEntry[] uprefs = DBRefUtils.selectRefs(
             seq.getDBRefs(), new String[] {
             // jalview.datamodel.DBRefSource.PDB,
-            jalview.datamodel.DBRefSource.UNIPROT,
+            DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
             // sys sources
             });
@@ -665,7 +666,7 @@ public class DasSequenceFeatureFetcher
 
         for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
         {
-          if (jalview.util.DBRefUtils.isDasCoordinateSystem(
+          if (DBRefUtils.isDasCoordinateSystem(
                   csys.getAuthority(), uprefs[j]))
           {
             debug("Launched fetcher for coordinate system "