X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=5f9b2d93748ccb848fe7bb08afcd332917843200;hb=c889fc8840c719390e49eb27adbf6b1bf156ae12;hp=a778ab148ff667ba470b9cea00b843c93066699c;hpb=2273eba5668e5340354da60fed329c6c716cc439;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index a778ab1..5f9b2d9 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -181,13 +183,12 @@ public class DasSequenceFeatureFetcher
     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[j].getSource().equals(
-                  jalview.datamodel.DBRefSource.UNIPROT))
+          if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
           {
             refCount++;
             break;
@@ -205,8 +206,10 @@ public class DasSequenceFeatureFetcher
         reply = JOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
-                        MessageManager.getString("label.find_uniprot_accession_ids"),
+                        MessageManager
+                                .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+                        MessageManager
+                                .getString("label.find_uniprot_accession_ids"),
                         JOptionPane.YES_NO_OPTION,
                         JOptionPane.QUESTION_MESSAGE);
       }
@@ -236,6 +239,7 @@ public class DasSequenceFeatureFetcher
 
   class FetchSeqFeatures implements Runnable
   {
+    @Override
     public void run()
     {
       startFetching();
@@ -245,10 +249,15 @@ public class DasSequenceFeatureFetcher
 
   class FetchDBRefs implements Runnable
   {
+    @Override
     public void run()
     {
       running = true;
-      new DBRefFetcher(sequences, af).fetchDBRefs(true);
+      boolean isNucleotide = af.getViewport().getAlignment()
+              .isNucleotide();
+      new DBRefFetcher(sequences, af, null, af.featureSettings,
+              isNucleotide).fetchDBRefs(true);
+
       startFetching();
       setGuiFetchComplete();
     }
@@ -264,7 +273,9 @@ public class DasSequenceFeatureFetcher
     startTime = System.currentTimeMillis();
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.fetching_das_sequence_features"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.fetching_das_sequence_features"),
+              startTime);
     }
     if (sourceRegistry == null)
     {
@@ -276,7 +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();
@@ -378,8 +389,7 @@ public class DasSequenceFeatureFetcher
                         source));
         for (String id : idl)
         {
-          List<String> qid = Arrays.asList(new String[]
-          { id });
+          List<String> qid = Arrays.asList(new String[] { id });
           try
           {
             DasGFFAdapter dga = featuresc.fetchData(source, qid);
@@ -537,7 +547,9 @@ public class DasSequenceFeatureFetcher
 
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
+      af.setProgressBar(
+              MessageManager.getString("status.no_das_sources_active"),
+              startTime);
     }
     if (getFeatSettings() != null)
     {
@@ -567,7 +579,9 @@ public class DasSequenceFeatureFetcher
   {
     if (af != null)
     {
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_cancelled"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_cancelled"),
+              startTime);
     }
     cancelled = true;
   }
@@ -582,12 +596,13 @@ public class DasSequenceFeatureFetcher
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
-      af.setProgressBar(MessageManager.getString("status.das_feature_fetching_complete"), startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_complete"), startTime);
     }
 
     if (af != null && af.featureSettings != null)
     {
-      af.featureSettings.setTableData();
+      af.featureSettings.discoverAllFeatureData();
     }
 
     if (getFeatSettings() != null)
@@ -629,11 +644,10 @@ public class DasSequenceFeatureFetcher
     {
       return null;
     }
-    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-            seq.getDBRef(), new String[]
-            {
+    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
             });
@@ -652,7 +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 "
@@ -710,8 +724,7 @@ public class DasSequenceFeatureFetcher
       }
     }
 
-    return new Object[]
-    { ids, qstring };
+    return new Object[] { ids, qstring };
   }
 
   /**