JAL-2388 Applied ViewportRanges to code

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

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 808d9a0..4d3dd2f 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -22,11 +22,14 @@ 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.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
@@ -44,8 +47,6 @@ import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
 import org.biodas.jdas.client.FeaturesClient;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
@@ -181,13 +182,12 @@ 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;
@@ -199,21 +199,21 @@ public class DasSequenceFeatureFetcher
     if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
     {
 
-      int reply = JOptionPane.YES_OPTION;
+      int reply = JvOptionPane.YES_OPTION;
       if (promptFetchDbrefs)
       {
-        reply = JOptionPane
+        reply = JvOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
                         MessageManager
                                 .getString("info.you_want_jalview_to_find_uniprot_accessions"),
                         MessageManager
                                 .getString("label.find_uniprot_accession_ids"),
-                        JOptionPane.YES_NO_OPTION,
-                        JOptionPane.QUESTION_MESSAGE);
+                        JvOptionPane.YES_NO_OPTION,
+                        JvOptionPane.QUESTION_MESSAGE);
       }
 
-      if (reply == JOptionPane.YES_OPTION)
+      if (reply == JvOptionPane.YES_OPTION)
       {
         Thread thread = new Thread(new FetchDBRefs());
         thread.start();
@@ -238,6 +238,7 @@ public class DasSequenceFeatureFetcher
 
   class FetchSeqFeatures implements Runnable
   {
+    @Override
     public void run()
     {
       startFetching();
@@ -247,10 +248,14 @@ 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();
     }
@@ -280,8 +285,7 @@ public class DasSequenceFeatureFetcher
       {
         jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
                 new jalviewSourceI[0]);
-        String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
-                "uniprot");
+        String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
         StringTokenizer st = new StringTokenizer(active, "\t");
         selectedSources = new Vector();
         String token;
@@ -613,8 +617,8 @@ public class DasSequenceFeatureFetcher
     }
     af.getFeatureRenderer().featuresAdded();
 
-    int start = af.getViewport().getStartSeq();
-    int end = af.getViewport().getEndSeq();
+    int start = af.getViewport().getRanges().getStartSeq();
+    int end = af.getViewport().getRanges().getEndSeq();
     int index;
     for (index = start; index < end; index++)
     {
@@ -637,10 +641,10 @@ 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
             });
@@ -659,8 +663,8 @@ public class DasSequenceFeatureFetcher
 
         for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
         {
-          if (jalview.util.DBRefUtils.isDasCoordinateSystem(
-                  csys.getAuthority(), uprefs[j]))
+          if (DBRefUtils.isDasCoordinateSystem(csys.getAuthority(),
+                  uprefs[j]))
           {
             debug("Launched fetcher for coordinate system "
                     + csys.getAuthority());