X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=35690a95f2425796561d25b91b32dc9140f5fdd2;hb=e826112670b160df06adb4030835624248ac4a8a;hp=bc663e64d12621c548d612afa9b4e9b3cbb81a18;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index bc663e6..35690a9 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -19,11 +19,10 @@ package jalview.gui;
 
 import java.io.*;
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 
@@ -38,6 +37,7 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 public class FeatureSettings extends JPanel
 {
@@ -313,15 +313,15 @@ public class FeatureSettings extends JPanel
     Vector allGroups = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
-      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+      if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
               .getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
 
       int index = 0;
@@ -442,10 +442,10 @@ public class FeatureSettings extends JPanel
     // Find out which features should be visible depending on which groups
     // are selected / deselected
     // and recompute average width ordering
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
       if (tmpfeatures == null)
       {
@@ -1177,7 +1177,7 @@ public class FeatureSettings extends JPanel
    * @param checkDbRefs
    * @param promptFetchDbRefs
    */
-  private void doDasFeatureFetch(Vector selectedSources,
+  private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
           boolean checkDbRefs, boolean promptFetchDbRefs)
   {
     SequenceI[] dataset, seqs;
@@ -1225,9 +1225,9 @@ public class FeatureSettings extends JPanel
    *          Vector of Strings to resolve to DAS source nicknames.
    * @return sources that are present in source list.
    */
-  public Vector resolveSourceNicknames(Vector sources)
+  public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
   {
-    return dassourceBrowser.resolveSourceNicknames(sources);
+    return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
   }
 
   /**
@@ -1253,14 +1253,14 @@ public class FeatureSettings extends JPanel
   public void fetchDasFeatures(Vector sources, boolean block)
   {
     initDasSources();
-    Vector resolved = resolveSourceNicknames(sources);
+    List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
     if (resolved.size() == 0)
     {
       resolved = dassourceBrowser.getSelectedSources();
     }
     if (resolved.size() > 0)
     {
-      final Vector dassources = resolved;
+      final List<jalviewSourceI> dassources = resolved;
       fetchDAS.setEnabled(false);
       // cancelDAS.setEnabled(true); doDasFetch does this.
       Runnable fetcher = new Runnable()