JAL-2314 Tidy up

[jalview.git] / src / jalview / gui / IdPanel.java

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index e326a7a..2074900 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -36,9 +36,7 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.util.List;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
@@ -200,7 +198,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     int seq = alignPanel.getSeqPanel().findSeq(e);
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    String url = Preferences.sequenceUrlLinks.getDefaultUrl(id);
+    String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
     try
     {
@@ -244,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -328,7 +327,7 @@ public class IdPanel extends JPanel implements MouseListener,
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
     // build a new links menu based on the current links + any non-positional
     // features
-    Vector<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
     SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
     if (sfs != null)
     {
@@ -340,7 +339,7 @@ public class IdPanel extends JPanel implements MouseListener,
           {
             for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
             {
-              nlinks.addElement(sf.links.elementAt(l));
+              nlinks.add(sf.links.elementAt(l));
             }
           }
         }
@@ -444,9 +443,10 @@ public class IdPanel extends JPanel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -488,11 +488,11 @@ public class IdPanel extends JPanel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)