X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=66eb053159b2d4ac4d3e87488d995de750b83495;hb=7bd8dd38f8ba6cbec54343bc4ac04ee21b8de776;hp=4e7c9cd3de1961cfc0800fb3020adaa6a208aaee;hpb=a45bb4b4b3f6ce4067fc94acbfc546637fb30b06;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 4e7c9cd..66eb053 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -35,9 +35,9 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Vector;
 
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
@@ -79,7 +79,11 @@ public class IdPanel extends Panel implements MouseListener,
         label = av.applet.getParameter("linkLabel_" + i);
         url = av.applet.getParameter("linkURL_" + i);
 
-        urlList.put(label, url);
+        // only add non-null parameters
+        if (label != null)
+        {
+          urlList.put(label, url);
+        }
       }
 
       if (!urlList.isEmpty())
@@ -222,8 +226,12 @@ public class IdPanel extends Panel implements MouseListener,
     String id = sq.getName();
 
     // get the default url with the sequence details filled in
-    String url = urlProvider.getDefaultUrl(id);
-    String target = urlProvider.getDefaultTarget(id);
+    if (urlProvider == null)
+    {
+      return;
+    }
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
       alignPanel.alignFrame.showURL(url, target);
@@ -250,13 +258,13 @@ public class IdPanel extends Panel 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() >= getSize().height
-            && av.getAlignment().getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -284,8 +292,15 @@ public class IdPanel extends Panel implements MouseListener,
 
       // build a new links menu based on the current links + any non-positional
       // features
-      Vector<String> nlinks = urlProvider.getLinksForMenu();
-
+      List<String> nlinks;
+      if (urlProvider != null)
+      {
+        nlinks = urlProvider.getLinksForMenu();
+      }
+      else
+      {
+        nlinks = new ArrayList<String>();
+      }
       SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
@@ -295,7 +310,7 @@ public class IdPanel extends Panel implements MouseListener,
           {
             for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
             {
-              nlinks.addElement(sf[sl].links.elementAt(l));
+              nlinks.add(sf[sl].links.elementAt(l));
             }
           }
         }
@@ -395,9 +410,10 @@ public class IdPanel extends Panel 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);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -425,13 +441,13 @@ public class IdPanel extends Panel implements MouseListener,
       running = true;
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().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)