X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=a1726f1a62fa9939d061d051cdfe1bd009b1584b;hb=a1073a1f85c1a0c3f57cc85b8a7c49d6ad09ef27;hp=4ccfb2fc0ce6f52a8b91d9c37437897c861b8608;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 4ccfb2f..a1726f1 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -108,8 +108,7 @@ public class IdPanel extends JPanel
       SequenceI sequence = av.getAlignment().getSequenceAt(seq);
       StringBuilder tip = new StringBuilder(64);
       seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
-              av.isShowDBRefs(), av.isShowNPFeats(),
-              sp.seqCanvas.fr.getMinMax());
+              av.isShowDBRefs(), av.isShowNPFeats(), sp.seqCanvas.fr);
       setToolTipText(JvSwingUtils.wrapTooltip(true,
               sequence.getDisplayId(true) + " " + tip.toString()));
     }
@@ -138,7 +137,7 @@ public class IdPanel extends JPanel
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -154,7 +153,7 @@ public class IdPanel extends JPanel
       {
         av.getRanges().scrollRight(true);
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(false);
       }
@@ -165,7 +164,7 @@ public class IdPanel extends JPanel
       {
         av.getRanges().scrollRight(false);
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(true);
       }
@@ -313,7 +312,7 @@ public class IdPanel extends JPanel
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -325,28 +324,25 @@ public class IdPanel extends JPanel
   {
     int seq2 = alignPanel.getSeqPanel().findSeq(e);
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
-    // build a new links menu based on the current links + any non-positional
-    // features
+
+    /*
+     *  build a new links menu based on the current links
+     *  and any non-positional features
+     */
     List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
-    if (sfs != null)
+    List<SequenceFeature> features = sq.getFeatures().getNonPositionalFeatures();
+    for (SequenceFeature sf : features)
     {
-      for (SequenceFeature sf : sfs)
+      if (sf.links != null)
       {
-        if (sf.begin == sf.end && sf.begin == 0)
+        for (String link : sf.links)
         {
-          if (sf.links != null && sf.links.size() > 0)
-          {
-            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
-            {
-              nlinks.add(sf.links.elementAt(l));
-            }
-          }
+          nlinks.add(link);
         }
       }
     }
 
-    PopupMenu pop = new PopupMenu(alignPanel, sq, nlinks,
+    PopupMenu pop = new PopupMenu(alignPanel, sq, features,
             Preferences.getGroupURLLinks());
     pop.show(this, e.getX(), e.getY());
   }
@@ -511,7 +507,7 @@ public class IdPanel extends JPanel
           running = false;
         }
 
-        alignPanel.paintAlignment(false);
+        alignPanel.paintAlignment(false, false);
 
         try
         {