Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 6ae19f0..29bb522 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -152,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
       else
       {
-        alignPanel.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
       else
       {
-        alignPanel.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
   }
@@ -242,13 +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);
     }
@@ -324,23 +325,19 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     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)
+    for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
     {
-      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);
         }
       }
     }
@@ -442,9 +439,10 @@ 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);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -483,14 +481,14 @@ public class IdPanel extends JPanel implements MouseListener,
 
       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)