X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=8ac02be707ed229319417039f4f7a5b70e10c0f3;hb=a4aca9cd975791d85eb6123b31a4b812689520dc;hp=cc021f53bfc94f3cf6fa08a117ae78e7c471f71d;hpb=a1bf90058be8be92554ecbc5868982dcdbed5a80;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index cc021f5..8ac02be 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -35,11 +35,12 @@ 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;
 
-public class IdPanel extends Panel implements MouseListener,
-        MouseMotionListener
+public class IdPanel extends Panel
+        implements MouseListener, MouseMotionListener
 {
 
   protected IdCanvas idCanvas;
@@ -78,7 +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())
@@ -172,13 +177,14 @@ public class IdPanel extends Panel implements MouseListener,
     }
     if (tooltip == null)
     {
-      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString(), idCanvas);
+      tooltip = new Tooltip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString(),
+              idCanvas);
     }
     else
     {
-      tooltip.setTip(sequence.getDisplayId(true) + "\n"
-              + tooltiptext.toString());
+      tooltip.setTip(
+              sequence.getDisplayId(true) + "\n" + tooltiptext.toString());
     }
     tooltiptext = null;
   }
@@ -221,6 +227,10 @@ public class IdPanel extends Panel implements MouseListener,
     String id = sq.getName();
 
     // get the default url with the sequence details filled in
+    if (urlProvider == null)
+    {
+      return;
+    }
     String url = urlProvider.getPrimaryUrl(id);
     String target = urlProvider.getPrimaryTarget(id);
     try
@@ -249,13 +259,13 @@ 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);
     }
@@ -277,14 +287,22 @@ public class IdPanel extends Panel implements MouseListener,
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((e.getModifiers()
+            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
       Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
 
       // build a new links menu based on the current links + any non-positional
       // features
-      List<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++)
       {
@@ -307,8 +325,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!jalview.util.Platform.isControlDown(e) && !e
-                    .isShiftDown()) && av.getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e)
+                    && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -357,8 +375,8 @@ public class IdPanel extends Panel implements MouseListener,
     }
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
 
   }
@@ -394,9 +412,10 @@ 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);
     }
   }
 
@@ -424,13 +443,13 @@ 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)