(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 38912fd..9d1cae4 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -85,9 +85,9 @@ public class IdPanel extends JPanel implements MouseListener,
     SeqPanel sp = alignPanel.seqPanel;
     int seq = Math.max(0, sp.findSeq(e));
     String tmp;
-    if (seq > -1 && seq < av.alignment.getHeight())
+    if (seq > -1 && seq < av.getAlignment().getHeight())
     {
-      SequenceI sequence = av.alignment.getSequenceAt(seq);
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
       StringBuffer tip = new StringBuffer();
       tip.append("<i>");
 
@@ -287,7 +287,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.alignment.getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -314,7 +314,7 @@ public class IdPanel extends JPanel implements MouseListener,
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq.getDatasetSequence().getSequenceFeatures();
+      SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -342,7 +342,7 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
     if (e.isShiftDown() && (lastid != -1))
@@ -419,15 +419,11 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       scrollThread.running = false;
     }
-    // if (mouseDragging)
-    {
-      // always send selection message when mouse is released
-      av.sendSelection();
-
-    }
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
   }
 
   /**
@@ -445,7 +441,7 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    int index = av.alignment.findIndex((SequenceI) found.get(0));
+    int index = av.getAlignment().findIndex((SequenceI) found.get(0));
 
     // do we need to scroll the panel?
     if ((av.getStartSeq() > index) || (av.getEndSeq() < index))