Make sure annots are alignment width

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a5ffb80..aaad2ae 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -86,20 +86,20 @@ public class SeqPanel
    * @param avp DOCUMENT ME!\r
    * @param p DOCUMENT ME!\r
    */\r
-  public SeqPanel(AlignViewport avp, AlignmentPanel p)\r
+  public SeqPanel(AlignViewport av, AlignmentPanel ap)\r
   {\r
     linkImageURL = getClass().getResource("/images/link.gif");\r
     ToolTipManager.sharedInstance().registerComponent(this);\r
     ToolTipManager.sharedInstance().setInitialDelay(0);\r
     ToolTipManager.sharedInstance().setDismissDelay(10000);\r
-    this.av = avp;\r
+    this.av = av;\r
     setBackground(Color.white);\r
 \r
-    seqCanvas = new SeqCanvas(avp);\r
+    seqCanvas = new SeqCanvas(ap);\r
     setLayout(new BorderLayout());\r
     add(seqCanvas, BorderLayout.CENTER);\r
 \r
-    ap = p;\r
+    this.ap = ap;\r
 \r
     if (!av.isDataset())\r
     {\r
@@ -204,6 +204,13 @@ public class SeqPanel
           continue;\r
         }\r
 \r
+        if (features[i].featureGroup != null\r
+           && seqCanvas.fr.featureGroups!=null\r
+            && seqCanvas.fr.featureGroups.containsKey(features[i].featureGroup)\r
+            && !((Boolean)seqCanvas.fr.featureGroups.get(features[i].featureGroup)).booleanValue())\r
+          continue;\r
+\r
+\r
         if ( (features[i].getBegin() <= res) &&\r
             (features[i].getEnd() >= res))\r
         {\r
@@ -509,8 +516,6 @@ public class SeqPanel
     }\r
 \r
     endEditing();\r
-\r
-    ap.paintAlignment(true);\r
   }\r
 \r
   /**\r
@@ -1568,13 +1573,14 @@ public class SeqPanel
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,\r
                                        stretchGroup.getName());\r
       }\r
+      PaintRefresher.Refresh(this, av.getSequenceSetId());\r
+      ap.paintAlignment(true);\r
     }\r
+\r
     changeEndRes = false;\r
     changeStartRes = false;\r
     stretchGroup = null;\r
 \r
-    PaintRefresher.Refresh(this, av.getSequenceSetId());\r
-    ap.paintAlignment(true);\r
   }\r
 \r
   /**\r