X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1a133f33aaa1480ce3551c901207b2c897438b22;hb=84a9beec424185c5ce0f2da9af5b71857588b846;hp=51e703dc594b80dc072b9344d4a7863f952935f7;hpb=985fd5ff517f3eb5221a7aefec88138341514779;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 51e703d..1a133f3 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -532,7 +532,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     addNotify();
     // TODO: many places call this method and also paintAlignment with various
     // different settings. this means multiple redraws are triggered...
-    paintAlignment(true, false);
+    paintAlignment(true, av.needToUpdateStructureViews());
   }
 
   /**
@@ -1414,6 +1414,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   }
 
+  /**
+   * Answers the height of the entire alignment in pixels, assuming it is in
+   * wrapped mode
+   * 
+   * @return
+   */
   int getWrappedHeight()
   {
     int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
@@ -1438,6 +1444,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int annotationHeight = 0;
     if (av.isShowAnnotation())
     {
+      hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
       annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }