X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1a133f33aaa1480ce3551c901207b2c897438b22;hb=84a9beec424185c5ce0f2da9af5b71857588b846;hp=82e2113eccc5f31bb39636ae7dd3b6347985e1a1;hpb=6007f0f4e720ede8ca8ff70e866f2f2b870cde3e;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 82e2113..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());
   }
 
   /**
@@ -637,16 +637,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        // reset the width to exclude hidden columns
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
-
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
       vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -958,8 +951,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    final int alignmentWidth = av.getAlignment().getWidth();
-    final int pagesWide = (alignmentWidth / totalRes) + 1;
+    final int alignmentWidth = av.getAlignment().getVisibleWidth();
+    int pagesWide = (alignmentWidth / totalRes) + 1;
 
     final int startRes = (pageIndex % pagesWide) * totalRes;
     final int endRes = Math.min(startRes + totalRes - 1,
@@ -1076,12 +1069,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int idWidth = getVisibleIdWidth(false);
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int resWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(pageWidth - idWidth);
@@ -1243,12 +1231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public AlignmentDimension getAlignmentDimension()
   {
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
             + getScalePanel().getHeight();
@@ -1431,6 +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();
@@ -1455,6 +1444,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int annotationHeight = 0;
     if (av.isShowAnnotation())
     {
+      hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
       annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }