X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=1a133f33aaa1480ce3551c901207b2c897438b22;hb=84a9beec424185c5ce0f2da9af5b71857588b846;hp=c03b56dacd0fa6d9d5933940d001f577775255a1;hpb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c03b56d..1a133f3 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -328,12 +328,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Highlight the given results on the alignment.
+   * Highlight the given results on the alignment
    * 
    */
   public void highlightSearchResults(SearchResultsI results)
   {
-    boolean scrolled = scrollToPosition(results, 0, true, false);
+    boolean scrolled = scrollToPosition(results, 0, false);
 
     boolean noFastPaint = scrolled && av.getWrapAlignment();
 
@@ -345,13 +345,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * (if any)
    * 
    * @param searchResults
-   * @param redrawOverview
    * @return
    */
-  public boolean scrollToPosition(SearchResultsI searchResults,
-          boolean redrawOverview)
+  public boolean scrollToPosition(SearchResultsI searchResults)
   {
-    return scrollToPosition(searchResults, 0, redrawOverview, false);
+    return scrollToPosition(searchResults, 0, false);
   }
 
   /**
@@ -364,14 +362,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @param verticalOffset
    *          if greater than zero, allows scrolling to a position below the
    *          first displayed sequence
-   * @param redrawOverview
-   *          - when set, the overview will be recalculated (takes longer)
    * @param centre
    *          if true, try to centre the search results horizontally in the view
    * @return
    */
   protected boolean scrollToPosition(SearchResultsI results,
-          int verticalOffset, boolean redrawOverview, boolean centre)
+          int verticalOffset, boolean centre)
   {
     int startv, endv, starts, ends;
     ViewportRanges ranges = av.getRanges();
@@ -477,7 +473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview, false);
+    paintAlignment(false, false);
 
     return scrollNeeded;
   }
@@ -536,7 +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());
   }
 
   /**
@@ -641,16 +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();
 
@@ -962,8 +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,
@@ -1080,12 +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);
@@ -1247,12 +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();
@@ -1435,6 +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();
@@ -1459,6 +1444,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int annotationHeight = 0;
     if (av.isShowAnnotation())
     {
+      hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
       annotationHeight = getAnnotationPanel().adjustPanelHeight();
     }
 
@@ -1698,7 +1684,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    scrollToPosition(sr, verticalOffset, true, true);
+    scrollToPosition(sr, verticalOffset, true);
   }
 
   /**