Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 0ea2b8a..2aa21bb 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -329,12 +329,12 @@ 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 fastPaint = !(scrolled && av.getWrapAlignment());
 
@@ -346,13 +346,11 @@ 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);
   }
 
   /**
@@ -365,14 +363,12 @@ 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();
@@ -478,7 +474,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       scrollNeeded = ranges.scrollToWrappedVisible(start);
     }
 
-    paintAlignment(redrawOverview, false);
+    paintAlignment(false, false);
 
     return scrollNeeded;
   }
@@ -537,7 +533,7 @@ 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());
   }
 
   /**
@@ -642,16 +638,9 @@ 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();
 
@@ -964,8 +953,8 @@ 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,
@@ -1082,12 +1071,7 @@ 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);
@@ -1215,12 +1199,7 @@ 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();
@@ -1645,7 +1624,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    scrollToPosition(sr, verticalOffset, true, true);
+    scrollToPosition(sr, verticalOffset, true);
   }
 
   /**