X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=2c5684a8a168c5ccd0876b20f2614d83447a66a2;hb=bab4b08733a9543bdce5c0b9d1c32ca7d18ad9e3;hp=ab6a7813d6d1d03c33a1b6e7f9239eb20e239fd3;hpb=8aa68d0642ccf38d8c971edb717982f6d509675f;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ab6a781..2c5684a 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -48,7 +48,6 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
-import java.awt.Insets;
 import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
@@ -419,8 +418,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      start = hidden.findColumnPosition(start);
-      end = hidden.findColumnPosition(end);
+      start = hidden.absoluteToVisibleColumn(start);
+      end = hidden.absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!hidden.isVisible(r[0]))
@@ -556,13 +555,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       /*
        * Estimate available height in the AlignFrame for alignment +
        * annotations. Deduct an estimate for title bar, menu bar, scale panel,
-       * hscroll, status bar (as these are not laid out we can't inspect their
-       * actual heights). Insets gives frame borders.
+       * hscroll, status bar, insets. 
        */
-      int stuff = Platform.isAMac() ? 80 : 100;
-      Insets insets = alignFrame.getInsets();
-      int availableHeight = alignFrame.getHeight() - stuff - insets.top
-              - insets.bottom;
+      int stuff = Platform.isAMac() ? 120 : 140;
+      int availableHeight = alignFrame.getHeight() - stuff;
 
       /*
        * If not enough vertical space, maximize annotation height while keeping
@@ -678,7 +674,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         // reset the width to exclude hidden columns
         width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
+                .absoluteToVisibleColumn(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -874,10 +870,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
+    invalidate(); // needed so that the id width adjuster works correctly
+
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
 
+    validate(); // needed so that the id width adjuster works correctly
+
     /*
      * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
      * though I still think this call should be elsewhere.
@@ -1172,7 +1172,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas
@@ -1364,7 +1364,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1582,7 +1582,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1811,35 +1811,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    /*
-     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
-     * mapped), we can make the scroll-to location a sequence above the one
-     * actually mapped.
-     */
-    SequenceI mappedTo = sr.getResults().get(0).getSequence();
-    List<SequenceI> seqs = av.getAlignment().getSequences();
-
-    /*
-     * This is like AlignmentI.findIndex(seq) but here we are matching the
-     * dataset sequence not the aligned sequence
-     */
-    boolean matched = false;
-    for (SequenceI seq : seqs)
-    {
-      if (mappedTo == seq.getDatasetSequence())
-      {
-        matched = true;
-        break;
-      }
-    }
-    if (!matched)
-    {
-      return; // failsafe, shouldn't happen
-    }
-
-    /*
-     * Scroll to position but centring the target residue.
-     */
     scrollToPosition(sr, verticalOffset, true, true);
   }