X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=2c5684a8a168c5ccd0876b20f2614d83447a66a2;hb=95d7a34b009144b172d60bbb5827df2fbb43524e;hp=6491c22fe6f31f49bdb03891afffa401911e518b;hpb=0cdeb96f949f136ee7103960ecd8a8e155c94a34;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 6491c22..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();
@@ -874,15 +870,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
-    invalidate();
+    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();
+
+    validate(); // needed so that the id width adjuster works correctly
 
     /*
-     * set scroll bar positions
+     * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+     * though I still think this call should be elsewhere.
      */
     ViewportRanges ranges = av.getRanges();
     setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
@@ -1174,7 +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
@@ -1366,7 +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())
@@ -1584,7 +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;