X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=7f2a943d9425ee5a6958b35661f7d314d12844e1;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=b34a5bbb561339759be9c01fa9db71f037eea5a9;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index b34a5bb..7f2a943 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -84,7 +84,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
 
     sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-
     alabels = new AnnotationLabels(this);
 
     setAnnotationVisible(av.showAnnotation);
@@ -138,7 +137,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
         }
       }
     });
-
   }
 
   public SequenceRenderer getSequenceRenderer()
@@ -480,12 +478,27 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     int mheight = height;
     Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
     int seqandannot = d.height - scalePanelHolder.getSize().height;
-    // sets initial preferred height
-    if ((height + 40) > seqandannot / 2)
+
+    if (adjustPanelHeight)
     {
-      height = seqandannot / 2;
+      // NOTE: this logic is different in the application. Need a better algorithm to define behaviour
+      // sets initial preferred height
+      // try and set height according to alignment
+      float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight));
+      if (sscaling > 0.5)
+      {
+        // if the alignment is too big then
+        // default is 0.5 split
+        height = seqandannot / 2;
+      }
+      else
+      {
+        // otherwise just set the panel so that one row of sequence is visible 
+        height = -av.getCharHeight() * 1
+                + (int) (seqandannot * (1 - sscaling));
+      }
     }
-    if (!adjustPanelHeight)
+    else
     {
       // maintain same window layout whilst updating sliders
       height = annotationPanelHolder.getSize().height;