X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=7f2a943d9425ee5a6958b35661f7d314d12844e1;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=51ade37f77ca73b3028d487aa9ce5488e863feca;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 51ade37..7f2a943 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,26 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Hashtable;
-import java.util.Vector;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.*;
@@ -85,7 +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);
@@ -139,7 +137,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
         }
       }
     });
-
   }
 
   public SequenceRenderer getSequenceRenderer()
@@ -481,12 +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;