From 34348a4079b425ce7fda3eb75e5e6a2b62cf16b9 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 4 Apr 2014 16:38:24 +0100
Subject: [PATCH] JAL-1211 - set annotation panel height according to the
 amount of annotation present on the alignment and the
 relative size of the alignment.

---
 src/jalview/appletgui/AlignmentPanel.java |   25 ++++++++++++++++------
 src/jalview/gui/AlignmentPanel.java       |   32 +++++++++++++++++++++--------
 2 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index b34a5bb..5a49281 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -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;
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 541c7c2..6bfe4bd 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -422,16 +422,30 @@ public class AlignmentPanel extends GAlignmentPanel implements
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
     int height = annotationPanel.adjustPanelHeight();
-
-    if (hscroll.isVisible())
-    {
-      height += hscroll.getPreferredSize().height;
-    }
-    if (height > alignFrame.getHeight() / 2)
-    {
-      height = alignFrame.getHeight() / 2;
+    
+    int theight = av.getCharHeight() * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 : av.getAlignment().getHiddenSequences().getSize()));
+    float sscaling = (float) (theight/(1.0*theight+height));
+    float ascaling=(float)(height*1.0/alignFrame.getHeight());
+    int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+    if (adjustPanelHeight)
+    {
+      // NOTE: this logic is different in the applet. Need a better algorithm to define behaviour
+      // try and set height according to alignment
+      if (ascaling>0 && sscaling < 0.5)
+      {
+        // if the alignment is too big then
+        // default is 0.5 split
+        height = alignFrame.getHeight() / 2;
+      }
+      else
+      {
+        // if space for more than one sequence row left when annotation is fully displayed then set height to annotation height
+        // otherwise, leave at least two lines of sequence shown.  
+        height = (rheight>av.getCharHeight()) ? height : (-av.getCharHeight() * 3
+                + (int) (alignFrame.getHeight() * (1 - sscaling)));
+      }
     }
-    if (!adjustPanelHeight)
+    else
     {
       // maintain same window layout whilst updating sliders
       height = annotationScroller.getSize().height;
-- 
1.7.10.2