From 124d129cc007fbfc84039610b364df62efc72707 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 6 Sep 2018 20:33:43 +0100
Subject: [PATCH] JAL-2854 compute visible annotation panel height and provide
 it directly to via Scrollable interface

---
 help/html/releases.html              |    4 +++
 src/jalview/gui/AlignmentPanel.java  |   33 +++--------------------
 src/jalview/gui/AnnotationPanel.java |   49 +++++++++++++++++++++++++++++++++-
 3 files changed, 55 insertions(+), 31 deletions(-)

diff --git a/help/html/releases.html b/help/html/releases.html
index 33b54ec..0bc9e4e 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -111,6 +111,10 @@ li:before {
         <em></em>
         <ul>
             <li>
+              <!-- JAL-2854 -->Annotation obscures sequences if lots of
+              annotation displayed.
+            </li>
+            <li>
               <!-- JAL-3087 -->Corrupted display when switching to
               wrapped mode when sequence panel's vertical scrollbar is
               visible.
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index c46a2ab..60ef480 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -37,7 +37,6 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
-import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
@@ -547,37 +546,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
   protected void validateAnnotationDimensions(boolean adjustPanelHeight)
   {
     int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+    annotationHeight = getAnnotationPanel()
+            .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
 
-    if (adjustPanelHeight)
-    {
-      int rowHeight = av.getCharHeight();
-      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
-
-      /*
-       * Estimate available height in the AlignFrame for alignment +
-       * annotations. Deduct an estimate for title bar, menu bar, scale panel,
-       * hscroll, status bar, insets. 
-       */
-      int stuff = Platform.isAMac() ? 120 : 140;
-      int availableHeight = alignFrame.getHeight() - stuff;
-
-      /*
-       * If not enough vertical space, maximize annotation height while keeping
-       * at least two rows of alignment visible
-       */
-      if (annotationHeight + alignmentHeight > availableHeight)
-      {
-        annotationHeight = Math.min(annotationHeight,
-                availableHeight - 2 * rowHeight);
-      }
-    }
-    else
-    {
-      // maintain same window layout whilst updating sliders
-      annotationHeight = annotationScroller.getSize().height;
-    }
     hscroll.addNotify();
-
     annotationScroller.setPreferredSize(
             new Dimension(annotationScroller.getWidth(), annotationHeight));
 
@@ -616,6 +588,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
+      validateAnnotationDimensions(false);
     }
 
     int canvasWidth = getSeqPanel().seqCanvas.getWidth();
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index dee56b0..50971c7 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -30,6 +30,7 @@ import jalview.renderer.AwtRenderPanelI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
 
@@ -206,7 +207,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public Dimension getPreferredScrollableViewportSize()
   {
-    return getPreferredSize();
+    Dimension ps = getPreferredSize();
+    return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
   }
 
   @Override
@@ -1196,4 +1198,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
     }
   }
+
+  /**
+   * computes the visible height of the annotation panel
+   * 
+   * @param adjustPanelHeight
+   *          - when false, just adjust existing height according to other
+   *          windows
+   * @param annotationHeight
+   * @return height to use for the ScrollerPreferredVisibleSize
+   */
+  public int adjustForAlignFrame(boolean adjustPanelHeight,
+          int annotationHeight)
+  {
+    /*
+     * Estimate available height in the AlignFrame for alignment +
+     * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+     * hscroll, status bar, insets. 
+     */
+    int stuff = (ap.getViewName() != null ? 30 : 0)
+            + (Platform.isAMac() ? 120 : 140);
+    int availableHeight = ap.alignFrame.getHeight() - stuff;
+    int rowHeight = av.getCharHeight();
+
+    if (adjustPanelHeight)
+    {
+      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+      /*
+       * If not enough vertical space, maximize annotation height while keeping
+       * at least two rows of alignment visible
+       */
+      if (annotationHeight + alignmentHeight > availableHeight)
+      {
+        annotationHeight = Math.min(annotationHeight,
+                availableHeight - 2 * rowHeight);
+      }
+    }
+    else
+    {
+      // maintain same window layout whilst updating sliders
+      annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+              availableHeight - 2 * rowHeight);
+    }
+    return annotationHeight;
+  }
 }
-- 
1.7.10.2